Cascade debris overlap mechanism of 〈100〉 dislocation loop formation in Fe and FeCr

NASA Astrophysics Data System (ADS)

Granberg, F.; Byggmästar, J.; Sand, A. E.; Nordlund, K.

2017-09-01

Two types of dislocation loops are observed in irradiated α-Fe, the 1/2〈111〉 loop and the 〈100〉 loop. Atomistic simulations consistently predict that only the energetically more favourable 1/2〈111〉 loops are formed directly in cascades, leaving the formation mechanism of 〈100〉 loops an unsolved question. We show how 〈100〉 loops can be formed when cascades overlap with random pre-existing primary radiation damage in Fe and FeCr. This indicates that there are no specific constraints involved in the formation of 〈100〉 loops, and can explain their common occurrence.

Fine flow structures in the transition region small-scale loops

NASA Astrophysics Data System (ADS)

Yan, L.; Peter, H.; He, J.; Wei, Y.

2016-12-01

The observation and model have suggested that the transition region EUV emission from the quiet sun region is contributed by very small scale loops which have not been resolved. Recently, the observation from IRIS has revealed that this kind of small scale loops. Based on the high resolution spectral and imaging observation from IRIS, much more detail work needs to be done to reveal the fine flow features in this kind of loop to help us understand the loop heating. Here, we present a detail statistical study of the spatial and temporal evolution of Si IV line profiles of small scale loops and report the spectral features: there is a transition from blue (red) wing enhancement dominant to red (blue) wing enhancement dominant along the cross-section of the loop, which is independent of time. This feature appears as the loop appear and disappear as the loop un-visible. This is probably the signature of helical flow along the loop. The result suggests that the brightening of this kind of loop is probably due to the current dissipation heating in the twisted magnetic field flux tube.

A Markov chain technique for determining the acquisition behavior of a digital tracking loop

NASA Technical Reports Server (NTRS)

Chadwick, H. D.

1972-01-01

An iterative procedure is presented for determining the acquisition behavior of discrete or digital implementations of a tracking loop. The technique is based on the theory of Markov chains and provides the cumulative probability of acquisition in the loop as a function of time in the presence of noise and a given set of initial condition probabilities. A digital second-order tracking loop to be used in the Viking command receiver for continuous tracking of the command subcarrier phase was analyzed using this technique, and the results agree closely with experimental data.

Analysis of a first order phase locked loop in the presence of Gaussian noise

NASA Technical Reports Server (NTRS)

Blasche, P. R.

1977-01-01

A first-order digital phase locked loop is analyzed by application of a Markov chain model. Steady state loop error probabilities, phase standard deviation, and mean loop transient times are determined for various input signal to noise ratios. Results for direct loop simulation are presented for comparison.

Transcription of telomeric DNA leads to high levels of homologous recombination and t-loops.

PubMed

Kar, Anirban; Willcox, Smaranda; Griffith, Jack D

2016-11-02

The formation of DNA loops at chromosome ends (t-loops) and the transcription of telomeres producing G-rich RNA (TERRA) represent two central features of telomeres. To explore a possible link between them we employed artificial human telomeres containing long arrays of TTAGGG repeats flanked by the T7 or T3 promoters. Transcription of these DNAs generates a high frequency of t-loops within individual molecules and homologous recombination events between different DNAs at their telomeric sequences. T-loop formation does not require a single strand overhang, arguing that both terminal strands insert into the preceding duplex. The loops are very stable and some RNase H resistant TERRA remains at the t-loop, likely adding to their stability. Transcription of DNAs containing TTAGTG or TGAGTG repeats showed greatly reduced loop formation. While in the cell multiple pathways may lead to t-loop formation, the pathway revealed here does not depend on the shelterins but rather on the unique character of telomeric DNA when it is opened for transcription. Hence, telomeric sequences may have evolved to facilitate their ability to loop back on themselves. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Solar Tornadoes Triggered by Interaction between Filaments and EUV Jets

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

Chen, Huadong; Zhang, Jun; Ma, Suli

We investigate the formations and evolutions of two successive solar tornadoes in/near AR 12297 during 2015 March 19–20. Recurrent EUV jets close to two filaments were detected along a large-scale coronal loop prior to the appearances of the tornadoes. Under the disturbances from the activities, the filaments continually ascended and finally interacted with the loops tracked by the jets. Subsequently, the structures of the filaments and the loop were merged together, probably via magnetic reconnections, and formed tornado-like structures with a long spiral arm. Our observations suggest that solar tornadoes can be triggered by the interaction between filaments and nearbymore » coronal jets, which has rarely been reported before. At the earlier development phase of the first tornado, about 30 small-scale sub-jets appeared in the tornado’s arm, accompanied by local EUV brightenings. They have an ejection direction approximately vertical to the axis of the arm and a typical maximum speed of ∼280 km s{sup −1}. During the ruinations of the two tornadoes, fast plasma outflows from the strong EUV brightenings inside tornadoes are observed, in company with the untangling or unwinding of the highly twisted tornado structures. These observational features indicate that self reconnections probably occurred between the tangled magnetic fields of the tornadoes and resulted in the rapid disintegrations and disappearances of the tornadoes. According to the reconnection theory, we also derive the field strength of the tornado core to be ∼8 G.« less

Solar Tornadoes Triggered by Interaction between Filaments and EUV Jets

NASA Astrophysics Data System (ADS)

Chen, Huadong; Zhang, Jun; Ma, Suli; Yan, Xiaoli; Xue, Jianchao

2017-05-01

We investigate the formations and evolutions of two successive solar tornadoes in/near AR 12297 during 2015 March 19-20. Recurrent EUV jets close to two filaments were detected along a large-scale coronal loop prior to the appearances of the tornadoes. Under the disturbances from the activities, the filaments continually ascended and finally interacted with the loops tracked by the jets. Subsequently, the structures of the filaments and the loop were merged together, probably via magnetic reconnections, and formed tornado-like structures with a long spiral arm. Our observations suggest that solar tornadoes can be triggered by the interaction between filaments and nearby coronal jets, which has rarely been reported before. At the earlier development phase of the first tornado, about 30 small-scale sub-jets appeared in the tornado’s arm, accompanied by local EUV brightenings. They have an ejection direction approximately vertical to the axis of the arm and a typical maximum speed of ˜280 km s-1. During the ruinations of the two tornadoes, fast plasma outflows from the strong EUV brightenings inside tornadoes are observed, in company with the untangling or unwinding of the highly twisted tornado structures. These observational features indicate that self reconnections probably occurred between the tangled magnetic fields of the tornadoes and resulted in the rapid disintegrations and disappearances of the tornadoes. According to the reconnection theory, we also derive the field strength of the tornado core to be ˜8 G.

Steady-state probability density function of the phase error for a DPLL with an integrate-and-dump device

NASA Technical Reports Server (NTRS)

Simon, M.; Mileant, A.

1986-01-01

The steady-state behavior of a particular type of digital phase-locked loop (DPLL) with an integrate-and-dump circuit following the phase detector is characterized in terms of the probability density function (pdf) of the phase error in the loop. Although the loop is entirely digital from an implementation standpoint, it operates at two extremely different sampling rates. In particular, the combination of a phase detector and an integrate-and-dump circuit operates at a very high rate whereas the loop update rate is very slow by comparison. Because of this dichotomy, the loop can be analyzed by hybrid analog/digital (s/z domain) techniques. The loop is modeled in such a general fashion that previous analyses of the Real-Time Combiner (RTC), Subcarrier Demodulator Assembly (SDA), and Symbol Synchronization Assembly (SSA) fall out as special cases.

R-loop-mediated genomic instability is caused by impairment of replication fork progression

PubMed Central

Gan, Wenjian; Guan, Zhishuang; Liu, Jie; Gui, Ting; Shen, Keng; Manley, James L.; Li, Xialu

2011-01-01

Transcriptional R loops are anomalous RNA:DNA hybrids that have been detected in organisms from bacteria to humans. These structures have been shown in eukaryotes to result in DNA damage and rearrangements; however, the mechanisms underlying these effects have remained largely unknown. To investigate this, we first show that R-loop formation induces chromosomal DNA rearrangements and recombination in Escherichia coli, just as it does in eukaryotes. More importantly, we then show that R-loop formation causes DNA replication fork stalling, and that this in fact underlies the effects of R loops on genomic stability. Strikingly, we found that attenuation of replication strongly suppresses R-loop-mediated DNA rearrangements in both E. coli and HeLa cells. Our findings thus provide a direct demonstration that R-loop formation impairs DNA replication and that this is responsible for the deleterious effects of R loops on genome stability from bacteria to humans. PMID:21979917

Laser beam pulse formatting method

DOEpatents

Daly, T.P.; Moses, E.I.; Patterson, R.W.; Sawicki, R.H.

1994-08-09

A method for formatting a laser beam pulse using one or more delay loops is disclosed. The delay loops have a partially reflective beam splitter and a plurality of highly reflective mirrors arranged such that the laser beam pulse enters into the delay loop through the beam splitter and circulates therein along a delay loop length defined by the mirrors. As the laser beam pulse circulates within the delay loop a portion thereof is emitted upon each completed circuit when the laser beam pulse strikes the beam splitter. The laser beam pulse is thereby formatted into a plurality of sub-pulses. The delay loops are used in combination to produce complex waveforms by combining the sub-pulses using additive waveform synthesis. 8 figs.

An Environmental for Hardware-in-the-Loop Formation Navigation and Control

NASA Technical Reports Server (NTRS)

Burns, Rich; Naasz, Bo; Gaylor, Dave; Higinbotham, John

2004-01-01

Recent interest in formation flying satellite systems has spurred a considerable amount of research in the relative navigation and control of satellites. Development in this area has included new estimation and control algorithms as well as sensor and actuator development specifically geared toward the relative control problem. This paper describes a simulation facility, the Formation Flying Test Bed (FFTB) at NASA Goddard Space Flight Center, which allows engineers to test new algorithms for the formation flying problem with relevant GN&C hardware in a closed loop simulation. The FFTB currently supports the inclusion of GPS receiver hardware in the simulation loop. Support for satellite crosslink ranging technology is at a prototype stage. This closed-loop, hardware inclusive simulation capability permits testing of navigation and control software in the presence of the actual hardware with which the algorithms must interact. This capability provides the navigation or control developer with a perspective on how the algorithms perform as part of the closed-loop system. In this paper, the overall design and evolution of the FFTB are presented. Each component of the FFTB is then described. Interfaces between the components of the FFTB are shown and the interfaces to and between navigation and control software are described. Finally, an example of closed-loop formation control with GPS receivers in the loop is presented.

Laser beam pulse formatting method

DOEpatents

Daly, Thomas P.; Moses, Edward I.; Patterson, Ralph W.; Sawicki, Richard H.

1994-01-01

A method for formatting a laser beam pulse (20) using one or more delay loops (10). The delay loops (10) have a partially reflective beam splitter (12) and a plurality of highly reflective mirrors (14) arranged such that the laser beam pulse (20) enters into the delay loop (10) through the beam splitter (12) and circulates therein along a delay loop length (24) defined by the mirrors (14). As the laser beam pulse (20) circulates within the delay loop (10) a portion thereof is emitted upon each completed circuit when the laser beam pulse (20) strikes the beam splitter (12). The laser beam pulse (20) is thereby formatted into a plurality of sub-pulses (50, 52, 54 and 56). The delay loops (10) are used in combination to produce complex waveforms by combining the sub-pulses (50, 52, 54 and 56) using additive waveform synthesis.

First Results from a Hardware-in-the-Loop Demonstration of Closed-Loop Autonomous Formation Flying

NASA Technical Reports Server (NTRS)

Gill, E.; Naasz, Bo; Ebinuma, T.

2003-01-01

A closed-loop system for the demonstration of formation flying technologies has been developed at NASA s Goddard Space Flight Center. Making use of a GPS signal simulator with a dual radio frequency outlet, the system includes two GPS space receivers as well as a powerful onboard navigation processor dedicated to the GPS-based guidance, navigation, and control of a satellite formation in real-time. The closed-loop system allows realistic simulations of autonomous formation flying scenarios, enabling research in the fields of tracking and orbit control strategies for a wide range of applications. A sample scenario has been set up where the autonomous transition of a satellite formation from an initial along-track separation of 800 m to a final distance of 100 m has been demonstrated. As a result, a typical control accuracy of about 5 m has been achieved which proves the applicability of autonomous formation flying techniques to formations of satellites as close as 50 m.

Open-loop frequency acquisition for suppressed-carrier biphase signals using one-pole arm filters

NASA Technical Reports Server (NTRS)

Shah, B.; Holmes, J. K.

1991-01-01

Open loop frequency acquisition performance is discussed for suppressed carrier binary phase shift keyed signals in terms of the probability of detecting the carrier frequency offset when the arms of the Costas loop detector have one pole filters. The approach, which does not require symbol timing, uses fast Fourier transforms (FFTs) to detect the carrier frequency offset. The detection probability, which depends on both the 3 dB arm filter bandwidth and the received symbol signal to noise ratio, is derived and is shown to be independent of symbol timing. It is shown that the performance of this technique is slightly better that other open loop acquisition techniques which use integrators in the arms and whose detection performance varies with symbol timing.

An Environment for Hardware-in-the-Loop Formation Navigation and Control Simulation

NASA Technical Reports Server (NTRS)

Burns, Rich

2004-01-01

Recent interest in formation flying satellite systems has spurred a considerable amount of research in the relative navigation and control of satellites. Development in this area has included new estimation and control algorithms as well as sensor and actuator development specifically geared toward the relative control problem. This paper describes a simulation facility, the Formation Flying Testbed (FFTB) at NASA's Goddard Space Flight Center, which allows engineers to test new algorithms for the formation flying problem with relevant GN&C hardware in a closed loop simulation. The FFTB currently supports the injection of GPS receiver hardware into the simulation loop, and support for satellite crosslink ranging technology is at a prototype stage. This closed-loop, hardware inclusive simulation capability permits testing of navigation and control software in the presence of the actual hardware with which the algorithms must interact. This capability provides the navigation or control developer with a perspective on how the algorithms perform as part of the closed-loop system. In this paper, the overall design and evolution of the FFTB are presented. Each component of the FFTB is then described in detail. Interfaces between the components of the FFTB are shown and the interfaces to and between navigation and control software are described in detail. Finally, an example of closed-loop formation control with GPS receivers in the loop is presented and results are analyzed.

High-altitude closed magnetic loops at Mars observed by MAVEN

NASA Astrophysics Data System (ADS)

Xu, Shaosui; Mitchell, David; Luhmann, Janet; Ma, Yingjuan; Fang, Xiaohua; Harada, Yuki; Hara, Takuya; Brain, David; Webber, Tristan; Mazelle, Christian; DiBraccio, Gina A.

2017-10-01

With electron and magnetic field data obtained by the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft, we have identified closed magnetic field lines, with both footpoints embedded in the dayside ionosphere, extending up to 6200 km altitude (2.8 $R_m$) into the Martian tail. This topology is deduced from photoelectrons produced in the dayside ionosphere being observed in both parallel and anti-parallel directions along the magnetic field line. At perpendicular pitch angles, cases with either solar wind electrons or photoelectrons have been found, indicative of different formation mechanisms of these closed loops. These large closed loops are predicted by MHD simulations. The case with field-aligned photoelectrons mixed with perpendicular solar wind electrons is likely to be associated with reconnection, while the case with photoelectrons in all directions are probably due to closed field lines being pulled back down tail. We have developed an automated algorithm for distinguishing photoelectrons from solar wind electrons in pitch angle resolved energy spectra. This allows us to systematically analyze the MAVEN database and map the spatial distribution and occurrence rate of these closed magnetic loops, ranging from a few percent to a few tens percent outside of the optical shadow and less than one percent within the wake. These observations can be used to investigate the general magnetic topology in the tail, which is relevant to ion escape, reconnection, and flux ropes.

Interplay of protein and DNA structure revealed in simulations of the lac operon.

PubMed

Czapla, Luke; Grosner, Michael A; Swigon, David; Olson, Wilma K

2013-01-01

The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gene control. The molecular simulations presented here examine two likely structural contributions to the in-vivo looping of bacterial DNA: the distortions of the double helix introduced upon association of the highly abundant, nonspecific nucleoid protein HU and the large-scale deformations of the repressor detected in low-resolution experiments. The computations take account of the three-dimensional arrangements of nucleotides and amino acids found in crystal structures of DNA with the two proteins, the natural rest state and deformational properties of protein-free DNA, and the constraints on looping imposed by the conformation of the repressor and the orientation of bound DNA. The predicted looping propensities capture the complex, chain-length-dependent variation in repression efficacy extracted from gene expression studies and in vitro experiments and reveal unexpected chain-length-dependent variations in the uptake of HU, the deformation of repressor, and the folding of DNA. Both the opening of repressor and the presence of HU, at levels approximating those found in vivo, enhance the probability of loop formation. HU affects the global organization of the repressor and the opening of repressor influences the levels of HU binding to DNA. The length of the loop determines whether the DNA adopts antiparallel or parallel orientations on the repressor, whether the repressor is opened or closed, and how many HU molecules bind to the loop. The collective behavior of proteins and DNA is greater than the sum of the parts and hints of ways in which multiple proteins may coordinate the packaging and processing of genetic information.

A causal loop analysis of the sustainability of integrated community case management in Rwanda.

PubMed

Sarriot, Eric; Morrow, Melanie; Langston, Anne; Weiss, Jennifer; Landegger, Justine; Tsuma, Laban

2015-04-01

Expansion of community health services in Rwanda has come with the national scale up of integrated Community Case Management (iCCM) of malaria, pneumonia and diarrhea. We used a sustainability assessment framework as part of a large-scale project evaluation to identify factors affecting iCCM sustainability (2011). We then (2012) used causal-loop analysis to identify systems determinants of iCCM sustainability from a national systems perspective. This allows us to develop three high-probability future scenarios putting the achievements of community health at risk, and to recommend mitigating strategies. Our causal loop diagram highlights both balancing and reinforcing loops of cause and effect in the national iCCM system. Financial, political and technical scenarios carry high probability for threatening the sustainability through: (1) reduction in performance-based financing resources, (2) political shocks and erosion of political commitment for community health, and (3) insufficient progress in resolving district health systems--"building blocks"--performance gaps. In a complex health system, the consequences of choices may be delayed and hard to predict precisely. Causal loop analysis and scenario mapping make explicit complex cause-and-effects relationships and high probability risks, which need to be anticipated and mitigated. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Intensity of emission lines of the quiescent solar corona: comparison between calculated and observed values

NASA Astrophysics Data System (ADS)

Krissinel, Boris

2018-03-01

The paper reports the results of calculations of the center-to-limb intensity of optically thin line emission in EUV and FUV wavelength ranges. The calculations employ a multicomponent model for the quiescent solar corona. The model includes a collection of loops of various sizes, spicules, and free (inter-loop) matter. Theoretical intensity values are found from probabilities of encountering parts of loops in the line of sight with respect to the probability of absence of other coronal components. The model uses 12 loops with sizes from 3200 to 210000 km with different values of rarefaction index and pressure at the loop base and apex. The temperature at loop apices is 1 400 000 K. The calculations utilize the CHIANTI database. The comparison between theoretical and observed emission intensity values for coronal and transition region lines obtained by the SUMER, CDS, and EIS telescopes shows quite satisfactory agreement between them, particularly for the solar disk center. For the data acquired above the limb, the enhanced discrepancies after the analysis refer to errors in EIS measurements.

Turbulence and the Formation of Filaments, Loops, and Shock Fronts in NGC 1275

NASA Astrophysics Data System (ADS)

Falceta-Gonçalves, D.; de Gouveia Dal Pino, E. M.; Gallagher, J. S.; Lazarian, A.

2010-01-01

NGC 1275, the central galaxy in the Perseus cluster, is the host of gigantic hot bipolar bubbles inflated by active galactic nucleus (AGN) jets observed in the radio as Perseus A. It presents a spectacular Hα-emitting nebulosity surrounding NGC 1275, with loops and filaments of gas extending to over 50 kpc. The origin of the filaments is still unknown, but probably correlates with the mechanism responsible for the giant buoyant bubbles. We present 2.5 and three-dimensional magnetohydrodynamical (MHD) simulations of the central region of the cluster in which turbulent energy, possibly triggered by star formation and supernovae (SNe) explosions, is introduced. The simulations reveal that the turbulence injected by massive stars could be responsible for the nearly isotropic distribution of filaments and loops that drag magnetic fields upward as indicated by recent observations. Weak shell-like shock fronts propagating into the intracluster medium (ICM) with velocities of 100-500 km s-1 are found, also resembling the observations. The isotropic outflow momentum of the turbulence slows the infall of the ICM, thus limiting further starburst activity in NGC 1275. As the turbulence is subsonic over most of the simulated volume, the turbulent kinetic energy is not efficiently converted into heat and additional heating is required to suppress the cooling flow at the core of the cluster. Simulations combining the MHD turbulence with the AGN outflow can reproduce the temperature radial profile observed around NGC 1275. While the AGN mechanism is the main heating source, the SNe are crucial to isotropize the energy distribution.

Basic helix-loop-helix transcription factors in evolution: Roles in development of mesoderm and neural tissues.

PubMed

Gyoja, Fuki

2017-09-01

Basic helix-loop-helix (bHLH) transcription factors have attracted the attention of developmental and evolutionary biologists for decades because of their conserved functions in mesodermal and neural tissue formation in both vertebrates and fruit flies. Their evolutionary history is of special interest because it will likely provide insights into developmental processes and refinement of metazoan-specific traits. This review briefly considers advances in developmental biological studies on bHLHs/HLHs. I also discuss recent genome-wide surveys and molecular phylogenetic analyses of these factors in a wide range of metazoans. I hypothesize that interactions between metazoan-specific Group A, D, and E bHLH/HLH factors enabled a sophisticated transition system from cell proliferation to differentiation in multicellular development. This control mechanism probably emerged initially to organize a multicellular animal body and was subsequently recruited to form evolutionarily novel tissues, which differentiated during a later ontogenetic phase. © 2017 Wiley Periodicals, Inc.

A short autocomplementary sequence plays an essential role in avian sarcoma-leukosis virus RNA dimerization.

PubMed

Fossé, P; Motté, N; Roumier, A; Gabus, C; Muriaux, D; Darlix, J L; Paoletti, J

1996-12-24

Retroviral genomes consist of two identical RNA molecules joined noncovalently near their 5'-ends. Recently, two models have been proposed for RNA dimer formation on the basis of results obtained in vitro with human immunodeficiency virus type 1 RNA and Moloney murine leukemia virus RNA. It was first proposed that viral RNA dimerizes by forming an interstrand quadruple helix with purine tetrads. The second model postulates that RNA dimerization is initiated by a loop-loop interaction between the two RNA molecules. In order to better characterize the dimerization process of retroviral genomic RNA, we analyzed the in vitro dimerization of avian sarcoma-leukosis virus (ASLV) RNA using different transcripts. We determined the requirements for heterodimer formation, the thermal dissociation of RNA dimers, and the influence of antisense DNA oligonucleotides on dimer formation. Our results strongly suggest that purine tetrads are not involved in dimer formation. Data show that an autocomplementary sequence located upstream from the splice donor site and within a major packaging signal plays a crucial role in ASLV RNA dimer formation in vitro. This sequence is able to form a stem-loop structure, and phylogenetic analysis reveals that it is conserved in 28 different avian sarcoma and leukosis viruses. These results suggest that dimerization of ASLV RNA is initiated by a loop-loop interaction between two RNA molecules and provide an additional argument for the ubiquity of the dimerization process via loop-loop interaction.

Shrunk loop theorem for the topology probabilities of closed Brownian (or Feynman) paths on the twice punctured plane

NASA Astrophysics Data System (ADS)

Giraud, O.; Thain, A.; Hannay, J. H.

2004-02-01

The shrunk loop theorem proved here is an integral identity which facilitates the calculation of the relative probability (or probability amplitude) of any given topology that a free, closed Brownian (or Feynman) path of a given 'duration' might have on the twice punctured plane (plane with two marked points). The result is expressed as a 'scattering' series of integrals of increasing dimensionality based on the maximally shrunk version of the path. Physically, this applies in different contexts: (i) the topology probability of a closed ideal polymer chain on a plane with two impassable points, (ii) the trace of the Schrödinger Green function, and thence spectral information, in the presence of two Aharonov-Bohm fluxes and (iii) the same with two branch points of a Riemann surface instead of fluxes. Our theorem starts from the Stovicek scattering expansion for the Green function in the presence of two Aharonov-Bohm flux lines, which itself is based on the famous Sommerfeld one puncture point solution of 1896 (the one puncture case has much easier topology, just one winding number). Stovicek's expansion itself can supply the results at the expense of choosing a base point on the loop and then integrating it away. The shrunk loop theorem eliminates this extra two-dimensional integration, distilling the topology from the geometry.

Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability.

PubMed

Bonnet, Amandine; Grosso, Ana R; Elkaoutari, Abdessamad; Coleno, Emeline; Presle, Adrien; Sridhara, Sreerama C; Janbon, Guilhem; Géli, Vincent; de Almeida, Sérgio F; Palancade, Benoit

2017-08-17

Transcription is a source of genetic instability that can notably result from the formation of genotoxic DNA:RNA hybrids, or R-loops, between the nascent mRNA and its template. Here we report an unexpected function for introns in counteracting R-loop accumulation in eukaryotic genomes. Deletion of endogenous introns increases R-loop formation, while insertion of an intron into an intronless gene suppresses R-loop accumulation and its deleterious impact on transcription and recombination in yeast. Recruitment of the spliceosome onto the mRNA, but not splicing per se, is shown to be critical to attenuate R-loop formation and transcription-associated genetic instability. Genome-wide analyses in a number of distant species differing in their intron content, including human, further revealed that intron-containing genes and the intron-richest genomes are best protected against R-loop accumulation and subsequent genetic instability. Our results thereby provide a possible rationale for the conservation of introns throughout the eukaryotic lineage. Copyright © 2017 Elsevier Inc. All rights reserved.

Atomistic Simulation of Interstitial Dislocation Loop Evolution under Applied Stresses in BCC Iron

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

Long, Xue Hao; Wang, Dong; Setyawan, Wahyu

Evolution of an interstitial 1/2⟨111⟩ dislocation loop under tensile, shear, and torsion stresses is studied with molecular statics method. Under a tensile stress, the dependence of ultimate tensile strength on size of loop is calculated. The formation of small shear loops around the initial prismatic loop is confirmed as an intermediate state to form the final dislocation network. Under a shear stress, the rotation of a loop is observed not only by a change of the habit plane but also through a transformation between a shear and a prismatic loop. Under torsion, a perfect BCC crystal may undergo a BCCmore » to FCC or BCC to HCP transformation. The present work indicates that a 1/2⟨111⟩ loop can delay these transformations, resulting in the formation of micro-crack on the surface.« less

Formation of prismatic loops from C15 Laves phase interstitial clusters in body-centered cubic iron

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

Zhang, Yongfeng; Bai, Xian-Ming; Tonks, Michael R.

2015-03-01

This Letter reports the transition of C15 phase self-interstitial clusters to loops in body-centered-cubic Iron. Molecular dynamics simulations are performed to evaluate the relative stabilities of difference interstitial cluster configurations including C15 phase structure and <100> and <111>/2 loops. Within a certain size range, C15 cluster are found more stable than loops, and the relative stabilities are reversed beyond that range. In accordance to the crossover in relative stabilities, C15 clusters may grow by absorbing individual interstitials at small sizes and transitions into loops eventually. The transition takes place by nucleation and reaction of <111>/2 loop segments. These observations explainmore » the absence of C15 phase interstitial clusters predicted by density-functional-theory calculations in previous experimental observations. More importantly, the current results provide a new formation mechanism of <100> loops which requires no interaction of loops.« less

Costas loop lock detection in the advanced receiver

NASA Technical Reports Server (NTRS)

Mileant, A.; Hinedi, S.

1989-01-01

The advanced receiver currently being developed uses a Costas digital loop to demodulate the subcarrier. Previous analyses of lock detector algorithms for Costas loops have ignored the effects of the inherent correlation between the samples of the phase-error process. Accounting for this correlation is necessary to achieve the desired lock-detection probability for a given false-alarm rate. Both analysis and simulations are used to quantify the effects of phase correlation on lock detection for the square-law and the absolute-value type detectors. Results are obtained which depict the lock-detection probability as a function of loop signal-to-noise ratio for a given false-alarm rate. The mathematical model and computer simulation show that the square-law detector experiences less degradation due to phase jitter than the absolute-value detector and that the degradation in detector signal-to-noise ratio is more pronounced for square-wave than for sine-wave signals.

First Results from a Hardware-in-the-Loop Demonstration of Closed-Loop Autonomous Formation Flying

NASA Technical Reports Server (NTRS)

Gill, E.; Naasz, Bo; Ebinuma, T.

2003-01-01

A closed-loop system for the demonstration of autonomous satellite formation flying technologies using hardware-in-the-loop has been developed. Making use of a GPS signal simulator with a dual radio frequency outlet, the system includes two GPS space receivers as well as a powerful onboard navigation processor dedicated to the GPS-based guidance, navigation, and control of a satellite formation in real-time. The closed-loop system allows realistic simulations of autonomous formation flying scenarios, enabling research in the fields of tracking and orbit control strategies for a wide range of applications. The autonomous closed-loop formation acquisition and keeping strategy is based on Lyapunov's direct control method as applied to the standard set of Keplerian elements. This approach not only assures global and asymptotic stability of the control but also maintains valuable physical insight into the applied control vectors. Furthermore, the approach can account for system uncertainties and effectively avoids a computationally expensive solution of the two point boundary problem, which renders the concept particularly attractive for implementation in onboard processors. A guidance law has been developed which strictly separates the relative from the absolute motion, thus avoiding the numerical integration of a target trajectory in the onboard processor. Moreover, upon using precise kinematic relative GPS solutions, a dynamical modeling or filtering is avoided which provides for an efficient implementation of the process on an onboard processor. A sample formation flying scenario has been created aiming at the autonomous transition of a Low Earth Orbit satellite formation from an initial along-track separation of 800 m to a target distance of 100 m. Assuming a low-thrust actuator which may be accommodated on a small satellite, a typical control accuracy of less than 5 m has been achieved which proves the applicability of autonomous formation flying techniques to formations of satellites as close as 50 m.

Formation of chromosomal domains in interphase by loop extrusion

NASA Astrophysics Data System (ADS)

Fudenberg, Geoffrey

While genomes are often considered as one-dimensional sequences, interphase chromosomes are organized in three dimensions with an essential role for regulating gene expression. Recent studies have shown that Topologically Associating Domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes. Despite observations that architectural proteins, including CTCF, demarcate and maintain the borders of TADs, the mechanisms underlying TAD formation remain unknown. Here we propose that loop extrusion underlies the formation TADs. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops, but stall at TAD boundaries due to interactions with boundary proteins, including CTCF. This process dynamically forms loops of various sizes within but not between TADs. Using polymer simulations, we find that loop extrusion can produce TADs as determined by our analyses of the highest-resolution experimental data. Moreover, we find that loop extrusion can explain many diverse experimental observations, including: the preferential orientation of CTCF motifs and enrichments of architectural proteins at TAD boundaries; TAD boundary deletion experiments; and experiments with knockdown or depletion of CTCF, cohesin, and cohesin-loading factors. Together, the emerging picture from our work is that TADs are formed by rapidly associating, growing, and dissociating loops, presenting a clear framework for understanding interphase chromosomal organization.

A synthetic neural cell adhesion molecule mimetic peptide promotes synaptogenesis, enhances presynaptic function, and facilitates memory consolidation.

PubMed

Cambon, Karine; Hansen, Stine M; Venero, Cesar; Herrero, A Isabel; Skibo, Galina; Berezin, Vladimir; Bock, Elisabeth; Sandi, Carmen

2004-04-28

The neural cell adhesion molecule (NCAM) plays a critical role in development and plasticity of the nervous system and is involved in the mechanisms of learning and memory. Here, we show that intracerebroventricular administration of the FG loop (FGL), a synthetic 15 amino acid peptide corresponding to the binding site of NCAM for the fibroblast growth factor receptor 1 (FGFR1), immediately after training rats in fear conditioning or water maze learning, induced a long-lasting improvement of memory. In primary cultures of hippocampal neurons, FGL enhanced the presynaptic function through activation of FGFR1 and promoted synapse formation. These results provide the first evidence for a memory-facilitating effect resulting from a treatment that mimics NCAM function. They suggest that increased efficacy of synaptic transmission and formation of new synapses probably mediate the cognition-enhancing properties displayed by the peptide.

Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq

PubMed Central

Dumelie, Jason G

2017-01-01

R-loops are features of chromatin consisting of a strand of DNA hybridized to RNA, as well as the expelled complementary DNA strand. R-loops are enriched at promoters where they have recently been shown to have important roles in modifying gene expression. However, the location of promoter-associated R-loops and the genomic domains they perturb to modify gene expression remain unclear. To resolve this issue, we developed a bisulfite-based approach, bisDRIP-seq, to map R-loops across the genome at near-nucleotide resolution in MCF-7 cells. We found the location of promoter-associated R-loops is dependent on the presence of introns. In intron-containing genes, R-loops are bounded between the transcription start site and the first exon-intron junction. In intronless genes, the 3' boundary displays gene-specific heterogeneity. Moreover, intronless genes are often associated with promoter-associated R-loop formation. Together, these studies provide a high-resolution map of R-loops and identify gene structure as a critical determinant of R-loop formation. PMID:29072160

Undersize solute element effects on defect structure development in copper under electron irradiation

NASA Astrophysics Data System (ADS)

Satoh, Y.; Yoshiie, T.; Arai, S.

2018-03-01

We conducted systematic experiments of defect structure development in Cu base binary alloys under 1000 kV electron irradiation at temperatures higher than 300 K, using in situ observations with high voltage electron microscopy. This report describes the effects of undersize elements: Co (-3.78%), Ni (-8.45%) and Be (-26.45%). The volume size factors are given in parentheses. The amounts of the respective elements were 2, 0.3, 0.05 at.%, or less. In Cu-Ni and Cu-Co and in the reference Cu, temperature dependence of the number density of interstitial-type dislocation loops had a down peak (i.e. loops hardly formed) at approximately 373 K, attributed to unexpected impurity atoms. Above the down-peak temperature, the addition of Co or Ni increased the loop number density through continuous nucleation of loops, extended the loop formation to higher temperatures, and decreased the apparent activation energy of loop growth rate. The addition of Be for 0.3 at.% or more delayed loop formation after formation of stacking fault tetrahedra (SFTs) around 300 K. The apparent mobility of self-interstitial atoms is expected to be smaller than that of vacancies because of strong binding with Be. Loop formation at temperatures higher than 373 K was enhanced by Be for 0.3 or 2 at.%, although it was suppressed greatly for 0.05 at.% or less. All undersize atoms increased the stability of SFTs under irradiation. Mechanisms of those effects were discussed and were briefly compared with earlier results found for oversize elements in Cu.

Spatial-pattern-induced evolution of a self-replicating loop network.

PubMed

Suzuki, Keisuke; Ikegami, Takashi

2006-01-01

We study a system of self-replicating loops in which interaction rules between individuals allow competition that leads to the formation of a hypercycle-like network. The main feature of the model is the multiple layers of interaction between loops, which lead to both global spatial patterns and local replication. The network of loops manifests itself as a spiral structure from which new kinds of self-replicating loops emerge at the boundaries between different species. In these regions, larger and more complex self-replicating loops live for longer periods of time, managing to self-replicate in spite of their slower replication. Of particular interest is how micro-scale interactions between replicators lead to macro-scale spatial pattern formation, and how these macro-scale patterns in turn perturb the micro-scale replication dynamics.

Effect of supercoiling on formation of protein-mediated DNA loops

NASA Astrophysics Data System (ADS)

Purohit, P. K.; Nelson, P. C.

2006-12-01

DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic rod model of DNA to determine the free energy of forming short (50-100 basepair), protein mediated DNA loops. Superhelical stress in the DNA of living cells is a critical factor determining the energetics of loop formation, and we explicitly account for it in our calculations. The repressor protein itself is regarded as a rigid coupler; its geometry enters the problem through the boundary conditions it applies on the DNA. We show that a theory with these ingredients is sufficient to explain certain features observed in modulation of in vivo gene activity as a function of the distance between operator sites for the lac repressor. We also use our theory to make quantitative predictions for the dependence of looping on superhelical stress, which may be testable both in vivo and in single-molecule experiments such as the tethered particle assay and the magnetic bead assay.

Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses.

PubMed

Hamperl, Stephan; Bocek, Michael J; Saldivar, Joshua C; Swigut, Tomek; Cimprich, Karlene A

2017-08-10

Conflicts between transcription and replication are a potent source of DNA damage. Co-transcriptional R-loops could aggravate such conflicts by creating an additional barrier to replication fork progression. Here, we use a defined episomal system to investigate how conflict orientation and R-loop formation influence genome stability in human cells. R-loops, but not normal transcription complexes, induce DNA breaks and orientation-specific DNA damage responses during conflicts with replication forks. Unexpectedly, the replisome acts as an orientation-dependent regulator of R-loop levels, reducing R-loops in the co-directional (CD) orientation but promoting their formation in the head-on (HO) orientation. Replication stress and deregulated origin firing increase the number of HO collisions leading to genome-destabilizing R-loops. Our findings connect DNA replication to R-loop homeostasis and suggest a mechanistic basis for genome instability resulting from deregulated DNA replication, observed in cancer and other disease states. Copyright © 2017 Elsevier Inc. All rights reserved.

Eruption of a plasma blob, associated M-class flare, and large-scale extreme-ultraviolet wave observed by SDO

NASA Astrophysics Data System (ADS)

Kumar, P.; Manoharan, P. K.

2013-05-01

We present a multiwavelength study of the formation and ejection of a plasma blob and associated extreme ultraviolet (EUV) waves in active region (AR) NOAA 11176, observed by SDO/AIA and STEREO on 25 March 2011. The EUV images observed with the AIA instrument clearly show the formation and ejection of a plasma blob from the lower atmosphere of the Sun at ~9 min prior to the onset of the M1.0 flare. This onset of the M-class flare happened at the site of the blob formation, while the blob was rising in a parabolic path with an average speed of ~300 km s. The blob also showed twisting and de-twisting motion in the lower corona, and the blob speed varied from ~10-540 km s. The faster and slower EUV wavefronts were observed in front of the plasma blob during its impulsive acceleration phase. The faster EUV wave propagated with a speed of ~785 to 1020 km s, whereas the slower wavefront speed varied in between ~245 and 465 km s. The timing and speed of the faster wave match the shock speed estimated from the drift rate of the associated type II radio burst. The faster wave experiences a reflection by the nearby AR NOAA 11177. In addition, secondary waves were observed (only in the 171 Å channel), when the primary fast wave and plasma blob impacted the funnel-shaped coronal loops. The Helioseismic Magnetic Imager (HMI) magnetograms revealed the continuous emergence of new magnetic flux along with shear flows at the site of the blob formation. It is inferred that the emergence of twisted magnetic fields in the form of arch-filaments/"anemone-type" loops is the likely cause for the plasma blob formation and associated eruption along with the triggering of M-class flare. Furthermore, the faster EUV wave formed ahead of the blob shows the signature of fast-mode MHD wave, whereas the slower wave seems to be generated by the field line compression by the plasma blob. The secondary wave trains originated from the funnel-shaped loops are probably the fast magnetoacoustic waves. Three movies are available in electronic form at http://www.aanda.org

A Closed-Loop Hardware Simulation of Decentralized Satellite Formation Control

NASA Technical Reports Server (NTRS)

Ebimuma, Takuji; Lightsey, E. Glenn; Baur, Frank (Technical Monitor)

2002-01-01

In recent years, there has been significant interest in the use of formation flying spacecraft for a variety of earth and space science missions. Formation flying may provide smaller and cheaper satellites that, working together, have more capability than larger and more expensive satellites. Several decentralized architectures have been proposed for autonomous establishment and maintenance of satellite formations. In such architectures, each satellite cooperatively maintains the shape of the formation without a central supervisor, and processing only local measurement information. The Global Positioning System (GPS) sensors are ideally suited to provide such local position and velocity measurements to the individual satellites. An investigation of the feasibility of a decentralized approach to satellite formation flying was originally presented by Carpenter. He extended a decentralized linear-quadratic-Gaussian (LQG) framework proposed by Speyer in a fashion similar to an extended Kalman filter (EKE) which processed GPS position fix solutions. The new decentralized LQG architecture was demonstrated in a numerical simulation for a realistic scenario that is similar to missions that have been proposed by NASA and the U.S. Air Force. Another decentralized architecture was proposed by Park et al. using carrier differential-phase GPS (CDGPS). Recently, Busse et al demonstrated the decentralized CDGPS architecture in a hardware-in-the-loop simulation on the Formation Flying TestBed (FFTB) at Goddard Space Flight Center (GSFC), which features two Spirent Cox 16 channel GPS signal generator. Although representing a step forward by utilizing GPS signal simulators for a spacecraft formation flying simulation, only an open-loop performance, in which no maneuvers were executed based on the real-time state estimates, was considered. In this research, hardware experimentation has been extended to include closed-loop integrated guidance and navigation of multiple spacecraft formations using GPS receivers and real-time vehicle telemetry. A hardware closed-loop simulation has been performed using the decentralized LQG architecture proposed by Carpenter in the GPS test facility at the Center for Space Research (CSR). This is the first presentation using this type of hardware for demonstration of closed-loop spacecraft formation flying.

Prediction of induction time for methane hydrate formation in the presence or absence of THF in flow loop system by Natarajan model

NASA Astrophysics Data System (ADS)

Talaghat, Mohammad Reza; Jokar, Seyyed Mohammad

2018-03-01

The induction time is a time interval to detect the initial hydrate formation, which is counted from the moment when the stirrer is turned on until the first detection of hydrate formation. The main objective of the present work is to predict and measure the induction time of methane hydrate formation in the presence or absence of tetrahydrofuran (THF) as promoter in the flow loop system. A laboratory flow mini-loop apparatus was set up to measure the induction time of methane hydrate formation. The induction time is predicted using developed Kashchiev and Firoozabadi model and modified model of Natarajan for a flow loop system. Furthermore, the effects of volumetric flow rate of the fluid on the induction time were investigated. The results of the models were compared with experimental data. They show that the induction time of hydrate formation in the presence of THF is very short at high pressure and high volumetric flow rate of the fluid. It decreases with increasing pressure and liquid volumetric flow rate. It is also shown that the modified Natarajan model is more accurate than the Kashchiev and Firoozabadi ones in prediction of the induction time.

The Formation of Coronal Loops by Thermal Instability in Three Dimensions

NASA Technical Reports Server (NTRS)

Mok, Yung; Mikic, Zoran; Lionello, Roberto; Linker, Jon A.

2008-01-01

Plasma loops in solar active regions have been observed in EUV and soft X-rays for decades. Their formation mechanism and properties, however, are still not fully understood. Predictions by early models, based on 1D hydrostatic equilibria with uniform plasma heating, are not consistent with high-resolution measurements. In this Letter, we demonstrate, via 3D simulations, that a class of heating models can lead to the dynamic formation of plasma loops provided the plasma is heated sufficiently to match SXT soft X-ray measurements. We show that individual flux tubes in a 3D magnetic structure tend to stand out against their neighbors. The loops have large aspect ratios and nearly uniform cross sections in the corona, similar to those observed by EIT and TRACE. The coronal EUV emission from these thermally unstable solutions is roughly consistent with EIT measurements. The solution oscillates in time through a large-amplitude, nonlinear cycle, leading to repeated brightening and fading of the loops.

Sequence Effect on the Formation of DNA Minidumbbells.

PubMed

Liu, Yuan; Lam, Sik Lok

2017-11-16

The DNA minidumbbell (MDB) is a recently identified non-B structure. The reported MDBs contain two TTTA, CCTG, or CTTG type II loops. At present, the knowledge and understanding of the sequence criteria for MDB formation are still limited. In this study, we performed a systematic high-resolution nuclear magnetic resonance (NMR) and native gel study to investigate the effect of sequence variations in tandem repeats on the formation of MDBs. Our NMR results reveal the importance of hydrogen bonds, base-base stacking, and hydrophobic interactions from each of the participating residues. We conclude that in the MDBs formed by tandem repeats, C-G loop-closing base pairs are more stabilizing than T-A loop-closing base pairs, and thymine residues in both the second and third loop positions are more stabilizing than cytosine residues. The results from this study enrich our knowledge on the sequence criteria for the formation of MDBs, paving a path for better exploring their potential roles in biological systems and DNA nanotechnology.

Optimal spacecraft formation establishment and reconfiguration propelled by the geomagnetic Lorentz force

NASA Astrophysics Data System (ADS)

Huang, Xu; Yan, Ye; Zhou, Yang

2014-12-01

The Lorentz force acting on an electrostatically charged spacecraft as it moves through the planetary magnetic field could be utilized as propellantless electromagnetic propulsion for orbital maneuvering, such as spacecraft formation establishment and formation reconfiguration. By assuming that the Earth's magnetic field could be modeled as a tilted dipole located at the center of Earth that corotates with Earth, a dynamical model that describes the relative orbital motion of Lorentz spacecraft is developed. Based on the proposed dynamical model, the energy-optimal open-loop trajectories of control inputs, namely, the required specific charges of Lorentz spacecraft, for Lorentz-propelled spacecraft formation establishment or reconfiguration problems with both fixed and free final conditions constraints are derived via Gauss pseudospectral method. The effect of the magnetic dipole tilt angle on the optimal control inputs and the relative transfer trajectories for formation establishment or reconfiguration is also investigated by comparisons with the results derived from a nontilted dipole model. Furthermore, a closed-loop integral sliding mode controller is designed to guarantee the trajectory tracking in the presence of external disturbances and modeling errors. The stability of the closed-loop system is proved by a Lyapunov-based approach. Numerical simulations are presented to verify the validity of the proposed open-loop control methods and demonstrate the performance of the closed-loop controller. Also, the results indicate the dipole tilt angle should be considered when designing control strategies for Lorentz-propelled spacecraft formation establishment or reconfiguration.

PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation.

PubMed

Belotserkovskii, Boris P; Hanawalt, Philip C

2015-11-01

Peptide Nucleic Acids (PNAs) are artificial DNA mimics with superior nucleic acid binding capabilities. T7 RNA polymerase (T7 RNAP) transcription upon encountering PNA bound to the non-template DNA strand was studied in vitro. A characteristic pattern of blockage signals was observed, extending downstream from the PNA binding site, similar to that produced by G-rich homopurine-homopyrimidine (hPu-hPy) sequences and likely caused by R-loop formation. Since blocked transcription complexes in association with stable R-loops may interfere with replication and in some cases trigger apoptosis, targeted R-loop formation might be employed to inactivate selected cells, such as those in tumors, based upon their unique complement of expressed genes. © 2014 The Authors. Molecular Carcinogenesis published by Wiley Periodicals, Inc.

Scattering of Cosmic Strings by Black Holes:. Loop Formation

NASA Astrophysics Data System (ADS)

Dubath, Florian; Sakellariadou, Mairi; Viallet, Claude Michel

We study the deformation of a long cosmic string by a nearby rotating black hole. We examine whether the deformation of a cosmic string, induced by the gravitational field of a Kerr black hole, may lead to the formation of a string loop. The segment of the string which enters the ergo-sphere of a rotating black hole gets deformed and, if it is sufficiently twisted, it can self-intersect, chopping off a loop. We find that the formation of a loop, via such a mechanism, is a rare event. It will only arise in a small region of the collision phase space, which depends on the string velocity, the impact parameter and the black hole angular momentum. We conclude that, generically, a long cosmic string is simply scattered, or captured, by a nearby rotating black hole.

Control of polymer network topology in semi-batch systems

NASA Astrophysics Data System (ADS)

Wang, Rui; Olsen, Bradley; Johnson, Jeremiah

Polymer networks invariably possess topological defects: loops of different orders. Since small loops (primary loops and secondary loops) both lower the modulus of network and lead to stress concentration that causes material failure at low deformation, it is desirable to greatly reduce the loop fraction. We have shown that achieving loop fraction close to zero is extremely difficult in the batch process due to the slow decay of loop fraction with the polymer concentration and chain length. Here, we develop a modified kinetic graph theory that can model network formation reactions in semi-batch systems. We demonstrate that the loop fraction is not sensitive to the feeding policy if the reaction volume maintains constant during the network formation. However, if we initially put concentrated solution of small junction molecules in the reactor and continuously adding polymer solutions, the fractions of both primary loop and higher-order loops will be significantly reduced. There is a limiting value (nonzero) of loop fraction that can be achieved in the semi-batch system in condition of extremely slow feeding rate. This minimum loop fraction only depends on a single dimensionless variable, the product of concentration and with single chain pervaded volume, and defines an operating zone in which the loop fraction of polymer networks can be controlled through adjusting the feeding rate of the semi-batch process.

An efficient algorithm to compute marginal posterior genotype probabilities for every member of a pedigree with loops

PubMed Central

2009-01-01

Background Marginal posterior genotype probabilities need to be computed for genetic analyses such as geneticcounseling in humans and selective breeding in animal and plant species. Methods In this paper, we describe a peeling based, deterministic, exact algorithm to compute efficiently genotype probabilities for every member of a pedigree with loops without recourse to junction-tree methods from graph theory. The efficiency in computing the likelihood by peeling comes from storing intermediate results in multidimensional tables called cutsets. Computing marginal genotype probabilities for individual i requires recomputing the likelihood for each of the possible genotypes of individual i. This can be done efficiently by storing intermediate results in two types of cutsets called anterior and posterior cutsets and reusing these intermediate results to compute the likelihood. Examples A small example is used to illustrate the theoretical concepts discussed in this paper, and marginal genotype probabilities are computed at a monogenic disease locus for every member in a real cattle pedigree. PMID:19958551

A novel method for reducing gap formation in tendon repair.

PubMed

Dean, Ryan; Sethi, Paul

2018-03-01

This study investigates gap formation in tendon repair using a novel tensioning method. The novel stitch will demonstrate less gap formation than the other suture configurations tested. Porcine tendons stitched with classic Krackow stitch configurations were compared to a Krackow stitch modified with a proximal Tension-Assist Loop. Each group was cyclically loaded followed by analysis of the tendon-suture construct for gap formation. The Tension-Assist Loop group produced significantly less gap formation than each of the other stitch groups. Decreasing early gap formation may be beneficial in allowing early rehabilitation and range of motion.

Small-scale Magnetic Flux Emergence in the Quiet Sun

NASA Astrophysics Data System (ADS)

Moreno-Insertis, F.; Martinez-Sykora, J.; Hansteen, V. H.; Muñoz, D.

2018-06-01

Small bipolar magnetic features are observed to appear in the interior of individual granules in the quiet Sun, signaling the emergence of tiny magnetic loops from the solar interior. We study the origin of those features as part of the magnetoconvection process in the top layers of the convection zone. Two quiet-Sun magnetoconvection models, calculated with the radiation-magnetohydrodynamic (MHD) Bifrost code and with domain stretching from the top layers of the convection zone to the corona, are analyzed. Using 3D visualization as well as a posteriori spectral synthesis of Stokes parameters, we detect the repeated emergence of small magnetic elements in the interior of granules, as in the observations. Additionally, we identify the formation of organized horizontal magnetic sheets covering whole granules. Our approach is twofold, calculating statistical properties of the system, like joint probability density functions (JPDFs), and pursuing individual events via visualization tools. We conclude that the small magnetic loops surfacing within individual granules in the observations may originate from sites at or near the downflows in the granular and mesogranular levels, probably in the first 1 or 1.5 Mm below the surface. We also document the creation of granule-covering magnetic sheet-like structures through the sideways expansion of a small subphotospheric magnetic concentration picked up and pulled out of the interior by a nascent granule. The sheet-like structures that we found in the models may match the recent observations of Centeno et al.

High-Altitude Closed Magnetic Loops at Mars Observed by MAVEN

NASA Astrophysics Data System (ADS)

Xu, Shaosui; Mitchell, David; Luhmann, Janet; Ma, Yingjuan; Fang, Xiaohua; Harada, Yuki; Hara, Takuya; Brain, David; Weber, Tristan; Mazelle, Christian; DiBraccio, Gina A.

2017-11-01

With electron and magnetic field data obtained by the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft, we have identified closed magnetic field lines, with both foot points embedded in the dayside ionosphere, extending up to 6,200 km altitude into the Martian tail. This topology is deduced from photoelectrons produced in the dayside ionosphere being observed traveling both parallel and antiparallel to the magnetic field. At trapped-zone pitch angles (within a range centered on 90° where electrons magnetically reflect before interacting with the atmosphere), cases with either solar wind electrons or photoelectrons have been found, indicating different formation mechanisms for these closed loops. These large closed loops are present in MHD simulations. The case with field-aligned photoelectrons mixed with solar wind electrons having trapped-zone pitch angles is likely to be associated with reconnection, while the case with photoelectrons at all pitch angles is probably due to closed field lines being pulled tailward by the surrounding plasma flow. By utilizing an algorithm for distinguishing photoelectrons from solar wind electrons in pitch angle-resolved energy spectra, we systematically map the spatial distribution and occurrence rate of these closed magnetic loops over the region sampled by the MAVEN orbit. We find that the occurrence rate ranges from a few percent to a few tens of percent outside of the optical shadow and less than one percent within the shadow. These observations can be used to investigate the general magnetic topology in the tail, which is relevant to cold ion escape, reconnection, and flux ropes.

How a short double-stranded DNA bends

NASA Astrophysics Data System (ADS)

Shin, Jaeoh; Lee, O.-Chul; Sung, Wokyung

2015-04-01

A recent experiment using fluorescence microscopy showed that double-stranded DNA fragments shorter than 100 base pairs loop with the probabilities higher by the factor of 102-106 than predicted by the worm-like chain (WLC) model [R. Vafabakhsh and T. Ha, Science 337, 1101(2012)]. Furthermore, the looping probabilities were found to be nearly independent of the loop size. The results signify a breakdown of the WLC model for DNA mechanics which works well on long length scales and calls for fundamental understanding for stressed DNA on shorter length scales. We develop an analytical, statistical mechanical model to investigate what emerges to the short DNA under a tight bending. A bending above a critical level initiates nucleation of a thermally induced bubble, which could be trapped for a long time, in contrast to the bubbles in both free and uniformly bent DNAs, which are either transient or unstable. The trapped bubble is none other than the previously hypothesized kink, which releases the bending energy more easily as the contour length decreases. It leads to tremendous enhancement of the cyclization probabilities, in a reasonable agreement with experiment.

Hardware-In-The-Loop Testing of Continuous Control Algorithms for a Precision Formation Flying Demonstration Mission

NASA Technical Reports Server (NTRS)

Naasz, Bo J.; Burns, Richard D.; Gaylor, David; Higinbotham, John

2004-01-01

A sample mission sequence is defined for a low earth orbit demonstration of Precision Formation Flying (PFF). Various guidance navigation and control strategies are discussed for use in the PFF experiment phases. A sample PFF experiment is implemented and tested in a realistic Hardware-in-the-Loop (HWIL) simulation using the Formation Flying Test Bed (FFTB) at NASA's Goddard Space Flight Center.

Processing of double-R-loops in (CAG)·(CTG) and C9orf72 (GGGGCC)·(GGCCCC) repeats causes instability

PubMed Central

Reddy, Kaalak; Schmidt, Monika H.M.; Geist, Jaimie M.; Thakkar, Neha P.; Panigrahi, Gagan B.; Wang, Yuh-Hwa; Pearson, Christopher E.

2014-01-01

R-loops, transcriptionally-induced RNA:DNA hybrids, occurring at repeat tracts (CTG)n, (CAG)n, (CGG)n, (CCG)n and (GAA)n, are associated with diseases including myotonic dystrophy, Huntington's disease, fragile X and Friedreich's ataxia. Many of these repeats are bidirectionally transcribed, allowing for single- and double-R-loop configurations, where either or both DNA strands may be RNA-bound. R-loops can trigger repeat instability at (CTG)·(CAG) repeats, but the mechanism of this is unclear. We demonstrate R-loop-mediated instability through processing of R-loops by HeLa and human neuron-like cell extracts. Double-R-loops induced greater instability than single-R-loops. Pre-treatment with RNase H only partially suppressed instability, supporting a model in which R-loops directly generate instability by aberrant processing, or via slipped-DNA formation upon RNA removal and its subsequent aberrant processing. Slipped-DNAs were observed to form following removal of the RNA from R-loops. Since transcriptionally-induced R-loops can occur in the absence of DNA replication, R-loop processing may be a source of repeat instability in the brain. Double-R-loop formation and processing to instability was extended to the expanded C9orf72 (GGGGCC)·(GGCCCC) repeats, known to cause amyotrophic lateral sclerosis and frontotemporal dementia, providing the first suggestion through which these repeats may become unstable. These findings provide a mechanistic basis for R-loop-mediated instability at disease-associated repeats. PMID:25147206

R-loops in bacterial transcription: their causes and consequences.

PubMed

Gowrishankar, J; Leela, J Krishna; Anupama, K

2013-01-01

Nascent untranslated transcripts in bacteria are prone to generating RNA-DNA hybrids (R-loops); Rho-dependent transcription termination acts to reduce their prevalence. Here we discuss the mechanisms of R-loop formation and growth inhibition in bacteria.

Wavefront tilt feedforward for the formation interferometer testbad (FIT)

NASA Technical Reports Server (NTRS)

Shields, J. F.; Liewer, K.; Wehmeier, U.

2002-01-01

Separated spacecraft interferometry is a candidate architecture for several future NASA missions. The Formation Interferometer Testbed (FIT) is a ground based testbed dedicated to the validation of this key technology for a formation of two spacecraft. In separated spacecraft interferometry, the residual relative motion of the component spacecraft must be compensated for by articulation of the optical components. In this paper, the design of the FIT interferometer pointing control system is described. This control system is composed of a metrology pointing loop that maintains an optical link between the two spacecraft and two stellar pointing loops for stabilizing the stellar wavefront at both the right and left apertures of the instrument. A novel feedforward algorithm is used to decouple the metrology loop from the left side stellar loop. Experimental results from the testbed are presented that verify this approach and that fully demonstrate the performance of the algorithm.

A cosmic book. [of physics of early universe

NASA Technical Reports Server (NTRS)

Peebles, P. J. E.; Silk, Joseph

1988-01-01

A system of assigning odds to the basic elements of cosmological theories is proposed in order to evaluate the strengths and weaknesses of the theories. A figure of merit for the theories is obtained by counting and weighing the plausibility of each of the basic elements that is not substantially supported by observation or mature fundamental theory. The magnetized strong model is found to be the most probable. In order of decreasing probability, the ranking for the rest of the models is: (1) the magnetized string model with no exotic matter and the baryon adiabatic model; (2) the hot dark matter model and the model of cosmic string loops; (3) the canonical cold dark matter model, the cosmic string loops model with hot dark matter, and the baryonic isocurvature model; and (4) the cosmic string loops model with no exotic matter.

The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.

PubMed

Tsuchiya, Yuko; Mizuguchi, Kenji

2016-04-01

Of the complementarity-determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen-binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen-binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen-binding tendencies of all the CDR loops. © 2016 The Protein Society.

Analytical solutions to optimal underactuated spacecraft formation reconfiguration

NASA Astrophysics Data System (ADS)

Huang, Xu; Yan, Ye; Zhou, Yang

2015-11-01

Underactuated systems can generally be defined as systems with fewer number of control inputs than that of the degrees of freedom to be controlled. In this paper, analytical solutions to optimal underactuated spacecraft formation reconfiguration without either the radial or the in-track control are derived. By using a linear dynamical model of underactuated spacecraft formation in circular orbits, controllability analysis is conducted for either underactuated case. Indirect optimization methods based on the minimum principle are then introduced to generate analytical solutions to optimal open-loop underactuated reconfiguration problems. Both fixed and free final conditions constraints are considered for either underactuated case and comparisons between these two final conditions indicate that the optimal control strategies with free final conditions require less control efforts than those with the fixed ones. Meanwhile, closed-loop adaptive sliding mode controllers for both underactuated cases are designed to guarantee optimal trajectory tracking in the presence of unmatched external perturbations, linearization errors, and system uncertainties. The adaptation laws are designed via a Lyapunov-based method to ensure the overall stability of the closed-loop system. The explicit expressions of the terminal convergent regions of each system states have also been obtained. Numerical simulations demonstrate the validity and feasibility of the proposed open-loop and closed-loop control schemes for optimal underactuated spacecraft formation reconfiguration in circular orbits.

The Strength of an Ig Switch Region is Determined by its Ability to Drive R-loop Formation and its Number of WGCW Sites

PubMed Central

Zhang, Zheng Z.; Pannunzio, Nicholas R.; Han, Li; Hsieh, Chih-Lin; Yu, Kefei; Lieber, Michael R.

2014-01-01

SUMMARY R-loops exist at the murine IgH switch regions and possibly other locations, but their functional importance is unclear. In biochemical systems, R-loop initiation requires DNA sequence regions containing clusters of G nucleotides, but cellular studies have not been done. Here, we vary the G-clustering, total switch region length, and the number of target sites (WGCW sites for the activation-induced deaminase) at synthetic switch regions in a murine B cell line to determine the effect on class switch recombination (CSR). G-clusters increase CSR, regardless of their immediate proximity to the WGCW sites. This increase is accompanied by an increase in R-loop formation. CSR efficiency correlates better with the absolute number of WGCW sites in the switch region rather than the total switch region length or density of WGCW sites. Thus, the overall strength of the switch region depends on G-clusters, which initiate R-loop formation, and on the number of WGCW sites. PMID:25017067

Efficient Ligation of the Schistosoma Hammerhead Ribozyme †

PubMed Central

Canny, Marella D.; Jucker, Fiona M.; Pardi, Arthur

2011-01-01

The hammerhead ribozyme from Schistosoma mansoni is the best characterized of the natural hammerhead ribozymes. Biophysical, biochemical, and structural studies have shown that the formation of the loop-loop tertiary interaction between stems I and II alters the global folding, cleavage kinetics, and conformation of the catalytic core of this hammerhead, leading to a ribozyme that is readily cleaved under physiological conditions. This study investigates the ligation kinetics and the internal equilibrium between cleavage and ligation for the Schistosoma hammerhead. Single turnover kinetic studies on a construct where the ribozyme cleaves and ligates substrate(s) in trans showed up to 23% ligation when starting from fully cleaved products. This was achieved by a ~2,000-fold increase in the rate of ligation compared to a minimal hammerhead without the loop-loop tertiary interaction, yielding an internal equilibrium that ranges from 2–3 at physiological Mg2+ ion concentrations (0.1 –1 mM). Thus, the natural Schistosoma hammerhead ribozyme is almost as efficient at ligation as it is at cleavage. The results here are consistent with a model where formation of the loop-loop tertiary interaction leads to a higher population of catalytically active molecules, and where formation of this tertiary interaction has a much larger effect on the ligation than the cleavage activity of the Schistosoma hammerhead ribozyme. PMID:17319693

Probing the elastic limit of DNA bending

PubMed Central

Le, Tung T.; Kim, Harold D.

2014-01-01

Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using single-molecule Fluorescence Resonance Energy Transfer. The relationship of loop lifetime to loop size revealed a critical transition in bending stress. Above the critical loop size, the loop lifetime changed with loop size in a manner consistent with elastic bending stress, but below it, became less sensitive to loop size, indicative of softened dsDNA. The critical loop size increased from ∼60 bp to ∼100 bp with the addition of 5 mM magnesium. We show that our result is in quantitative agreement with the kinkable worm-like chain model, and furthermore, can reproduce previously reported looping probabilities of dsDNA over the range between 50 and 200 bp. Our findings shed new light on the energetics of sharply bent dsDNA. PMID:25122748

The formation flare loops by magnetic reconnection and chromospheric ablation

NASA Technical Reports Server (NTRS)

Forbes, T. G.; Malherbe, J. M.; Priest, E. R.

1989-01-01

Noncoplanar compressible reconnection theory is combined here with simple scaling arguments for ablation and radiative cooling to predict average properties of hot and cool flare loops as a function of the coronal vector magnetic field. For a coronal field strength of 100 G, the temperature of the hot flare loops decreases from 1.2 x 10 to the 7th K to 4.0 x 10 to the 6th K as the component of the coronal magnetic field perpendicular to the plane of the loops increases from 0 percent to 86 percent of the total field. When the perpendicular component exceeds 86 percent of the total field or when the altitude of the reconnection site exceeds 10 to the 6th km, flare loops no longer occur. Shock-enhanced radiative cooling triggers the formation of cool H-alpha flare loops with predicted densities of roughly 10 to the 13th/cu cm, and a small gap of roughly 1000 km is predicted to exist between the footpoints of the cool flare loops and the inner edges of the flare ribbons.

Kinetics of interior loop formation in semiflexible chains.

PubMed

Hyeon, Changbong; Thirumalai, D

2006-03-14

Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using a mean field approach. Using the potential of mean force derived from the distance distribution function we present a simple expression for the kinetics of interior looping by adopting Kramers theory. For the parameters, that are appropriate for DNA, the theoretical predictions in comparison with the case are in excellent agreement with explicit Brownian dynamics simulations of wormlike chain (WLC) model. The interior looping times (tauIC) can be greatly altered in the cases when the stiffness of the loop differs from that of the dangling ends. If the dangling end is stiffer than the loop then tauIC increases for the case of the WLC with uniform persistence length. In contrast, attachment of flexible dangling ends enhances rate of interior loop formation. The theory also shows that if the monomers are charged and interact via screened Coulomb potential then both the cyclization (tauc) and interior looping (tauIC) times greatly increase at low ionic concentration. Because both tauc and tauIC are determined essentially by the effective persistence length [lp(R)] we computed lp(R) by varying the range of the repulsive interaction between the monomers. For short range interactions lp(R) nearly coincides with the bare persistence length which is determined largely by the backbone chain connectivity. This finding rationalizes the efficacy of describing a number of experimental observations (response of biopolymers to force and cyclization kinetics) in biomolecules using WLC model with an effective persistence length.

The Statistical Loop Analyzer (SLA)

NASA Technical Reports Server (NTRS)

Lindsey, W. C.

1985-01-01

The statistical loop analyzer (SLA) is designed to automatically measure the acquisition, tracking and frequency stability performance characteristics of symbol synchronizers, code synchronizers, carrier tracking loops, and coherent transponders. Automated phase lock and system level tests can also be made using the SLA. Standard baseband, carrier and spread spectrum modulation techniques can be accomodated. Through the SLA's phase error jitter and cycle slip measurements the acquisition and tracking thresholds of the unit under test are determined; any false phase and frequency lock events are statistically analyzed and reported in the SLA output in probabilistic terms. Automated signal drop out tests can be performed in order to trouble shoot algorithms and evaluate the reacquisition statistics of the unit under test. Cycle slip rates and cycle slip probabilities can be measured using the SLA. These measurements, combined with bit error probability measurements, are all that are needed to fully characterize the acquisition and tracking performance of a digital communication system.

RFI in hybrid loops - Simulation and experimental results.

NASA Technical Reports Server (NTRS)

Ziemer, R. E.; Nelson, D. R.; Raghavan, H. R.

1972-01-01

A digital simulation of an imperfect second-order hybrid phase-locked loop (HPLL) operating in radio frequency interference (RFI) is described. Its performance is characterized in terms of phase error variance and phase error probability density function (PDF). Monte-Carlo simulation is used to show that the HPLL can be superior to the conventional phase-locked loops in RFI backgrounds when minimum phase error variance is the goodness criterion. Similar experimentally obtained data are given in support of the simulation data.

Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.

PubMed

White, Neil A; Hoogstraten, Charles G

2017-09-01

The hairpin ribozyme consists of two RNA internal loops that interact to form the catalytically active structure. This docking transition is a rare example of intermolecular formation of RNA tertiary structure without coupling to helix annealing. We have used temperature-dependent surface plasmon resonance (SPR) to characterize the thermodynamics and kinetics of RNA tertiary structure formation for the junctionless form of the ribozyme, in which loops A and B reside on separate molecules. We find docking to be strongly enthalpy-driven and to be accompanied by substantial activation barriers for association and dissociation, consistent with the structural reorganization of both internal loops upon complex formation. Comparisons with the parallel analysis of a ribozyme variant carrying a 2'-O-methyl modification at the self-cleavage site and with published data in other systems reveal a surprising diversity of thermodynamic signatures, emphasizing the delicate balance of contributions to the free energy of formation of RNA tertiary structure. Copyright © 2017 Elsevier B.V. All rights reserved.

Frequency-Locked Detector Threshold Setting Criteria Based on Mean-Time-To-Lose-Lock (MTLL) for GPS Receivers

PubMed Central

Zhao, Na; Qin, Honglei; Sun, Kewen; Ji, Yuanfa

2017-01-01

Frequency-locked detector (FLD) has been widely utilized in tracking loops of Global Positioning System (GPS) receivers to indicate their locking status. The relation between FLD and lock status has been seldom discussed. The traditional PLL experience is not suitable for FLL. In this paper, the threshold setting criteria for frequency-locked detector in the GPS receiver has been proposed by analyzing statistical characteristic of FLD output. The approximate probability distribution of frequency-locked detector is theoretically derived by using a statistical approach, which reveals the relationship between probabilities of frequency-locked detector and the carrier-to-noise ratio (C/N0) of the received GPS signal. The relationship among mean-time-to-lose-lock (MTLL), detection threshold and lock probability related to C/N0 can be further discovered by utilizing this probability. Therefore, a theoretical basis for threshold setting criteria in frequency locked loops for GPS receivers is provided based on mean-time-to-lose-lock analysis. PMID:29207546

Frequency-Locked Detector Threshold Setting Criteria Based on Mean-Time-To-Lose-Lock (MTLL) for GPS Receivers.

PubMed

Jin, Tian; Yuan, Heliang; Zhao, Na; Qin, Honglei; Sun, Kewen; Ji, Yuanfa

2017-12-04

Frequency-locked detector (FLD) has been widely utilized in tracking loops of Global Positioning System (GPS) receivers to indicate their locking status. The relation between FLD and lock status has been seldom discussed. The traditional PLL experience is not suitable for FLL. In this paper, the threshold setting criteria for frequency-locked detector in the GPS receiver has been proposed by analyzing statistical characteristic of FLD output. The approximate probability distribution of frequency-locked detector is theoretically derived by using a statistical approach, which reveals the relationship between probabilities of frequency-locked detector and the carrier-to-noise ratio ( C / N ₀) of the received GPS signal. The relationship among mean-time-to-lose-lock (MTLL), detection threshold and lock probability related to C / N ₀ can be further discovered by utilizing this probability. Therefore, a theoretical basis for threshold setting criteria in frequency locked loops for GPS receivers is provided based on mean-time-to-lose-lock analysis.

Chemical Distances for Percolation of Planar Gaussian Free Fields and Critical Random Walk Loop Soups

NASA Astrophysics Data System (ADS)

Ding, Jian; Li, Li

2018-05-01

We initiate the study on chemical distances of percolation clusters for level sets of two-dimensional discrete Gaussian free fields as well as loop clusters generated by two-dimensional random walk loop soups. One of our results states that the chemical distance between two macroscopic annuli away from the boundary for the random walk loop soup at the critical intensity is of dimension 1 with positive probability. Our proof method is based on an interesting combination of a theorem of Makarov, isomorphism theory, and an entropic repulsion estimate for Gaussian free fields in the presence of a hard wall.

Chemical Distances for Percolation of Planar Gaussian Free Fields and Critical Random Walk Loop Soups

NASA Astrophysics Data System (ADS)

Ding, Jian; Li, Li

2018-06-01

We initiate the study on chemical distances of percolation clusters for level sets of two-dimensional discrete Gaussian free fields as well as loop clusters generated by two-dimensional random walk loop soups. One of our results states that the chemical distance between two macroscopic annuli away from the boundary for the random walk loop soup at the critical intensity is of dimension 1 with positive probability. Our proof method is based on an interesting combination of a theorem of Makarov, isomorphism theory, and an entropic repulsion estimate for Gaussian free fields in the presence of a hard wall.

The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast.

PubMed

Hartono, Stella R; Malapert, Amélie; Legros, Pénélope; Bernard, Pascal; Chédin, Frédéric; Vanoosthuyse, Vincent

2018-02-02

R-loops, which result from the formation of stable DNA:RNA hybrids, can both threaten genome integrity and act as physiological regulators of gene expression and chromatin patterning. To characterize R-loops in fission yeast, we used the S9.6 antibody-based DRIPc-seq method to sequence the RNA strand of R-loops and obtain strand-specific R-loop maps at near nucleotide resolution. Surprisingly, preliminary DRIPc-seq experiments identified mostly RNase H-resistant but exosome-sensitive RNAs that mapped to both DNA strands and resembled RNA:RNA hybrids (dsRNAs), suggesting that dsRNAs form widely in fission yeast. We confirmed in vitro that S9.6 can immuno-precipitate dsRNAs and provide evidence that dsRNAs can interfere with its binding to R-loops. dsRNA elimination by RNase III treatment prior to DRIPc-seq allowed the genome-wide and strand-specific identification of genuine R-loops that responded in vivo to RNase H levels and displayed classical features associated with R-loop formation. We also found that most transcripts whose levels were altered by in vivo manipulation of RNase H levels did not form detectable R-loops, suggesting that prolonged manipulation of R-loop levels could indirectly alter the transcriptome. We discuss the implications of our work in the design of experimental strategies to probe R-loop functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dynamic formation and magnetic support of loop or arcade prominences

NASA Technical Reports Server (NTRS)

Vanhoven, Gerard; Mok, Y.; Drake, J. F.

1992-01-01

The results of model dynamic simulations of the formation and support of a narrow prominence at the apex of a coronal magnetic loop or arcade are described. The condensation process proceeds via an initial radiative cooling and pressure drop, and a secondary siphon flow from the dense chromospheric ends. The antibuoyancy effect as the prominence forms causes a bending of a confining magnetic field, which propagates toward the semirigid ends of the magnetic loop. Thus, a wide magnetic 'hammock' or well (of a normal polarity Kippenhahn-Schlueter type) is formed, which supports the prominence at or near the field apex.

Propensities of Aromatic Amino Acids versus Leucine and Proline to Induce Residual Structure in the Denatured State Ensemble of Iso-1-cytochrome c

PubMed Central

Finnegan, Michaela L.; Bowler, Bruce E.

2010-01-01

Histidine-heme loop formation in the denatured state of a protein is a sensitive means to probe for residual structure under unfolding conditions. In this study, we use a host-guest approach to investigate the relative tendencies of different amino acids to promote residual structure under denaturing conditions. The host for this work is a 6 amino acid insert of five alanines followed by a lysine engineered immediately following a unique histidine near the N-terminus of yeast iso-1-cytochrome c. We substitute the 4th alanine in this sequence, HAAAXAK, with X = Trp, Phe, Tyr and Leu. The effects of proline are tested with substitutions at positions 1 and 5 in the insert, HPAAAAK and HAAAAPK, respectively. Thermodynamic studies on His-heme loop formation in 3 M guanidine hydrochloride reveal significant stabilization of residual structure by aromatic amino acids, particularly, Trp and Phe, and minimal stabilization of residual structure by Leu. Prolines disfavor His-heme loop formation slightly, presumably due to enhanced chain stiffness. Kinetic studies reveal that much of the change in His-heme loop stability for the aromatic amino acids is caused by a slowing of the rate of His-heme loop breakage, indicating that residual structure is preferentially stabilized in the closed-loop form of the denatured state. PMID:20850458

Molecular dynamics simulations of electrostatics and hydration distributions around RNA and DNA motifs

NASA Astrophysics Data System (ADS)

Marlowe, Ashley E.; Singh, Abhishek; Semichaevsky, Andrey V.; Yingling, Yaroslava G.

2009-03-01

Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this presentation we use explicit molecular dynamics simulations to examine the variations in cationic distributions and hydration environment around DNA and RNA helices and loop-loop interactions. Our simulations show that the potassium and sodium ionic distributions are different around RNA and DNA motifs which could be indicative of ion mediated relative stability of loop-loop complexes. Moreover in RNA loop-loop motifs ions are consistently present and exchanged through a distinct electronegative channel. We will also show how we used the specific RNA loop-loop motif to design a RNA hexagonal nanoparticle.

MAP Kinase-Mediated Negative Regulation of Symbiotic Nodule Formation in Medicago truncatula.

PubMed

Ryu, Hojin; Laffont, Carole; Frugier, Florian; Hwang, Ildoo

2017-01-01

Mitogen-activated protein kinase (MAPK) signaling cascades play critical roles in various cellular events in plants, including stress responses, innate immunity, hormone signaling, and cell specificity. MAPK-mediated stress signaling is also known to negatively regulate nitrogen-fixing symbiotic interactions, but the molecular mechanism of the MAPK signaling cascades underlying the symbiotic nodule development remains largely unknown. We show that the MtMKK5-MtMPK3/6 signaling module negatively regulates the early symbiotic nodule formation, probably upstream of ERN1 (ERF Required for Nodulation 1) and NSP1 (Nod factor Signaling Pathway 1) in Medicago truncatula . The overexpression of MtMKK5 stimulated stress and defense signaling pathways but also reduced nodule formation in M. truncatula roots. Conversely, a MAPK specific inhibitor, U0126, enhanced nodule formation and the expression of an early nodulation marker gene, MtNIN . We found that MtMKK5 directly activates MtMPK3/6 by phosphorylating the TEY motif within the activation loop and that the MtMPK3/6 proteins physically interact with the early nodulation-related transcription factors ERN1 and NSP1. These data suggest that the stress signaling-mediated MtMKK5/MtMPK3/6 module suppresses symbiotic nodule development via the action of early nodulation transcription factors.

MAP Kinase-Mediated Negative Regulation of Symbiotic Nodule Formation in Medicago truncatula

PubMed Central

Ryu, Hojin; Laffont, Carole; Frugier, Florian; Hwang, Ildoo

2017-01-01

Mitogen-activated protein kinase (MAPK) signaling cascades play critical roles in various cellular events in plants, including stress responses, innate immunity, hormone signaling, and cell specificity. MAPK-mediated stress signaling is also known to negatively regulate nitrogen-fixing symbiotic interactions, but the molecular mechanism of the MAPK signaling cascades underlying the symbiotic nodule development remains largely unknown. We show that the MtMKK5-MtMPK3/6 signaling module negatively regulates the early symbiotic nodule formation, probably upstream of ERN1 (ERF Required for Nodulation 1) and NSP1 (Nod factor Signaling Pathway 1) in Medicago truncatula. The overexpression of MtMKK5 stimulated stress and defense signaling pathways but also reduced nodule formation in M. truncatula roots. Conversely, a MAPK specific inhibitor, U0126, enhanced nodule formation and the expression of an early nodulation marker gene, MtNIN. We found that MtMKK5 directly activates MtMPK3/6 by phosphorylating the TEY motif within the activation loop and that the MtMPK3/6 proteins physically interact with the early nodulation-related transcription factors ERN1 and NSP1. These data suggest that the stress signaling-mediated MtMKK5/MtMPK3/6 module suppresses symbiotic nodule development via the action of early nodulation transcription factors. PMID:28152300

Analysis and design of a second-order digital phase-locked loop

NASA Technical Reports Server (NTRS)

Blasche, P. R.

1979-01-01

A specific second-order digital phase-locked loop (DPLL) was modeled as a first-order Markov chain with alternatives. From the matrix of transition probabilities of the Markov chain, the steady-state phase error of the DPLL was determined. In a similar manner the loop's response was calculated for a fading input. Additionally, a hardware DPLL was constructed and tested to provide a comparison to the results obtained from the Markov chain model. In all cases tested, good agreement was found between the theoretical predictions and the experimental data.

Continuous infusion or bolus injection of loop diuretics for congestive heart failure?

PubMed

Zepeda, Patricio; Rain, Carmen; Sepúlveda, Paola

2016-04-22

Loop diuretics are widely used in acute heart failure. However, there is controversy about the superiority of continuous infusion over bolus administration. Searching in Epistemonikos database, which is maintained by screening 30 databases, we identified four systematic reviews including 11 pertinent randomized controlled trials overall. We combined the evidence using meta-analysis and generated a summary of findings following the GRADE approach. We concluded continuous administration of loop diuretics probably reduces mortality and length of stay compared to intermittent administration in patients with acute heart failure.

Offset quadrature communications with decision-feedback carrier synchronization

NASA Technical Reports Server (NTRS)

Simon, M. K.; Smith, J. G.

1974-01-01

In order to accommodate a quadrature amplitude-shift-keyed (QASK) signal, Simon and Smith (1974) have modified the decision-feedback loop which tracks a quadrature phase-shift-keyed (QPSK). In the investigation reported approaches are considered to modify the loops in such a way that offset QASK signals can be tracked, giving attention to the special case of an offset QPSK. The development of the stochastic integro-differential equation of operation for a decision-feedback offset QASK loop is discussed along with the probability density function of the phase error process.

New method of computing the contributions of graphs without lepton loops to the electron anomalous magnetic moment in QED

NASA Astrophysics Data System (ADS)

Volkov, Sergey

2017-11-01

This paper presents a new method of numerical computation of the mass-independent QED contributions to the electron anomalous magnetic moment which arise from Feynman graphs without closed electron loops. The method is based on a forestlike subtraction formula that removes all ultraviolet and infrared divergences in each Feynman graph before integration in Feynman-parametric space. The integration is performed by an importance sampling Monte-Carlo algorithm with the probability density function that is constructed for each Feynman graph individually. The method is fully automated at any order of the perturbation series. The results of applying the method to 2-loop, 3-loop, 4-loop Feynman graphs, and to some individual 5-loop graphs are presented, as well as the comparison of this method with other ones with respect to Monte Carlo convergence speed.

Optimal Lorentz-augmented spacecraft formation flying in elliptic orbits

NASA Astrophysics Data System (ADS)

Huang, Xu; Yan, Ye; Zhou, Yang

2015-06-01

An electrostatically charged spacecraft accelerates as it moves through the Earth's magnetic field due to the induced Lorentz force, providing a new means of propellantless electromagnetic propulsion for orbital maneuvers. The feasibility of Lorentz-augmented spacecraft formation flying in elliptic orbits is investigated in this paper. Assuming the Earth's magnetic field as a tilted dipole corotating with Earth, a nonlinear dynamical model that characterizes the orbital motion of Lorentz spacecraft in the vicinity of arbitrary elliptic orbits is developed. To establish a predetermined formation configuration at given terminal time, pseudospectral method is used to solve the optimal open-loop trajectories of hybrid control inputs consisted of Lorentz acceleration and thruster-generated control acceleration. A nontilted dipole model is also introduced to analyze the effect of dipole tilt angle via comparisons with the tilted one. Meanwhile, to guarantee finite-time convergence and system robustness against external perturbations, a continuous fast nonsingular terminal sliding mode controller is designed and the closed-loop system stability is proved by Lyapunov theory. Numerical simulations substantiate the validity of proposed open-loop and closed-loop control schemes, and the results indicate that an almost propellantless formation establishment can be achieved by choosing appropriate objective function in the pseudospectral method. Furthermore, compared to the nonsingular terminal sliding mode controller, the closed-loop controller presents superior convergence rate with only a bit more control effort. And the proposed controller can be applied in other Lorentz-augmented relative orbital control problems.

Open-loop-feedback control of serum drug concentrations: pharmacokinetic approaches to drug therapy.

PubMed

Jelliffe, R W

1983-01-01

Recent developments to optimize open-loop-feedback control of drug dosage regimens, generally applicable to pharmacokinetically oriented therapy with many drugs, involve computation of patient-individualized strategies for obtaining desired serum drug concentrations. Analyses of past therapy are performed by least squares, extended least squares, and maximum a posteriori probability Bayesian methods of fitting pharmacokinetic models to serum level data. Future possibilities for truly optimal open-loop-feedback therapy with full Bayesian methods, and conceivably for optimal closed-loop therapy in such data-poor clinical situations, are also discussed. Implementation of these various therapeutic strategies, using automated, locally controlled infusion devices, has also been achieved in prototype form.

A cytotoxic haemolysin from Treponema hyodysenteriae--a probable virulence determinant in swine dysentery.

PubMed

Lysons, R J; Kent, K A; Bland, A P; Sellwood, R; Robinson, W F; Frost, A J

1991-02-01

The haemolysin from a virulent strain of Treponema hyodysenteriae was extracted and injected into ligated loops of the ileum and colon of germ-free pigs. It caused severe epithelial damage, especially to the differentiated cells at the tips of the villi in the ileum and the cells in the intercrypt zones of the colon; goblet cells were less affected. The changes in the colon were similar to those seen in natural cases of swine dysentery. The ligated loop offers a means of investigating pathogenic mechanisms and the mode of action of the toxin. This study demonstrated that the haemolysin was a potent cytotoxin for pig enterocytes, and a probable virulence determinant in swine dysentery.

Transequatorial loops interconnecting McMath regions 12472 and 12474

NASA Technical Reports Server (NTRS)

Svestka, Z.; Krieger, A. S.; Chase, R. C.; Howard, R.

1977-01-01

The paper reviews the life history of one transequatorial loop in a system observed in soft X-rays for at least 1.5 days and which interconnected a newly born active region with an old region. The birth of the selected loop is discussed along with properties of the interconnected active regions, sharpening and brightening of the loop, decay of the loop system, and physical relations between the interconnected regions. It is concluded that: (1) the loop was most probably born via reconnection of magnetic-field lines extending from the two active regions toward the equator, which occurred later than 33 hr after the younger region was born; (2) the fully developed interconnection was composed of several loops, all of which appeared to be rooted in a spotless magnetic hill of preceding northern polarity but were spread over two separate spotty regions of southern polarity in the magnetically complex new region; (3) the loop electron temperature increased from 2.1 million to 3.1 million K in one to three hours when the loop system brightened; and (4) the loops became twisted during the brightening, possibly due to their rise in the corona while remaining rooted in moving magnetic features in the younger region.

Mechanism of retinoic acid-induced transcription: histone code, DNA oxidation and formation of chromatin loops.

PubMed

Zuchegna, Candida; Aceto, Fabiana; Bertoni, Alessandra; Romano, Antonella; Perillo, Bruno; Laccetti, Paolo; Gottesman, Max E; Avvedimento, Enrico V; Porcellini, Antonio

2014-01-01

Histone methylation changes and formation of chromatin loops involving enhancers, promoters and 3' end regions of genes have been variously associated with active transcription in eukaryotes. We have studied the effect of activation of the retinoic A receptor, at the RARE-promoter chromatin of CASP9 and CYP26A1 genes, 15 and 45 min following RA exposure, and we found that histone H3 lysines 4 and 9 are demethylated by the lysine-specific demethylase, LSD1 and by the JMJ-domain containing demethylase, D2A. The action of the oxidase (LSD1) and a dioxygenase (JMJD2A) in the presence of Fe++ elicits an oxidation wave that locally modifies the DNA and recruits the enzymes involved in base and nucleotide excision repair (BER and NER). These events are essential for the formation of chromatin loop(s) that juxtapose the RARE element with the 5' transcription start site and the 3' end of the genes. The RARE bound-receptor governs the 5' and 3' end selection and directs the productive transcription cycle of RNA polymerase. These data mechanistically link chromatin loops, histone methylation changes and localized DNA repair with transcription. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Cutting a Drop of Water Pinned by Wire Loops Using a Superhydrophobic Surface and Knife

PubMed Central

Yanashima, Ryan; García, Antonio A.; Aldridge, James; Weiss, Noah; Hayes, Mark A.; Andrews, James H.

2012-01-01

A water drop on a superhydrophobic surface that is pinned by wire loops can be reproducibly cut without formation of satellite droplets. Drops placed on low-density polyethylene surfaces and Teflon-coated glass slides were cut with superhydrophobic knives of low-density polyethylene and treated copper or zinc sheets, respectively. Distortion of drop shape by the superhydrophobic knife enables a clean break. The driving force for droplet formation arises from the lower surface free energy for two separate drops, and it is modeled as a 2-D system. An estimate of the free energy change serves to guide when droplets will form based on the variation of drop volume, loop spacing and knife depth. Combining the cutting process with an electrofocusing driving force could enable a reproducible biomolecular separation without troubling satellite drop formation. PMID:23029297

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.

PubMed

Di Palma, Francesco; Bottaro, Sandro; Bussi, Giovanni

2015-01-01

Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The structural mechanism regulating its conformational changes upon ligand binding mostly remains to be elucidated. In this open framework it has been suggested that the ligand stabilizes the interaction of the distal "kissing loop" complex. Using accurate full-atom molecular dynamics with explicit solvent in combination with enhanced sampling techniques and advanced analysis methods it could be possible to provide a more detailed perspective on the formation of these tertiary contacts. In this work, we used umbrella sampling simulations to study the thermodynamics of the kissing loop complex in the presence and in the absence of the cognate ligand. We enforced the breaking/formation of the loop-loop interaction restraining the distance between the two loops. We also assessed the convergence of the results by using two alternative initialization protocols. A structural analysis was performed using a novel approach to analyze base contacts. Contacts between the two loops were progressively lost when larger inter-loop distances were enforced. Inter-loop Watson-Crick contacts survived at larger separation when compared with non-canonical pairing and stacking interactions. Intra-loop stacking contacts remained formed upon loop undocking. Our simulations qualitatively indicated that the ligand could stabilize the kissing loop complex. We also compared with previously published simulation studies. Kissing complex stabilization given by the ligand was compatible with available experimental data. However, the dependence of its value on the initialization protocol of the umbrella sampling simulations posed some questions on the quantitative interpretation of the results and called for better converged enhanced sampling simulations.

Proceedings from the 2nd International Symposium on Formation Flying Missions and Technologies

NASA Technical Reports Server (NTRS)

2004-01-01

Topics discussed include: The Stellar Imager (SI) "Vision Mission"; First Formation Flying Demonstration Mission Including on Flight Nulling; Formation Flying X-ray Telescope in L2 Orbit; SPECS: The Kilometer-baseline Far-IR Interferometer in NASA's Space Science Roadmap Presentation; A Tight Formation for Along-track SAR Interferometry; Realization of the Solar Power Satellite using the Formation Flying Solar Reflector; SIMBOL-X : Formation Flying for High-Energy Astrophysics; High Precision Optical Metrology for DARWIN; Close Formation Flight of Micro-Satellites for SAR Interferometry; Station-Keeping Requirements for Astronomical Imaging with Constellations of Free-Flying Collectors; Closed-Loop Control of Formation Flying Satellites; Formation Control for the MAXIM Mission; Precision Formation Keeping at L2 Using the Autonomous Formation Flying Sensor; Robust Control of Multiple Spacecraft Formation Flying; Virtual Rigid Body (VRB) Satellite Formation Control: Stable Mode-Switching and Cross-Coupling; Electromagnetic Formation Flight (EMFF) System Design, Mission Capabilities, and Testbed Development; Navigation Algorithms for Formation Flying Missions; Use of Formation Flying Small Satellites Incorporating OISL's in a Tandem Cluster Mission; Semimajor Axis Estimation Strategies; Relative Attitude Determination of Earth Orbiting Formations Using GPS Receivers; Analysis of Formation Flying in Eccentric Orbits Using Linearized Equations of Relative Motion; Conservative Analytical Collision Probabilities for Orbital Formation Flying; Equations of Motion and Stability of Two Spacecraft in Formation at the Earth/Moon Triangular Libration Points; Formations Near the Libration Points: Design Strategies Using Natural and Non-Natural Ares; An Overview of the Formation and Attitude Control System for the Terrestrial Planet Finder Formation Flying Interferometer; GVE-Based Dynamics and Control for Formation Flying Spacecraft; GNC System Design for a New Concept of X-Ray Distributed Telescope; GNC System for the Deployment and Fine Control of the DARWIN Free-Flying Interferometer; Formation Algorithm and Simulation Testbed; and PLATFORM: A Formation Flying, RvD and Robotic Validation Test-bench.

Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model

PubMed Central

Mitra, Rajib; Jordan, Michael I.; Dunbrack, Roland L.

2010-01-01

Distributions of the backbone dihedral angles of proteins have been studied for over 40 years. While many statistical analyses have been presented, only a handful of probability densities are publicly available for use in structure validation and structure prediction methods. The available distributions differ in a number of important ways, which determine their usefulness for various purposes. These include: 1) input data size and criteria for structure inclusion (resolution, R-factor, etc.); 2) filtering of suspect conformations and outliers using B-factors or other features; 3) secondary structure of input data (e.g., whether helix and sheet are included; whether beta turns are included); 4) the method used for determining probability densities ranging from simple histograms to modern nonparametric density estimation; and 5) whether they include nearest neighbor effects on the distribution of conformations in different regions of the Ramachandran map. In this work, Ramachandran probability distributions are presented for residues in protein loops from a high-resolution data set with filtering based on calculated electron densities. Distributions for all 20 amino acids (with cis and trans proline treated separately) have been determined, as well as 420 left-neighbor and 420 right-neighbor dependent distributions. The neighbor-independent and neighbor-dependent probability densities have been accurately estimated using Bayesian nonparametric statistical analysis based on the Dirichlet process. In particular, we used hierarchical Dirichlet process priors, which allow sharing of information between densities for a particular residue type and different neighbor residue types. The resulting distributions are tested in a loop modeling benchmark with the program Rosetta, and are shown to improve protein loop conformation prediction significantly. The distributions are available at http://dunbrack.fccc.edu/hdp. PMID:20442867

Interactions driving the collapse of islet amyloid polypeptide: Implications for amyloid aggregation

NASA Astrophysics Data System (ADS)

Cope, Stephanie M.

Human islet amyloid polypeptide (hIAPP), also known as amylin, is a 37-residue intrinsically disordered hormone involved in glucose regulation and gastric emptying. The aggregation of hIAPP into amyloid fibrils is believed to play a causal role in type 2 diabetes. To date, not much is known about the monomeric state of hIAPP or how it undergoes an irreversible transformation from disordered peptide to insoluble aggregate. IAPP contains a highly conserved disulfide bond that restricts hIAPP(1-8) into a short ring-like structure: N_loop. Removal or chemical reduction of N_loop not only prevents cell response upon binding to the CGRP receptor, but also alters the mass per length distribution of hIAPP fibers and the kinetics of fibril formation. The mechanism by which N_loop affects hIAPP aggregation is not yet understood, but is important for rationalizing kinetics and developing potential inhibitors. By measuring end-to-end contact formation rates, Vaiana et al. showed that N_loop induces collapsed states in IAPP monomers, implying attractive interactions between N_loop and other regions of the disordered polypeptide chain . We show that in addition to being involved in intra-protein interactions, the N_loop is involved in inter-protein interactions, which lead to the formation of extremely long and stable beta-turn fibers. These non-amyloid fibers are present in the 10 muM concentration range, under the same solution conditions in which hIAPP forms amyloid fibers. We discuss the effect of peptide cyclization on both intra- and inter-protein interactions, and its possible implications for aggregation. Our findings indicate a potential role of N_loop-N_loop interactions in hIAPP aggregation, which has not previously been explored. Though our findings suggest that N_loop plays an important role in the pathway of amyloid formation, other naturally occurring IAPP variants that contain this structural feature are incapable of forming amyloids. For example, hIAPP readily forms amyloid fibrils in vitro, whereas the rat variant (rIAPP), differing by six amino acids, does not. In addition to being highly soluble, rIAPP is an effective inhibitor of hIAPP fibril formation . Both of these properties have been attributed to rIAPP's three proline residues: A25P, S28P and S29P. Single proline mutants of hIAPP have also been shown to kinetically inhibit hIAPP fibril formation. Because of their intrinsic dihedral angle preferences, prolines are expected to affect conformational ensembles of intrinsically disordered proteins. The specific effect of proline substitutions on IAPP structure and dynamics has not yet been explored, as the detection of such properties is experimentally challenging due to the low molecular weight, fast reconfiguration times, and very low solubility of IAPP peptides. High-resolution techniques able to measure tertiary contact formations are needed to address this issue. We employ a nanosecond laser spectroscopy technique to measure end-to-end contact formation rates in IAPP mutants. We explore the proline substitutions in IAPP and quantify their effects in terms of intrinsic chain stiffness. We find that the three proline mutations found in rIAPP increase chain stiffness. Interestingly, we also find that residue R18 plays an important role in rIAPP's unique chain stiffness and, together with the proline residues, is a determinant for its non-amyloidogenic properties. We discuss the implications of our findings on the role of prolines in IDPs.

Diagnostic yield of a routine magnetic resonance imaging in tinnitus and clinical relevance of the anterior inferior cerebellar artery loops.

PubMed

Hoekstra, Carlijn E L; Prijs, Vera F; van Zanten, Gijsbert A

2015-02-01

To assess the diagnostic yield of a routine magnetic resonance imaging (MRI) scan in patients with (unilateral) chronic tinnitus, to define the frequency of incidental findings, and to assess the clinical relevance of potentially found anterior inferior cerebellar artery (AICA) loops. Retrospective cohort study. Tertiary Tinnitus Care Group at the University Medical Center Utrecht. Three hundred twenty-one patients with chronic tinnitus. Routine diagnostic magnetic resonance imaging (MRI) and diagnostic auditory brainstem responses (ABR) when an AICA loop was found. Relationship between abnormalities on MRI and tinnitus. In 138 patients (45%), an abnormality on the MRI scan was described. In only 7 patients (2.2%), the abnormality probably related to the patient's tinnitus. Results were not significantly better in patients with unilateral tinnitus (abnormalities in 3.2%). Incidental findings, not related to the tinnitus, were found in 41% of the patients. In 70 patients (23%), an AICA loop was found in the internal auditory canal. No significant relationships were found between the presence of an AICA loop and the side of the tinnitus, abnormalities on the ABR or complaints specific to nerve compression syndrome. A routine MRI is of little or no value in patients with tinnitus with persistent complaints. Anterior inferior cerebellar artery loops are often encountered on an MRI scan but rarely relate to the tinnitus and should thus be considered incidental findings. It is advised to only perform an MRI when on clinical grounds a specific etiology with tinnitus as the symptom seems probable.

Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription.

PubMed

Gerasimova, N S; Pestov, N A; Kulaeva, O I; Clark, D J; Studitsky, V M

2016-05-26

RNA polymerase II (Pol II) transcription through chromatin is accompanied by formation of small intranucleosomal DNA loops. Pol II captured within a small loop drives accumulation of DNA supercoiling, facilitating further transcription. DNA breaks relieve supercoiling and induce Pol II arrest, allowing detection of DNA damage hidden in chromatin structure.

Successive Two-sided Loop Jets Caused by Magnetic Reconnection between Two Adjacent Filamentary Threads

NASA Astrophysics Data System (ADS)

Tian, Zhanjun; Liu, Yu; Shen, Yuandeng; Elmhamdi, Abouazza; Su, Jiangtao; Liu, Ying D.; Kordi, Ayman. S.

2017-08-01

We present observational analysis of two successive two-sided loop jets observed by the ground-based New Vacuum Solar Telescope and the space-borne Solar Dynamics Observatory. The two successive two-sided loop jets manifested similar evolution processes and both were associated with the interaction of two small-scale adjacent filamentary threads, magnetic emerging, and cancellation processes at the jet’s source region. High temporal and high spatial resolution observations reveal that the two adjacent ends of the two filamentary threads are rooted in opposite magnetic polarities within the source region. The two threads approached each other, and then an obvious brightening patch is observed at the interaction position. Subsequently, a pair of hot plasma ejections are observed heading in opposite directions along the paths of the two filamentary threads at a typical speed for two-sided loop jets of the order 150 km s-1. Close to the end of the second jet, we report the formation of a bright hot loop structure at the source region, which suggests the formation of new loops during the interaction. Based on the observational results, we propose that the observed two-sided loop jets are caused by magnetic reconnection between the two adjacent filamentary threads, largely different from the previous scenario that a two-sided loop jet is generated by magnetic reconnection between an emerging bipole and the overlying horizontal magnetic fields.

THE EFFECT OF THE {sup 14}N(p, {gamma}){sup 15}O REACTION ON THE BLUE LOOPS IN INTERMEDIATE-MASS STARS

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

Halabi, Ghina M.; El Eid, Mounib F.; Champagne, Arthur

2012-12-10

We present stellar evolutionary sequences of stars in the mass range 5-12 M{sub Sun }, having solar-like initial composition. The stellar models are obtained using updated input physics, including recent rates of thermonuclear reactions. We investigate the effects of a modification of the {sup 14}N(p, {gamma}){sup 15}O reaction rate, as suggested by recent evaluations, on the formation and extension of the blue loops encountered during the evolution of the stars in the above mass range. We find that a reduced {sup 14}N(p, {gamma}){sup 15}O rate, as described in the text, has a striking impact on the physical conditions of burningmore » and mixing during shell hydrogen burning when the blue loops are formed. In particular, we find that the efficiency of shell hydrogen burning is crucial for the formation of an extended blue loop. We show that a significantly reduced {sup 14}N(p, {gamma}){sup 15}O rate affects severely the extension of the blue loops and the time spent by the star in the blue part of the Hertzsprung-Russell diagram in the mass range 5-7 M{sub Sun} if the treatment of convection is based on the Schwarzschild criterion only. In this case, envelope overshooting helps to restore well-extended blue loops as supported by the observations of the Cepheid stars. If core overshooting is included during the core hydrogen and core helium burning phases, the loop formation and its properties depend on how this overshooting is treated for a given stellar mass range, as well as on its efficiency.« less

Height Dependence of Plasma Properties of a Dark Lane and a Cool Loop in a Solar Limb Active Region Observed by Hinode/EIS

NASA Astrophysics Data System (ADS)

Lee, K.; Imada, S.; Moon, Y.; Lee, J.

2013-12-01

We investigate spectral properties of a cool loop and a dark lane over a limb active region on 2007 March 14 by the Hinode/EUV Imaging Spectrometer. The cool loop is clearly seen in the spectral lines formed at the transition region temperature. The dark lane is characterized by an elongated faint structure in coronal spectral lines and rooted on a bright point. We determine their electron densities, Doppler velocities, and non-thermal velocities with height over the limb. We derived electron densities using the density sensitive line pairs of Mg VII, Si X, Fe XII, Fe XIII and Fe XIV spectra. Under the hydrostatic equilibrium and isothermal assumption, we determine their temperatures from the density scale height. Comparing the scale height temperatures to the peak formation temperatures of the spectral lines, we note that the scale height temperature of the cool loop is consistent with a peak formation temperature of the Fe XII and the scale height temperatures of the dark lane from each spectral lines are much lower than their peak formation temperatures. The non-thermal velocity in the cool loop slightly decreases along the loop while that in the dark lane sharply falls off with height. The variation of non-thermal velocity with height in the cool loop and the dark lane is contrast to that in off-limb polar coronal holes which are considered as source of the solar wind. Such a decrease in the non-thermal velocity may be explained by wave damping near the solar surface or turbulence due to magnetic reconnection near the bright point.

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

DOE PAGES

Field, Kevin G.; Briggs, Samuel A.; Hu, Xunxiang; ...

2016-11-01

FeCrAl alloys are an attractive materials class for nuclear power applications due to their increased environmental compatibility over more traditional nuclear materials. Preliminary studies into the radiation tolerance of FeCrAl alloys under accelerated neutron testing between 300-400 °C have shown post-irradiation microstructures containing dislocation loops and Cr-rich ' phase. Although these initial works established the post-irradiation microstructures, little to no focus was applied towards the influence of pre-irradiation microstructures on this response. Here, a well annealed commercial FeCrAl alloy, Alkrothal 720, was neutron irradiated to 1.8 dpa at 382 °C and then the role of random high angle grain boundariesmore » on the spatial distribution and size of dislocation loops, dislocation loops, and black dot damage was analyzed using on-zone scanning transmission electron microscopy. Results showed a clear heterogeneous dislocation loop formation with dislocation loops showing an increased number density and size, black dot damage showing a significant number density decrease, and an increased size of dislocation loops in the vicinity directly adjacent to the grain boundary. Lastly, these results suggest the importance of the pre-irradiation microstructure on the radiation tolerance of FeCrAl alloys.« less

Mass and energy supply of a cool coronal loop near its apex

NASA Astrophysics Data System (ADS)

Yan, Limei; Peter, Hardi; He, Jiansen; Xia, Lidong; Wang, Linghua

2018-03-01

Context. Different models for the heating of solar corona assume or predict different locations of the energy input: concentrated at the footpoints, at the apex, or uniformly distributed. The brightening of a loop could be due to the increase in electron density ne, the temperature T, or a mixture of both. Aim. We investigate possible reasons for the brightening of a cool loop at transition region temperatures through imaging and spectral observation. Methods: We observed a loop with the Interface Region Imaging Spectrograph (IRIS) and used the slit-jaw images together with spectra taken at a fixed slit position to study the evolution of plasma properties in and below the loop. We used spectra of Si IV, which forms at around 80 000 K in equilibrium, to identify plasma motions and derive electron densities from the ratio of inter-combination lines of O IV. Additional observations from the Solar Dynamics Observatory (SDO) were employed to study the response at coronal temperatures (Atmospheric Imaging Assembly, AIA) and to investigate the surface magnetic field below the loop (Helioseismic and Magnetic Imager, HMI). Results: The loop first appears at transition region temperatures and later also at coronal temperatures, indicating a heating of the plasma in the loop. The appearance of hot plasma in the loop coincides with a possible accelerating upflow seen in Si IV, with the Doppler velocity shifting continuously from -70 km s-1 to -265 km s-1. The 3D magnetic field lines extrapolated from the HMI magnetogram indicate possible magnetic reconnection between small-scale magnetic flux tubes below or near the loop apex. At the same time, an additional intensity enhancement near the loop apex is visible in the IRIS slit-jaw images at 1400 Å. These observations suggest that the loop is probably heated by the interaction between the loop and the upflows, which are accelerated by the magnetic reconnection between small-scale magnetic flux tubes at lower altitudes. Before and after the possible heating phase, the intensity changes in the optically thin (Si IV) and optical thick line (C II) are mainly contributed by the density variation without significant heating. Conclusions: We therefore provide evidence for the heating of an envelope loop that is affected by accelerating upflows, which are probably launched by magnetic reconnection between small-scale magnetic flux tubes underneath the envelope loop. This study emphasizes that in the complex upper atmosphere of the Sun, the dynamics of the 3D coupled magnetic field and flow field plays a key role in thermalizing 1D structures such as coronal loops. An animation associated to Fig. 1 is available at http://https://www.aanda.org

Radiation Enhanced Absorption of Frank Loops by Nanovoids in Cu

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

Chen, Youxing; Zhang, Xinghang; Wang, Jian

Neutron and heavy ion irradiation generally induces voids in metallic materials, and continuous radiations typically result in void swelling and mechanical failure of the irradiated materials. Recent experiments showed that nanovoids in nanotwinned copper could act as sinks for radiation-induced Frank loops, significantly mitigating radiation damage [Y. Chen et al., Nat. Commun. 6:7036 (2015)]. In this paper, we report on structural evolution of Frank loops under cascades and address the role of nanovoids in absorbing Frank loops in detail by using molecular dynamics simulations. Results show that a stand-alone Frank loop is stable under cascades. When Frank loops are adjacentmore » to nanovoids, the diffusion of a group of atoms from the loop into nanovoids is accomplished via the formation and propagation of dislocation loops. The loop-nanovoid interactions result in the shrinkage of the nanovoids and the Frank loops.« less

Radiation Enhanced Absorption of Frank Loops by Nanovoids in Cu

DOE PAGES

Chen, Youxing; Zhang, Xinghang; Wang, Jian

2016-11-01

Neutron and heavy ion irradiation generally induces voids in metallic materials, and continuous radiations typically result in void swelling and mechanical failure of the irradiated materials. Recent experiments showed that nanovoids in nanotwinned copper could act as sinks for radiation-induced Frank loops, significantly mitigating radiation damage [Y. Chen et al., Nat. Commun. 6:7036 (2015)]. In this paper, we report on structural evolution of Frank loops under cascades and address the role of nanovoids in absorbing Frank loops in detail by using molecular dynamics simulations. Results show that a stand-alone Frank loop is stable under cascades. When Frank loops are adjacentmore » to nanovoids, the diffusion of a group of atoms from the loop into nanovoids is accomplished via the formation and propagation of dislocation loops. The loop-nanovoid interactions result in the shrinkage of the nanovoids and the Frank loops.« less

Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription

PubMed Central

Gerasimova, N. S.; Pestov, N. A.; Kulaeva, O. I.; Clark, D. J.; Studitsky, V. M.

2016-01-01

ABSTRACT RNA polymerase II (Pol II) transcription through chromatin is accompanied by formation of small intranucleosomal DNA loops. Pol II captured within a small loop drives accumulation of DNA supercoiling, facilitating further transcription. DNA breaks relieve supercoiling and induce Pol II arrest, allowing detection of DNA damage hidden in chromatin structure. PMID:27115204

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

PubMed

Stirling, Peter C; Hieter, Philip

2017-10-27

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

Stopped-in-loop flow analysis of trace vanadium in water.

PubMed

Teshima, Norio; Ohno, Shinsuke; Sakai, Tadao

2007-01-01

The new concept of stopped-in-loop flow analysis (SIL-FA) is proposed, and an SIL-FA method for the catalytic determination of vanadium is demonstrated. In an SIL format, a sample solution merges with reagent(s), and the well-mixed solution is loaded into a loop. The solution in the loop is separated by a six-way switching valve from the main stream. While the reaction proceeds in the stationary loop, the SIL-FA system does not need to establish a baseline continuously. This leads to a reduction in reagent consumption and waste generation compared with traditional flow injection analysis.

The response of structure and function of the gravireceptor in a vertebrate to near weightlessness.

PubMed

Neubert, J; Briegleb, W; Schatz, A; Hertwig, I; Kruse, B

1988-02-01

The paper sums up results of a 7-day space flight experiment (D-l-Mission-BW-STA 00-STATEX) using growing frog embryos and larvae (Xenopus laevis) as a model system. Evaluation of photographs taken from the surface of sectioned deep-frozen objects, and micrographs using TEM and SEM show no aberrations in the shape, size, position, or respective electron density of the otolith membranes in larvae developed for 154 h under near-zero g. The further evaluation of the "weightless larvae" revealed a probably not yet described otolith-like formation below the dorsal wall of the vestibulum. In the weightless larvae this formation outnumbers, also qualitatively, strongly the 1-g control samples. The swimming behavior of the tadpoles which was observed about one hour after landing of the Space Shuttle showed a typical anomaly (loop swimming), which is known from larvae developed on the clinostat or from fish flown aboard Apollo capsules. An extra result is the lack of striking effects of cosmic radiation on the embryonic development of the flown Xenopus eggs.

The response of structure and function of the gravireceptor in a vertebrate to near weightlessness

NASA Astrophysics Data System (ADS)

Neubert, J.; Briegleb, W.; Schatz, A.; Hertwig, I.; Kruse, B.

The paper sums up results of a 7-day space flight experiment (D-1-Mission-BW-STA 00-STATEX) using growing frog embryos and larvae ( Xenopus laevis) as a model system. Evaluation of photographs taken from the surface of sectioned deep-frozen objects, and micrographs using TEM and SEM show no aberrations in the shape, size, position, or respective electron density of the otolith membranes in larvae developed for 154 h under near-zero g. The further evaluation of the "weightless larvae" revealed a probably not yet described otolith-like formation below the dorsal wall of the vestibulum. In the weightless larvae this formation outnumbers, also qualitatively, strongly the 1- g control samples. The swimming behavior of the tadpoles which was observed about one hour after landing of the Space Shuttle showed a typical anomaly (loop swimming), which is known from larvae developed on the clinostat or from fish flown aboard Apollo capsules. An extra result is the lack of striking effects of cosmic radiation on the embryonic development of the flown Xenopus eggs.

An improved method of renal tissue engineering, by combining renal dissociation and reaggregation with a low-volume culture technique, results in development of engineered kidneys complete with loops of Henle.

PubMed

Chang, C-Hong; Davies, Jamie A

2012-01-01

Tissue engineering of functional kidney tissue is an important goal for clinical restoration of renal function in patients damaged by infectious, toxicological, or genetic disease. One promising approach is the use of the self-organizing abilities of embryonic kidney cells to arrange themselves, from a simply reaggregated cell suspension, into engineered organs similar to fetal kidneys. The previous state-of-the-art method for this results in the formation of a branched collecting duct tree, immature nephrons (S-shaped bodies) beside and connected to it, and supportive stroma. It does not, though, result in the significant formation of morphologically detectable loops of Henle - anatomical features of the nephron that are critical to physiological function. We have combined the best existing technique for renal tissue engineering from cell suspensions with a low-volume culture technique that allows intact kidney rudiments to make loops of Henle to test whether engineered kidneys can produce these loops. The result is the formation of loops of Henle in engineered cultured 'fetal kidneys', very similar in both morphology and in number to those formed by intact organ rudiments. This brings the engineering technique one important step closer to production of a fully realistic organ. Copyright © 2012 S. Karger AG, Basel.

Activation of Latent Dihydroorotase from Aquifex aeolicus by Pressure*

PubMed Central

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

2017-01-01

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

Multiwavelength observations of a flux rope formation by series of magnetic reconnection in the chromosphere

NASA Astrophysics Data System (ADS)

Kumar, Pankaj; Yurchyshyn, Vasyl; Cho, Kyung-Suk; Wang, Haimin

2017-07-01

Using high-resolution observations from the 1.6 m New Solar Telescope (NST) operating at the Big Bear Solar Observatory (BBSO), we report direct evidence of merging and reconnection of cool Hα loops in the chromosphere during two homologous flares (B and C class) caused by a shear motion at the footpoints of two loops. The reconnection between these loops caused the formation of an unstable flux rope that showed counterclockwise rotation. The flux rope could not reach the height of torus instability and failed to form a coronal mass ejection. The HMI magnetograms revealed rotation of the negative and positive (N1/P2) polarity sunspots in the opposite directions, which increased the right- and left-handed twist in the magnetic structures rooted at N1/P2. Rapid photospheric flux cancellation (duration 20-30 min, rate ≈3.44 × 1020 Mx h-1) was observed during and even after the first B6.0 flare and continued until the end of the second C2.3 flare. The RHESSI X-ray sources were located at the site of the loop coalescence. To the best of our knowledge, such a clear interaction of chromospheric loops along with rapid flux cancellation has not been reported before. These high-resolution observations suggest the formation of a small flux rope by a series of magnetic reconnections within chromospheric loops that are associated with very rapid flux cancellation. Movies attached to Figs. 2, 7, 8, and 10 are available at http://www.aanda.org

Loop L5 Assumes Three Distinct Orientations during the ATPase Cycle of the Mitotic Kinesin Eg5

PubMed Central

Muretta, Joseph M.; Behnke-Parks, William M.; Major, Jennifer; Petersen, Karl J.; Goulet, Adeline; Moores, Carolyn A.; Thomas, David D.; Rosenfeld, Steven S.

2013-01-01

Members of the kinesin superfamily of molecular motors differ in several key structural domains, which probably allows these molecular motors to serve the different physiologies required of them. One of the most variable of these is a stem-loop motif referred to as L5. This loop is longest in the mitotic kinesin Eg5, and previous structural studies have shown that it can assume different conformations in different nucleotide states. However, enzymatic domains often consist of a mixture of conformations whose distribution shifts in response to substrate binding or product release, and this information is not available from the “static” images that structural studies provide. We have addressed this issue in the case of Eg5 by attaching a fluorescent probe to L5 and examining its fluorescence, using both steady state and time-resolved methods. This reveals that L5 assumes an equilibrium mixture of three orientations that differ in their local environment and segmental mobility. Combining these studies with transient state kinetics demonstrates that there is a major shift in this distribution during transitions that interconvert weak and strong microtubule binding states. Finally, in conjunction with previous cryo-EM reconstructions of Eg5·microtubule complexes, these fluorescence studies suggest a model in which L5 regulates both nucleotide and microtubule binding through a set of reversible interactions with helix α3. We propose that these features facilitate the production of sustained opposing force by Eg5, which underlies its role in supporting formation of a bipolar spindle in mitosis. PMID:24145034

Spherical nanoindentation study of the deformation micromechanisms of LiTaO{sub 3} single crystals

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

Anasori, B.; Barsoum, M. W.; Sickafus, K. E.

2011-07-15

Herein, spherical nanoindentation (NI) was used to investigate the room temperature deformation behavior of C-plane LiTaO{sub 3} single crystals loaded along the [0001] direction as a function of ion irradiation. When the NI load-displacement curves of 3 different nanoindenter radii (1.4 {mu}m, 5 {mu}m, and 21 {mu}m) were converted to NI stress-strain curves, good agreement between them was found. The surface first deforms elastically - with a Young's modulus of 205 {+-} 5 GPa, calculated from the stiffness versus contact radii curves and 207 {+-} 3 GPa measured using a Berkovich tip - and then plastically deforms at {approx_equal} 6more » GPa. Repeated loading into the same location results in large, reproducible, fully reversible, nested hysteresis loops attributed to the formation of incipient kink bands (IKBs). The latter are coaxial fully reversible dislocation loops that spontaneously shrink when the load is removed. The IKBs most probably nucleate within the (1012) twins that form near the surface. The sharper radii resulted in twin nucleation at lower stresses. The changes in the reversible loops' shape and areas can be related to the width of the twins that form. The latter were proportional to the nanoindenter tip radii and confirmed by scanning electron microscopy and by the fact that larger threshold stresses were needed for IKB nucleation with the smaller tip sizes. No effect of irradiation was observed on the NI response, presumably because of the mildness of the irradiation damage.« less

Creating a Strain Relief Loop during S1 Transforaminal Lead Placement for Dorsal Root Ganglion Stimulation for Foot Pain: A Technical Note.

PubMed

van Velsen, Valery; van Helmond, Noud; Chapman, Kenneth B

2018-04-01

Chronic neuropathic pain is often refractory to conventional medical treatments and leads to significant disability and socio-economic burden. Dorsal root ganglion (DRG) stimulation has recently emerged as a treatment for persistent neuropathic pain, but creating a strain relief loop at the S1 level has thus far been a challenging technical component of DRG lead placement. We describe a refined technique for strain relief loop formation at the S1 level using a transforaminal approach that we employed in a 45-year-old patient with intractable foot pain. We successfully placed a strain relief loop in the sacral space in a predictable and easily reproducible manner using a transforaminal anchorless approach. The patient experienced a decrease in visual analog pain score (85%), and improvement in function during the trial period, and proceeded with permanent implantation. The described sacral transforaminal strain relief loop formation technique appears to be a more reliable and predictable technique of DRG lead placement in the sacrum than those previously documented. © 2017 World Institute of Pain.

Electrostatics Explains the Position-Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes.

PubMed

Abi-Ghanem, Josephine; Rabin, Clémence; Porrini, Massimiliano; Dausse, Eric; Toulmé, Jean-Jacques; Gabelica, Valérie

2017-10-06

In the RNA realm, non-Watson-Crick base pairs are abundant and can affect both the RNA 3D structure and its function. Here, we investigated the formation of RNA kissing complexes in which the loop-loop interaction is modulated by non-Watson-Crick pairs. Mass spectrometry, surface plasmon resonance, and UV-melting experiments show that the G⋅U wobble base pair favors kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modeling, including molecular mechanics Poisson-Boltzmann surface area (MMPBSA) thermodynamics calculations and PBSA calculations of the electrostatic potential surfaces. Modeling reveals that the G⋅U stabilization is due to a specific electrostatic environment defined by the base pairs of the entire loop-loop region. The loop is not symmetric, and therefore the identity and position of each base pair matters. Predicting and visualizing the electrostatic environment created by a given sequence can help to design specific kissing complexes with high affinity, for potential therapeutic, nanotechnology or analytical applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectroscopic Study of a Dark Lane and a Cool Loop in a Solar Limb Active Region by Hinode/EIS

NASA Astrophysics Data System (ADS)

Lee, K.; Imada, S.; Moon, Y.; Lee, J.

2012-12-01

We investigate a cool loop and a dark lane over a limb active region on 2007 March 14 by the Hinode/EUV Imaging Spectrometer (EIS). The cool loop is clearly seen in the EIS spectral lines formed at the transition region temperature (log T = 5.8). The dark lane is characterized by an elongated faint structure in coronal spectral lines (log T = 5.8 - 6.1) and rooted on a bright point. We examine their electron densities, Doppler velocities, and non-thermal velocities as a function of distance from the limb using the spectral lines formed at different temperatures (log T = 5.4 - 6.4). The electron densities of the cool loop and the dark lane are derived from the density sensitive line pairs of Mg VII, Fe XII, and Fe XIV spectra. Under the hydrostatic equilibrium and isothermal assumption, we determine their temperatures from the density scale height. Comparing the scale height temperatures to the peak formation temperatures of the spectral lines, we note that the scale height temperature of the cool loop is consistent with a peak formation temperature of the Mg VII (log T = 5.8) and the scale height temperature of the dark lane is close to a peak formation temperature of the Fe XII and Fe XIII (log T = 6.1 - 6.2). It is interesting to note that the structures of the cool loop and the dark lane are most visible in these temperature lines. While the non-thermal velocity in the cool loop slightly decreases (less than 7 km {s-1}) along the loop, that in the dark lane sharply falls off with height. The variation of non-thermal velocity with height in the cool loop and the dark lane is contrast to that in off-limb polar coronal holes which are considered as source of the fast solar wind. Such a decrease in the non-thermal velocity may be explained by wave damping near the solar surface or turbulence due to magnetic reconnection near the bright point.

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

Toeroek, T.; Aulanier, G.; Schmieder, B.

We address the formation of three-dimensional nullpoint topologies in the solar corona by combining Hinode/X-ray Telescope (XRT) observations of a small dynamic limb event, which occurred beside a non-erupting prominence cavity, with a three-dimensional (3D) zero-beta magnetohydrodynamics (MHD) simulation. To this end, we model the boundary-driven 'kinematic' emergence of a compact, intense, and uniformly twisted flux tube into a potential field arcade that overlies a weakly twisted coronal flux rope. The expansion of the emerging flux in the corona gives rise to the formation of a nullpoint at the interface of the emerging and the pre-existing fields. We unveil amore » two-step reconnection process at the nullpoint that eventually yields the formation of a broad 3D fan-spine configuration above the emerging bipole. The first reconnection involves emerging fields and a set of large-scale arcade field lines. It results in the launch of a torsional MHD wave that propagates along the arcades, and in the formation of a sheared loop system on one side of the emerging flux. The second reconnection occurs between these newly formed loops and remote arcade fields, and yields the formation of a second loop system on the opposite side of the emerging flux. The two loop systems collectively display an anenome pattern that is located below the fan surface. The flux that surrounds the inner spine field line of the nullpoint retains a fraction of the emerged twist, while the remaining twist is evacuated along the reconnected arcades. The nature and timing of the features which occur in the simulation do qualititatively reproduce those observed by XRT in the particular event studied in this paper. Moreover, the two-step reconnection process suggests a new consistent and generic model for the formation of anemone regions in the solar corona.« less

Successive Two-sided Loop Jets Caused by Magnetic Reconnection between Two Adjacent Filamentary Threads

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

Tian, Zhanjun; Liu, Yu; Shen, Yuandeng

We present observational analysis of two successive two-sided loop jets observed by the ground-based New Vacuum Solar Telescope and the space-borne Solar Dynamics Observatory . The two successive two-sided loop jets manifested similar evolution processes and both were associated with the interaction of two small-scale adjacent filamentary threads, magnetic emerging, and cancellation processes at the jet’s source region. High temporal and high spatial resolution observations reveal that the two adjacent ends of the two filamentary threads are rooted in opposite magnetic polarities within the source region. The two threads approached each other, and then an obvious brightening patch is observedmore » at the interaction position. Subsequently, a pair of hot plasma ejections are observed heading in opposite directions along the paths of the two filamentary threads at a typical speed for two-sided loop jets of the order 150 km s{sup −1}. Close to the end of the second jet, we report the formation of a bright hot loop structure at the source region, which suggests the formation of new loops during the interaction. Based on the observational results, we propose that the observed two-sided loop jets are caused by magnetic reconnection between the two adjacent filamentary threads, largely different from the previous scenario that a two-sided loop jet is generated by magnetic reconnection between an emerging bipole and the overlying horizontal magnetic fields.« less

Recent Developments in Hardware-in-the-Loop Formation Navigation and Control

NASA Technical Reports Server (NTRS)

Mitchell, Jason W.; Luquette, Richard J.

2005-01-01

The Formation Flying Test-Bed (FFTB) at NASA Goddard Space Flight Center (GSFC) provides a hardware-in-the-loop test environment for formation navigation and control. The facility is evolving as a modular, hybrid, dynamic simulation facility for end-tc-end guidance, navigation, and control (GN&C) design and analysis of formation flying spacecraft. The core capabilities of the FFTB, as a platform for testing critical hardware and software algorithms in-the-loop, are reviewed with a focus on many recent improvements. Two significant upgrades to the FFTB are a message-oriented middleware (MOM) architecture, and a software crosslink for inter-spacecraft ranging. The MOM architecture provides a common messaging bus for software agents, easing integration, arid supporting the GSFC Mission Services Evolution Center (GMSEC) architecture via software bridge. Additionally, the FFTB s hardware capabilities are expanding. Recently, two Low-Power Transceivers (LPTs) with ranging capability have been introduced into the FFTB. The LPT crosslinks will be connected to a modified Crosslink Channel Simulator (CCS), which applies realistic space-environment effects to the Radio Frequency (RF) signals produced by the LPTs.

Expanding Hardware-in-the-Loop Formation Navigation and Control with Radio Frequency Crosslink Ranging

NASA Technical Reports Server (NTRS)

Mitchell, Jason W.; Barbee, Brent W.; Baldwin, Philip J.; Luquette, Richard J.

2007-01-01

The Formation Flying Testbed (FFTB) at the National Aeronautics and Space Administration (NASA) Goddard Space Flight Center (GSFC) provides a hardware-in-the-loop test environment for formation navigation and control. The facility continues to evolve as a modular, hybrid, dynamic simulation facility for end-to-end guidance, navigation, and control (GN&C) design and analysis of formation flying spacecraft. The core capabilities of the FFTB, as a platform for testing critical hardware and software algorithms in-the-loop, are reviewed with a focus on recent improvements. With the most recent improvement, in support of Technology Readiness Level (TRL) 6 testing of the Inter-spacecraft Ranging and Alarm System (IRAS) for the Magnetospheric Multiscale (MMS) mission, the FFTB has significantly expanded its ability to perform realistic simulations that require Radio Frequency (RF) ranging sensors for relative navigation with the Path Emulator for RF Signals (PERFS). The PERFS, currently under development at NASA GSFC, modulates RF signals exchanged between spacecraft. The RF signals are modified to accurately reflect the dynamic environment through which they travel, including the effects of medium, moving platforms, and radiated power.

Kinks, loops, and protein folding, with protein A as an example

PubMed Central

Krokhotin, Andrey; Liwo, Adam; Maisuradze, Gia G.; Niemi, Antti J.; Scheraga, Harold A.

2014-01-01

The dynamics and energetics of formation of loops in the 46-residue N-terminal fragment of the B-domain of staphylococcal protein A has been studied. Numerical simulations have been performed using coarse-grained molecular dynamics with the united-residue (UNRES) force field. The results have been analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger (DNLS) equation. In the case of proteins, the DNLS equation arises from a Cα-trace-based energy function. Three individual kink profiles were identified in the experimental three-α-helix structure of protein A, in the range of the Glu16-Asn29, Leu20-Asn29, and Gln33-Asn44 residues, respectively; these correspond to two loops in the native structure. UNRES simulations were started from the full right-handed α-helix to obtain a clear picture of kink formation, which would otherwise be blurred by helix formation. All three kinks emerged during coarse-grained simulations. It was found that the formation of each is accompanied by a local free energy increase; this is expressed as the change of UNRES energy which has the physical sense of the potential of mean force of a polypeptide chain. The increase is about 7 kcal/mol. This value can thus be considered as the free energy barrier to kink formation in full α-helical segments of polypeptide chains. During the simulations, the kinks emerge, disappear, propagate, and annihilate each other many times. It was found that the formation of a kink is initiated by an abrupt change in the orientation of a pair of consecutive side chains in the loop region. This resembles the formation of a Bloch wall along a spin chain, where the Cα backbone corresponds to the chain, and the amino acid side chains are interpreted as the spin variables. This observation suggests that nearest-neighbor side chain–side chain interactions are responsible for initiation of loop formation. It was also found that the individual kinks are reflected as clear peaks in the principal modes of the analyzed trajectory of protein A, the shapes of which resemble the directional derivatives of the kinks along the chain. These observations suggest that the kinks of the DNLS equation determine the functionally important motions of proteins. PMID:24437917

Minimum Winfree loop determines self-sustained oscillations in excitable Erdös-Rényi random networks.

PubMed

Qian, Yu; Cui, Xiaohua; Zheng, Zhigang

2017-07-18

The investigation of self-sustained oscillations in excitable complex networks is very important in understanding various activities in brain systems, among which the exploration of the key determinants of oscillations is a challenging task. In this paper, by investigating the influence of system parameters on self-sustained oscillations in excitable Erdös-Rényi random networks (EERRNs), the minimum Winfree loop (MWL) is revealed to be the key factor in determining the emergence of collective oscillations. Specifically, the one-to-one correspondence between the optimal connection probability (OCP) and the MWL length is exposed. Moreover, many important quantities such as the lower critical connection probability (LCCP), the OCP, and the upper critical connection probability (UCCP) are determined by the MWL. Most importantly, they can be approximately predicted by the network structure analysis, which have been verified in numerical simulations. Our results will be of great importance to help us in understanding the key factors in determining persistent activities in biological systems.

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

NASA Astrophysics Data System (ADS)

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

2017-01-01

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

Method-Unifying View of Loop-Formation Kinetics in Peptide and Protein Folding.

PubMed

Jacob, Maik H; D'Souza, Roy N; Schwarzlose, Thomas; Wang, Xiaojuan; Huang, Fang; Haas, Elisha; Nau, Werner M

2018-04-26

Protein folding can be described as a probabilistic succession of events in which the peptide chain forms loops closed by specific amino acid residue contacts, herein referred to as loop nodes. To measure loop rates, several photophysical methods have been introduced where a pair of optically active probes is incorporated at selected chain positions and the excited probe undergoes contact quenching (CQ) upon collision with the second probe. The quenching mechanisms involved triplet-triplet energy transfer, photoinduced electron transfer, and collision-induced fluorescence quenching, where the fluorescence of Dbo, an asparagine residue conjugated to 2,3-diazabicyclo[2.2.2]octane, is quenched by tryptophan. The discrepancy between the loop rates afforded from these three CQ techniques has, however, remained unresolved. In analyzing this discrepancy, we now report two short-distance FRET methods where Dbo acts as an energy acceptor in combination with tryptophan and naphtylalanine, two donors with largely different fluorescence lifetimes of 1.3 and 33 ns, respectively. Despite the different quenching mechanisms, the rates from FRET and CQ methods were, surprisingly, of comparable magnitude. This combination of FRET and CQ data led to a unifying physical model and to the conclusion that the rate of loop formation in folding reactions varies not only with the kind and number of residues that constitute the chain but also in particular with the size and properties of the residues that constitute the loop node.

Docking, thermodynamics and molecular dynamics (MD) studies of a non-canonical protease inhibitor, MP-4, from Mucuna pruriens.

PubMed

Kumar, Ashish; Kaur, Harmeet; Jain, Abha; Nair, Deepak T; Salunke, Dinakar M

2018-01-12

Sequence and structural homology suggests that MP-4 protein from Mucuna pruriens belongs to Kunitz-type protease inhibitor family. However, biochemical assays showed that this protein is a poor inhibitor of trypsin. To understand the basis of observed poor inhibition, thermodynamics and molecular dynamics (MD) simulation studies on binding of MP-4 to trypsin were carried out. Molecular dynamics simulations revealed that temperature influences the spectrum of conformations adopted by the loop regions in the MP-4 structure. At an optimal temperature, MP-4 achieves maximal binding while above and below the optimum temperature, its functional activity is hampered due to unfavourable flexibility and relative rigidity, respectively. The low activity at normal temperature is due to the widening of the conformational spectrum of the Reactive Site Loop (RSL) that reduces the probability of formation of stabilizing contacts with trypsin. The unique sequence of the RSL enhances flexibility at ambient temperature and thus reduces its ability to inhibit trypsin. This study shows that temperature influences the function of a protein through modulation in the structure of functional domain of the protein. Modulation of function through appearance of new sequences that are more sensitive to temperature may be a general strategy for evolution of new proteins.

Structural and Biochemical Consequences of Disease-Causing Mutations in the Ankyrin Repeat Domain of the Human TRPV4 Channel

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

Inada, Hitoshi; Procko, Erik; Sotomayor, Marcos

2012-10-23

The TRPV4 calcium-permeable cation channel plays important physiological roles in osmosensation, mechanosensation, cell barrier formation, and bone homeostasis. Recent studies reported that mutations in TRPV4, including some in its ankyrin repeat domain (ARD), are associated with human inherited diseases, including neuropathies and skeletal dysplasias, probably because of the increased constitutive activity of the channel. TRPV4 activity is regulated by the binding of calmodulin and small molecules such as ATP to the ARD at its cytoplasmic N-terminus. We determined structures of ATP-free and -bound forms of human TRPV4-ARD and compared them with available TRPV-ARD structures. The third inter-repeat loop region (Fingermore » 3 loop) is flexible and may act as a switch to regulate channel activity. Comparisons of TRPV-ARD structures also suggest an evolutionary link between ARD structure and ATP binding ability. Thermal stability analyses and molecular dynamics simulations suggest that ATP increases stability in TRPV-ARDs that can bind ATP. Biochemical analyses of a large panel of TRPV4-ARD mutations associated with human inherited diseases showed that some impaired thermal stability while others weakened ATP binding ability, suggesting molecular mechanisms for the diseases.« less

Knowledge Representation Standards and Interchange Formats for Causal Graphs

NASA Technical Reports Server (NTRS)

Throop, David R.; Malin, Jane T.; Fleming, Land

2005-01-01

In many domains, automated reasoning tools must represent graphs of causally linked events. These include fault-tree analysis, probabilistic risk assessment (PRA), planning, procedures, medical reasoning about disease progression, and functional architectures. Each of these fields has its own requirements for the representation of causation, events, actors and conditions. The representations include ontologies of function and cause, data dictionaries for causal dependency, failure and hazard, and interchange formats between some existing tools. In none of the domains has a generally accepted interchange format emerged. The paper makes progress towards interoperability across the wide range of causal analysis methodologies. We survey existing practice and emerging interchange formats in each of these fields. Setting forth a set of terms and concepts that are broadly shared across the domains, we examine the several ways in which current practice represents them. Some phenomena are difficult to represent or to analyze in several domains. These include mode transitions, reachability analysis, positive and negative feedback loops, conditions correlated but not causally linked and bimodal probability distributions. We work through examples and contrast the differing methods for addressing them. We detail recent work in knowledge interchange formats for causal trees in aerospace analysis applications in early design, safety and reliability. Several examples are discussed, with a particular focus on reachability analysis and mode transitions. We generalize the aerospace analysis work across the several other domains. We also recommend features and capabilities for the next generation of causal knowledge representation standards.

First LIGO search for gravitational wave bursts from cosmic (super)strings

NASA Astrophysics Data System (ADS)

Abbott, B. P.; Abbott, R.; Adhikari, R.; Ajith, P.; Allen, B.; Allen, G.; Amin, R. S.; Anderson, S. B.; Anderson, W. G.; Arain, M. A.; Araya, M.; Armandula, H.; Armor, P.; Aso, Y.; Aston, S.; Aufmuth, P.; Aulbert, C.; Babak, S.; Baker, P.; Ballmer, S.; Barker, C.; Barker, D.; Barr, B.; Barriga, P.; Barsotti, L.; Barton, M. A.; Bartos, I.; Bassiri, R.; Bastarrika, M.; Behnke, B.; Benacquista, M.; Betzwieser, J.; Beyersdorf, P. T.; Bilenko, I. A.; Billingsley, G.; Biswas, R.; Black, E.; Blackburn, J. K.; Blackburn, L.; Blair, D.; Bland, B.; Bodiya, T. P.; Bogue, L.; Bork, R.; Boschi, V.; Bose, S.; Brady, P. R.; Braginsky, V. B.; Brau, J. E.; Bridges, D. O.; Brinkmann, M.; Brooks, A. F.; Brown, D. A.; Brummit, A.; Brunet, G.; Bullington, A.; Buonanno, A.; Burmeister, O.; Byer, R. L.; Cadonati, L.; Camp, J. B.; Cannizzo, J.; Cannon, K. C.; Cao, J.; Cardenas, L.; Caride, S.; Castaldi, G.; Caudill, S.; Cavaglià, M.; Cepeda, C.; Chalermsongsak, T.; Chalkley, E.; Charlton, P.; Chatterji, S.; Chelkowski, S.; Chen, Y.; Christensen, N.; Chung, C. T. Y.; Clark, D.; Clark, J.; Clayton, J. H.; Cokelaer, T.; Colacino, C. N.; Conte, R.; Cook, D.; Corbitt, T. R. C.; Cornish, N.; Coward, D.; Coyne, D. C.; Creighton, J. D. E.; Creighton, T. D.; Cruise, A. M.; Culter, R. M.; Cumming, A.; Cunningham, L.; Danilishin, S. L.; Danzmann, K.; Daudert, B.; Davies, G.; Daw, E. J.; Debra, D.; Degallaix, J.; Dergachev, V.; Desai, S.; Desalvo, R.; Dhurandhar, S.; Díaz, M.; Dietz, A.; Donovan, F.; Dooley, K. L.; Doomes, E. E.; Drever, R. W. P.; Dueck, J.; Duke, I.; Dumas, J.-C.; Dwyer, J. G.; Echols, C.; Edgar, M.; Effler, A.; Ehrens, P.; Espinoza, E.; Etzel, T.; Evans, M.; Evans, T.; Fairhurst, S.; Faltas, Y.; Fan, Y.; Fazi, D.; Fehrmann, H.; Finn, L. S.; Flasch, K.; Foley, S.; Forrest, C.; Fotopoulos, N.; Franzen, A.; Frede, M.; Frei, M.; Frei, Z.; Freise, A.; Frey, R.; Fricke, T.; Fritschel, P.; Frolov, V. V.; Fyffe, M.; Galdi, V.; Garofoli, J. A.; Gholami, I.; Giaime, J. A.; Giampanis, S.; Giardina, K. D.; Goda, K.; Goetz, E.; Goggin, L. M.; González, G.; Gorodetsky, M. L.; Goßler, S.; Gouaty, R.; Grant, A.; Gras, S.; Gray, C.; Gray, M.; Greenhalgh, R. J. S.; Gretarsson, A. M.; Grimaldi, F.; Grosso, R.; Grote, H.; Grunewald, S.; Guenther, M.; Gustafson, E. K.; Gustafson, R.; Hage, B.; Hallam, J. M.; Hammer, D.; Hammond, G. D.; Hanna, C.; Hanson, J.; Harms, J.; Harry, G. M.; Harry, I. W.; Harstad, E. D.; Haughian, K.; Hayama, K.; Heefner, J.; Heng, I. S.; Heptonstall, A.; Hewitson, M.; Hild, S.; Hirose, E.; Hoak, D.; Hodge, K. A.; Holt, K.; Hosken, D. J.; Hough, J.; Hoyland, D.; Hughey, B.; Huttner, S. H.; Ingram, D. R.; Isogai, T.; Ito, M.; Ivanov, A.; Johnson, B.; Johnson, W. W.; Jones, D. I.; Jones, G.; Jones, R.; Ju, L.; Kalmus, P.; Kalogera, V.; Kandhasamy, S.; Kanner, J.; Kasprzyk, D.; Katsavounidis, E.; Kawabe, K.; Kawamura, S.; Kawazoe, F.; Kells, W.; Keppel, D. G.; Khalaidovski, A.; Khalili, F. Y.; Khan, R.; Khazanov, E.; King, P.; Kissel, J. S.; Klimenko, S.; Kokeyama, K.; Kondrashov, V.; Kopparapu, R.; Koranda, S.; Kozak, D.; Krishnan, B.; Kumar, R.; Kwee, P.; Lam, P. K.; Landry, M.; Lantz, B.; Lazzarini, A.; Lei, H.; Lei, M.; Leindecker, N.; Leonor, I.; Li, C.; Lin, H.; Lindquist, P. E.; Littenberg, T. B.; Lockerbie, N. A.; Lodhia, D.; Longo, M.; Lormand, M.; Lu, P.; Lubiński, M.; Lucianetti, A.; Lück, H.; Machenschalk, B.; Macinnis, M.; Mageswaran, M.; Mailand, K.; Mandel, I.; Mandic, V.; Márka, S.; Márka, Z.; Markosyan, A.; Markowitz, J.; Maros, E.; Martin, I. W.; Martin, R. M.; Marx, J. N.; Mason, K.; Matichard, F.; Matone, L.; Matzner, R. A.; Mavalvala, N.; McCarthy, R.; McClelland, D. E.; McGuire, S. C.; McHugh, M.; McIntyre, G.; McKechan, D. J. A.; McKenzie, K.; Mehmet, M.; Melatos, A.; Melissinos, A. C.; Menéndez, D. F.; Mendell, G.; Mercer, R. A.; Meshkov, S.; Messenger, C.; Meyer, M. S.; Miller, J.; Minelli, J.; Mino, Y.; Mitrofanov, V. P.; Mitselmakher, G.; Mittleman, R.; Miyakawa, O.; Moe, B.; Mohanty, S. D.; Mohapatra, S. R. P.; Moreno, G.; Morioka, T.; Mors, K.; Mossavi, K.; Mowlowry, C.; Mueller, G.; Müller-Ebhardt, H.; Muhammad, D.; Mukherjee, S.; Mukhopadhyay, H.; Mullavey, A.; Munch, J.; Murray, P. G.; Myers, E.; Myers, J.; Nash, T.; Nelson, J.; Newton, G.; Nishizawa, A.; Numata, K.; O'Dell, J.; O'Reilly, B.; O'Shaughnessy, R.; Ochsner, E.; Ogin, G. H.; Ottaway, D. J.; Ottens, R. S.; Overmier, H.; Owen, B. J.; Pan, Y.; Pankow, C.; Papa, M. A.; Parameshwaraiah, V.; Patel, P.; Pedraza, M.; Penn, S.; Perreca, A.; Pierro, V.; Pinto, I. M.; Pitkin, M.; Pletsch, H. J.; Plissi, M. V.; Postiglione, F.; Principe, M.; Prix, R.; Prokhorov, L.; Punken, O.; Quetschke, V.; Raab, F. J.; Rabeling, D. S.; Radkins, H.; Raffai, P.; Raics, Z.; Rainer, N.; Rakhmanov, M.; Raymond, V.; Reed, C. M.; Reed, T.; Rehbein, H.; Reid, S.; Reitze, D. H.; Riesen, R.; Riles, K.; Rivera, B.; Roberts, P.; Robertson, N. A.; Robinson, C.; Robinson, E. L.; Roddy, S.; Röver, C.; Rollins, J.; Romano, J. D.; Romie, J. H.; Rowan, S.; Rüdiger, A.; Russell, P.; Ryan, K.; Sakata, S.; Sancho de La Jordana, L.; Sandberg, V.; Sannibale, V.; Santamaría, L.; Saraf, S.; Sarin, P.; Sathyaprakash, B. S.; Sato, S.; Satterthwaite, M.; Saulson, P. R.; Savage, R.; Savov, P.; Scanlan, M.; Schilling, R.; Schnabel, R.; Schofield, R.; Schulz, B.; Schutz, B. F.; Schwinberg, P.; Scott, J.; Scott, S. M.; Searle, A. C.; Sears, B.; Seifert, F.; Sellers, D.; Sengupta, A. S.; Sergeev, A.; Shapiro, B.; Shawhan, P.; Shoemaker, D. H.; Sibley, A.; Siemens, X.; Sigg, D.; Sinha, S.; Sintes, A. M.; Slagmolen, B. J. J.; Slutsky, J.; Smith, J. R.; Smith, M. R.; Smith, N. D.; Somiya, K.; Sorazu, B.; Stein, A.; Stein, L. C.; Steplewski, S.; Stochino, A.; Stone, R.; Strain, K. A.; Strigin, S.; Stroeer, A.; Stuver, A. L.; Summerscales, T. Z.; Sun, K.-X.; Sung, M.; Sutton, P. J.; Szokoly, G. P.; Talukder, D.; Tang, L.; Tanner, D. B.; Tarabrin, S. P.; Taylor, J. R.; Taylor, R.; Thacker, J.; Thorne, K. A.; Thorne, K. S.; Thüring, A.; Tokmakov, K. V.; Torres, C.; Torrie, C.; Traylor, G.; Trias, M.; Ugolini, D.; Ulmen, J.; Urbanek, K.; Vahlbruch, H.; Vallisneri, M.; van den Broeck, C.; van der Sluys, M. V.; van Veggel, A. A.; Vass, S.; Vaulin, R.; Vecchio, A.; Veitch, J.; Veitch, P.; Veltkamp, C.; Villar, A.; Vorvick, C.; Vyachanin, S. P.; Waldman, S. J.; Wallace, L.; Ward, R. L.; Weidner, A.; Weinert, M.; Weinstein, A. J.; Weiss, R.; Wen, L.; Wen, S.; Wette, K.; Whelan, J. T.; Whitcomb, S. E.; Whiting, B. F.; Wilkinson, C.; Willems, P. A.; Williams, H. R.; Williams, L.; Willke, B.; Wilmut, I.; Winkelmann, L.; Winkler, W.; Wipf, C. C.; Wiseman, A. G.; Woan, G.; Wooley, R.; Worden, J.; Wu, W.; Yakushin, I.; Yamamoto, H.; Yan, Z.; Yoshida, S.; Zanolin, M.; Zhang, J.; Zhang, L.; Zhao, C.; Zotov, N.; Zucker, M. E.; Zur Mühlen, H.; Zweizig, J.; Robinet, F.

2009-09-01

We report on a matched-filter search for gravitational wave bursts from cosmic string cusps using LIGO data from the fourth science run (S4) which took place in February and March 2005. No gravitational waves were detected in 14.9 days of data from times when all three LIGO detectors were operating. We interpret the result in terms of a frequentist upper limit on the rate of gravitational wave bursts and use the limits on the rate to constrain the parameter space (string tension, reconnection probability, and loop sizes) of cosmic string models. Many grand unified theory-scale models (with string tension Gμ/c2≈10-6) can be ruled out at 90% confidence for reconnection probabilities p≤10-3 if loop sizes are set by gravitational back reaction.

Günther Tulip inferior vena cava filter retrieval using a bidirectional loop-snare technique.

PubMed

Ross, Jordan; Allison, Stephen; Vaidya, Sandeep; Monroe, Eric

2016-01-01

Many advanced techniques have been reported in the literature for difficult Günther Tulip filter removal. This report describes a bidirectional loop-snare technique in the setting of a fibrin scar formation around the filter leg anchors. The bidirectional loop-snare technique allows for maximal axial tension and alignment for stripping fibrin scar from the filter legs, a commonly encountered complication of prolonged dwell times.

Unfolding and Targeting Thermodynamics of a DNA Intramolecular Complex with Joined Triplex-Duplex Domains.

PubMed

Johnson, Sarah E; Reiling-Steffensmeier, Calliste; Lee, Hui-Ting; Marky, Luis A

2018-01-25

Our laboratory is interested in developing methods that can be used for the control of gene expression. In this work, we are investigating the reaction of an intramolecular complex containing a triplex-duplex junction with partially complementary strands. We used a combination of isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), and spectroscopy techniques to determine standard thermodynamic profiles for these targeting reactions. Specifically, we have designed single strands to target one loop (CTTTC) or two loops (CTTTC and GCAA) of this complex. Both reactions yielded exothermic enthalpies of -66.3 and -82.8 kcal/mol by ITC, in excellent agreement with the reaction enthalpies of -72.7 and -88.7 kcal/mol, respectively, obtained from DSC Hess cycles. The favorable heat contributions result from the formation of base-pair stacks involving mainly the unpaired bases of the loops. This shows that each complementary strand is able to invade and disrupt the secondary structure. The simultaneous targeting of two loops yielded a more favorable reaction free energy, by approximately -8 kcal/mol, which corresponds to the formation of roughly four base-pair stacks involving the unpaired bases of the 5'-GCAA loop. The main conclusion is that the targeting of loops with a large number of unpaired bases results in a more favorable reaction free energy.

Energetics analysis of interstitial loops in single-phase concentrated solid-solution alloys

NASA Astrophysics Data System (ADS)

Wang, Xin-Xin; Niu, Liang-Liang; Wang, Shaoqing

2018-04-01

Systematic energetics analysis on the shape preference, relative stability and radiation-induced segregation of interstitial loops in nickel-containing single-phase concentrated solid-solution alloys have been conducted using atomistic simulations. It is shown that the perfect loops prefer rhombus shape for its low potential energy, while the Frank faulted loops favor ellipse for its low potential energy and the possible large configurational entropy. The decrease of stacking fault energy with increasing compositional complexity provides the energetic driving force for the formation of faulted loops, which, in conjunction with the kinetic factors, explains the experimental observation that the fraction of faulted loops rises with increasing compositional complexity. Notably, the kinetics is primarily responsible for the absence of faulted loops in nickel-cobalt with a very low stacking fault energy. We further demonstrate that the simultaneous nickel enrichment and iron/chromium depletion on interstitial loops can be fully accounted for by their energetics.

Improving materials and methods for installing inductive loop detectors : final report.

DOT National Transportation Integrated Search

1986-06-01

This report is the final report of this research project. It describes a compiling of materials utilized by various agencies for use in formation of inductive loop detectors. It further lists methods by which different agencies install materials in o...

Point mutations in the extracytosolic loop between transmembrane segments M5 and M6 of the yeast Pma1 H+-ATPase: alanine-scanning mutagenesis.

PubMed

Petrov, Valery V

2015-01-01

Membrane-spanning segments M4, M5, M6, and M8 of the H(+)-, Ca(2+)-, and K(+), Na(+)-ATPases, which belong to the P2-type pumps are the core through which cations are transported. M5 and M6 loop is a short extracytoplasmic stretch of the seven amino acid residues (714-DNSLDID) connecting two of these segments, M5 and M6, where residues involved in the formation of the proton-binding site(s) are located. In the present study, we have used alanine-scanning mutagenesis to explore the structural and functional relationships within this loop of the yeast plasma membrane Pma1 H(+)-ATPase. Of the 7 Ala mutants made, substitution for the most conserved residue (Leu-717) has led to a severe misfolding and complete block in biogenesis of the mutant enzyme. The replacement of Asp-714 has also caused misfolding leading to significant decrease in the expression of the mutant and loss of activity. The remaining mutants were expressed in secretory vesicles at 21-119% of the wild-type level and were active enough to be analyzed in detail. One of these mutants (I719A) showed five- to threefold decrease in both expression and ATP hydrolyzing and H(+) pumping activities and also threefold reduction in the coupling ratio between ATP hydrolysis and H(+) transport. Thus, Ala substitutions at three positions of the seven seriously affected biogenesis, folding, stability and/or functioning of the enzyme. Taken together, these results lead to suggestion that M5 and M6 loop play an important role in the protein stability and function and is responsible for proper arrangement of transmembrane segments M5 and M6 and probably other domains of the enzyme. Results for additional conserved substitutions (Asn and Glu) at Asp-714 and Asp-720 confirmed this suggestion.

Molecular Velcro constructed from polymer loop brushes showing enhanced adhesion force

NASA Astrophysics Data System (ADS)

Zhou, Tian; Han, Biao; Han, Lin; Li, Christopher; Department of Materials Science; Engineering Team; School of Biomedical Engineering, Science; Health Systems Team

2015-03-01

Molecular Velcro is commonly seen in biological systems as the formation of strong physical entanglement at molecular scale could induce strong adhesion, which is crucial to many biological processes. To mimic this structure, we designed, and fabricated polymer loop brushes using polymer single crystals with desired surface functionality and controlled chain folding. Compared with reported loop brushes fabricated using triblock copolymers, the present loop bushes have precise loop sizes, loop grafting density, and well controlled tethering locations on the solid surface. Atomic force microscopy-based force spectroscopy measurements using a polymer chain coated probe reveal that the adhesion force are significantly enhanced on the loop brush surface as compared with its single-strand counterpart. This study directly shows the effect of polymer brush conformation on their properties, and suggests a promising strategy for advanced polymer surface design.

Enhanced stiffness of silk-like fibers by loop formation in the corona leads to stronger gels.

PubMed

Rombouts, Wolf H; Domeradzka, Natalia E; Werten, Marc W T; Leermakers, Frans A M; de Vries, Renko J; de Wolf, Frits A; van der Gucht, Jasper

2016-11-01

We study the self-assembly of protein polymers consisting of a silk-like block flanked by two hydrophilic blocks, with a cysteine residue attached to the C-terminal end. The silk blocks self-assemble to form fibers while the hydrophilic blocks form a stabilizing corona. Entanglement of the fibers leads to the formation of hydrogels. Under oxidizing conditions the cysteine residues form disulfide bridges, effectively connecting two corona chains at their ends to form a loop. We find that this leads to a significant increase in the elastic modulus of the gels. Using atomic force microscopy, we show that this stiffening is due to an increase of the persistence length of the fibers. Self-consistent-field calculations indicate a slight decrease of the lateral pressure in the corona upon loop formation. We argue that this small decrease in the repulsive interactions affects the stacking of the silk-like blocks in the core, resulting in a more rigid fiber. © 2016 Wiley Periodicals, Inc.

Promoter-Terminator Gene Loops Affect Alternative 3'-End Processing in Yeast.

PubMed

Lamas-Maceiras, Mónica; Singh, Badri Nath; Hampsey, Michael; Freire-Picos, María A

2016-04-22

Many eukaryotic genes undergo alternative 3'-end poly(A)-site selection producing transcript isoforms with 3'-UTRs of different lengths and post-transcriptional fates. Gene loops are dynamic structures that juxtapose the 3'-ends of genes with their promoters. Several functions have been attributed to looping, including memory of recent transcriptional activity and polarity of transcription initiation. In this study, we investigated the relationship between gene loops and alternative poly(A)-site. Using the KlCYC1 gene of the yeast Kluyveromyces lactis, which includes a single promoter and two poly(A) sites separated by 394 nucleotides, we demonstrate in two yeast species the formation of alternative gene loops (L1 and L2) that juxtapose the KlCYC1 promoter with either proximal or distal 3'-end processing sites, resulting in the synthesis of short and long forms of KlCYC1 mRNA. Furthermore, synthesis of short and long mRNAs and formation of the L1 and L2 loops are growth phase-dependent. Chromatin immunoprecipitation experiments revealed that the Ssu72 RNA polymerase II carboxyl-terminal domain phosphatase, a critical determinant of looping, peaks in early log phase at the proximal poly(A) site, but as growth phase advances, it extends to the distal site. These results define a cause-and-effect relationship between gene loops and alternative poly(A) site selection that responds to different physiological signals manifested by RNA polymerase II carboxyl-terminal domain phosphorylation status. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Multifunctional Dumbbell-Shaped DNA-Templated Selective Formation of Fluorescent Silver Nanoclusters or Copper Nanoparticles for Sensitive Detection of Biomolecules.

PubMed

Chen, Jinyang; Ji, Xinghu; Tinnefeld, Philip; He, Zhike

2016-01-27

In this work, a multifunctional template for selective formation of fluorescent silver nanoclusters (AgNCs) or copper nanoparticles (CuNPs) is put forward. This dumbbell-shaped (DS) DNA template is made up of two cytosine hairpin loops and an adenine-thymine-rich double-helical stem which is closed by the loops. The cytosine loops act as specific regions for the growth of AgNCs, and the double-helical stem serves as template for the CuNPs formation. By carefully investigating the sequence and length of DS DNA, we present the optimal design of the template. Benefiting from the smart design and facile synthesis, a simple, label-free, and ultrasensitive fluorescence strategy for adenosine triphosphate (ATP) detection is proposed. Through the systematic comparison, it is found that the strategy based on CuNPs formation is more sensitive for ATP assay than that based on AgNCs synthesis, and the detection limitation was found to be 81 pM. What's more, the CuNPs formation-based method is successfully applied in the detection of ATP in human serum as well as the determination of cellular ATP. In addition to small target molecule, the sensing strategy was also extended to the detection of biomacromolecule (DNA), which illustrates the generality of this biosensor.

Chromosomal Organization by an Interplay of Loop Extrusion and Compartment Interaction

NASA Astrophysics Data System (ADS)

Nuebler, Johannes; Fudenberg, Geoffrey; Imakaev, Maxim; Lu, Carolyn; Goloborodko, Anton; Abdennur, Nezar; Mirny, Leonid

The chromatin fiber in eukaryotic nuclei is far from being simply a confined but otherwise randomly arranged polymer. Rather, it shows a high degree of spatial organization on all length scales, from individual nucleosomes up to well-segregated chromosome territories. On intermediate scales, chromosome conformation capture techniques have revealed two ubiquitous modes of organization: an alternating structure of A/B compartments, where each type preferentially associates with other base pairs of its type, and, typically on a smaller scale, the formation of topologically associating domains (TADs) with increased association within each domain but not across boundaries. The mechanisms behind this organization are only beginning to emerge. We review how the model of active loop extrusion can explain in a unified way such diverse phenomena as TAD formation and mitotic compaction and segregation, and we address in particular to what extent the interplay of active loop extrusion and compartment structure is compatible with recent experiments that interfere with the loading of the proposed loop extrusion factor cohesin. 4D Nucleome.

Detection of digital FSK using a phase-locked loop

NASA Technical Reports Server (NTRS)

Lindsey, W. C.; Simon, M. K.

1975-01-01

A theory is presented for the design of a digital FSK receiver which employs a phase-locked loop to set up the desired matched filter as the arriving signal frequency switches. The developed mathematical model makes it possible to establish the error probability performance of systems which employ a class of digital FM modulations. The noise mechanism which accounts for decision errors is modeled on the basis of the Meyr distribution and renewal Markov process theory.

Unbiased, scalable sampling of protein loop conformations from probabilistic priors.

PubMed

Zhang, Yajia; Hauser, Kris

2013-01-01

Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion.

Unbiased, scalable sampling of protein loop conformations from probabilistic priors

PubMed Central

2013-01-01

Background Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Results Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Conclusion Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion. PMID:24565175

Vanadium—lithium in-pile loop for comprehensive tests of vanadium alloys and multipurpose coatings

NASA Astrophysics Data System (ADS)

Lyublinski, I. E.; Evtikhin, V. A.; Ivanov, V. B.; Kazakov, V. A.; Korjavin, V. M.; Markovchev, V. K.; Melder, R. R.; Revyakin, Y. L.; Shpolyanskiy, V. N.

1996-10-01

The reliable information on design and material properties of self-cooled Li sbnd Li blanket and liquid metal divertor under neutron radiation conditions can be obtained using the concept of combined technological and material in-pile tests in a vanadium—lithium loop. The method of in-pile loop tests includes studies of vanadium—base alloys resistance, weld resistance under mechanical stress, multipurpose coating formation processes and coatings' resistance under the following conditions: high temperature (600-700°C), lithium velocities up to 10 m/s, lithium with controlled concentration of impurities and technological additions, a neutron load of 0.4-0.5 MW/m 2 and level of irradiation doses up to 5 dpa. The design of such an in-pile loop is considered. The experimental data on corrosion and compatibility with lithium, mechanical properties and welding technology of the vanadium alloys, methods of coatings formation and its radiation tests in lithium environment in the BOR-60 reactor (fast neutron fluence up to 10 26 m -2, irradiation temperature range of 500-523°C) are presented and analyzed as a basis for such loop development.

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

PubMed Central

Daidone, Isabella; Neuweiler, Hannes; Doose, Sören; Sauer, Markus; Smith, Jeremy C.

2010-01-01

Characterization of the length dependence of end-to-end loop-closure kinetics in unfolded polypeptide chains provides an understanding of early steps in protein folding. Here, loop-closure in poly-glycine-serine peptides is investigated by combining single-molecule fluorescence spectroscopy with molecular dynamics simulation. For chains containing more than 10 peptide bonds loop-closing rate constants on the 20–100 nanosecond time range exhibit a power-law length dependence. However, this scaling breaks down for shorter peptides, which exhibit slower kinetics arising from a perturbation induced by the dye reporter system used in the experimental setup. The loop-closure kinetics in the longer peptides is found to be determined by the formation of intra-peptide hydrogen bonds and transient β-sheet structure, that accelerate the search for contacts among residues distant in sequence relative to the case of a polypeptide chain in which hydrogen bonds cannot form. Hydrogen-bond-driven polypeptide-chain collapse in unfolded peptides under physiological conditions found here is not only consistent with hierarchical models of protein folding, that highlights the importance of secondary structure formation early in the folding process, but is also shown to speed up the search for productive folding events. PMID:20098498

Observations of the 12.3 micron Mg I emission line during a major solar flare

NASA Technical Reports Server (NTRS)

Deming, Drake; Jennings, Donald E.; Osherovich, Vladimir; Wiedemann, Gunter; Hewagama, Tilak

1990-01-01

The extremely Zeeman-sensitive 12.32 micron Mg I solar emission line was observed during a 3B/X5.7 solar flare on October 24, 1989. When compared to postflare values, Mg I emission-line intensity in the penumbral flare ribbon was 20 percent greater at the peak of the flare in soft X-rays, and the 12 micron continuum intensity was 7 percent greater. The flare also excited the emission line in the umbra where it is normally absent. The umbral flare emission exhibits a Zeeman splitting 200 G less than the adjacent penumbra, suggesting that it is excited at higher altitude. The absolute penumbral magnetic field strength did not change by more than 100 G between the flare peak and postflare period. However, a change in the inclination of the field lines, probably related to the formation and development of the flare loop system, was seen.

Effect of orientation of prismatic dislocation loops on interaction with free surfaces in BCC iron

NASA Astrophysics Data System (ADS)

Fikar, Jan; Gröger, Roman; Schäublin, Robin

2017-12-01

The prismatic loops appear in metals as a result of high-energy irradiation. Understanding their formation and interaction is important for quantification of irradiation-induced deterioration of mechanical properties. Characterization of dislocation loops in thin foils is commonly made using transmission electron microscopy (TEM), but the results are inevitably influenced by the proximity of free surfaces. The prismatic loops are attracted to free surfaces by image forces. Depending on the type, shape, size, orientation and depth of the loop in the foil, they can escape to the free surface creating denuded loop-free zones and thus invalidating TEM observations. In our previous studies we described a simple general method to determine the critical depth and the critical stress to move prismatic dislocation loops. The critical depths can be further used to correct measurements of the loop density by TEM. Here, we use this procedure to compare 〈100〉 loops and 1/2 〈111〉 loops in body-centered cubic (BCC) iron. The influences of the interatomic potential and the loop orientation are studied in detail. The difference between interstitial and vacancy type loop is also investigated.

Design and Implementation of an RTK-Based Vector Phase Locked Loop

PubMed Central

Shafaati, Ahmad; Lin, Tao; Broumandan, Ali; Lachapelle, Gérard

2018-01-01

This paper introduces a novel double-differential vector phase-locked loop (DD-VPLL) for Global Navigation Satellite Systems (GNSS) that leverages carrier phase position solutions as well as base station measurements in the estimation of rover tracking loop parameters. The use of double differencing alleviates the need for estimating receiver clock dynamics and atmospheric delays; therefore, the navigation filter consists of the baseline dynamic states only. It is shown that using vector processing for carrier phase tracking leads to a significant enhancement in the receiver sensitivity compared to using the conventional scalar-based tracking loop (STL) and vector frequency locked loop (VFLL). The sensitivity improvement of 8 to 10 dB compared to STL, and 7 to 8 dB compared to VFLL, is obtained based on the test cases reported in the paper. Also, an increased probability of ambiguity resolution in the proposed method results in better availability for real time kinematic (RTK) applications. PMID:29533994

On the asymptotic states and the quantum S matrix of the η-deformed AdS 5 × S 5 superstring

DOE PAGES

Engelund, Oluf Tang; Roiban, Radu

2015-03-31

We investigate the worldsheet S matrix of string theory in η-deformed AdS 5 × S 5. By computing the six-point tree-level S matrix we explicitly show that there is no particle production at this level, as required by the classical integrability of the theory. At one and two loops we show that integrability requires that the classical two-particle states be redefined in a non-local and η-dependent way. This is a significant departure from the undeformed theory which is probably related to the quantum group symmetry of the worldsheet theory. We use generalized unitarity to carry out the loop calculations andmore » identify a set of integrals that allow us to give a two-loop Feynman integral representation of the logarithmic terms of the two-loop S matrix. We finally also discuss aspects of the calculation of the two-loop rational terms.« less

RCD+: Fast loop modeling server.

PubMed

López-Blanco, José Ramón; Canosa-Valls, Alejandro Jesús; Li, Yaohang; Chacón, Pablo

2016-07-08

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10-fold faster. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Multiple symbol partially coherent detection of MPSK

NASA Technical Reports Server (NTRS)

Simon, M. K.; Divsalar, D.

1992-01-01

It is shown that by using the known (or estimated) value of carrier tracking loop signal to noise ratio (SNR) in the decision metric, it is possible to improve the error probability performance of a partially coherent multiple phase-shift-keying (MPSK) system relative to that corresponding to the commonly used ideal coherent decision rule. Using a maximum-likeihood approach, an optimum decision metric is derived and shown to take the form of a weighted sum of the ideal coherent decision metric (i.e., correlation) and the noncoherent decision metric which is optimum for differential detection of MPSK. The performance of a receiver based on this optimum decision rule is derived and shown to provide continued improvement with increasing length of observation interval (data symbol sequence length). Unfortunately, increasing the observation length does not eliminate the error floor associated with the finite loop SNR. Nevertheless, in the limit of infinite observation length, the average error probability performance approaches the algebraic sum of the error floor and the performance of ideal coherent detection, i.e., at any error probability above the error floor, there is no degradation due to the partial coherence. It is shown that this limiting behavior is virtually achievable with practical size observation lengths. Furthermore, the performance is quite insensitive to mismatch between the estimate of loop SNR (e.g., obtained from measurement) fed to the decision metric and its true value. These results may be of use in low-cost Earth-orbiting or deep-space missions employing coded modulations.

Looping probabilities of elastic chains: a path integral approach.

PubMed

Cotta-Ramusino, Ludovica; Maddocks, John H

2010-11-01

We consider an elastic chain at thermodynamic equilibrium with a heat bath, and derive an approximation to the probability density function, or pdf, governing the relative location and orientation of the two ends of the chain. Our motivation is to exploit continuum mechanics models for the computation of DNA looping probabilities, but here we focus on explaining the novel analytical aspects in the derivation of our approximation formula. Accordingly, and for simplicity, the current presentation is limited to the illustrative case of planar configurations. A path integral formalism is adopted, and, in the standard way, the first approximation to the looping pdf is obtained from a minimal energy configuration satisfying prescribed end conditions. Then we compute an additional factor in the pdf which encompasses the contributions of quadratic fluctuations about the minimum energy configuration along with a simultaneous evaluation of the partition function. The original aspects of our analysis are twofold. First, the quadratic Lagrangian describing the fluctuations has cross-terms that are linear in first derivatives. This, seemingly small, deviation from the structure of standard path integral examples complicates the necessary analysis significantly. Nevertheless, after a nonlinear change of variable of Riccati type, we show that the correction factor to the pdf can still be evaluated in terms of the solution to an initial value problem for the linear system of Jacobi ordinary differential equations associated with the second variation. The second novel aspect of our analysis is that we show that the Hamiltonian form of these linear Jacobi equations still provides the appropriate correction term in the inextensible, unshearable limit that is commonly adopted in polymer physics models of, e.g. DNA. Prior analyses of the inextensible case have had to introduce nonlinear and nonlocal integral constraints to express conditions on the relative displacement of the end points. Our approximation formula for the looping pdf is of quite general applicability as, in contrast to most prior approaches, no assumption is made of either uniformity of the elastic chain, nor of a straight intrinsic shape. If the chain is uniform the Jacobi system evaluated at certain minimum energy configurations has constant coefficients. In such cases our approximate pdf can be evaluated in an entirely explicit, closed form. We illustrate our analysis with a planar example of this type and compute an approximate probability of cyclization, i.e., of forming a closed loop, from a uniform elastic chain whose intrinsic shape is an open circular arc.

Particulate Formation from a Copper Oxide-Based Oxygen Carrier in Chemical Looping Combustion for CO2 Capture

EPA Science Inventory

Attrition behavior and particle loss of a copper oxide-based oxygen carrier from a methane chemical looping combustion (CLC) process was investigated in a fluidized bed reactor. The aerodynamic diameters of most elutriated particulates, after passing through a horizontal settling...

Amyloid peptide Aβ40 inhibits aggregation of Aβ42: Evidence from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Viet, Man Hoang; Li, Mai Suan

2012-06-01

Effects of amyloid beta (Aβ) peptide Aβ40 on secondary structures of Aβ42 are studied by all-atom simulations using the GROMOS96 43a1 force field with explicit water. It is shown that in the presence of Aβ40 the beta-content of monomer Aβ42 is reduced. Since the fibril-prone conformation N* of full-length Aβ peptides has the shape of beta strand-loop-beta strand this result suggests that Aβ40 decreases the probability of observing N* of Aβ42 in monomer state. Based on this and the hypothesis that the higher is the population of N* the higher fibril formation rates, one can expect that, in agreement with the recent experiment, Aβ40 inhibit fibril formation of Aβ42. It is shown that the presence of Aβ40 makes the salt bridge D23-K28 and fragment 18-33 of Aβ42 more flexible providing additional support for this experimental fact. Our estimation of the binding free energy by the molecular mechanics-Poisson-Boltzmann surface area method reveals the inhibition mechanism that Aβ40 binds to Aβ42 modifying its morphology.

Heating of the Solar Corona and its Loops

NASA Technical Reports Server (NTRS)

Klimchuk, James A.

2009-01-01

At several million degrees, the solar corona is more than two orders of magnitude hotter than the underlying solar surface. The reason for these extreme conditions has been a puzzle for decades and is considered one of the fundamental problems in astrophysics. Much of the coronal plasma is organized by the magnetic field into arch-like structures called loops. Recent observational and theoretical advances have led to great progress in understanding the nature of these loops. In particular, we now believe they are bundles of unresolved magnetic strands that are heated by storms of impulsive energy bursts called nanoflares. Turbulent convection at the solar surface shuffles the footpoints of the strands and causes them to become tangled. A nanoflare occurs when the magnetic stresses reach a critical threshold, probably by way of a mechanism called the secondary instability. I will describe our current state of knowledge concerning the corona, its loops, and how they are heated.

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

PubMed

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

2016-02-04

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

Impact of primer dimers and self-amplifying hairpins on reverse transcription loop-mediated isothermal amplification detection of viral RNA

DOE PAGES

Meagher, Robert J.; Priye, Aashish; Light, Yooli K.; ...

2018-03-27

Loop-mediated isothermal amplification (LAMP), coupled with reverse transcription (RT), has become a popular technique for detection of viral RNA due to several desirable characteristics for use in point-of-care or low-resource settings. The large number of primers in LAMP (six per target) leads to an increased likelihood of primer-dimer interactions, and the inner primers in particular are prone to formation of stable hairpin structures due to their length (typically 40-45 bases). Although primer-dimers and hairpin structures are known features to avoid in nucleic acid amplification techniques, there is little quantitative information in literature regarding the impact of these structures on LAMPmore » or RT-LAMP assays. In this study, we examine the impact of primer-dimers and hairpins on previously-published primer sets for dengue virus and yellow fever virus. We demonstrate that minor changes to the primers to eliminate amplifiable primer dimers and hairpins improves the performance of the assays when monitored in real time with intercalating dyes, and when monitoring a fluorescent endpoint using the QUASR technique. We also discuss the thermodynamic implications of these minor changes on the overall stability of amplifiable secondary structures, and we present a single thermodynamic parameter to predict the probability of non-specific amplification associated with LAMP primers.« less

Impact of primer dimers and self-amplifying hairpins on reverse transcription loop-mediated isothermal amplification detection of viral RNA

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

Meagher, Robert J.; Priye, Aashish; Light, Yooli K.

Loop-mediated isothermal amplification (LAMP), coupled with reverse transcription (RT), has become a popular technique for detection of viral RNA due to several desirable characteristics for use in point-of-care or low-resource settings. The large number of primers in LAMP (six per target) leads to an increased likelihood of primer-dimer interactions, and the inner primers in particular are prone to formation of stable hairpin structures due to their length (typically 40-45 bases). Although primer-dimers and hairpin structures are known features to avoid in nucleic acid amplification techniques, there is little quantitative information in literature regarding the impact of these structures on LAMPmore » or RT-LAMP assays. In this study, we examine the impact of primer-dimers and hairpins on previously-published primer sets for dengue virus and yellow fever virus. We demonstrate that minor changes to the primers to eliminate amplifiable primer dimers and hairpins improves the performance of the assays when monitored in real time with intercalating dyes, and when monitoring a fluorescent endpoint using the QUASR technique. We also discuss the thermodynamic implications of these minor changes on the overall stability of amplifiable secondary structures, and we present a single thermodynamic parameter to predict the probability of non-specific amplification associated with LAMP primers.« less

Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster

PubMed Central

Mishiro, Tsuyoshi; Ishihara, Ko; Hino, Shinjiro; Tsutsumi, Shuichi; Aburatani, Hiroyuki; Shirahige, Katsuhiko; Kinoshita, Yoshikazu; Nakao, Mitsuyoshi

2009-01-01

Long-range regulatory elements and higher-order chromatin structure coordinate the expression of multiple genes in cluster, and CTCF/cohesin-mediated chromatin insulator may be a key in this regulation. The human apolipoprotein (APO) A1/C3/A4/A5 gene region, whose alterations increase the risk of dyslipidemia and atherosclerosis, is partitioned at least by three CTCF-enriched sites and three cohesin protein RAD21-enriched sites (two overlap with the CTCF sites), resulting in the formation of two transcribed chromatin loops by interactions between insulators. The C3 enhancer and APOC3/A4/A5 promoters reside in the same loop, where the APOC3/A4 promoters are pointed towards the C3 enhancer, whereas the APOA1 promoter is present in the different loop. The depletion of either CTCF or RAD21 disrupts the chromatin loop structure, together with significant changes in the APO expression and the localization of transcription factor hepatocyte nuclear factor (HNF)-4α and transcriptionally active form of RNA polymerase II at the APO promoters. Thus, CTCF/cohesin-mediated insulators maintain the chromatin loop formation and the localization of transcriptional apparatus at the promoters, suggesting an essential role of chromatin insulation in controlling the expression of clustered genes. PMID:19322193

Complex folding and misfolding effects of deer-specific amino acid substitutions in the β2-α2 loop of murine prion protein

NASA Astrophysics Data System (ADS)

Agarwal, Sonya; Döring, Kristina; Gierusz, Leszek A.; Iyer, Pooja; Lane, Fiona M.; Graham, James F.; Goldmann, Wilfred; Pinheiro, Teresa J. T.; Gill, Andrew C.

2015-10-01

The β2-α2 loop of PrPC is a key modulator of disease-associated prion protein misfolding. Amino acids that differentiate mouse (Ser169, Asn173) and deer (Asn169, Thr173) PrPC appear to confer dramatically different structural properties in this region and it has been suggested that amino acid sequences associated with structural rigidity of the loop also confer susceptibility to prion disease. Using mouse recombinant PrP, we show that mutating residue 173 from Asn to Thr alters protein stability and misfolding only subtly, whilst changing Ser to Asn at codon 169 causes instability in the protein, promotes oligomer formation and dramatically potentiates fibril formation. The doubly mutated protein exhibits more complex folding and misfolding behaviour than either single mutant, suggestive of differential effects of the β2-α2 loop sequence on both protein stability and on specific misfolding pathways. Molecular dynamics simulation of protein structure suggests a key role for the solvent accessibility of Tyr168 in promoting molecular interactions that may lead to prion protein misfolding. Thus, we conclude that ‘rigidity’ in the β2-α2 loop region of the normal conformer of PrP has less effect on misfolding than other sequence-related effects in this region.

An automatic frequency control loop using overlapping DFTs (Discrete Fourier Transforms)

NASA Technical Reports Server (NTRS)

Aguirre, S.

1988-01-01

An automatic frequency control (AFC) loop is introduced and analyzed in detail. The new scheme is a generalization of the well known Cross Product AFC loop that uses running overlapping discrete Fourier transforms (DFTs) to create a discriminator curve. Linear analysis is included and supported with computer simulations. The algorithm is tested in a low carrier to noise ratio (CNR) dynamic environment, and the probability of loss of lock is estimated via computer simulations. The algorithm discussed is a suboptimum tracking scheme with a larger frequency error variance compared to an optimum strategy, but offers simplicity of implementation and a very low operating threshold CNR. This technique can be applied during the carrier acquisition and re-acquisition process in the Advanced Receiver.

Design of a Modular Test Loop for Study of Two-Phase Flow and Heat Transfer in Low and High Accelerations

DTIC Science & Technology

1990-07-01

probably cannot afford to have such a large pressure drop (orifice or throttling valve ) in the loop to stabilize the flow. For a given flow rate, the...rate was set by a calibrated valve and the water flow rate was set by the pump speed. The loop was not equipped with flowmeters and it was assumed that...Configuration. 3-28 jCk z < [D - a~ - Z Li-c I Li CL- a ow L~j Z 4) ,,l C0 0 Q.(-C - CL Li Ln LJ r o~C:) Z CC Ck LLj ZJ LOL Li Ln ( 3-2 ~ Tf1 FFFFF ~< L~iK

Effects of low sampling rate in the digital data-transition tracking loop

NASA Technical Reports Server (NTRS)

Mileant, A.; Million, S.; Hinedi, S.

1994-01-01

This article describes the performance of the all-digital data-transition tracking loop (DTTL) with coherent and noncoherent sampling using nonlinear theory. The effects of few samples per symbol and of noncommensurate sampling and symbol rates are addressed and analyzed. Their impact on the probability density and variance of the phase error are quantified through computer simulations. It is shown that the performance of the all-digital DTTL approaches its analog counterpart when the sampling and symbol rates are noncommensurate (i.e., the number of samples per symbol is an irrational number). The loop signal-to-noise ratio (SNR) (inverse of phase error variance) degrades when the number of samples per symbol is an odd integer but degrades even further for even integers.

Unfolding thermodynamics of intramolecular G-quadruplexes: base sequence contributions of the loops.

PubMed

Olsen, Chris M; Lee, Hui-Ting; Marky, Luis A

2009-03-05

G-quadruplexes are a highly studied DNA motif with a potential role in a variety of cellular processes and more recently are considered novel targets for drug therapy in aging and anticancer research. In this work, we have investigated the thermodynamic contributions of the loops on the stable formation of G-quadruplexes. Specifically, we use a combination of UV, circular dichroism (CD) and fluorescence spectroscopies, and differential scanning calorimetry (DSC) to determine thermodynamic profiles, including the differential binding of ions and water, for the unfolding of the thrombin aptamer: d(GGT2GGTGTGGT2GG) that is referred to as G2. The sequences in italics, TGT and T2, are known to form loops. Other sequences examined contained base substitutions in the TGT loop (TAT, TCT, TTT, TAPT, and UUU), in the T2 loops (T4, U2), or in both loops (UGU and U2, UUU and U2). The CD spectra of all molecules show a positive band centered at 292 nm, which corresponds to the "chair" conformation. The UV and DSC melting curves of each G-quadruplex show monophasic transitions with transition temperatures (T(M)s) that remained constant with increasing strand concentration, confirming their intramolecular formation. These G-quadruplexes unfold with T(M)s in the range from 43.2 to 56.5 degrees C and endothermic enthalpies from 22.9 to 37.2 kcal/mol. Subtracting the contribution of a G-quartet stack from each experimental profile indicated that the presence of the loops stabilize each G-quadruplex by favorable enthalpy contributions, larger differential binding of K+ ions (0.1-0.6 mol K+/ mol), and a variable uptake/release of water molecules (-6 to 8 mol H2O/mol). The thermodynamic contributions for these specific base substitutions are discussed in terms of loop stacking (base-base stacking within the loops) and their hydration effects.

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

PubMed

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

2014-01-29

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

Closed-Loop Control of Vortex Formation in Separated Flows

NASA Technical Reports Server (NTRS)

Colonius, Tim; Joe, Won Tae; MacMynowski, Doug; Rowley, Clancy; Taira, Sam; Ahuja, Sunil

2010-01-01

In order to phase lock the flow at the desired shedding cycle, particularly at Phi,best, We designed a feedback compensator. (Even though the open-loop forcing at Wf below Wn can lead to phase-locked limit cycles with a high average lift,) This feedback controller resulted in the phase-locked limit cycles that the open-loop control could not achieve for alpha=30 and 40 Particularly for alpha=40, the feedback was able to stabilize the limit cycle that was not stable with any of the open-loop periodic forcing. This results in stable phase-locked limit cycles for a larger range of forcing frequencies than the open-loop control. Also, it was shown that the feedback achieved the high-lift unsteady flow states that open-loop control could not sustain even after the states have been achieved for a long period of time.

Investigation of the factors responsible for burns during MRI.

PubMed

Dempsey, M F; Condon, B; Hadley, D M

2001-04-01

Numerous reported burn injuries have been sustained during clinical MRI procedures. The aim of this study was to investigate the possible factors that may be responsible for such burns. Experiments were performed to investigate three possible mechanisms for causing heating in copper wire during MRI: direct electromagnetic induction in a conductive loop, induction in a resonant conducting loop, and electric field resonant coupling with a wire (the antenna effect). Maximum recorded temperature rises were 0.6 degrees C for the loop, 61.1 degrees C for the resonant loop, and 63.5 degrees C for the resonant antenna. These experimental findings suggest that, contrary to common belief, it is unlikely that direct induction in a conductive loop will result in thermal injury. Burn incidents are more likely to occur due to the formation of resonant conducting loops and from extended wires forming resonant antenna. The characteristics of resonance should be considered when formulating safety guidelines.

Affective and cognitive factors influencing sensitivity to probabilistic information.

PubMed

Tyszka, Tadeusz; Sawicki, Przemyslaw

2011-11-01

In study 1 different groups of female students were randomly assigned to one of four probabilistic information formats. Five different levels of probability of a genetic disease in an unborn child were presented to participants (within-subject factor). After the presentation of the probability level, participants were requested to indicate the acceptable level of pain they would tolerate to avoid the disease (in their unborn child), their subjective evaluation of the disease risk, and their subjective evaluation of being worried by this risk. The results of study 1 confirmed the hypothesis that an experience-based probability format decreases the subjective sense of worry about the disease, thus, presumably, weakening the tendency to overrate the probability of rare events. Study 2 showed that for the emotionally laden stimuli, the experience-based probability format resulted in higher sensitivity to probability variations than other formats of probabilistic information. These advantages of the experience-based probability format are interpreted in terms of two systems of information processing: the rational deliberative versus the affective experiential and the principle of stimulus-response compatibility. © 2011 Society for Risk Analysis.

Nonequilibrium Chromosome Looping via Molecular Slip Links

NASA Astrophysics Data System (ADS)

Brackley, C. A.; Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

2017-09-01

We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.

Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene.

PubMed

Tan-Wong, Sue Mei; French, Juliet D; Proudfoot, Nicholas J; Brown, Melissa A

2008-04-01

The 85-kb breast cancer-associated gene BRCA1 is an established tumor suppressor gene, but its regulation is poorly understood. We demonstrate by gene conformation analysis in both human cell lines and mouse mammary tissue that gene loops are imposed on BRCA1 between the promoter, introns, and terminator region. Significantly, association between the BRCA1 promoter and terminator regions change upon estrogen stimulation and during lactational development. Loop formation is transcription-dependent, suggesting that transcriptional elongation plays an active role in BRCA1 loop formation. We show that the BRCA1 terminator region can suppress estrogen-induced transcription and so may regulate BRCA1 expression. Significantly, BRCA1 promoter and terminator interactions vary in different breast cancer cell lines, indicating that defects in BRCA1 chromatin structure may contribute to dysregulated expression of BRCA1 seen in breast tumors.

The pH-dependent tertiary structure of a designed helix-loop-helix dimer.

PubMed

Dolphin, G T; Baltzer, L

1997-01-01

De novo designed helix-loop-helix motifs can fold into well-defined tertiary structures if residues or groups of residues are incorporated at the helix-helix boundary to form helix-recognition sites that restrict the conformational degrees of freedom of the helical segments. Understanding the relationship between structure and function of conformational constraints therefore forms the basis for the engineering of non-natural proteins. This paper describes the design of an interhelical HisH+-Asp- hydrogen-bonded ion pair and the conformational stability of the folded helix-loop-helix motif. GTD-C, a polypeptide with 43 amino acid residues, has been designed to fold into a hairpin helix-loop-helix motif that can dimerise to form a four-helix bundle. The folded motif is in slow conformational exchange on the NMR timescale and has a well-dispersed 1H NMR spectrum, a narrow temperature interval for thermal denaturation and a near-UV CD spectrum with some fine structure. The conformational stability is pH dependent with an optimum that corresponds to the pH for maximum formation of a hydrogen-bonded ion pair between HisH17+ in helix I and Asp27- in helix II. The formation of an interhelical salt bridge is strongly suggested by the pH dependence of a number of spectroscopic probes to generate a well-defined tertiary structure in a designed helix-loop-helix motif. The thermodynamic stability of the folded motif is not increased by the formation of the salt bridge, but neighbouring conformations are destabilised. The use of this novel design principle in combination with hydrophobic interactions that provide sufficient binding energy in the folded structure should be of general use in de novo design of native-like proteins.

Dislocation loops in ultra-high purity Fe(Cr) alloys after 7.2 MeV proton irradiation

NASA Astrophysics Data System (ADS)

Chen, J.; Duval, F.; Jung, P.; Schäublin, R.; Gao, N.; Barthe, M. F.

2018-05-01

Ultra-high purity Fe(Cr) alloys (from 0 wt% Cr to 14 wt% Cr) were 3D homogeneously irradiated by 0-7.2 MeV protons to 0.3 dpa at nominal temperatures from 270 °C to 500 °C. Microstructural changes were observed by transmission electron microscopy (TEM). The results showed that evolution of dislocation loops depends on the Cr content. Below 300 °C, large ½ a0 <111> loops are dominating. Above 300 °C, a0 <100> loops with a habit plane {100} appear. Loop sizes of both types are more or less the same. At temperatures from 310 °C to 400 °C, a0 <100> loops form clusters with the same {100} habit plane as the one of the loops forming them. This indicates that <100> loops of the same variant start gliding under mutual elastic interaction. At 500 °C, dislocation loops form disc shaped clusters about 1000 nm in diameter and sitting on {111} and/or {100} planes in the pure Fe samples. Based on these observations a quantitative analysis of the dislocation loops configurations and their temperature dependence is made, leading to an understanding of the basic mechanisms of formation of these loops.

Most-probable-number loop-mediated isothermal amplification-based procedure enhanced with K antigen-specific immunomagnetic separation for quantifying tdh(+) Vibrio parahaemolyticus in molluscan Shellfish.

PubMed

Tanaka, Natsuko; Iwade, Yoshito; Yamazaki, Wataru; Gondaira, Fumio; Vuddhakul, Varaporn; Nakaguchi, Yoshitsugu; Nishibuchi, Mitsuaki

2014-07-01

Although thermostable direct hemolysin-producing (tdh(+)) Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis, the enumeration of tdh(+) V. parahaemolyticus remains challenging due to its low densities in the environment. In this study, we developed a most-probable-number (MPN)-based procedure designated A-IS(1)-LAMP, in which an immunomagnetic separation (IMS) technique targeting as many as 69 established K antigens and a loop-mediated isothermal amplification (LAMP) assay targeting the thermostable direct hemolysin (tdh) gene were applied in an MPN format. Our IMS employed PickPen, an eight-channel intrasolution magnetic particle separation device, which enabled a straightforward microtiter plate-based IMS procedure (designated as PickPen-IMS). The ability of the procedure to quantify a wide range of tdh(+) V. parahaemolyticus levels was evaluated by testing shellfish samples in Japan and southern Thailand, where shellfish products are known to contain relatively low and high levels of total V. parahaemolyticus, respectively. The Japanese and Thai shellfish samples showed, respectively, relatively low (< 3 to 11 MPN/10 g) and considerably higher (930 to 110,000 MPN/10 g) levels of tdh(+) V. parahaemolyticus, raising concern about the safety of Thai shellfish products sold to domestic consumers at local morning markets. LAMP showed similar or higher performance than conventional PCR in the detection and quantification of a wide range of tdh(+) V. parahaemolyticus levels in shellfish products. Whereas a positive effect of PickPen-IMS was not observed in MPN determination, PickPen-IMS was able to concentrate tdh(+) V. parahaemolyticus 32-fold on average from the Japanese shellfish samples at an individual tube level, suggesting a possibility of using PickPen-IMS as an optional tool for specific shellfish samples. The A-IS(1)-LAMP procedure can be used by any health authority in the world to measure the tdh(+) V. parahaemolyticus levels in shellfish products.

Stochastic properties of radiation-induced DSB: DSB distributions in large scale chromatin loops, the HPRT gene and within the visible volumes of DNA repair foci.

PubMed

Ponomarev, Artem L; Costes, Sylvain V; Cucinotta, Francis A

2008-11-01

We computed probabilities to have multiple double-strand breaks (DSB), which are produced in DNA on a regional scale, and not in close vicinity, in volumes matching the size of DNA damage foci, of a large chromatin loop, and in the physical volume of DNA containing the HPRT (human hypoxanthine phosphoribosyltransferase) locus. The model is based on a Monte Carlo description of DSB formation by heavy ions in the spatial context of the entire human genome contained within the cell nucleus, as well as at the gene sequence level. We showed that a finite physical volume corresponding to a visible DNA repair focus, believed to be associated with one DSB, can contain multiple DSB due to heavy ion track structure and the DNA supercoiled topography. A corrective distribution was introduced, which was a conditional probability to have excess DSB in a focus volume, given that there was already one present. The corrective distribution was calculated for 19.5 MeV/amu N ions, 3.77 MeV/amu alpha-particles, 1000 MeV/amu Fe ions, and X-rays. The corrected initial DSB yield from the experimental data on DNA repair foci was calculated. The DSB yield based on the corrective function converts the focus yield into the DSB yield, which is comparable with the DSB yield based on the earlier PFGE experiments. The distribution of DSB within the physical limits of the HPRT gene was analyzed by a similar method as well. This corrective procedure shows the applicability of the model and empowers the researcher with a tool to better analyze focus statistics. The model enables researchers to analyze the DSB yield based on focus statistics in real experimental situations that lack one-to-one focus-to-DSB correspondance.

Integration of Libration Point Orbit Dynamics into a Universal 3-D Autonomous Formation Flying Algorithm

NASA Technical Reports Server (NTRS)

Folta, David; Bauer, Frank H. (Technical Monitor)

2001-01-01

The autonomous formation flying control algorithm developed by the Goddard Space Flight Center (GSFC) for the New Millennium Program (NMP) Earth Observing-1 (EO-1) mission is investigated for applicability to libration point orbit formations. In the EO-1 formation-flying algorithm, control is accomplished via linearization about a reference transfer orbit with a state transition matrix (STM) computed from state inputs. The effect of libration point orbit dynamics on this algorithm architecture is explored via computation of STMs using the flight proven code, a monodromy matrix developed from a N-body model of a libration orbit, and a standard STM developed from the gravitational and coriolis effects as measured at the libration point. A comparison of formation flying Delta-Vs calculated from these methods is made to a standard linear quadratic regulator (LQR) method. The universal 3-D approach is optimal in the sense that it can be accommodated as an open-loop or closed-loop control using only state information.

On coincident loop transient electromagnetic induction logging

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

Swidinsky, Andrei; Weiss, Chester J.

Coincident loop transient induction wireline logging is examined as the borehole analog of the well-known land and airborne time-domain electromagnetic (EM) method. The concept of whole-space late-time apparent resistivity is modified from the half-space version commonly used in land and airborne geophysics and applied to the coincident loop voltages produced from various formation, borehole, and invasion models. Given typical tool diameters, off-time measurements with such an instrument must be made on the order of nanoseconds to microseconds — much more rapidly than for surface methods. Departure curves of the apparent resistivity for thin beds, calculated using an algorithm developed tomore » model the transient response of a loop in a multilayered earth, indicate that the depth of investigation scales with the bed thickness. Modeled resistivity logs are comparable in accuracy and resolution with standard frequency-domain focused induction logs. However, if measurement times are longer than a few microseconds, the thicknesses of conductors can be overestimated, whereas resistors are underestimated. Thin-bed resolution characteristics are explained by visualizing snapshots of the EM fields in the formation, where a conductor traps the electric field while two current maxima are produced in the shoulder beds surrounding a resistor. Radial profiling is studied using a concentric cylinder earth model. Results found that true formation resistivity can be determined in the presence of either oil- or water-based mud, although in the latter case, measurements must be taken several orders of magnitude later in time. Lastly, the ability to determine true formation resistivity is governed by the degree that the EM field heals after being distorted by borehole fluid and invasion, a process visualized and particularly evident in the case of conductive water-based mud.« less

On coincident loop transient electromagnetic induction logging

DOE PAGES

Swidinsky, Andrei; Weiss, Chester J.

2017-05-31

Coincident loop transient induction wireline logging is examined as the borehole analog of the well-known land and airborne time-domain electromagnetic (EM) method. The concept of whole-space late-time apparent resistivity is modified from the half-space version commonly used in land and airborne geophysics and applied to the coincident loop voltages produced from various formation, borehole, and invasion models. Given typical tool diameters, off-time measurements with such an instrument must be made on the order of nanoseconds to microseconds — much more rapidly than for surface methods. Departure curves of the apparent resistivity for thin beds, calculated using an algorithm developed tomore » model the transient response of a loop in a multilayered earth, indicate that the depth of investigation scales with the bed thickness. Modeled resistivity logs are comparable in accuracy and resolution with standard frequency-domain focused induction logs. However, if measurement times are longer than a few microseconds, the thicknesses of conductors can be overestimated, whereas resistors are underestimated. Thin-bed resolution characteristics are explained by visualizing snapshots of the EM fields in the formation, where a conductor traps the electric field while two current maxima are produced in the shoulder beds surrounding a resistor. Radial profiling is studied using a concentric cylinder earth model. Results found that true formation resistivity can be determined in the presence of either oil- or water-based mud, although in the latter case, measurements must be taken several orders of magnitude later in time. Lastly, the ability to determine true formation resistivity is governed by the degree that the EM field heals after being distorted by borehole fluid and invasion, a process visualized and particularly evident in the case of conductive water-based mud.« less

Passive mode locking and formation of dissipative solitons in electron oscillators with a bleaching absorber in the feedback loop

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

Ginzburg, N. S., E-mail: ginzburg@appl.sci-nnov.ru; Kocharovskaya, E. R.; Vilkov, M. N.

The mechanisms of passive mode locking and formation of ultrashort pulses in microwave electron oscillators with a bleaching absorber in the feedback loop have been analyzed. It is shown that in the group synchronism regime in which the translational velocity of particles coincides with the group velocity of the electromagnetic wave, the pulse formation can be described by the equations known in the theory of dissipative solitons. At the same time, the regimes in which the translational velocity of electrons differs from the group velocity and the soliton being formed and moving along the electron beam consecutively (cumulatively) receives energymore » from various electron fractions are optimal for generating pulses with the maximal peak amplitudes.« less

Submembranous recruitment of creatine kinase B supports formation of dynamic actin-based protrusions of macrophages and relies on its C-terminal flexible loop.

PubMed

Venter, Gerda; Polling, Saskia; Pluk, Helma; Venselaar, Hanka; Wijers, Mietske; Willemse, Marieke; Fransen, Jack A M; Wieringa, Bé

2015-02-01

Subcellular partitioning of creatine kinase contributes to the formation of patterns in intracellular ATP distribution and the fuelling of cellular processes with a high and sudden energy demand. We have previously shown that brain-type creatine kinase (CK-B) accumulates at the phagocytic cup in macrophages where it is involved in the compartmentalized generation of ATP for actin remodeling. Here, we report that CK-B catalytic activity also helps in the formation of protrusive ruffle structures which are actin-dependent and abundant on the surface of both unstimulated and LPS-activated macrophages. Recruitment of CK-B to these structures occurred transiently and inhibition of the enzyme's catalytic activity with cyclocreatine led to a general smoothening of surface morphology as visualized by scanning electron microscopy. Comparison of the dynamics of distribution of YFP-tagged CK-mutants and isoforms by live imaging revealed that amino acid residues in the C-terminal segment (aa positions 323-330) that forms one of the protein's two mobile loops are involved in partitioning over inner regions of the cytosol and nearby sites where membrane protrusions occur during induction of phagocytic cup formation. Although wt CK-B, muscle-type CK (CK-M), and a catalytically dead CK-B-E232Q mutant with intact loop region were normally recruited from the cytosolic pool, no dynamic transition to the phagocytic cup area was seen for the CK-homologue arginine kinase and a CK-B-D326A mutant protein. Bioinformatics analysis helped us to predict that conformational flexibility of the C-terminal loop, independent of conformational changes induced by substrate binding or catalytic activity, is likely involved in exposing the enzyme for binding at or near the sites of membrane protrusion formation. Copyright © 2014 Elsevier GmbH. All rights reserved.

Prospect evaluation as a function of numeracy and probability denominator.

PubMed

Millroth, Philip; Juslin, Peter

2015-05-01

This study examines how numeracy and probability denominator (a direct-ratio probability, a relative frequency with denominator 100, a relative frequency with denominator 10,000) affect the evaluation of prospects in an expected-value based pricing task. We expected that numeracy would affect the results due to differences in the linearity of number perception and the susceptibility to denominator neglect with different probability formats. An analysis with functional measurement verified that participants integrated value and probability into an expected value. However, a significant interaction between numeracy and probability format and subsequent analyses of the parameters of cumulative prospect theory showed that the manipulation of probability denominator changed participants' psychophysical response to probability and value. Standard methods in decision research may thus confound people's genuine risk attitude with their numerical capacities and the probability format used. Copyright © 2015 Elsevier B.V. All rights reserved.

Experiences with Probabilistic Analysis Applied to Controlled Systems

NASA Technical Reports Server (NTRS)

Kenny, Sean P.; Giesy, Daniel P.

2004-01-01

This paper presents a semi-analytic method for computing frequency dependent means, variances, and failure probabilities for arbitrarily large-order closed-loop dynamical systems possessing a single uncertain parameter or with multiple highly correlated uncertain parameters. The approach will be shown to not suffer from the same computational challenges associated with computing failure probabilities using conventional FORM/SORM techniques. The approach is demonstrated by computing the probabilistic frequency domain performance of an optimal feed-forward disturbance rejection scheme.

Coined quantum walks on weighted graphs

NASA Astrophysics Data System (ADS)

Wong, Thomas G.

2017-11-01

We define a discrete-time, coined quantum walk on weighted graphs that is inspired by Szegedy’s quantum walk. Using this, we prove that many lackadaisical quantum walks, where each vertex has l integer self-loops, can be generalized to a quantum walk where each vertex has a single self-loop of real-valued weight l. We apply this real-valued lackadaisical quantum walk to two problems. First, we analyze it on the line or one-dimensional lattice, showing that it is exactly equivalent to a continuous deformation of the three-state Grover walk with faster ballistic dispersion. Second, we generalize Grover’s algorithm, or search on the complete graph, to have a weighted self-loop at each vertex, yielding an improved success probability when l < 3 + 2\\sqrt{2} ≈ 5.828 .

Encapsulation of Mesenchymal Stem Cells Improves Vascularization of Alginate-Based Scaffolds.

PubMed

Steiner, Dominik; Lingens, Lara; Fischer, Laura; Köhn, Katrin; Detsch, Rainer; Boccaccini, Aldo R; Fey, Tobias; Greil, Peter; Weis, Christian; Beier, Justus P; Horch, Raymund E; Arkudas, Andreas

2018-05-09

Vascularization of bioartificial tissues can be significantly enhanced by the generation of an arteriovenous (AV) loop. Besides the surgical vascularization, the choice of the scaffold and the applied cells are indispensable cofactors. The combination of alginate dialdehyde and gelatin (ADA-GEL) and mesenchymal stem cells (MSCs) is a promising approach with regard to biocompatibility, biodegradation, as well as de novo tissue formation. In this study, we targeted the investigation of the vascularization of ADA-GEL with and in the absence of encapsulated MSCs in the AV loop model. A Teflon chamber filled with ADA-GEL microcapsules was placed in the groin of Lewis rats and an AV loop was placed into the chamber. Group A encompassed the ADA-GEL without MSCs, whereas group B contained 2 × 10 6 DiI-labeled MSCs/mL ADA-GEL. Four weeks postoperatively, tissue formation and vascularization were investigated by histology and microcomputed tomography. We were able to prove vascularization originating from the AV loop in both groups with statistically significant more vessels in group B containing MSCs. Moreover, encapsulated MSCs promoted biodegradation of the ADA-GEL microcapsules. In the present study, we were able to demonstrate for the first time, the successful vascularization of ADA-GEL microcapsules by means of the AV loop. Furthermore, ADA-GEL displayed a good biocompatibility and encapsulation of MSCs into ADA-GEL microcapsule-enhanced vascularization as well as biodegradation.

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

PubMed Central

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

2013-01-01

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

Accumulation of dislocation loops in the α phase of Zr Excel alloy under heavy ion irradiation

NASA Astrophysics Data System (ADS)

Yu, Hongbing; Yao, Zhongwen; Idrees, Yasir; Zhang, He K.; Kirk, Mark A.; Daymond, Mark R.

2017-08-01

In-situ heavy ion irradiations were performed on the high Sn content Zr alloy 'Excel', measuring type dislocation loop accumulation up to irradiation damage doses of 10 dpa at a range of temperatures. The high content of Sn, which diffuses slowly, and the thin foil geometry of the sample provide a unique opportunity to study an extreme case where displacement cascades dominate the loop formation and evolution. The dynamic observation of dislocation loop evolution under irradiation at 200 °C reveals that type dislocation loops can form at very low dose (0.0025 dpa). The size of the dislocation loops increases slightly with irradiation damage dose. The mechanism controlling loop growth in this study is different from that in neutron irradiation; in this study, larger dislocation loops can condense directly from the interaction of displacement cascades and the high concentration of point defects in the matrix. The size of the dislocation loop is dependent on the point defect concentration in the matrix. A negative correlation between the irradiation temperature and the dislocation loop size was observed. A comparison between cascade dominated loop evolution (this study), diffusion dominated loop evolution (electron irradiation) and neutron irradiation suggests that heavy ion irradiation alone may not be enough to accurately reproduce neutron irradiation induced loop structures. An alternative method is proposed in this paper. The effects of Sn on the displacement cascades, defect yield, and the diffusion behavior of point defects are established.

Functional characteristics of a double positive feedback loop coupled with autorepression

NASA Astrophysics Data System (ADS)

Banerjee, Subhasis; Bose, Indrani

2008-12-01

We study the functional characteristics of a two-gene motif consisting of a double positive feedback loop and an autoregulatory negative feedback loop. The motif appears in the gene regulatory network controlling the functional activity of pancreatic β-cells. The model exhibits bistability and hysteresis in appropriate parameter regions. The two stable steady states correspond to low (OFF state) and high (ON state) protein levels, respectively. Using a deterministic approach, we show that the region of bistability increases in extent when the copy number of one of the genes is reduced from 2 to 1. The negative feedback loop has the effect of reducing the size of the bistable region. Loss of a gene copy, brought about by mutations, hampers the normal functioning of the β-cells giving rise to the genetic disorder, maturity-onset diabetes of the young (MODY). The diabetic phenotype makes its appearance when a sizable fraction of the β-cells is in the OFF state. Using stochastic simulation techniques we show that, on reduction of the gene copy number, there is a transition from the monostable ON to the ON state in the bistable region of the parameter space. Fluctuations in the protein levels, arising due to the stochastic nature of gene expression, can give rise to transitions between the ON and OFF states. We show that as the strength of autorepression increases, the ON → OFF state transitions become less probable whereas the reverse transitions are more probable. The implications of the results in the context of the occurrence of MODY are pointed out.

Cosmic string loops as the seeds of super-massive black holes

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

Bramberger, Sebastian F.; Brandenberger, Robert H.; Jreidini, Paul

2015-06-01

Recent discoveries of super-massive black holes at high redshifts indicate a possible tension with the standard ΛCDM paradigm of early universe cosmology which has difficulties in explaining the origin of the required nonlinear compact seeds which trigger the formation of these super-massive black holes. Here we show that cosmic string loops which result from a scaling solution of strings formed during a phase transition in the very early universe lead to an additional source of compact seeds. The number density of string-induced seeds dominates at high redshifts and can help trigger the formation of the observed super-massive black holes.

Transverse Oscillations of Coronal Loops

NASA Astrophysics Data System (ADS)

Ruderman, Michael S.; Erdélyi, Robert

2009-12-01

On 14 July 1998 TRACE observed transverse oscillations of a coronal loop generated by an external disturbance most probably caused by a solar flare. These oscillations were interpreted as standing fast kink waves in a magnetic flux tube. Firstly, in this review we embark on the discussion of the theory of waves and oscillations in a homogeneous straight magnetic cylinder with the particular emphasis on fast kink waves. Next, we consider the effects of stratification, loop expansion, loop curvature, non-circular cross-section, loop shape and magnetic twist. An important property of observed transverse coronal loop oscillations is their fast damping. We briefly review the different mechanisms suggested for explaining the rapid damping phenomenon. After that we concentrate on damping due to resonant absorption. We describe the latest analytical results obtained with the use of thin transition layer approximation, and then compare these results with numerical findings obtained for arbitrary density variation inside the flux tube. Very often collective oscillations of an array of coronal magnetic loops are observed. It is natural to start studying this phenomenon from the system of two coronal loops. We describe very recent analytical and numerical results of studying collective oscillations of two parallel homogeneous coronal loops. The implication of the theoretical results for coronal seismology is briefly discussed. We describe the estimates of magnetic field magnitude obtained from the observed fundamental frequency of oscillations, and the estimates of the coronal scale height obtained using the simultaneous observations of the fundamental frequency and the frequency of the first overtone of kink oscillations. In the last part of the review we summarise the most outstanding and acute problems in the theory of the coronal loop transverse oscillations.

Closed-loop motor control using high-speed fiber optics

NASA Technical Reports Server (NTRS)

Dawson, Reginald (Inventor); Rodriquiz, Dagobert (Inventor)

1991-01-01

A closed-loop control system for controlling the operation of one or more servo motors or other controllable devices is described. The system employs a fiber optics link immune to electromagnetic interference, for transmission of control signals from a controller or controllers at a remote station to the power electronics located in proximity to the motors or other devices at the local station. At the remote station the electrical control signals are time-multiplexed, converted to a formatted serial bit stream, and converted to light signals for transmission over a single fiber of the fiber optics link. At the local station, the received optical signals are reconstructed as electrical control signals for the controlled motors or other devices. At the local station, an encoder sensor linked to the driven device generates encoded feedback signals which provide information as to a condition of the controlled device. The encoded signals are placed in a formatted serial bit stream, multiplexed, and transmitted as optical signals over a second fiber of the fiber optic link which closes the control loop of the closed-loop motor controller. The encoded optical signals received at the remote station are demultiplexed, reconstructed and coupled to the controller(s) as electrical feedback signals.

CHROMOSOMAL DIFFERENTIATIONS OF THE LAMPBRUSH TYPE FORMED BY THE Y CHROMOSOME IN DROSOPHILA HYDEI AND DROSOPHILA NEOHYDEI

PubMed Central

Hess, Oswald; Meyer, Günther F.

1963-01-01

The nuclei of growing spermatocytes in Drosophila hydei and D. neohydei are characterized by the appearance of phase-specific, paired, loop-shaped structures thought to be similar to the loops in lampbrush chromosomes of amphibian oocytes. In X/O-males of D. hydei spermatogenesis is completely blocked before the first maturation division. No spermatozoa are formed in such testes. In the nuclei of X/O-spermatocytes, paired loop formations are absent. This shows the dependence of these chromosomal functional structures upon the Y chromosome. The basis of this dependence could be shown through an investigation of males with two Y chromosomes. All loop pairs are present in duplicate in XYY males. This proves that the intranuclear formations are structural modifications of the Y chromosome itself. These functional structures are species-specific and characteristically different in Drosophila hydei and D. neohydei. Reciprocal species crosses and a backcross showed that the spermatocyte nuclei of all hybrid males possess the functional structures corresponding to the species which donated the Y chromosome. This shows that the morphological character of the functional structures is also determined by the Y chromosome. PMID:13954225

The effect of jitter on the performance of space coherent optical communication system with Costas loop

NASA Astrophysics Data System (ADS)

Li, Xin; Hong, Yifeng; Wang, Jinfang; Liu, Yang; Sun, Xun; Li, Mi

2018-01-01

Numerous communication techniques and optical devices successfully applied in space optical communication system indicates a good portability of it. With this good portability, typical coherent demodulation technique of Costas loop can be easily adopted in space optical communication system. As one of the components of pointing error, the effect of jitter plays an important role in the communication quality of such system. Here, we obtain the probability density functions (PDF) of different jitter degrees and explain their essential effect on the bit error rate (BER) space optical communication system. Also, under the effect of jitter, we research the bit error rate of space coherent optical communication system using Costas loop with different system parameters of transmission power, divergence angle, receiving diameter, avalanche photodiode (APD) gain, and phase deviation caused by Costas loop. Through a numerical simulation of this kind of communication system, we demonstrate the relationship between the BER and these system parameters, and some corresponding methods of system optimization are presented to enhance the communication quality.

A competent catalytic active site is necessary for substrate induced dimer assembly in triosephosphate isomerase.

PubMed

Jimenez-Sandoval, Pedro; Vique-Sanchez, Jose Luis; Hidalgo, Marisol López; Velazquez-Juarez, Gilberto; Diaz-Quezada, Corina; Arroyo-Navarro, Luis Fernando; Moran, Gabriela Montero; Fattori, Juliana; Jessica Diaz-Salazar, A; Rudiño-Pinera, Enrique; Sotelo-Mundo, Rogerio; Figueira, Ana Carolina Migliorini; Lara-Gonzalez, Samuel; Benítez-Cardoza, Claudia G; Brieba, Luis G

2017-11-01

The protozoan parasite Trichomonas vaginalis contains two nearly identical triosephosphate isomerases (TvTIMs) that dissociate into stable monomers and dimerize upon substrate binding. Herein, we compare the role of the "ball and socket" and loop 3 interactions in substrate assisted dimer assembly in both TvTIMs. We found that point mutants at the "ball" are only 39 and 29-fold less catalytically active than their corresponding wild-type counterparts, whereas Δloop 3 deletions are 1502 and 9400-fold less active. Point and deletion mutants dissociate into stable monomers. However, point mutants assemble as catalytic competent dimers upon binding of the transition state substrate analog PGH, whereas loop 3 deletions remain monomeric. A comparison between crystal structures of point and loop 3 deletion monomeric mutants illustrates that the catalytic residues in point mutants and wild-type TvTIMs are maintained in the same orientation, whereas the catalytic residues in deletion mutants show an increase in thermal mobility and present structural disorder that may hamper their catalytic role. The high enzymatic activity present in monomeric point mutants correlates with the formation of dimeric TvTIMs upon substrate binding. In contrast, the low activity and lack of dimer assembly in deletion mutants suggests a role of loop 3 in promoting the formation of the active site as well as dimer assembly. Our results suggest that in TvTIMs the active site is assembled during dimerization and that the integrity of loop 3 and ball and socket residues is crucial to stabilize the dimer. Copyright © 2017 Elsevier B.V. All rights reserved.

Getting in (and out of) the loop: regulating higher order telomere structures.

PubMed

Luke-Glaser, Sarah; Poschke, Heiko; Luke, Brian

2012-01-01

The DNA at the ends of linear chromosomes (the telomere) folds back onto itself and forms an intramolecular lariat-like structure. Although the telomere loop has been implicated in the protection of chromosome ends from nuclease-mediated resection and unscheduled DNA repair activities, it potentially poses an obstacle to the DNA replication machinery during S-phase. Therefore, the coordinated regulation of telomere loop formation, maintenance, and resolution is required in order to establish a balance between protecting the chromosome ends and promoting their duplication prior to cell division. Until recently, the only factor known to influence telomere looping in human cells was TRF2, a component of the shelterin complex. Recent work in yeast and mouse cells has uncovered additional regulatory factors that affect the loop structure at telomeres. In the following "perspective" we outline what is known about telomere looping and highlight the latest results regarding the regulation of this chromosome end structure. We speculate about how the manipulation of the telomere loop may have therapeutic implications in terms of diseases associated with telomere dysfunction and uncontrolled proliferation.

Structure-Directed and Tailored Diversity Synthetic Antibody Libraries Yield Novel Anti-EGFR Antagonists.

PubMed

Miersch, Shane; Maruthachalam, Bharathikumar Vellalore; Geyer, C Ronald; Sidhu, Sachdev S

2017-05-19

We tested whether grafting an interaction domain into the hypervariable loop of a combinatorial antibody library could promote targeting to a specific epitope. Formation of the epidermal growth factor receptor (EGFR) signaling heterodimer involves extensive contacts mediated by a "dimerization loop." We grafted the dimerization loop into the third hypervariable loop of a synthetic antigen-binding fragment (Fab) library and diversified other loops using a tailored diversity strategy. This structure-directed Fab library and a naı̈ve synthetic Fab library were used to select Fabs against EGFR. Both libraries yielded high affinity Fabs that bound to overlapping epitopes on cell-surface EGFR, inhibited receptor activation, and targeted epitopes distinct from those of cetuximab and panitumumab. Epitope mapping experiments revealed complex sites of interaction, comprised of domains I and II but not exclusively localized to the receptor dimerization loop. These results validate the grafting approach for designing Fab libraries and also underscore the versatility of naı̈ve synthetic libraries.

Split and sealing of dislocated pipes at the front of a growing crystal

NASA Astrophysics Data System (ADS)

Gutkin, M. Yu.; Sheinerman, A. G.

2004-07-01

A model is suggested for the split of dislocated pipes at the front a growing crystal. Within the model, the pipe split occurs through the generation of a dislocation semi-loop at the pipe and crystal surfaces and its subsequent expansion into the crystal interior. The strain energy of such a dislocation semi-loop as well as the stress field of a dislocated pipe perpendicular to a flat crystal surface are calculated. The parameter regions are determined at which the expansion of the dislocation semi-loop is energetically favorable and, thus, the pipe split becomes irreversible. A mechanism is proposed for the formation of a stable semi-loop resulting in the split and possible subsequent overgrowth of the dislocated pipe.

Atomistic Simulations of the pH Induced Functional Rearrangement of Influenza Hemagglutinin

NASA Astrophysics Data System (ADS)

Lin, Xingcheng; Noel, Jeffrey; Wang, Qinghua; Ma, Jianpeng; Onuchic, Jose

Influenza hemagglutinin (HA), a surface glycoprotein responsible for the entry and replication of flu viruses in their host cells, functions by starting a dramatic conformational rearrangement, which leads to a fusion of the viral and endosomal membranes. It has been claimed that a loop-to-coiled-coil transition of the B-loop domain of HA drives the HA-induced membrane fusion. On the lack of dynamical details, however, the microscopic picture for this proposed ``spring-loaded'' movement is missing. To elaborate on the transition of the B-loop, we performed a set of unbiased all-atom molecular dynamics simulations of the full B-loop structure with the CHARMM36 force field. The complete free-energy profile constructed from our simulations reveals a slow transition rate for the B-loop that is incompatible with a downhill process. Additionally, our simulations indicate two potential sources of kinetic traps in the structural switch of the B-loop: Desolvation barriers and non-native secondary structure formation. The slow timescale of the B-loop transition also confirms our previous discovery from simulations using a coarse-grained structure-based model, which identified two competitive pathways both with a slow B-loop transition for HA to guide the membrane fusion.

THE ROLE OF KELVIN–HELMHOLTZ INSTABILITY FOR PRODUCING LOOP-TOP HARD X-RAY SOURCES IN SOLAR FLARES

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

Fang, Xia; Yuan, Ding; Xia, Chun

We propose a model for the formation of loop-top hard X-ray (HXR) sources in solar flares through the inverse Compton mechanism, scattering the surrounding soft X-ray (SXR) photons to higher energy HXR photons. We simulate the consequences of a flare-driven energy deposit in the upper chromosphere in the impulsive phase of single loop flares. The consequent chromosphere evaporation flows from both footpoints reach speeds up to hundreds of kilometers per second, and we demonstrate how this triggers Kelvin–Helmholtz instability (KHI) in the loop top, under mildly asymmetric conditions, or more toward the loop flank for strongly asymmetric cases. The KHImore » vortices further fragment the magnetic topology into multiple magnetic islands and current sheets, and the hot plasma within leads to a bright loop-top SXR source region. We argue that the magnetohydrodynamic turbulence that appears at the loop apex could be an efficient accelerator of non-thermal particles, which the island structures can trap at the loop-top. These accelerated non-thermal particles can upscatter the surrounding thermal SXR photons emitted by the extremely hot evaporated plasma to HXR photons.« less

Investigation of new techniques for aircraft navigation using the omega navigation

NASA Technical Reports Server (NTRS)

Baxa, E. G., Jr.

1978-01-01

An OMEGA navigation receiver with a microprocessor as the computational component was investigated. A version of the INTEL 4004 microprocessor macroassembler suitable for use on the CDC-6600 system and development of a FORTRAN IV simulator program for the microprocessor was developed. Supporting studies included development and evaluation of navigation algorithms to generate relative position information from OMEGA VLF phase measurements. Simulation studies were used to evaluate assumptions made in developing a navigation equation in OMEGA Line of Position (LOP) coordinates. Included in the navigation algorithms was a procedure for calculating a position in latitude/longitude given an OMEGA LOP fix. Implementation of a digital phase locked loop (DPLL) was evaluated on the basic of phase response characteristics over a range of input phase variations. Included also is an analytical evaluation on the basis of error probability of an algorithm for automatic time synchronization of the receiver to the OMEGA broadcast format. The use of actual OMEGA phase data and published propagation prediction corrections to determine phase velocity estimates was discussed.

Effects of alloying elements on the formation of < c >-component loops in Zr alloy Excel under heavy ion irradiation.

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

Idrees, Yasir; Francis, Elisabeth M.; Yao, Zhongwen

2015-05-14

We report here the microstructural changes occurring in the zirconium alloy Excel (Zr-3.5 wt% Sn-0.8Nb-0.8Mo-0.2Fe) during heavy ion irradiation. In situ irradiation experiments were conducted at reactor operating temperatures on two Zr Excel alloy microstructures with different states of alloying elements, with the states achieved by different solution heat treatments. In the first case, the alloying elements were mostly concentrated in the beta (beta) phase, whereas, in the second case, large Zr-3(Mo,Nb,Fe)(4) secondary phase precipitates (SPPs) were grown in the alpha (alpha) phase by long term aging. The heavy ion induced damage and resultant compositional changes were examined using transmissionmore » electron microscopy (TEM) in combination with scanning transmission electron microscope (STEM)-energy dispersive x-ray spectroscopy (EDS) mapping. Significant differences were seen in microstructural evolution between the two different microstructures that were irradiated under similar conditions. Nucleation and growth of < c >-component loops and their dependence on the alloying elements are a major focus of the current investigation. It was observed that the < c >-component loops nucleate readily at 100, 300, and 400 degrees C after a threshold incubation dose (TID), which varies with irradiation temperature and the state of alloying elements. It was found that the TID for the formation of < c >-component loops increases with decrease in irradiation temperature. Alloying elements that are present in the form of SPPs increase the TID compared to when they are in the beta phase solid solution. Dose and temperature dependence of loop size and density are presented. Radiation induced redistribution and clustering of alloying elements (Sn, Mo, and Fe) have been observed and related to the formation of < c >-component loops. It has been shown that at the higher temperature tests, irradiation induced dissolution of precipitates occurs whereas irradiation induced amorphization occurs at 100 degrees C. Furthermore, dose and temperature seem to be the main factors governing the dissolution of SPPs and redistribution of alloying elements, which in turn controls the nucleation and growth of < c >-component loops. The correlation between the microstructural evolution and microchemistry has been found by EDS and is discussed in detail.« less

Extrusion without a motor: a new take on the loop extrusion model of genome organization

PubMed Central

Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

2018-01-01

ABSTRACT Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and extrusion is the only model to date which can explain this. However, the model requires a motor to generate the loops, and although cohesin is a strong candidate for the extruding factor, a suitable motor protein (or a motor activity in cohesin itself) has yet to be found. Here we explore a new hypothesis: that there is no motor, and thermal motion within the nucleus drives extrusion. Using theoretical modelling and computer simulations we ask whether such diffusive extrusion could feasibly generate loops. Our simulations uncover an interesting ratchet effect (where an osmotic pressure promotes loop growth), and suggest, by comparison to recent in vitro and in vivo measurements, that diffusive extrusion can in principle generate loops of the size observed in the data. Extra View on : C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, and D. Marenduzzo “Non-equilibrium chromosome looping via molecular slip-links”, Physical Review Letters 119 138101 (2017) PMID:29300120

Extended molecular dynamics of a c-kit promoter quadruplex

PubMed Central

Islam, Barira; Stadlbauer, Petr; Krepl, Miroslav; Koca, Jaroslav; Neidle, Stephen; Haider, Shozeb; Sponer, Jiri

2015-01-01

The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 μs long, ∼50 μs in total) molecular dynamics simulations to explore conformational stability and loop dynamics of this quadruplex. Unfolding no-salt simulations are consistent with a multi-pathway model of quadruplex folding and identify the single-nucleotide propeller loops as the most fragile part of the quadruplex. Thus, formation of propeller loops represents a peculiar atomistic aspect of quadruplex folding. Unbiased simulations reveal μs-scale transitions in the loops, which emphasizes the need for extended simulations in studies of quadruplex loops. We identify ion binding in the loops which may contribute to quadruplex stability. The long lateral-propeller loop is internally very stable but extensively fluctuates as a rigid entity. It creates a size-adaptable cleft between the loop and the stem, which can facilitate ligand binding. The stability gain by forming the internal network of GA base pairs and stacks of this loop may be dictating which of the many possible quadruplex topologies is observed in the ground state by this promoter quadruplex. PMID:26245347

Probing the closed-loop model of mRNA translation in living cells

PubMed Central

Archer, Stuart K; Shirokikh, Nikolay E; Hallwirth, Claus V; Beilharz, Traude H; Preiss, Thomas

2015-01-01

The mRNA closed-loop, formed through interactions between the cap structure, poly(A) tail, eIF4E, eIF4G and PAB, features centrally in models of eukaryotic translation initiation, although direct support for its existence in vivo is not well established. Here, we investigated the closed-loop using a combination of mRNP isolation from rapidly cross-linked cells and high-throughput qPCR. Using the interaction between these factors and the opposing ends of mRNAs as a proxy for the closed-loop, we provide evidence that it is prevalent for eIF4E/4G-bound but unexpectedly sparse for PAB1-bound mRNAs, suggesting it primarily occurs during a distinct phase of polysome assembly. We observed mRNA-specific variation in the extent of closed-loop formation, consistent with a role for polysome topology in the control of gene expression. PMID:25826658

Neutron irradiation effects in Fe and Fe-Cr at 300 °C

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

Chen, Wei-Ying; Miao, Yinbin; Gan, Jian

2016-06-01

Fe and Fe-Cr (Cr = 10–16 at.%) specimens were neutron-irradiated at 300 °C to 0.01, 0.1 and 1 dpa. The TEM observations indicated that the Cr significantly reduced the mobility of dislocation loops and suppressed vacancy clustering, leading to distinct damage microstructures between Fe and Fe-Cr. Irradiation-induced dislocation loops in Fe were heterogeneously observed in the vicinity of grown-in dislocations, whereas the loop distribution observed in Fe-Cr is much more uniform. Voids were observed in the irradiated Fe samples, but not in irradiated Fe-Cr samples. Increasing Cr content in Fe-Cr results in a higher density, and a smaller size ofmore » irradiation-induced dislocation loops. Orowan mechanism was used to correlate the observed microstructure and hardening, which showed that the hardening in Fe-Cr can be attributed to the formation of dislocation loops and α' precipitates.« less

Bisphenol A and its methylated congeners inhibit growth and interfere with microtubules in human fibroblasts in vitro.

PubMed

Lehmann, Leane; Metzler, Manfred

2004-04-15

Bisphenol A (BPA), a monomer of polycarbonate plastics and epoxy resins, has previously been reported to induce micronuclei containing whole chromosomes in Chinese hamster V79 cells. In the present study, the aneuploidogenic potential of BPA was investigated in cultured human AG01522C fibroblasts. In contrast to the known aneugens diethylstilbestrol (DES) and 17beta-estradiol, which caused mitotic arrest and the induction of kinetochore-positive micronuclei, BPA did not induce micronuclei and inhibited the proliferation of AG01522C cells in G2 phase and probably also in G1 phase. Fluorescence microscopy of the BPA-treated cells after immunofluorescent staining of microtubules revealed structural abnormalities of the cytoplasmic microtubule complex (CMTC): densely stained rings and loops of tubulin were observed, which increased in number with increasing BPA concentration and were more stable against low temperature than normal microtubules. The mechanisms of the growth inhibition and the interference with microtubules elicited by BPA in AG01522C cells are presently unknown. The formation of rings and loops in the CMTC of AG01522C cells was also observed with two congeners of BPA carrying one and two, respectively, additional methyl groups in ortho-position to the phenolic hydroxyl group at each aromatic ring. However, in contrast to BPA itself, these congeners of BPA behaved "DES-like" by inducing mitotic arrest and kinetochore-positive micronuclei in AG01522C cells.

Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient β-sheet

PubMed Central

Buchanan, Lauren E.; Dunkelberger, Emily B.; Tran, Huong Q.; Cheng, Pin-Nan; Chiu, Chi-Cheng; Cao, Ping; Raleigh, Daniel P.; de Pablo, Juan J.; Nowick, James S.; Zanni, Martin T.

2013-01-01

Amyloid formation is implicated in more than 20 human diseases, yet the mechanism by which fibrils form is not well understood. We use 2D infrared spectroscopy and isotope labeling to monitor the kinetics of fibril formation by human islet amyloid polypeptide (hIAPP or amylin) that is associated with type 2 diabetes. We find that an oligomeric intermediate forms during the lag phase with parallel β-sheet structure in a region that is ultimately a partially disordered loop in the fibril. We confirm the presence of this intermediate, using a set of homologous macrocyclic peptides designed to recognize β-sheets. Mutations and molecular dynamics simulations indicate that the intermediate is on pathway. Disrupting the oligomeric β-sheet to form the partially disordered loop of the fibrils creates a free energy barrier that is the origin of the lag phase during aggregation. These results help rationalize a wide range of previous fragment and mutation studies including mutations in other species that prevent the formation of amyloid plaques. PMID:24218609

[Pharmacogenic osteoporosis beyond cortisone. Proton pump inhibitors, glitazones and diuretics].

PubMed

Kann, P H; Hadji, P; Bergmann, R S

2014-05-01

[corrected] There are many drugs which can cause osteoporosis or at least favor its initiation. The effect of hormones and drugs with antihormonal activity, such as glucocorticoids and aromatase inhibitors, on initiation of osteoporosis is well known. In addition, proton pump inhibitors, glitazones and diuretics also influence the formation of osteoporosis. The results of currently available studies on the correlation between proton pump inhibitors, glitazones and diuretics on formation of osteoporosis were evaluated and summarized. Proton pump inhibitors and glitazones increase the risk for osteoporotic fractures. Loop diuretics may slightly increase fracture risk, whereas thiazides were shown to be osteoprotective by reducing fracture probability on a relevant scale. Proton pump inhibitors should not be prescribed without serious consideration and then only as long as necessary. Alternatively, the administration of the less effective H2 antagonists should be considered when possible due to the reduction of acid secretion. Because the long-term intake of thiazides is associated with a clinically relevant reduction in the risk of fractures and they are economic and well-tolerated, prescription can be thoroughly recommended within the framework of differential diagnostic considerations in an appropriate clinical context. The briefly increased risk of falling immediately after starting diuretic therapy is the only point which needs to be considered.

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

DOE PAGES

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

2017-08-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.

PubMed Central

van Dongen, M J; Mooren, M M; Willems, E F; van der Marel, G A; van Boom, J H; Wijmenga, S S; Hilbers, C W

1997-01-01

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA-TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and the last residues of the tetraloop of this hairpin form a sheared G-A base pair on top of the six Watson-Crick base pairs in the stem. The glycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high- anti domain ( approximately -60 degrees ) respectively. Several dihedral angles in the loop adopt non-standard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residue is directed away from the loop region. The loop structure can be classified as a so-called type-I loop, in which the bases at the 5'-end of the loop stack in a continuous fashion. In this situation, loop stability is unlikely to depend heavily on the nature of the unpaired bases in the loop. Moreover, the present study indicates that the influence of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair. PMID:9092659

Prognostic Impact of Loop Diuretics in Patients With Chronic Heart Failure　- Effects of Addition of Renin-Angiotensin-Aldosterone System Inhibitors and β-Blockers.

PubMed

Miura, Masanobu; Sugimura, Koichiro; Sakata, Yasuhiko; Miyata, Satoshi; Tadaki, Soichiro; Yamauchi, Takeshi; Onose, Takeo; Tsuji, Kanako; Abe, Ruri; Oikawa, Takuya; Kasahara, Shintaro; Nochioka, Kotaro; Takahashi, Jun; Shimokawa, Hiroaki

2016-05-25

It remains to be elucidated whether addition of renin-angiotensin-aldosterone system (RAAS) inhibitors and/or β-blockers to loop diuretics has a beneficial prognostic impact on chronic heart failure (CHF) patients. From the Chronic Heart failure Analysis and Registry in the Tohoku district 2 (CHART-2) Study (n=10,219), we enrolled 4,134 consecutive patients with symptomatic stage C/D CHF (mean age, 69.3 years, 67.7% male). We constructed Cox models for composite of death, myocardial infarction, stroke and HF admission. On multivariate inverse probability of treatment weighted (IPTW) Cox modeling, loop diuretics use was associated with worse prognosis with hazard ratio (HR) 1.28 (P<0001). Furthermore, on IPTW multivariate Cox modeling for multiple treatments, both low-dose (<40 mg/day) and high-dose (≥40 mg/day) loop diuretics were associated with worse prognosis with HR 1.32 and 1.56, respectively (both P<0.001). Triple blockade with RAS inhibitor(s), mineral corticoid (aldosterone) receptor antagonist(s) (MRA), and β-blocker(s) was significantly associated with better prognosis in those on low-dose but not on high-dose loop diuretics. Chronic use of loop diuretics is significantly associated with worse prognosis in CHF patients in a dose-dependent manner, whereas the triple combination of RAAS inhibitor(s), MRA, and β-blocker(s) is associated with better prognosis when combined with low-dose loop diuretics. (Circ J 2016; 80: 1396-1403).

Cluster-based control of a separating flow over a smoothly contoured ramp

NASA Astrophysics Data System (ADS)

Kaiser, Eurika; Noack, Bernd R.; Spohn, Andreas; Cattafesta, Louis N.; Morzyński, Marek

2017-12-01

The ability to manipulate and control fluid flows is of great importance in many scientific and engineering applications. The proposed closed-loop control framework addresses a key issue of model-based control: The actuation effect often results from slow dynamics of strongly nonlinear interactions which the flow reveals at timescales much longer than the prediction horizon of any model. Hence, we employ a probabilistic approach based on a cluster-based discretization of the Liouville equation for the evolution of the probability distribution. The proposed methodology frames high-dimensional, nonlinear dynamics into low-dimensional, probabilistic, linear dynamics which considerably simplifies the optimal control problem while preserving nonlinear actuation mechanisms. The data-driven approach builds upon a state space discretization using a clustering algorithm which groups kinematically similar flow states into a low number of clusters. The temporal evolution of the probability distribution on this set of clusters is then described by a control-dependent Markov model. This Markov model can be used as predictor for the ergodic probability distribution for a particular control law. This probability distribution approximates the long-term behavior of the original system on which basis the optimal control law is determined. We examine how the approach can be used to improve the open-loop actuation in a separating flow dominated by Kelvin-Helmholtz shedding. For this purpose, the feature space, in which the model is learned, and the admissible control inputs are tailored to strongly oscillatory flows.

Stochastic gravitational wave background from light cosmic strings

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

DePies, Matthew R.; Hogan, Craig J.

2007-06-15

Spectra of the stochastic gravitational wave backgrounds from cosmic strings are calculated and compared with present and future experimental limits. Motivated by theoretical expectations of light cosmic strings in superstring cosmology, improvements in experimental sensitivity, and recent demonstrations of large, stable loop formation from a primordial network, this study explores a new range of string parameters with masses lighter than previously investigated. A standard 'one-scale' model for string loop formation is assumed. Background spectra are calculated numerically for dimensionless string tensions G{mu}/c{sup 2} between 10{sup -7} and 10{sup -18}, and initial loop sizes as a fraction of the Hubble radiusmore » {alpha} from 0.1 to 10{sup -6}. The spectra show a low frequency power-law tail, a broad spectral peak due to loops decaying at the present epoch (including frequencies higher than their fundamental mode, and radiation associated with cusps), and a flat (constant energy density) spectrum at high frequencies due to radiation from loops that decayed during the radiation-dominated era. The string spectrum is distinctive and unlike any other known source. The peak of the spectrum for light strings appears at high frequencies, significantly affecting predicted signals. The spectra of the cosmic string backgrounds are compared with current millisecond pulsar limits and Laser Interferometer Space Antenna (LISA) sensitivity curves. For models with large stable loops ({alpha}=0.1), current pulsar-timing limits exclude G{mu}/c{sup 2}>10{sup -9}, a much tighter limit on string tension than achievable with other techniques, and within the range of current models based on brane inflation. LISA may detect a background from strings as light as G{mu}/c{sup 2}{approx_equal}10{sup -16}, corresponding to field theory strings formed at roughly 10{sup 11} GeV.« less

Investigation of RNA Hairpin Loop Folding with Time-Resolved Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Stancik, Aaron Lee

Ribonucleic acids (RNAs) are a group of functional biopolymers central to the molecular underpinnings of life. To complete the many processes they mediate, RNAs must fold into precise three-dimensional structures. Hairpin loops are the most ubiquitous and basic structural elements present in all folded RNAs, and are the foundation upon which all complex tertiary structures are built. A hairpin loop forms when a single stranded RNA molecule folds back on itself creating a helical stem of paired bases capped by a loop. This work investigates the formation of UNCG hairpin loops with the sequence 5'-GC(UNCG)GC-3' (N = A, U, G, or C) using both equilibrium infrared (IR) and time-resolved IR spectroscopy. Equilibrium IR melting data were used to determine thermodynamic parameters. Melting temperatures ranged from 50 to 60°C, and enthalpies of unfolding were on the order of 100 kJ/mol. In the time-resolved work, temperature jumps of up to 20°C at 2.5°C increments were obtained with transient relaxation kinetics spanning nanoseconds to hundreds of microseconds. The relaxation kinetics for all of the oligomers studied were fit to first or second order exponentials. Multiple vibrational transitions were probed on each oligomer for fully folded and partially denatured structures. In the time-resolved limit, in contrast to equilibrium melting, RNA does not fold according to two-state behavior. These results are some of the first to show that RNA hairpins fold according to a rugged energy landscape, which contradicts their relatively simple nature. In addition, this work has proven that time-resolved IR spectroscopy is a powerful and novel tool for investigating the earliest events of RNA folding, the formation of the hairpin loop.

Measurements of gas hydrate formation probability distributions on a quasi-free water droplet

NASA Astrophysics Data System (ADS)

Maeda, Nobuo

2014-06-01

A High Pressure Automated Lag Time Apparatus (HP-ALTA) can measure gas hydrate formation probability distributions from water in a glass sample cell. In an HP-ALTA gas hydrate formation originates near the edges of the sample cell and gas hydrate films subsequently grow across the water-guest gas interface. It would ideally be desirable to be able to measure gas hydrate formation probability distributions of a single water droplet or mist that is freely levitating in a guest gas, but this is technically challenging. The next best option is to let a water droplet sit on top of a denser, immiscible, inert, and wall-wetting hydrophobic liquid to avoid contact of a water droplet with the solid walls. Here we report the development of a second generation HP-ALTA which can measure gas hydrate formation probability distributions of a water droplet which sits on a perfluorocarbon oil in a container that is coated with 1H,1H,2H,2H-Perfluorodecyltriethoxysilane. It was found that the gas hydrate formation probability distributions of such a quasi-free water droplet were significantly lower than those of water in a glass sample cell.

Effects of applied strain on nanoscale self-interstitial cluster formation in BCC iron

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

Gao, Ning; Setyawan, Wahyu; Kurtz, Richard J.

2017-09-01

The effect of applied strains on the configurational evolution of self-interstitial clusters in BCC iron (Fe) is explored with atomistic simulations. A novel cluster configuration is discovered at low temperatures (<600 K), which consists of <110> dumbbells and <111> crowdions in a specific configuration, resulting in an immobile defect. The stability and diffusion of this cluster at higher temperatures is explored. In addition, an anisotropy distribution factor of a particular [hkl] interstitial loop within the family of loops is calculated as a function of strain. The results show that loop anisotropy is governed by the angle between the stress directionmore » and the orientation of the <111> crowdions in the loop, and directly linked to the stress induced preferred nucleation of self-interstitial atoms.« less

Response simulation and theoretical calibration of a dual-induction resistivity LWD tool

NASA Astrophysics Data System (ADS)

Xu, Wei; Ke, Shi-Zhen; Li, An-Zong; Chen, Peng; Zhu, Jun; Zhang, Wei

2014-03-01

In this paper, responses of a new dual-induction resistivity logging-while-drilling (LWD) tool in 3D inhomogeneous formation models are simulated by the vector finite element method (VFEM), the influences of the borehole, invaded zone, surrounding strata, and tool eccentricity are analyzed, and calibration loop parameters and calibration coefficients of the LWD tool are discussed. The results show that the tool has a greater depth of investigation than that of the existing electromagnetic propagation LWD tools and is more sensitive to azimuthal conductivity. Both deep and medium induction responses have linear relationships with the formation conductivity, considering optimal calibration loop parameters and calibration coefficients. Due to the different depths of investigation and resolution, deep induction and medium induction are affected differently by the formation model parameters, thereby having different correction factors. The simulation results can provide theoretical references for the research and interpretation of the dual-induction resistivity LWD tools.

Relative position coordinated control for spacecraft formation flying with communication delays

NASA Astrophysics Data System (ADS)

Ran, Dechao; Chen, Xiaoqian; Misra, Arun K.; Xiao, Bing

2017-08-01

This study addresses a relative position coordinated control problem for spacecraft formation flying subject to directed communication topology. Two different kinds of communication delay cases, including time-varying delays and arbitrarily bounded delays are investigated. Using the backstepping control technique, two virtual velocity control inputs are firstly designed to achieve coordinated position tracking for the kinematic subsystem. Furthermore, a hyperbolic tangent function is introduced to guarantee the boundedness of the virtual controller. Then, a finite-time control algorithm is designed for the dynamic subsystem. It can guarantee that the virtual velocity can be followed by the real velocity after finite time. It is theoretically proved that the proposed control scheme can asymptotically stabilize the closed-loop system. Numerical simulations are further presented that not only highlight closed-loop performance benefiting from the proposed control scheme, but also illustrate its superiority in comparison with conventional formation control schemes.

Dynamic graciloplasty for urinary incontinence: the potential for sequential closed-loop stimulation.

PubMed

Zonnevijlle, Erik D H; Perez-Abadia, Gustavo; Stremel, Richard W; Maldonado, Claudio J; Kon, Moshe; Barker, John H

2003-11-01

Muscle tissue transplantation applied to regain or dynamically assist contractile functions is known as 'dynamic myoplasty'. Success rates of clinical applications are unpredictable, because of lack of endurance, ischemic lesions, abundant scar formation and inadequate performance of tasks due to lack of refined control. Electrical stimulation is used to control dynamic myoplasties and should be improved to reduce some of these drawbacks. Sequential segmental neuromuscular stimulation improves the endurance and closed-loop control offers refinement in rate of contraction of the muscle, while function-controlling stimulator algorithms present the possibility of performing more complex tasks. An acute feasibility study was performed in anaesthetised dogs combining these techniques. Electrically stimulated gracilis-based neo-sphincters were compared to native sphincters with regard to their ability to maintain continence. Measurements were made during fast bladder pressure changes, static high bladder pressure and slow filling of the bladder, mimicking among others posture changes, lifting heavy objects and diuresis. In general, neo-sphincter and native sphincter performance showed no significant difference during these measurements. However, during high bladder pressures reaching 40 cm H(2)O the neo-sphincters maintained positive pressure gradients, whereas most native sphincters relaxed. During slow filling of the bladder the neo-sphincters maintained a controlled positive pressure gradient for a prolonged time without any form of training. Furthermore, the accuracy of these maintained pressure gradients proved to be within the limits set up by the native sphincters. Refinements using more complicated self-learning function-controlling algorithms proved to be effective also and are briefly discussed. In conclusion, a combination of sequential stimulation, closed-loop control and function-controlling algorithms proved feasible in this dynamic graciloplasty-model. Neo-sphincters were created, which would probably provide an acceptable performance, when the stimulation system could be implanted and further tested. Sizing this technique down to implantable proportions seems to be justified and will enable exploration of the possible benefits.

Precision Closed-Loop Orbital Maneuvering System Design and Performance for the Magnetospheric Multi-Scale Mission (MMS) Formation

NASA Technical Reports Server (NTRS)

Chai, Dean; Queen, Steve; Placanica, Sam

2015-01-01

NASA's Magnetospheric Multi-Scale (MMS) mission successfully launched on March 13, 2015 (UTC) consists of four identically instrumented spin-stabilized observatories that function as a constellation to study magnetic reconnection in space. The need to maintain sufficiently accurate spatial and temporal formation resolution of the observatories must be balanced against the logistical constraints of executing overly-frequent maneuvers on a small fleet of spacecraft. These two considerations make for an extremely challenging maneuver design problem. This paper focuses on the design elements of a 6-DOF spacecraft attitude control and maneuvering system capable of delivering the high-precision adjustments required by the constellation designers---specifically, the design, implementation, and on-orbit performance of the closed-loop formation-class maneuvers that include initialization, maintenance, and re-sizing. The maneuvering control system flown on MMS utilizes a micro-gravity resolution accelerometer sampled at a high rate in order to achieve closed-loop velocity tracking of an inertial target with arc-minute directional and millimeter-per-second magnitude accuracy. This paper summarizes the techniques used for correcting bias drift, sensor-head offsets, and centripetal aliasing in the acceleration measurements. It also discusses the on-board pre-maneuver calibration and compensation algorithms as well as the implementation of the post-maneuver attitude adjustments.

Precision Closed-Loop Orbital Maneuvering System Design and Performance for the Magnetospheric Multiscale Formation

NASA Technical Reports Server (NTRS)

Chai, Dean J.; Queen, Steven Z.; Placanica, Samuel J.

2015-01-01

NASAs Magnetospheric Multiscale (MMS) mission successfully launched on March 13,2015 (UTC) consists of four identically instrumented spin-stabilized observatories that function as a constellation to study magnetic reconnection in space. The need to maintain sufficiently accurate spatial and temporal formation resolution of the observatories must be balanced against the logistical constraints of executing overly-frequent maneuvers on a small fleet of spacecraft. These two considerations make for an extremely challenging maneuver design problem. This paper focuses on the design elements of a 6-DOF spacecraft attitude control and maneuvering system capable of delivering the high-precision adjustments required by the constellation designers specifically, the design, implementation, and on-orbit performance of the closed-loop formation-class maneuvers that include initialization, maintenance, and re-sizing. The maneuvering control system flown on MMS utilizes a micro-gravity resolution accelerometer sampled at a high rate in order to achieve closed-loop velocity tracking of an inertial target with arc-minute directional and millimeter-per second magnitude accuracy. This paper summarizes the techniques used for correcting bias drift, sensor-head offsets, and centripetal aliasing in the acceleration measurements. It also discusses the on-board pre-maneuver calibration and compensation algorithms as well as the implementation of the post-maneuver attitude adjustments.

TWO INNEXINS OF Spodoptera litura INFLUENCES HEMICHANNEL AND GAP JUNCTION FUNCTIONS IN CELLULAR IMMUNE RESPONSES.

PubMed

Pang, Zunyu; Li, Ming; Yu, Dongshuai; Yan, Zhang; Liu, Xinyi; Ji, Xinglai; Yang, Yang; Hu, Jiansheng; Luo, Kaijun

2015-09-01

Insect cellular immune responses include encapsulation, nodule formation, and phagocytosis. Hemichannels and gap junctions are involved in these cellular actions. Innexins (Inxs: analogous to the vertebrate connexins) form hemichannels and gap junctions, but the molecular mechanisms underlying their biology is still unclear. In this article, we reported a steady-state level of Inxs (SpliInxs) in hemocytes of Spodoptera litura, which formed nonfunctional hemichannels on the cell surface to maintain normal metabolism. We also reported that two innnexins (SpliInx2 and SpliInx3) were expressed significantly higher in hemocytes compared to other tissues, suggesting that they play important roles in hemocytes. Amino acid analysis found that two cysteine residues in two extracellular loops provided the capability for SpliInx2 and SpliInx3 hemichannels to dock into gap junctions. Western blotting demonstrated that both extracellular and intracellular loops of SpliInx3 and the extracellular loops of SpliInx2 might undergo posttranslational modification during the formation of a steady-state hemichannel. During hemichannel formation, SpliInx2 presented as one isoform, while SpliInx3 presented as three isoforms. These results provide fundamental knowledge for further study of how steady-state levels of SpliInxs are dynamically adjusted to perform cellular immune responses under immune challenge. © 2015 Wiley Periodicals, Inc.

Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1

DOE PAGES

Michael, Alicia K.; Fribourgh, Jennifer L.; Chelliah, Yogarany; ...

2017-01-31

The basic helix-loop-helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ~24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here in this paper, we show that CRY1 binds directly to the PAS domain core of CLOCK: BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solutionmore » X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1.« less

A new method for the adjustment of neochordal length: the adjustable slip knot technique.

PubMed

Yano, Mitsuhiro; Sakaguchi, Syuuhei; Furukawa, Kohji; Nakamura, Eisaku

2015-08-01

The use of expanded polytetrafluoroethylene (ePTFE) sutures for the correction of mitral valve prolapse has become a standardized procedure. Adjustment of neochordal length is crucial to the efficacy of this technique. Various methods have been described for this purpose; however, the fine adjustment of neochordal length is technically challenging. We describe a simple and effective technique for the implantation of neochordae, which we have termed the 'adjustable slip knot technique'. The first step of this technique is reinforcement of the papillary muscle by a Teflon pledget with or without polytetrafluoroethylene (CV-4) loops. The second step is the formation of a neochordal loop by introducing an ePTFE suture between the affected mitral leaflet and the papillary muscle or ePTFE loops. The third step is the adjustment of the length of neochordae. The formation of a slip knot in one arm of the ePTFE suture is the pivot of this technique. The neochordal loop can be constricted by the application of tension to one arm of the suture. We applied this technique in 5 patients with satisfactory results. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

The free-energy cost of interaction between DNA loops.

PubMed

Huang, Lifang; Liu, Peijiang; Yuan, Zhanjiang; Zhou, Tianshou; Yu, Jianshe

2017-10-03

From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.

Spatial-temporal evolution of self-organized loop-patterns on a water surface and a diffuse discharge in the gap

NASA Astrophysics Data System (ADS)

Li, Xuechen; Geng, Jinling; Jia, Pengying; Zhang, Panpan; Zhang, Qi; Li, Yaru

2017-11-01

Excited by an alternating current voltage, a patterned discharge and a diffuse discharge are generated in a needle to liquid configuration. Using an intensified charge-coupled device (ICCD), temporal evolution of the discharge between the two electrodes is investigated for the diffuse mode and the patterned mode, respectively. For the diffuse mode, the positive discharge is in a glow regime, and the negative discharge is in a Townsend discharge regime. For the patterned mode, the discharge always belongs to the Townsend discharge regime. Moreover, in the patterned mode, various patterns including the single loop, single loop with the surrounding corona, triple loops, and concentric loops with a central spot are observed on the water surface with the increasing positive peak-value of the applied voltage (Upp). Temporally resolved images of the loop-patterns are captured on the water surface. From the electrical measurements and the ICCD imaging, it is found that the loop pattern emerges after the discharge bridges the two electrodes. Then, it begins to evolve and finally degenerates with the decrease in the discharge current. The pattern does not disappear until the discharge quenches. Formation of the loop-patterns is attributed to the role of negative ions.

Mitotic chromosome compaction via active loop extrusion

NASA Astrophysics Data System (ADS)

Goloborodko, Anton; Imakaev, Maxim; Marko, John; Mirny, Leonid; MIT-Northwestern Team

During cell division, two copies of each chromosome are segregated from each other and compacted more than hundred-fold into the canonical X-shaped structures. According to earlier microscopic observations and the recent Hi-C study, chromosomes are compacted into arrays of consecutive loops of ~100 kilobases. Mechanisms that lead to formation of such loop arrays are largely unknown. Here we propose that, during cell division, chromosomes can be compacted by enzymes that extrude loops on chromatin fibers. First, we use computer simulations and analytical modeling to show that a system of loop-extruding enzymes on a chromatin fiber self-organizes into an array of consecutive dynamic loops. Second, we model the process of loop extrusion in 3D and show that, coupled with the topo II strand-passing activity, it leads to robust compaction and segregation of sister chromatids. This mechanism of chromosomal condensation and segregation does not require additional proteins or specific DNA markup and is robust against variations in the number and properties of such loop extruding enzymes. Work at NU was supported by the NSF through Grants DMR-1206868 and MCB-1022117, and by the NIH through Grants GM105847 and CA193419. Work at MIT was supported by the NIH through Grants GM114190 R01HG003143.

Atomistic study of the hardening of ferritic iron by Ni-Cr decorated dislocation loops

NASA Astrophysics Data System (ADS)

Bonny, G.; Bakaev, A.; Terentyev, D.; Zhurkin, E.; Posselt, M.

2018-01-01

The exact nature of the radiation defects causing hardening in reactor structural steels consists of several components that are not yet clearly determined. While generally, the hardening is attributed to dislocation loops, voids and secondary phases (radiation-induced precipitates), recent advanced experimental and computational studies point to the importance of solute-rich clusters (SRCs). Depending on the exact composition of the steel, SRCs may contain Mn, Ni and Cu (e.g. in reactor pressure vessel steels) or Ni, Cr, Si, Mn (e.g. in high-chromium steels for generation IV and fusion applications). One of the hypotheses currently implied to explain their formation is the process of radiation-induced diffusion and segregation of these elements to small dislocation loops (heterogeneous nucleation), so that the distinction between SRCs and loops becomes somewhat blurred. In this work, we perform an atomistic study to investigate the enrichment of loops by Ni and Cr solutes and their interaction with an edge dislocation. The dislocation loops decorated with Ni and Cr solutes are obtained by Monte Carlo simulations, while the effect of solute segregation on the loop's strength and interaction mechanism is then addressed by large scale molecular dynamics simulations. The synergy of the Cr-Ni interaction and their competition to occupy positions in the dislocation loop core are specifically clarified.

Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation

PubMed Central

Swigon, David; Coleman, Bernard D.; Olson, Wilma K.

2006-01-01

Repression of transcription of the Escherichia coli Lac operon by the Lac repressor (LacR) is accompanied by the simultaneous binding of LacR to two operators and the formation of a DNA loop. A recently developed theory of sequence-dependent DNA elasticity enables one to relate the fine structure of the LacR–DNA complex to a wide range of heretofore-unconnected experimental observations. Here, that theory is used to calculate the configuration and free energy of the DNA loop as a function of its length and base-pair sequence, its linking number, and the end conditions imposed by the LacR tetramer. The tetramer can assume two types of conformations. Whereas a rigid V-shaped structure is observed in the crystal, EM images show extended forms in which two dimer subunits are flexibly joined. Upon comparing our computed loop configurations with published experimental observations of permanganate sensitivities, DNase I cutting patterns, and loop stabilities, we conclude that linear DNA segments of short-to-medium chain length (50–180 bp) give rise to loops with the extended form of LacR and that loops formed within negatively supercoiled plasmids induce the V-shaped structure. PMID:16785444

Technical notes and correspondence: Stochastic robustness of linear time-invariant control systems

NASA Technical Reports Server (NTRS)

Stengel, Robert F.; Ray, Laura R.

1991-01-01

A simple numerical procedure for estimating the stochastic robustness of a linear time-invariant system is described. Monte Carlo evaluations of the system's eigenvalues allows the probability of instability and the related stochastic root locus to be estimated. This analysis approach treats not only Gaussian parameter uncertainties but non-Gaussian cases, including uncertain-but-bounded variation. Confidence intervals for the scalar probability of instability address computational issues inherent in Monte Carlo simulation. Trivial extensions of the procedure admit consideration of alternate discriminants; thus, the probabilities that stipulated degrees of instability will be exceeded or that closed-loop roots will leave desirable regions can also be estimated. Results are particularly amenable to graphical presentation.

Transfer of Solutions to Conditional Probability Problems: Effects of Example Problem Format, Solution Format, and Problem Context

ERIC Educational Resources Information Center

Chow, Alan F.; Van Haneghan, James P.

2016-01-01

This study reports the results of a study examining how easily students are able to transfer frequency solutions to conditional probability problems to novel situations. University students studied either a problem solved using the traditional Bayes formula format or using a natural frequency (tree diagram) format. In addition, the example problem…

Analytical Solutions to Backreaction on Cosmic Strings

NASA Astrophysics Data System (ADS)

Wachter, Jeremy M.

2017-08-01

We present analytical studies of gravitational and electromagnetic backreaction on cosmic strings. For oscillating loops of cosmic string, we present a general argument for how kinks must change; additionally, we apply this general argument to the geometrically simple case of the Garfinkle-Vachaspati loop. Our results suggest that the formation of cusps on loops is delayed, and so we should expect fewer cuspy signatures to be seen in gravitational wave observations. Electromagnetic backreaction we show to reduce currents on a string at least as rapidly as necessary to avoid a paradox, and currents induced on a superconducting straight string will be asymptotically reduced to zero.

Probability density function of non-reactive solute concentration in heterogeneous porous formations

Treesearch

Alberto Bellin; Daniele Tonina

2007-01-01

Available models of solute transport in heterogeneous formations lack in providing complete characterization of the predicted concentration. This is a serious drawback especially in risk analysis where confidence intervals and probability of exceeding threshold values are required. Our contribution to fill this gap of knowledge is a probability distribution model for...

Dislocation dynamics simulations of interactions between gliding dislocations and radiation induced prismatic loops in zirconium

NASA Astrophysics Data System (ADS)

Drouet, Julie; Dupuy, Laurent; Onimus, Fabien; Mompiou, Frédéric; Perusin, Simon; Ambard, Antoine

2014-06-01

The mechanical behavior of Pressurized Water Reactor fuel cladding tubes made of zirconium alloys is strongly affected by neutron irradiation due to the high density of radiation induced dislocation loops. In order to investigate the interaction mechanisms between gliding dislocations and loops in zirconium, a new nodal dislocation dynamics code, adapted to Hexagonal Close Packed metals, has been used. Various configurations have been systematically computed considering different glide planes, basal or prismatic, and different characters, edge or screw, for gliding dislocations with -type Burgers vectors. Simulations show various interaction mechanisms such as (i) absorption of a loop on an edge dislocation leading to the formation of a double super-jog, (ii) creation of a helical turn, on a screw dislocation, that acts as a strong pinning point or (iii) sweeping of a loop by a gliding dislocation. It is shown that the clearing of loops is more favorable when the dislocation glides in the basal plane than in the prismatic plane explaining the easy dislocation channeling in the basal plane observed after neutron irradiation by transmission electron microscopy.

Interaction of irradiation-induced prismatic dislocation loops with free surfaces in tungsten

NASA Astrophysics Data System (ADS)

Fikar, Jan; Gröger, Roman; Schäublin, Robin

2017-02-01

The prismatic dislocation loops appear in metals as a result of high-energy irradiation. Understanding their formation and interaction is important for quantification of irradiation-induced deterioration of mechanical properties. Characterization of dislocation loops in thin foils is commonly made using transmission electron microscopy (TEM), but the results are inevitably influenced by the proximity of free surfaces. The prismatic loops are attracted to free surfaces by image forces. Depending on the type, size and depth of the loop in the foil, they can escape to the free surface, thus invalidating TEM observations and conclusions. In this article small prismatic hexagonal and circular dislocation loops in tungsten with the Burgers vectors 1/2 〈 1 1 1 〉 and 〈 1 0 0 〉 are studied by molecular statics simulations using three embedded atom method (EAM) potentials. The calculated image forces are compared to known elastic solutions. A particular attention is paid to the critical stress to move edge dislocations. The escape of the loop to the free surface is quantified by a combination of atomistic simulations and elastic calculations. For example, for the 1/2 〈 1 1 1 〉 loop with diameter 7.4 nm in a 55 nm thick foil we calculated that about one half of the loops will escape to the free surface. This implies that TEM observations detect only approx. 50% of the loops that were originally present in the foil.

Buoyancy-induced flow studies in thermally stratified loop of a double-envelope building

NASA Astrophysics Data System (ADS)

Ghaffari, H. T.; Jones, R. F.

There is a wide interest in the flow studies of thermally stratified loops of double-envelope houses. These loops primarily serve to hold a moderate air temperature around the inner buildings, and to reduce thermal losses and air movements into the house by diminishing infiltration. Further, if the thermal mechanism of the buildng is well designed, it may be possible to cause a solar-assisted, buoyancy-induced cycling of the flow during the day and a probable reverse cycling during the night. The benefits of this flow pattern are a possible storage of heat in the ground level of the crawl space during the day, its retrieval at night, and a better mixing of warmed air in various zones of the loop. The double-envelope section of the buildng was monitored from October 1981 to October 1982. Data collected were debugged and the monitoring system was adjusted and calibrated. Results from this experiment concerning significant local flows are analyzed. Hence, a validation of the conceptual thermal mechanism is obtained, and empirical and analytical assessments are compared.

Open magnetic fields in active regions

NASA Technical Reports Server (NTRS)

Svestka, Z.; Solodyna, C. V.; Howard, R.; Levine, R. H.

1977-01-01

Soft X-ray images and magnetograms of several active regions and coronal holes are examined which support the interpretation that some of the dark X-ray gaps seen between interconnecting loops and inner cores of active regions are foot points of open field lines inside the active regions. Characteristics of the investigated dark gaps are summarized. All the active regions with dark X-ray gaps at the proper place and with the correct polarity predicted by global potential extrapolation of photospheric magnetic fields are shown to be old active regions, indicating that field opening is accomplished only in a late phase of active-region development. It is noted that some of the observed dark gaps probably have nothing in common with open fields, but are either due to the decreased temperature in low-lying portions of interconnecting loops or are the roots of higher and less dense or cooler loops.

Duration of inflation and conditions at the bounce as a prediction of effective isotropic loop quantum cosmology

NASA Astrophysics Data System (ADS)

Linsefors, Linda; Barrau, Aurelien

2013-06-01

Loop quantum cosmology with a scalar field is known to be closely linked with an inflationary phase. In this article, we study probabilistic predictions for the duration of slow-roll inflation, by assuming a minimalist massive scalar field as the main content of the Universe. The phase of the field in its “prebounce” oscillatory state is taken as a natural random parameter. We find that the probability for a given number of inflationary e-folds is quite sharply peaked around 145, which is consistent with the most favored minimum values. In this precise sense, a satisfactory inflation is therefore a clear prediction of loop gravity. In addition, we derive an original and stringent upper limit on the Barbero-Immirzi parameter. The general picture of inflation, superinflation, deflation, and superdeflation is also much clarified in the framework of bouncing cosmologies.

Membrane-Based Gas Traps for Ammonia, Freon-21, and Water Systems to Simplify Ground Processing

NASA Technical Reports Server (NTRS)

Ritchie, Stephen M. C.

2003-01-01

Gas traps are critical for the smooth operation of coolant loops because gas bubbles can cause loss of centrifugal pump prime, interference with sensor readings, inhibition of heat transfer, and blockage of passages to remote systems. Coolant loops are ubiquitous in space flight hardware, and thus there is a great need for this technology. Conventional gas traps will not function in micro-gravity due to the absence of buoyancy forces. Therefore, clever designs that make use of adhesion and momentum are required for adequate separation, preferable in a single pass. The gas traps currently used in water coolant loops on the International Space Station are composed of membrane tube sets in a shell. Each tube set is composed of a hydrophilic membrane (used for water transport and capture of bubbles) and a hydrophobic membrane (used for venting of air bubbles). For the hydrophilic membrane, there are two critical pressures, the pressure drop and the bubble pressure. The pressure drop is the decrease in system pressure across the gas trap. The bubble pressure is the pressure required for air bubbles to pass across the water filled membrane. A significant difference between these pressures is needed to ensure complete capture of air bubbles in a single pass. Bubbles trapped by the device adsorb on the hydrophobic membrane in the interior of the hydrophilic membrane tube. After adsorption, the air is vented due to a pressure drop of approximately 1 atmosphere across the membrane. For water systems, the air is vented to the ambient (cabin). Because water vapor can also transport across the hydrophobic membrane, it is critical that a minimum surface area is used to avoid excessive water loss (would like to have a closed loop for the coolant). The currently used gas traps only provide a difference in pressure drop and bubble pressure of 3-4 psid. This makes the gas traps susceptible to failure at high bubble loading and if gas venting is impaired. One mechanism for the latter is when particles adhere to the hydrophobic membrane, promoting formation of a water layer about it that can blind the membrane for gas transport (Figure 1). This mechanism is the most probable cause for observed failures with the existing design. The objective of this project was to devise a strategy for choosing new membrane materials (database development and procedure), redesign of the gas trap to mitigate blinding effects, and to develop a design that can be used in ammonia and Freon-21 coolant loops.

Cosmic string induced peculiar velocities

NASA Technical Reports Server (NTRS)

Van Dalen, Anthony; Schramm, David N.

1988-01-01

This paper considers the scenario of a flat universe with a network of heavy cosmic strings as the primordial fluctuation spectrum. The joint probability of finding streaming velocities of at least 600 km/s on large scales and local peculiar velocities of less than 800 km/s is calculated. It is shown how the effects of loops breaking up and being born with a spectrum of sizes can be estimated. It is found that to obtain large-scale streaming velocities of at least 600 km/s, it is necessary that either a large value for beta G mu exist or the effect of loop fissioning and production details be considerable.

Asking better questions: How presentation formats influence information search.

PubMed

Wu, Charley M; Meder, Björn; Filimon, Flavia; Nelson, Jonathan D

2017-08-01

While the influence of presentation formats have been widely studied in Bayesian reasoning tasks, we present the first systematic investigation of how presentation formats influence information search decisions. Four experiments were conducted across different probabilistic environments, where subjects (N = 2,858) chose between 2 possible search queries, each with binary probabilistic outcomes, with the goal of maximizing classification accuracy. We studied 14 different numerical and visual formats for presenting information about the search environment, constructed across 6 design features that have been prominently related to improvements in Bayesian reasoning accuracy (natural frequencies, posteriors, complement, spatial extent, countability, and part-to-whole information). The posterior variants of the icon array and bar graph formats led to the highest proportion of correct responses, and were substantially better than the standard probability format. Results suggest that presenting information in terms of posterior probabilities and visualizing natural frequencies using spatial extent (a perceptual feature) were especially helpful in guiding search decisions, although environments with a mixture of probabilistic and certain outcomes were challenging across all formats. Subjects who made more accurate probability judgments did not perform better on the search task, suggesting that simple decision heuristics may be used to make search decisions without explicitly applying Bayesian inference to compute probabilities. We propose a new take-the-difference (TTD) heuristic that identifies the accuracy-maximizing query without explicit computation of posterior probabilities. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

FAST CONTRACTION OF CORONAL LOOPS AT THE FLARE PEAK

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

Liu Rui; Wang Haimin

On 2005 September 8, a coronal loop overlying the active region NOAA 10808 was observed in TRACE 171 A to contract at {approx}100 km s{sup -1} at the peak of an X5.4-2B flare at 21:05 UT. Prior to the fast contraction, the loop underwent a much slower contraction at {approx}6 km s{sup -1} for about 8 minutes, initiating during the flare preheating phase. The sudden switch to fast contraction is presumably corresponding to the onset of the impulsive phase. The contraction resulted in the oscillation of a group of loops located below, with the period of about 10 minutes. Meanwhile,more » the contracting loop exhibited a similar oscillatory pattern superimposed on the dominant downward motion. We suggest that the fast contraction reflects a suddenly reduced magnetic pressure underneath due either to (1) the eruption of magnetic structures located at lower altitudes or to (2) the rapid conversion of magnetic free energy in the flare core region. Electrons accelerated in the shrinking trap formed by the contracting loop can theoretically contribute to a late-phase hard X-ray burst, which is associated with Type IV radio emission. To complement the X5.4 flare which was probably confined, a similar event observed in SOHO/EIT 195 A on 2004 July 20 in an eruptive, M8.6 flare is briefly described, in which the contraction was followed by the expansion of the same loop leading up to a halo coronal mass ejection. These observations further substantiate the conjecture of coronal implosion and suggest coronal implosion as a new exciter mechanism for coronal loop oscillations.« less

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.

PubMed

Arnautova, Yelena A; Abagyan, Ruben A; Totrov, Maxim

2011-02-01

We report the development of internal coordinate mechanics force field (ICMFF), new force field parameterized using a combination of experimental data for crystals of small molecules and quantum mechanics calculations. The main features of ICMFF include: (a) parameterization for the dielectric constant relevant to the condensed state (ε = 2) instead of vacuum, (b) an improved description of hydrogen-bond interactions using duplicate sets of van der Waals parameters for heavy atom-hydrogen interactions, and (c) improved backbone covalent geometry and energetics achieved using novel backbone torsional potentials and inclusion of the bond angles at the C(α) atoms into the internal variable set. The performance of ICMFF was evaluated through loop modeling simulations for 4-13 residue loops. ICMFF was combined with a solvent-accessible surface area solvation model optimized using a large set of loop decoys. Conformational sampling was carried out using the biased probability Monte Carlo method. Average/median backbone root-mean-square deviations of the lowest energy conformations from the native structures were 0.25/0.21 Å for four residues loops, 0.84/0.46 Å for eight residue loops, and 1.16/0.73 Å for 12 residue loops. To our knowledge, these results are significantly better than or comparable with those reported to date for any loop modeling method that does not take crystal packing into account. Moreover, the accuracy of our method is on par with the best previously reported results obtained considering the crystal environment. We attribute this success to the high accuracy of the new ICM force field achieved by meticulous parameterization, to the optimized solvent model, and the efficiency of the search method. © 2010 Wiley-Liss, Inc.

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

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

Wendler, E.

2011-06-01

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

Pattern of Bone Generation after Irradiation in Vascularized Tissue Engineered Constructs.

PubMed

Eweida, Ahmad; Fathi, Ibrahim; Eltawila, Ahmed M; Elsherif, Ahmad M; Elkerm, Yasser; Harhaus, Leila; Kneser, Ulrich; Sakr, Mahmoud F

2018-02-01

 Regenerative medicine modalities provide promising alternatives to conventional reconstruction techniques but are still deficient after malignant tumor excision or irradiation due to defective vascularization.  We investigated the pattern of bone formation in axially vascularized tissue engineering constructs (AVTECs) after irradiation in a study that mimics the clinical scenario after head and neck cancer. Heterotopic bone generation was induced in a subcutaneously implanted AVTEC in the thigh of six male New Zealand rabbits. The tissue construct was made up of Nanobone (Artoss GmbH; Rostock, Germany) granules mixed with autogenous bone marrow and 80 μL of bone morphogenic protein-2 at a concentration of 1.5 μg/μL. An arteriovenous loop was created microsurgically between the saphenous vessels and implanted in the core of the construct to induce axial vascularization. The constructs were subjected to external beam irradiation on postoperative day 20 with a single dose of 15 Gy. The constructs were removed 20 days after irradiation and subjected to histological and immunohistochemical analysis for vascularization, bone formation, apoptosis, and cellular proliferation.  The vascularized constructs showed homogenous vascularization and bone formation both in their central and peripheral regions. Although vascularity, proliferation, and apoptosis were similar between central and peripheral regions of the constructs, significantly more bone was formed in the central regions of the constructs.  The study shows for the first time the pattern of bone formation in AVTECs after irradiation using doses comparable to those applied after head and neck cancer. Axial vascularization probably enhances the osteoinductive properties in the central regions of AVTECs after irradiation. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Formation of large-scale structure from cosmic-string loops and cold dark matter

NASA Technical Reports Server (NTRS)

Melott, Adrian L.; Scherrer, Robert J.

1987-01-01

Some results from a numerical simulation of the formation of large-scale structure from cosmic-string loops are presented. It is found that even though G x mu is required to be lower than 2 x 10 to the -6th (where mu is the mass per unit length of the string) to give a low enough autocorrelation amplitude, there is excessive power on smaller scales, so that galaxies would be more dense than observed. The large-scale structure does not include a filamentary or connected appearance and shares with more conventional models based on Gaussian perturbations the lack of cluster-cluster correlation at the mean cluster separation scale as well as excessively small bulk velocities at these scales.

The structural coupling between ATPase activation and recovery stroke in the myosin II motor

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

Koppole, Sampath; Smith, Jeremy C; Fischer, S.

2007-07-01

Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates {approx} 65{sup o}. Simultaneous with this 'recovery stroke', myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 {angstrom}-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transitionmore » at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.« less

The structural coupling between ATPase activation and recovery stroke in the myosin II motor.

PubMed

Koppole, Sampath; Smith, Jeremy C; Fischer, Stefan

2007-07-01

Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates approximately 65 degrees . Simultaneous with this "recovery stroke," myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 A-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transition at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.

Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure

PubMed Central

Koczyk, Grzegorz; Berezovsky, Igor N.

2008-01-01

Domain hierarchy and closed loops (DHcL) (http://sitron.bccs.uib.no/dhcl/) is a web server that delineates energy hierarchy of protein domain structure and detects domains at different levels of this hierarchy. The server also identifies closed loops and van der Waals locks, which constitute a structural basis for the protein domain hierarchy. The DHcL can be a useful tool for an express analysis of protein structures and their alternative domain decompositions. The user submits a PDB identifier(s) or uploads a 3D protein structure in a PDB format. The results of the analysis are the location of domains at different levels of hierarchy, closed loops, van der Waals locks and their interactive visualization. The server maintains a regularly updated database of domains, closed loop and van der Waals locks for all X-ray structures in PDB. DHcL server is available at: http://sitron.bccs.uib.no/dhcl. PMID:18502776

Visualization of chromatin domains created by the gypsy insulator of Drosophila.

PubMed

Byrd, Keith; Corces, Victor G

2003-08-18

Insulators might regulate gene expression by establishing and maintaining the organization of the chromatin fiber within the nucleus. Biochemical fractionation and in situ high salt extraction of lysed cells show that two known protein components of the gypsy insulator are present in the nuclear matrix. Using FISH with DNA probes located between two endogenous Su(Hw) binding sites, we show that the intervening DNA is arranged in a loop, with the two insulators located at the base. Mutations in insulator proteins, subjecting the cells to a brief heat shock, or destruction of the nuclear matrix lead to disruption of the loop. Insertion of an additional gypsy insulator in the center of the loop results in the formation of paired loops through the attachment of the inserted sequences to the nuclear matrix. These results suggest that the gypsy insulator might establish higher-order domains of chromatin structure and regulate nuclear organization by tethering the DNA to the nuclear matrix and creating chromatin loops.

Effects of applied strain on nanoscale self-interstitial cluster formation in BCC iron

NASA Astrophysics Data System (ADS)

Gao, Ning; Setyawan, Wahyu; Kurtz, Richard J.; Wang, Zhiguang

2017-09-01

The effect of applied strains on the configurational evolution of self-interstitial clusters in BCC iron (Fe) is explored with atomistic simulations. A novel cluster configuration is discovered at low temperatures (<600 K), which consists of 〈 110 〉 dumbbells and 〈 111 〉 crowdions in a specific configuration, resulting in an immobile defect. The stability and diffusion of this cluster at higher temperatures is explored. In addition, an anisotropy distribution factor of a particular [ hkl ] interstitial loop within the family of 〈 hkl 〉 loops is calculated as a function of strain. The results show that loop anisotropy is governed by the angle between the stress direction and the orientation of the 〈 111 〉 crowdions in the loop, and directly linked to the stress induced preferred nucleation of self-interstitial atoms.

Purification of bacteriophage lambda repressor

PubMed Central

Gao, Ning; Shearwin, Keith; Mack, John; Finzi, Laura; Dunlap, David

2013-01-01

Bacteriophage lambda repressor controls the lysogeny/lytic growth switch after infection of E. coli by lambda phage. In order to study in detail the looping of DNA mediated by the protein, tag-free repressor and a loss-of-cooperativity mutant were expressed in E.coli and purified by (1) ammonium sulfate fractionation, (2) anion-exchange chromatography and (3) heparin affinity chromatography. This method employs more recently developed and readily available chromatography resins to produce highly pure protein in good yield. In tethered particle motion looping assays and atomic force microscopy “footprinting” assays, both the wild-type protein and a C-terminal His-tagged variant, purified using immobilized metal affinity chromatography, bound specifically to high affinity sites to mediate loop formation. In contrast the G147D loss-of-cooperativity mutant bound specifically but did not secure loops. PMID:23831434

Microstructure evolution of recrystallized Zircaloy-4 under charged particles irradiation

NASA Astrophysics Data System (ADS)

Gaumé, M.; Onimus, F.; Dupuy, L.; Tissot, O.; Bachelet, C.; Mompiou, F.

2017-11-01

Recrystallized zirconium alloys are used as nuclear fuel cladding tubes of Pressurized Water Reactors. During operation, these alloys are submitted to fast neutron irradiation which leads to their in-reactor deformation and to a change of their mechanical properties. These phenomena are directly related to the microstructure evolution under irradiation and especially to the formation of -type dislocation loops. In the present work, the radiation damage evolution in recrystallized Zircaloy-4 has been studied using charged particles irradiation. The loop nucleation and growth kinetics, and also the helical climb of linear dislocations, were observed in-situ using a High Voltage Electron Microscope (HVEM) under 1 MeV electron irradiation at 673 and 723 K. In addition, 600 keV Zr+ ion irradiations were conducted at the same temperature. Transmission Electron Microscopy (TEM) characterizations have been performed after both types of irradiations, and show dislocation loops with a Burgers vector belonging to planes close to { 10 1 bar 0 } first order prismatic planes. The nature of the loops has been characterized. Only interstitial dislocation loops have been observed after ion irradiation at 723 K. However, after electron irradiation conducted at 673 and 723 K, both interstitial and vacancy loops were observed, the proportion of interstitial loops increasing as the temperature is increased. The loop growth kinetics analysis shows that as the temperature increases, the loop number density decreases and the loop growth rate tends to increase. An increase of the flux leads to an increase of the loop number density and a decrease of the loop growth rate. The results are compared to previous works and discussed in the light of point defects diffusion.

The Large Hydrophilic Loop of Presenilin 1 Is Important for Regulating γ-Secretase Complex Assembly and Dictating the Amyloid β Peptide (Aβ) Profile without Affecting Notch Processing*

PubMed Central

Wanngren, Johanna; Frånberg, Jenny; Svensson, Annelie I.; Laudon, Hanna; Olsson, Fredrik; Winblad, Bengt; Liu, Frank; Näslund, Jan; Lundkvist, Johan; Karlström, Helena

2010-01-01

γ-Secretase is an enzyme complex that mediates both Notch signaling and β-amyloid precursor protein (APP) processing, resulting in the generation of Notch intracellular domain, APP intracellular domain, and the amyloid β peptide (Aβ), the latter playing a central role in Alzheimer disease (AD). By a hitherto undefined mechanism, the activity of γ-secretase gives rise to Aβ peptides of different lengths, where Aβ42 is considered to play a particular role in AD. In this study we have examined the role of the large hydrophilic loop (amino acids 320–374, encoded by exon 10) of presenilin 1 (PS1), the catalytic subunit of γ-secretase, for γ-secretase complex formation and activity on Notch and APP processing. Deletion of exon 10 resulted in impaired PS1 endoproteolysis, γ-secretase complex formation, and had a differential effect on Aβ-peptide production. Although the production of Aβ38, Aβ39, and Aβ40 was severely impaired, the effect on Aβ42 was affected to a lesser extent, implying that the production of the AD-related Aβ42 peptide is separate from the production of the Aβ38, Aβ39, and Aβ40 peptides. Interestingly, formation of the intracellular domains of both APP and Notch was intact, implying a differential cleavage activity between the ϵ/S3 and γ sites. The most C-terminal amino acids of the hydrophilic loop were important for regulating APP processing. In summary, the large hydrophilic loop of PS1 appears to differentially regulate the relative production of different Aβ peptides without affecting Notch processing, two parameters of significance when considering γ-secretase as a target for pharmaceutical intervention in AD. PMID:20106965

Crystal structure of a looped-chain CoII coordination polymer: catena-poly[[bis-(nitrato-κO)cobalt(II)]bis-[μ-bis-(pyridin-3-ylmeth-yl)sulfane-κ2N:N'

PubMed

Moon, Suk-Hee; Seo, Joobeom; Park, Ki-Min

2017-11-01

The asymmetric unit of the title compound, [Co(NO 3 ) 2 (C 12 H 12 N 2 S) 2 ] n , contains a bis-(pyridin-3-ylmeth-yl)sulfane ( L ) ligand, an NO 3 - anion and half a Co II cation, which lies on an inversion centre. The Co II cation is six-coordinated, being bound to four pyridine N atoms from four symmetry-related L ligands. The remaining coordination sites are occupied by two O atoms from two symmetry-related nitrate anions in a monodentate manner. Thus, the Co II centre adopts a distorted octa-hedral geometry. Two symmetry-related L ligands are connected by two symmetry-related Co II cations, forming a 20-membered cyclic dimer, in which the Co II atoms are separated by 10.2922 (7) Å. The cyclic dimers are connected to each other by sharing Co II atoms, giving rise to the formation of an infinite looped chain propagating along the [101] direction. Inter-molecular C-H⋯π (H⋯ring centroid = 2.89 Å) inter-actions between one pair of corresponding L ligands and C-H⋯O hydrogen bonds between the L ligands and the nitrate anions occur in the looped chain. In the crystal, adjacent looped chains are connected by inter-molecular π-π stacking inter-actions [centroid-to-centroid distance = 3.8859 (14) Å] and C-H⋯π hydrogen bonds (H⋯ring centroid = 2.65 Å), leading to the formation of layers parallel to (101). These layers are further connected through C-H⋯O hydrogen bonds between the layers, resulting in the formation of a three-dimensional supra-molecular architecture.

A Closed Loop System Using a Brine Reservoir to Replace Fresh Water as the Frac Fluid Source

EPA Pesticide Factsheets

A non-fresh water source, the Debolt formation, has been proposed and tested in the laboratory and field for application as a fracturing fluid in shale gas formations, with potential to replace much of the fresh water used in the Horn River Basin.

Renormalizing a viscous fluid model for large scale structure formation

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

Führer, Florian; Rigopoulos, Gerasimos, E-mail: fuhrer@thphys.uni-heidelberg.de, E-mail: gerasimos.rigopoulos@ncl.ac.uk

2016-02-01

Using the Stochastic Adhesion Model (SAM) as a simple toy model for cosmic structure formation, we study renormalization and the removal of the cutoff dependence from loop integrals in perturbative calculations. SAM shares the same symmetry with the full system of continuity+Euler equations and includes a viscosity term and a stochastic noise term, similar to the effective theories recently put forward to model CDM clustering. We show in this context that if the viscosity and noise terms are treated as perturbative corrections to the standard eulerian perturbation theory, they are necessarily non-local in time. To ensure Galilean Invariance higher ordermore » vertices related to the viscosity and the noise must then be added and we explicitly show at one-loop that these terms act as counter terms for vertex diagrams. The Ward Identities ensure that the non-local-in-time theory can be renormalized consistently. Another possibility is to include the viscosity in the linear propagator, resulting in exponential damping at high wavenumber. The resulting local-in-time theory is then renormalizable to one loop, requiring less free parameters for its renormalization.« less

Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System.

PubMed

Xiao, Yibei; Luo, Min; Hayes, Robert P; Kim, Jonathan; Ng, Sherwin; Ding, Fang; Liao, Maofu; Ke, Ailong

2017-06-29

Type I CRISPR systems feature a sequential dsDNA target searching and degradation process, by crRNA-displaying Cascade and nuclease-helicase fusion enzyme Cas3, respectively. Here we present two cryo-EM snapshots of the Thermobifida fusca type I-E Cascade: (1) unwinding 11 bp of dsDNA at the seed-sequence region to scout for sequence complementarity, and (2) further unwinding of the entire protospacer to form a full R-loop. These structures provide the much-needed temporal and spatial resolution to resolve key mechanistic steps leading to Cas3 recruitment. In the early steps, PAM recognition causes severe DNA bending, leading to spontaneous DNA unwinding to form a seed-bubble. The full R-loop formation triggers conformational changes in Cascade, licensing Cas3 to bind. The same process also generates a bulge in the non-target DNA strand, enabling its handover to Cas3 for cleavage. The combination of both negative and positive checkpoints ensures stringent yet efficient target degradation in type I CRISPR-Cas systems. Copyright © 2017 Elsevier Inc. All rights reserved.

The Caltech experimental investigation of fast 3D non-equilbrium dynamics: an overview

NASA Astrophysics Data System (ADS)

Bellan, Paul; Shikama, Taiichi; Chai, Kilbyoung; Ha, Bao; Chaplin, Vernon; Kendall, Mark; Moser, Auna; Stenson, Eve; Tobin, Zachary; Zhai, Xiang

2012-10-01

The formation and dynamics of writhing, plasma-filled, twisted open magnetic flux tubes is being investigated using pulsed-power laboratory experiments. This work is relevant to solar corona loops, astrophysical jets, spheromak formation, and open field lines in tokamaks and RFP's. MHD forces have been observed to drive fast axial plasma flows into the flux tube from the boundary it intercepts. These flows fill the flux tube with plasma while simultaneously injecting linked frozen-in azimuthal flux; helicity injection is thus associated with mass injection. Recent results include observation of a secondary instability (Rayleigh-Taylor driven by the effective gravity of an exponentially growing kink mode), color-coded plasmas manifesting bidirectional axial flows in a geometry similar to a solar corona loop, and spectroscopic measurements of the internal vector magnetic field. Experiments underway include investigating how an external magnetic field straps down a solar loop, investigation of the details of the Rayleigh-Taylor instability, development of a fast EUV movie camera, increasing the jet velocity, excitation of Alfven waves, and investigating 3D magnetic reconnection.

A Hardware-in-the-Loop Testbed for Spacecraft Formation Flying Applications

NASA Technical Reports Server (NTRS)

Leitner, Jesse; Bauer, Frank H. (Technical Monitor)

2001-01-01

The Formation Flying Test Bed (FFTB) at NASA Goddard Space Flight Center (GSFC) is being developed as a modular, hybrid dynamic simulation facility employed for end-to-end guidance, navigation, and control (GN&C) analysis and design for formation flying clusters and constellations of satellites. The FFTB will support critical hardware and software technology development to enable current and future missions for NASA, other government agencies, and external customers for a wide range of missions, particularly those involving distributed spacecraft operations. The initial capabilities of the FFTB are based upon an integration of high fidelity hardware and software simulation, emulation, and test platforms developed at GSFC in recent years; including a high-fidelity GPS simulator which has been a fundamental component of the Guidance, Navigation, and Control Center's GPS Test Facility. The FFTB will be continuously evolving over the next several years from a too[ with initial capabilities in GPS navigation hardware/software- in-the- loop analysis and closed loop GPS-based orbit control algorithm assessment to one with cross-link communications and relative navigation analysis and simulation capability. Eventually the FFT13 will provide full capability to support all aspects of multi-sensor, absolute and relative position determination and control, in all (attitude and orbit) degrees of freedom, as well as information management for satellite clusters and constellations. In this paper we focus on the architecture for the FFT13 as a general GN&C analysis environment for the spacecraft formation flying community inside and outside of NASA GSFC and we briefly reference some current and future activities which will drive the requirements and development.

Evaluation of the 90-Day Inhalation Toxicity of Petroleum and Oil Shale JP-5 Jet Fuel

DTIC Science & Technology

1985-04-01

urothelium over the surface of the renal papillus, moderate to severe deposits of mineralized debris in medullary tubules (probably at the loop of Henle...and tubular degenera- tion. Hyperplastic areas along the pelvic urothelium were thought to result from mechanical irritation by mineralized de- bris

Growth rate effects on the formation of dislocation loops around deep helium bubbles in Tungsten

DOE PAGES

Sandoval, Luis; Perez, Danny; Uberuaga, Blas P.; ...

2016-11-15

Here, the growth process of spherical helium bubbles located 6 nm below a (100) surface is studied using molecular dynamics and parallel replica dynamics simulations, over growth rates from 10 6 to 10 12 helium atoms per second. Slower growth rates lead to a release of pressure and lower helium content as compared with fast growth cases. In addition, at slower growth rates, helium bubbles are not decorated by multiple dislocation loops, as these tend to merge or emit given sufficient time. At faster rates, dislocation loops nucleate faster than they can emit, leading to a more complicated dislocation structuremore » around the bubble.« less

Tracheophytes Contain Conserved Orthologs of a Basic Helix-Loop-Helix Transcription Factor That Modulate ROOT HAIR SPECIFIC Genes[OPEN

PubMed Central

Cho, Hyun-Min

2017-01-01

ROOT HAIR SPECIFIC (RHS) genes, which contain the root hair-specific cis-element (RHE) in their regulatory regions, function in root hair morphogenesis. Here, we demonstrate that an Arabidopsis thaliana basic helix-loop-helix transcription factor, ROOT HAIR DEFECTVE SIX-LIKE4 (RSL4), directly binds to the RHE in vitro and in vivo, upregulates RHS genes, and stimulates root hair formation in Arabidopsis. Orthologs of RSL4 from a eudicot (poplar [Populus trichocarpa]), a monocot (rice [Oryza sativa]), and a lycophyte (Selaginella moellendorffii) each restored root hair growth in the Arabidopsis rsl4 mutant. In addition, the rice and S. moellendorffii RSL4 orthologs bound to the RHE in in vitro and in vivo assays. The RSL4 orthologous genes contain RHEs in their promoter regions, and RSL4 was able to bind to its own RHEs in vivo and amplify its own expression. This process likely provides a positive feedback loop for sustainable root hair growth. When RSL4 and its orthologs were expressed in cells in non-root-hair positions, they induced ectopic root hair growth, indicating that these genes are sufficient to specify root hair formation. Our results suggest that RSL4 mediates root hair formation by regulating RHS genes and that this mechanism is conserved throughout the tracheophyte (vascular plant) lineage. PMID:28087829

Formation of Large-scale Coronal Loops Interconnecting Two Active Regions through Gradual Magnetic Reconnection and an Associated Heating Process

NASA Astrophysics Data System (ADS)

Du, Guohui; Chen, Yao; Zhu, Chunming; Liu, Chang; Ge, Lili; Wang, Bing; Li, Chuanyang; Wang, Haimin

2018-06-01

Coronal loops interconnecting two active regions (ARs), called interconnecting loops (ILs), are prominent large-scale structures in the solar atmosphere. They carry a significant amount of magnetic flux and therefore are considered to be an important element of the solar dynamo process. Earlier observations showed that eruptions of ILs are an important source of CMEs. It is generally believed that ILs are formed through magnetic reconnection in the high corona (>150″–200″), and several scenarios have been proposed to explain their brightening in soft X-rays (SXRs). However, the detailed IL formation process has not been fully explored, and the associated energy release in the corona still remains unresolved. Here, we report the complete formation process of a set of ILs connecting two nearby ARs, with successive observations by STEREO-A on the far side of the Sun and by SDO and Hinode on the Earth side. We conclude that ILs are formed by gradual reconnection high in the corona, in line with earlier postulations. In addition, we show evidence that ILs brighten in SXRs and EUVs through heating at or close to the reconnection site in the corona (i.e., through the direct heating process of reconnection), a process that has been largely overlooked in earlier studies of ILs.

Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization

DOE PAGES

Alexandrov, Ludmil B.; Rasmussen, Kim Ø.; Bishop, Alan R.; ...

2017-08-29

The innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer’s J-factor, which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA sequences revealed a discrepancy of up to six orders of magnitude between experimentally measured and theoretically predicted J-factors. These large differences suggest that, in addition to the elastic moduli of the double helix, other factors contribute to loop formation. We develop a new theoretical model that explores how coherent delocalized phonon-like modes in DNA provide single-stranded ”flexible hinges” to assist in loop formation. We also combine the Czapla-Swigon-Olson structural model of DNA with ourmore » extended Peyrard-Bishop-Dauxois model and, without changing any of the parameters of the two models, apply this new computational framework to 86 experimentally characterized DNA sequences. Our results demonstrate that the new computational framework can predict J-factors within an order of magnitude of experimental measurements for most ultra-short DNA sequences, while continuing to accurately describe the J-factors of longer sequences. Furthermore, we demonstrate that our computational framework can be used to describe the cyclization of DNA sequences that contain a base pair mismatch. Overall, our results support the conclusion that coherent delocalized phonon-like modes play an important role in DNA cyclization.« less

Evaluating the role of coherent delocalized phonon-like modes in DNA cyclization

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

Alexandrov, Ludmil B.; Rasmussen, Kim Ø.; Bishop, Alan R.

The innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer’s J-factor, which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA sequences revealed a discrepancy of up to six orders of magnitude between experimentally measured and theoretically predicted J-factors. These large differences suggest that, in addition to the elastic moduli of the double helix, other factors contribute to loop formation. We develop a new theoretical model that explores how coherent delocalized phonon-like modes in DNA provide single-stranded ”flexible hinges” to assist in loop formation. We also combine the Czapla-Swigon-Olson structural model of DNA with ourmore » extended Peyrard-Bishop-Dauxois model and, without changing any of the parameters of the two models, apply this new computational framework to 86 experimentally characterized DNA sequences. Our results demonstrate that the new computational framework can predict J-factors within an order of magnitude of experimental measurements for most ultra-short DNA sequences, while continuing to accurately describe the J-factors of longer sequences. Furthermore, we demonstrate that our computational framework can be used to describe the cyclization of DNA sequences that contain a base pair mismatch. Overall, our results support the conclusion that coherent delocalized phonon-like modes play an important role in DNA cyclization.« less

Evaluation of Bosch-Based Systems Using Non-Traditional Catalysts at Reduced Temperatures

NASA Technical Reports Server (NTRS)

Abney, Morgan B.; Mansell, J. Matthew

2011-01-01

Oxygen and water resupply make open loop atmosphere revitalization (AR) systems unfavorable for long-term missions beyond low Earth orbit. Crucial to closing the AR loop are carbon dioxide reduction systems with low mass and volume, minimal power requirements, and minimal consumables. For this purpose, NASA is exploring using Bosch-based systems. The Bosch process is favorable over state-of-the-art Sabatier-based processes due to complete loop closure. However, traditional operation of the Bosch required high reaction temperatures, high recycle rates, and significant consumables in the form of catalyst resupply due to carbon fouling. A number of configurations have been proposed for next-generation Bosch systems. First, alternative catalysts (catalysts other than steel wool) can be used in a traditional single-stage Bosch reactor to improve reaction kinetics and increase carbon packing density. Second, the Bosch reactor may be split into separate stages wherein the first reactor stage is dedicated to carbon monoxide and water formation via the reverse water-gas shift reaction and the second reactor stage is dedicated to carbon formation. A series system will enable maximum efficiency of both steps of the Bosch reaction, resulting in optimized operation and maximum carbon formation rate. This paper details the results of testing of both single-stage and two-stage Bosch systems with alternative catalysts at reduced temperatures. These results are compared to a traditional Bosch system operated with a steel wool catalyst.

Conceptualization and validation of an open-source closed-loop deep brain stimulation system in rat.

PubMed

Wu, Hemmings; Ghekiere, Hartwin; Beeckmans, Dorien; Tambuyzer, Tim; van Kuyck, Kris; Aerts, Jean-Marie; Nuttin, Bart

2015-04-21

Conventional deep brain stimulation (DBS) applies constant electrical stimulation to specific brain regions to treat neurological disorders. Closed-loop DBS with real-time feedback is gaining attention in recent years, after proved more effective than conventional DBS in terms of pathological symptom control clinically. Here we demonstrate the conceptualization and validation of a closed-loop DBS system using open-source hardware. We used hippocampal theta oscillations as system input, and electrical stimulation in the mesencephalic reticular formation (mRt) as controller output. It is well documented that hippocampal theta oscillations are highly related to locomotion, while electrical stimulation in the mRt induces freezing. We used an Arduino open-source microcontroller between input and output sources. This allowed us to use hippocampal local field potentials (LFPs) to steer electrical stimulation in the mRt. Our results showed that closed-loop DBS significantly suppressed locomotion compared to no stimulation, and required on average only 56% of the stimulation used in open-loop DBS to reach similar effects. The main advantages of open-source hardware include wide selection and availability, high customizability, and affordability. Our open-source closed-loop DBS system is effective, and warrants further research using open-source hardware for closed-loop neuromodulation.

Conceptualization and validation of an open-source closed-loop deep brain stimulation system in rat

PubMed Central

Wu, Hemmings; Ghekiere, Hartwin; Beeckmans, Dorien; Tambuyzer, Tim; van Kuyck, Kris; Aerts, Jean-Marie; Nuttin, Bart

2015-01-01

Conventional deep brain stimulation (DBS) applies constant electrical stimulation to specific brain regions to treat neurological disorders. Closed-loop DBS with real-time feedback is gaining attention in recent years, after proved more effective than conventional DBS in terms of pathological symptom control clinically. Here we demonstrate the conceptualization and validation of a closed-loop DBS system using open-source hardware. We used hippocampal theta oscillations as system input, and electrical stimulation in the mesencephalic reticular formation (mRt) as controller output. It is well documented that hippocampal theta oscillations are highly related to locomotion, while electrical stimulation in the mRt induces freezing. We used an Arduino open-source microcontroller between input and output sources. This allowed us to use hippocampal local field potentials (LFPs) to steer electrical stimulation in the mRt. Our results showed that closed-loop DBS significantly suppressed locomotion compared to no stimulation, and required on average only 56% of the stimulation used in open-loop DBS to reach similar effects. The main advantages of open-source hardware include wide selection and availability, high customizability, and affordability. Our open-source closed-loop DBS system is effective, and warrants further research using open-source hardware for closed-loop neuromodulation. PMID:25897892

Effective blocking of the white enhancer requires cooperation between two main mechanisms suggested for the insulator function.

PubMed

Kyrchanova, Olga; Maksimenko, Oksana; Stakhov, Viacheslav; Ivlieva, Tatyana; Parshikov, Alexander; Studitsky, Vasily M; Georgiev, Pavel

2013-01-01

Chromatin insulators block the action of transcriptional enhancers when interposed between an enhancer and a promoter. In this study, we examined the role of chromatin loops formed by two unrelated insulators, gypsy and Fab-7, in their enhancer-blocking activity. To test for this activity, we selected the white reporter gene that is activated by the eye-specific enhancer. The results showed that one copy of the gypsy or Fab-7 insulator failed to block the eye enhancer in most of genomic sites, whereas a chromatin loop formed by two gypsy insulators flanking either the eye enhancer or the reporter completely blocked white stimulation by the enhancer. However, strong enhancer blocking was achieved due not only to chromatin loop formation but also to the direct interaction of the gypsy insulator with the eye enhancer, which was confirmed by the 3C assay. In particular, it was observed that Mod(mdg4)-67.2, a component of the gypsy insulator, interacted with the Zeste protein, which is critical for the eye enhancer-white promoter communication. These results suggest that efficient enhancer blocking depends on the combination of two factors: chromatin loop formation by paired insulators, which generates physical constraints for enhancer-promoter communication, and the direct interaction of proteins recruited to an insulator and to the enhancer-promoter pair.

Effective Blocking of the White Enhancer Requires Cooperation between Two Main Mechanisms Suggested for the Insulator Function

PubMed Central

Stakhov, Viacheslav; Ivlieva, Tatyana; Parshikov, Alexander; Studitsky, Vasily M.; Georgiev, Pavel

2013-01-01

Chromatin insulators block the action of transcriptional enhancers when interposed between an enhancer and a promoter. In this study, we examined the role of chromatin loops formed by two unrelated insulators, gypsy and Fab-7, in their enhancer-blocking activity. To test for this activity, we selected the white reporter gene that is activated by the eye-specific enhancer. The results showed that one copy of the gypsy or Fab-7 insulator failed to block the eye enhancer in most of genomic sites, whereas a chromatin loop formed by two gypsy insulators flanking either the eye enhancer or the reporter completely blocked white stimulation by the enhancer. However, strong enhancer blocking was achieved due not only to chromatin loop formation but also to the direct interaction of the gypsy insulator with the eye enhancer, which was confirmed by the 3C assay. In particular, it was observed that Mod(mdg4)-67.2, a component of the gypsy insulator, interacted with the Zeste protein, which is critical for the eye enhancer–white promoter communication. These results suggest that efficient enhancer blocking depends on the combination of two factors: chromatin loop formation by paired insulators, which generates physical constraints for enhancer–promoter communication, and the direct interaction of proteins recruited to an insulator and to the enhancer–promoter pair. PMID:23861668

DETECTION OF SUPERSONIC DOWNFLOWS AND ASSOCIATED HEATING EVENTS IN THE TRANSITION REGION ABOVE SUNSPOTS

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

Kleint, L.; Martínez-Sykora, J.; Antolin, P.

Interface Region Imaging Spectrograph data allow us to study the solar transition region (TR) with an unprecedented spatial resolution of 0.''33. On 2013 August 30, we observed bursts of high Doppler shifts suggesting strong supersonic downflows of up to 200 km s{sup –1} and weaker, slightly slower upflows in the spectral lines Mg II h and k, C II 1336, Si IV 1394 Å, and 1403 Å, that are correlated with brightenings in the slitjaw images (SJIs). The bursty behavior lasts throughout the 2 hr observation, with average burst durations of about 20 s. The locations of these short-lived events appear to bemore » the umbral and penumbral footpoints of EUV loops. Fast apparent downflows are observed along these loops in the SJIs and in the Atmospheric Imaging Assembly, suggesting that the loops are thermally unstable. We interpret the observations as cool material falling from coronal heights, and especially coronal rain produced along the thermally unstable loops, which leads to an increase of intensity at the loop footpoints, probably indicating an increase of density and temperature in the TR. The rain speeds are on the higher end of previously reported speeds for this phenomenon, and possibly higher than the free-fall velocity along the loops. On other observing days, similar bright dots are sometimes aligned into ribbons, resembling small flare ribbons. These observations provide a first insight into small-scale heating events in sunspots in the TR.« less

Structurally conserved water molecules in ribonuclease T1.

PubMed

Malin, R; Zielenkiewicz, P; Saenger, W

1991-03-15

In the high resolution (1.7-1.9 A) crystal structures of ribonuclease T1 (RNase T1) in complex with guanosine, guanosine 2'-phosphate, guanylyl 2',5'-guanosine, and vanadate, there are 30 water sites in nearly identical (+/- 1 A) positions that are considered conserved. One water is tightly bound to Asp76(O delta), Thr93(O gamma), Cys6(O), and Asn9(N); another bridges two loops by hydrogen-bonding to Tyr68(O eta) and to Ser35(N), Asn36(N); a loop structure is stabilized by two waters coordinated to Gly31(O) and His27(N delta), and by water bound to cis-Pro39(O). Most notable is a hydrogen-bonded chain of 10 water molecules. Waters 1-5 of this chain are inaccessible to solvent, are anchored at Trp59(N), and stitch together the loop formed by segments 60-68; waters 5-8 coordinate to Ca2+, and waters 9 and 10 hydrogen-bond to N-terminal side chains of the alpha-helix. The water chain and two conserved water molecules are bound to amino acids adjacent to the active site residues His40, Glu58, Arg77, and His92; they are probably involved in maintaining their spatial orientation required for catalysis. Water sites must be considered in genetic engineering; the mutation Trp59Tyr, which probably influences the 10-water chain, doubles the catalytic activity of RNase T1.

Unmixing Magnetic Hysteresis Loops

NASA Astrophysics Data System (ADS)

Heslop, D.; Roberts, A. P.

2012-04-01

Magnetic hysteresis loops provide important information in rock and environmental magnetic studies. Natural samples often contain an assemblage of magnetic particles composed of components with different origins. Each component potentially carries important environmental information. Hysteresis loops, however, provide information concerning the bulk magnetic assemblage, which makes it difficult to isolate the specific contributions from different sources. For complex mineral assemblages an unmixing strategy with which to separate hysteresis loops into their component parts is therefore essential. Previous methods to unmix hysteresis data have aimed at separating individual loops into their constituent parts using libraries of type-curves thought to correspond to specific mineral types. We demonstrate an alternative approach, which rather than decomposing a single loop into monomineralic contributions, examines a collection of loops to determine their constituent source materials. These source materials may themselves be mineral mixtures, but they provide a genetically meaningful decomposition of a magnetic assemblage in terms of the processes that controlled its formation. We show how an empirically derived hysteresis mixing space can be created, without resorting to type-curves, based on the co-variation within a collection of measured loops. Physically realistic end-members, which respect the expected behaviour and symmetries of hysteresis loops, can then be extracted from the mixing space. These end-members allow the measured loops to be described as a combination of invariant parts that are assumed to represent the different sources in the mixing model. Particular attention is paid to model selection and estimating the complexity of the mixing model, specifically, how many end-members should be included. We demonstrate application of this approach using lake sediments from Butte Valley, northern California. Our method successfully separates the hysteresis loops into sources with a variety of terrigenous and authigenic origins.

Gas Hydrate Formation Probability Distributions: The Effect of Shear and Comparisons with Nucleation Theory.

PubMed

May, Eric F; Lim, Vincent W; Metaxas, Peter J; Du, Jianwei; Stanwix, Paul L; Rowland, Darren; Johns, Michael L; Haandrikman, Gert; Crosby, Daniel; Aman, Zachary M

2018-03-13

Gas hydrate formation is a stochastic phenomenon of considerable significance for any risk-based approach to flow assurance in the oil and gas industry. In principle, well-established results from nucleation theory offer the prospect of predictive models for hydrate formation probability in industrial production systems. In practice, however, heuristics are relied on when estimating formation risk for a given flowline subcooling or when quantifying kinetic hydrate inhibitor (KHI) performance. Here, we present statistically significant measurements of formation probability distributions for natural gas hydrate systems under shear, which are quantitatively compared with theoretical predictions. Distributions with over 100 points were generated using low-mass, Peltier-cooled pressure cells, cycled in temperature between 40 and -5 °C at up to 2 K·min -1 and analyzed with robust algorithms that automatically identify hydrate formation and initial growth rates from dynamic pressure data. The application of shear had a significant influence on the measured distributions: at 700 rpm mass-transfer limitations were minimal, as demonstrated by the kinetic growth rates observed. The formation probability distributions measured at this shear rate had mean subcoolings consistent with theoretical predictions and steel-hydrate-water contact angles of 14-26°. However, the experimental distributions were substantially wider than predicted, suggesting that phenomena acting on macroscopic length scales are responsible for much of the observed stochastic formation. Performance tests of a KHI provided new insights into how such chemicals can reduce the risk of hydrate blockage in flowlines. Our data demonstrate that the KHI not only reduces the probability of formation (by both shifting and sharpening the distribution) but also reduces hydrate growth rates by a factor of 2.

Identification of a high affinity nucleocapsid protein binding element within the Moloney murine leukemia virus Psi-RNA packaging signal: implications for genome recognition.

PubMed

D'Souza, V; Melamed, J; Habib, D; Pullen, K; Wallace, K; Summers, M F

2001-11-23

Murine leukemia virus (MLV) is currently the most widely used gene delivery system in gene therapy trials. The simple retrovirus packages two copies of its RNA genome by a mechanism that involves interactions between the nucleocapsid (NC) domain of a virally-encoded Gag polyprotein and a segment of the RNA genome located just upstream of the Gag initiation codon, known as the Psi-site. Previous studies indicated that the MLV Psi-site contains three stem loops (SLB-SLD), and that stem loops SLC and SLD play prominent roles in packaging. We have developed a method for the preparation and purification of large quantities of recombinant Moloney MLV NC protein, and have studied its interactions with a series of oligoribonucleotides that contain one or more of the Psi-RNA stem loops. At RNA concentrations above approximately 0.3 mM, isolated stem loop SLB forms a duplex and stem loops SL-C and SL-D form kissing complexes, as expected from previous studies. However, neither the monomeric nor the dimeric forms of these isolated stem loops binds NC with significant affinity. Longer constructs containing two stem loops (SL-BC and SL-CD) also exhibit low affinities for NC. However, NC binds with high affinity and stoichiometrically to both the monomeric and dimeric forms of an RNA construct that contains all three stem loops (SL-BCD; K(d)=132(+/-55) nM). Titration of SL-BCD with NC also shifts monomer-dimer equilibrium toward the dimer. Mutagenesis experiments demonstrate that the conserved GACG tetraloops of stem loops C and D do not influence the monomer-dimer equilibrium of SL-BCD, that the tetraloop of stem loop B does not participate directly in NC binding, and that the tetraloops of stem loops C and D probably also do not bind to NC. These surprising results differ considerably from those observed for HIV-1, where NC binds to individual stem loops with high affinity via interactions with exposed residues of the tetraloops. The present results indicate that MLV NC binds to a pocket or surface that only exists in the presence of all three stem loops. Copyright 2001 Academic Press.

Fire-scar formation in Jeffrey pine - mixed conifer forests in the Sierra San Pedro Martir, Mexico

Treesearch

Scott L. Stephens; Danny L. Fry; Brandon M. Collins; Carl N. Skinner; Ernesto Franco-Vizcaino; Travis J. Freed

2010-01-01

Little is known about the probability of fire-scar formation. In this study, we examined all mixed conifer trees for fire-scar formation in a 16 ha watershed that burned as part of a 2003 wildfire in Sierra San Pedro Ma´rtir National Park (SSPM), Mexico. In addition, we examine the probability of fire-scar formation in relation to the previous fire interval in forests...

Prediction of beta-turns in proteins using the first-order Markov models.

PubMed

Lin, Thy-Hou; Wang, Ging-Ming; Wang, Yen-Tseng

2002-01-01

We present a method based on the first-order Markov models for predicting simple beta-turns and loops containing multiple turns in proteins. Sequences of 338 proteins in a database are divided using the published turn criteria into the following three regions, namely, the turn, the boundary, and the nonturn ones. A transition probability matrix is constructed for either the turn or the nonturn region using the weighted transition probabilities computed for dipeptides identified from each region. There are two such matrices constructed for the boundary region since the transition probabilities for dipeptides immediately preceding or following a turn are different. The window used for scanning a protein sequence from amino (N-) to carboxyl (C-) terminal is a hexapeptide since the transition probability computed for a turn tetrapeptide is capped at both the N- and C- termini with a boundary transition probability indexed respectively from the two boundary transition matrices. A sum of the averaged product of the transition probabilities of all the hexapeptides involving each residue is computed. This is then weighted with a probability computed from assuming that all the hexapeptides are from the nonturn region to give the final prediction quantity. Both simple beta-turns and loops containing multiple turns in a protein are then identified by the rising of the prediction quantity computed. The performance of the prediction scheme or the percentage (%) of correct prediction is evaluated through computation of Matthews correlation coefficients for each protein predicted. It is found that the prediction method is capable of giving prediction results with better correlation between the percent of correct prediction and the Matthews correlation coefficients for a group of test proteins as compared with those predicted using some secondary structural prediction methods. The prediction accuracy for about 40% of proteins in the database or 50% of proteins in the test set is better than 70%. Such a percentage for the test set is reduced to 30 if the structures of all the proteins in the set are treated as unknown.

Optical phase locked loop for transparent inter-satellite communications.

PubMed

Herzog, F; Kudielka, K; Erni, D; Bächtold, W

2005-05-16

A novel type of optical phase locked loop (OPLL), optimized for homodyne inter-satellite communication, is presented. The loop employs a conventional 180? 3 dB optical hybrid and an AC-coupled balanced front end. No residual carrier transmission is required for phase locking. The loop accepts analog as well as digital data and various modulation formats. The only requirement to the transmitted user signal is a constant envelope. Phase error extraction occurs through applying a small sinusoidal local oscillator (LO) phase disturbance, while measuring its impact on the power of the baseband output signal. First experimental results indicate a receiver sensitivity of 36 photons/bit (-55.7 dBm) for a BER of 10 ;-9, when transmitting a PRBS-31 signal at a data rate of 400 Mbit/s. The system setup employs diode-pumped Nd:YAG lasers at a wavelength of 1.06 mum.

Optical phase locked loop for transparent inter-satellite communications

NASA Astrophysics Data System (ADS)

Herzog, F.; Kudielka, K.; Erni, D.; Bächtold, W.

2005-05-01

A novel type of optical phase locked loop (OPLL), optimized for homodyne inter-satellite communication, is presented. The loop employs a conventional 180◦ 3 dB optical hybrid and an AC-coupled balanced front end. No residual carrier transmission is required for phase locking. The loop accepts analog as well as digital data and various modulation formats. The only requirement to the transmitted user signal is a constant envelope. Phase error extraction occurs through applying a small sinusoidal local oscillator (LO) phase disturbance, while measuring its impact on the power of the baseband output signal. First experimental results indicate a receiver sensitivity of 36 photons/bit (-55.7 dBm) for a BER of 10 ^-9, when transmitting a PRBS-31 signal at a data rate of 400 Mbit/s. The system setup employs diode-pumped Nd:YAG lasers at a wavelength of 1.06 μm.

Analysis of the mechanism of nucleosome survival during transcription

PubMed Central

Chang, Han-Wen; Kulaeva, Olga I.; Shaytan, Alexey K.; Kibanov, Mikhail; Kuznedelov, Konstantin; Severinov, Konstantin V.; Kirpichnikov, Mikhail P.; Clark, David J.; Studitsky, Vasily M.

2014-01-01

Maintenance of nucleosomal structure in the cell nuclei is essential for cell viability, regulation of gene expression and normal aging. Our previous data identified a key intermediate (a small intranucleosomal DNA loop, Ø-loop) that is likely required for nucleosome survival during transcription by RNA polymerase II (Pol II) through chromatin, and suggested that strong nucleosomal pausing guarantees efficient nucleosome survival. To evaluate these predictions, we analysed transcription through a nucleosome by different, structurally related RNA polymerases and mutant yeast Pol II having different histone-interacting surfaces that presumably stabilize the Ø-loop. The height of the nucleosomal barrier to transcription and efficiency of nucleosome survival correlate with the net negative charges of the histone-interacting surfaces. Molecular modeling and analysis of Pol II-nucleosome intermediates by DNase I footprinting suggest that efficient Ø-loop formation and nucleosome survival are mediated by electrostatic interactions between the largest subunit of Pol II and core histones. PMID:24234452

SWAP Observations of Post Flare Giant Arches and Evidence of Run-Away Reconnection

NASA Astrophysics Data System (ADS)

West, M. J.; Seaton, D. B.; Savage, S. L.

2016-12-01

It was recently established that post-flare giant arches and regular post-flare loops are generated in the same way, with post-flare giant arches undergoing sustained magnetic reconnection allowing them to grow to heights of approximately 400000 km (>0.5 solar-radii). In this presentation we discuss how reconnection can be sustained to such great heights, and the role the background corona plays in maintaining this growth. We use observations from 14 October 2014, when the SWAP EUV solar telescope on-board the PROBA2 spacecraft observed an eruption that led to the formation of perhaps the largest post-flare loop system seen in the solar corona in solar cycle 24. We combine these observations with those of RHESSI and LASCO, as well as using a forward model to assess the reconnection and loop deposition rate in the post-eruptive loop system.

Structural mechanism of Smad4 recognition by the nuclear oncoprotein Ski: insights on Ski-mediated repression of TGF-beta signaling.

PubMed

Wu, Jia Wei; Krawitz, Ariel R; Chai, Jijie; Li, Wenyu; Zhang, Fangjiu; Luo, Kunxin; Shi, Yigong

2002-11-01

The Ski family of nuclear oncoproteins represses TGF-beta signaling through interactions with the Smad proteins. The crystal structure of the Smad4 binding domain of human c-Ski in complex with the MH2 domain of Smad4 reveals specific recognition of the Smad4 L3 loop region by a highly conserved interaction loop (I loop) from Ski. The Ski binding surface on Smad4 significantly overlaps with that required for binding of the R-Smads. Indeed, Ski disrupts the formation of a functional complex between the Co- and R-Smads, explaining how it could lead to repression of TGF-beta, activin, and BMP responses. Intriguingly, the structure of the Ski fragment, stabilized by a bound zinc atom, resembles the SAND domain, in which the corresponding I loop is responsible for DNA binding.

Paleomagnetism of the Late Proterozoic Tsezotene Formation of northwestern Canada

NASA Astrophysics Data System (ADS)

Park, John K.; Aitken, James D.

1986-04-01

Paleomagnetic evidence from 37 sites of the partly red-pigmented siliciclastic Tsezotene Formation supports a recently proposed apparent polar wander path for the Hadrynian Mackenzie Mountains supergroup (MMs). The probable primary remanence has a direction at D°, I° = 271, +24 (k = 15; α95° = 8) with an associated pole TA (12°N, 214°W; N = 23 specimens; δp°, δm° = 5, 9). TA becomes the oldest pole from the MMS. It helps bridge the gap between the apparently youngest poles of the Grenville Loop (about 0.88 Ga) and the suggested younger poles from the MMs. A secondary pole TB (23°N, 198°W; N = 18 sites; δp°, δm° = 3, 5), derived from a magnetic direction in hematite pigment (D°, I° = 263, +48; k = 73; α95° = 4), supports a magnetization found in the overlying "Copper cycle" and in younger units of the MMs as a pervasive overprint. Another secondary pole Tc (63°N, 141°W; N = 29 sites; δp°, δm° = 6, 6), derived from a magnetization (D°, I° = 317, +87; k = 89; α95° = 3) partly residing in another phase of hematite pigment, is of postfolding age (post-Paleocene). This study demonstrates the importance of using several treatment methods, singly and in combination, when analyzing complex magnetizations.

Evidence for Magnetic Reconnection in Three Homologous Solar Flares Observed by RHESSI

NASA Technical Reports Server (NTRS)

Sui, Lin-Hui; Holman, Gordon D.; Dennis, Brian R.

2004-01-01

We present RHESSI observF5oss of three homologous flares, which occurred between April 14 and 16, 2002. We find that the RHESSI images of all three flares at energies between 6 and 25 keV had some common features: (1) A. separate coronal source up to approx. 30 deg. above the flare loop appeared in the early impulsive phase and stayed stationary for several minutes. (2) Before the flare loop moved upward; previously reported by others, the flare loop-top centroid moved downward for 2-4 minutes during the early impulsive phase of the Ears: falling by 13 - 30% of its initial height with a speed between 8 and 23 km/s. We conclude that these features are associated with the formation and development of a current sheet between the loop-top and the coronal source. In the April 14-15 flare, we find that the hard X-ray flux (greater than 25 keV) is correlated with the rate at which the flare loop moves upward, indicating that the faster the loop grows, the faster the reconnection rate, and therefore, the greater the flux of accelerated electrons. Subject headings: Sun: L'iaies-Sun: X-1-ay-s -

Development of a Radio Frequency Space Environment Path Emulator for Evaluating Spacecraft Ranging Hardware

NASA Technical Reports Server (NTRS)

Mitchell, Jason W.; Baldwin, Philip J.; Kurichh, Rishi; Naasz, Bo J.; Luquette, Richard J.

2007-01-01

The Formation Flying Testbed (FFTB) at the National Aeronautics and Space Administration (NASA) Goddard Space Flight Center (GSFC) provides a hardware-in-the-loop test environment for formation navigation and control. The facility is evolving as a modular, hybrid, dynamic simulation facility for end-to-end guidance, navigation and. control (GN&C) design and analysis of formation flying spacecraft. The core capabilities of the FFTB, as a platform for testing critical hardware and software algorithms in-the-loop, have expanded to include S-band Radio Frequency (RF) modems for inter-spacecraft communication and ranging. To enable realistic simulations that require RF ranging sensors for relative navigation, a mechanism is needed to buffer the RF signals exchanged between spacecraft that accurately emulates the dynamic environment through which the RF signals travel, including the effects of medium, moving platforms, and radiated power. The Path Emulator for RF Signals (PERFS), currently under development at NASA GSFC, provides this capability. The function and performance of a prototype device are presented.

Characterization of a Prototype Radio Frequency Space Environment Path Emulator for Evaluating Spacecraft Ranging Hardware

NASA Technical Reports Server (NTRS)

Mitchell, Jason W.; Baldwin, Philip J.; Kurichh, Rishi; Naasz, Bo J.; Luquette, Richard J.

2007-01-01

The Formation Flying Testbed (FFTB) at the National Aeronautics and Space Administration (NASA) Goddard Space Flight Center (GSFC) provides a hardware-in-the-loop test environment for formation navigation and control. The facility is evolving as a modular, hybrid, dynamic simulation facility for end-to-end guidance, navigation and control (GN&C) design and analysis of formation flying spacecraft. The core capabilities of the FFTB, as a platform for testing critical hardware and software algorithms in-the-loop, have expanded to include S-band Radio Frequency (RF) modems for interspacecraft communication and ranging. To enable realistic simulations that require RF ranging sensors for relative navigation, a mechanism is needed to buffer the RF signals exchanged between spacecraft that accurately emulates the dynamic environment through which the RF signals travel, including the effects of the medium, moving platforms, and radiated power. The Path Emulator for Radio Frequency Signals (PERFS), currently under development at NASA GSFC, provides this capability. The function and performance of a prototype device are presented.

Simultaneous Determination of Two Subdomain Folding Rates Using the "Transfer-Quench" Method.

PubMed

Rahamim, Gil; Amir, Dan; Haas, Elisha

2017-05-09

The investigation of the mechanism of protein folding is complicated by the context dependence of the rates of intramolecular contact formation. Methods based on site-specific labeling and ultrafast spectroscopic detection of fluorescence signals were developed for monitoring the rates of individual subdomain folding transitions in situ, in the context of the whole molecule. However, each site-specific labeling modification might affect rates of folding of near-neighbor structural elements, and thus limit the ability to resolve fine differences in rates of folding of these elements. Therefore, it is highly desirable to be able to study the rates of folding of two or more neighboring subdomain structures using a single mutant to facilitate resolution of the order and interdependence of such steps. Here, we report the development of the "Transfer-Quench" method for measuring the rate of formation of two structural elements using a single triple-labeled mutant. This method is based on Förster resonance energy transfer combined with fluorescence quenching. We placed the donor and acceptor at the loop ends, and a quencher at an α-helical element involved in the node forming the loop. The folding of the triple-labeled mutant is monitored by the acceptor emission. The formation of nonlocal contact (loop closure) increases the time-dependent acceptor emission, while the closure of the labeled helix turn reduces this emission. The method was applied in a study of the folding mechanism of the common model protein, the B domain of staphylococcal protein A. Only natural amino acids were used as probes, and thus possible structural perturbations were minimized. Tyr and Trp residues served as donor and acceptor at the ends of a long loop between helices I and II, and a Cys residue as a quencher for the acceptor. We found that the closure of the loop (segment 14-33) occurs with the same rate constant as the nucleation of helix HII (segment 33-29), in line with the nucleation-condensation model. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Adaptive tracking control for a class of stochastic switched systems

NASA Astrophysics Data System (ADS)

Zhang, Hui; Xia, Yuanqing

2018-02-01

The problem of adaptive tracking is considered for a class of stochastic switched systems, in this paper. As preliminaries, the criterion of global asymptotical practical stability in probability is first presented by the aid of common Lyapunov function method. Based on the Lyapunov stability criterion, adaptive backstepping controllers are designed to guarantee that the closed-loop system has a unique global solution, which is globally asymptotically practically stable in probability, and the tracking error in the fourth moment converges to an arbitrarily small neighbourhood of zero. Simulation examples are given to demonstrate the efficiency of the proposed schemes.

Loop propensity of the sequence YKGQP from staphylococcal nuclease: implications for the folding of nuclease.

PubMed

Patel, Sunita; Sasidhar, Yellamraju U

2007-10-01

Recently we performed molecular dynamics (MD) simulations on the folding of the hairpin peptide DTVKLMYKGQPMTFR from staphylococcal nuclease in explicit water. We found that the peptide folds into a hairpin conformation with native and nonnative hydrogen-bonding patterns. In all the folding events observed in the folding of the hairpin peptide, loop formation involving the region YKGQP was an important event. In order to trace the origins of the loop propensity of the sequence YKGQP, we performed MD simulations on the sequence starting from extended, polyproline II and native type I' turn conformations for a total simulation length of 300 ns, using the GROMOS96 force field under constant volume and temperature (NVT) conditions. The free-energy landscape of the peptide YKGQP shows minima corresponding to loop conformation with Tyr and Pro side-chain association, turn and extended conformational forms, with modest free-energy barriers separating the minima. To elucidate the role of Gly in facilitating loop formation, we also performed MD simulations of the mutated peptide YKAQP (Gly --> Ala mutation) under similar conditions starting from polyproline II conformation for 100 ns. Two minima corresponding to bend/turn and extended conformations were observed in the free-energy landscape for the peptide YKAQP. The free-energy barrier between the minima in the free-energy landscape of the peptide YKAQP was also modest. Loop conformation is largely sampled by the YKGQP peptide, while extended conformation is largely sampled by the YKAQP peptide. We also explain why the YKGQP sequence samples type II turn conformation in these simulations, whereas the sequence as part of the hairpin peptide DTVKLMYKGQPMTFR samples type I' turn conformation both in the X-ray crystal structure and in our earlier simulations on the folding of the hairpin peptide. We discuss the implications of our results to the folding of the staphylococcal nuclease. Copyright (c) 2007 European Peptide Society and John Wiley & Sons, Ltd.

H-alpha Fabry-Perot interferometric observations of blue compact dwarf galaxies

NASA Technical Reports Server (NTRS)

Thuan, Trinh Xuan; Williams, T. B.; Malumuth, E.

1987-01-01

H-alpha Fabry-Perot interferometric observations of the two blue compact dwarf galaxies (BCDs) 7 Zw 403 and 1 Zw 49 are presented. The velocity field of 7 Zw 403 shows no clear large-scale organized motion but the velocity field is not completely chaotic either. The gas associated with the 8 H II regions in 7 Zw 403 has neither the highest nor lowest velocities. The BCD 1 Zw 49 is dominated by a single H II region which is about 50 times brighter than any other feature in the galaxy. There is a chain of fainter H II regions extending across the galaxy. The velocity field is well ordered along the H II region chain, but it is very complex around the dominant H II region, suggesting H-alpha loops and filaments around the latter. Both BCDs show velocity gradients of about 25 km/s on scales of about 10 pc in 7 Zw 403 and of about 50 pc in 1 Zw 49. These velocity discontinuities compress the gas and are probably responsible for the star formation.

Microwave detector

DOEpatents

Meldner, H.W.; Cusson, R.Y.; Johnson, R.M.

1985-02-08

A microwave detector is provided for measuring the envelope shape of a microwave pulse comprised of high-frequency oscillations. A biased ferrite produces a magnetization field flux that links a B-dot loop. The magnetic field of the microwave pulse participates in the formation of the magnetization field flux. High-frequency insensitive means are provided for measuring electric voltage or current induced in the B-dot loop. The recorded output of the detector is proportional to the time derivative of the square of the envelope shape of the microwave pulse.

Mutations reducing replication from R-loops suppress the defects of growth, chromosome segregation and DNA supercoiling in cells lacking topoisomerase I and RNase HI activity.

PubMed

Usongo, Valentine; Martel, Makisha; Balleydier, Aurélien; Drolet, Marc

2016-04-01

R-loop formation occurs when the nascent RNA hybridizes with the template DNA strand behind the RNA polymerase. R-loops affect a wide range of cellular processes and their use as origins of replication was the first function attributed to them. In Escherichia coli, R-loop formation is promoted by the ATP-dependent negative supercoiling activity of gyrase (gyrA and gyrB) and is inhibited by topoisomerase (topo) I (topA) relaxing transcription-induced negative supercoiling. RNase HI (rnhA) degrades the RNA moiety of R-loops. The depletion of RNase HI activity in topA null mutants was previously shown to lead to extensive DNA relaxation, due to DNA gyrase inhibition, and to severe growth and chromosome segregation defects that were partially corrected by overproducing topo III (topB). Here, DNA gyrase assays in crude cell extracts showed that the ATP-dependent activity (supercoiling) of gyrase but not its ATP-independent activity (relaxation) was inhibited in topA null cells lacking RNase HI. To characterize the cellular event(s) triggered by the absence of RNase HI, we performed a genetic screen for suppressors of the growth defect of topA rnhA null cells. Suppressors affecting genes in replication (holC2::aph and dnaT18::aph) nucleotide metabolism (dcd49::aph), RNA degradation (rne59::aph) and fimbriae synthesis (fimD22::aph) were found to reduce replication from R-loops and to restore supercoiling, thus pointing to a correlation between R-loop-dependent replication in topA rnhA mutants and the inhibition of gyrase activity and growth. Interestingly, the position of fimD on the E. coli chromosome corresponds to the site of one of the five main putative origins of replication from R-loops in rnhA null cells recently identified by next-generation sequencing, thus suggesting that the fimD22::aph mutation inactivated one of these origins. Furthermore, we show that topo III overproduction is unable to complement the growth defect of topA rnhA null mutants at low temperatures that stabilizes hyper-negatively supercoiled DNA. Copyright © 2016 Elsevier B.V. All rights reserved.

A novel mode for transcription inhibition mediated by PNA-induced R-loops with a model in vitro system.

PubMed

D'Souza, Alicia D; Belotserkovskii, Boris P; Hanawalt, Philip C

2018-02-01

The selective inhibition of transcription of a chosen gene by an artificial agent has numerous applications. Usually, these agents are designed to bind a specific nucleotide sequence in the promoter or within the transcribed region of the chosen gene. However, since optimal binding sites might not exist within the gene, it is of interest to explore the possibility of transcription inhibition when the agent is designed to bind at other locations. One of these possibilities arises when an additional transcription initiation site (e.g. secondary promoter) is present upstream from the primary promoter of the target gene. In this case, transcription inhibition might be achieved by inducing the formation of an RNA-DNA hybrid (R-loop) upon transcription from the secondary promoter. The R-loop could extend into the region of the primary promoter, to interfere with promoter recognition by RNA polymerase and thereby inhibit transcription. As a sequence-specific R-loop-inducing agent, a peptide nucleic acid (PNA) could be designed to facilitate R-loop formation by sequestering the non-template DNA strand. To investigate this mode for transcription inhibition, we have employed a model system in which a PNA binding site is localized between the T3 and T7 phage RNA polymerase promoters, which respectively assume the roles of primary and secondary promoters. In accord with our model, we have demonstrated that with PNA-bound DNA substrates, transcription from the T7 promoter reduces transcription from the T3 promoter by 30-fold, while in the absence of PNA binding there is no significant effect of T7 transcription upon T3 transcription. Copyright © 2018 Elsevier B.V. All rights reserved.

Health Professionals Prefer to Communicate Risk-Related Numerical Information Using "1-in-X" Ratios.

PubMed

Sirota, Miroslav; Juanchich, Marie; Petrova, Dafina; Garcia-Retamero, Rocio; Walasek, Lukasz; Bhatia, Sudeep

2018-04-01

Previous research has shown that format effects, such as the "1-in-X" effect-whereby "1-in-X" ratios lead to a higher perceived probability than "N-in-N*X" ratios-alter perceptions of medical probabilities. We do not know, however, how prevalent this effect is in practice; i.e., how often health professionals use the "1-in-X" ratio. We assembled 4 different sources of evidence, involving experimental work and corpus studies, to examine the use of "1-in-X" and other numerical formats quantifying probability. Our results revealed that the use of the "1-in-X" ratio is prevalent and that health professionals prefer this format compared with other numerical formats (i.e., the "N-in-N*X", %, and decimal formats). In Study 1, UK family physicians preferred to communicate prenatal risk using a "1-in-X" ratio (80.4%, n = 131) across different risk levels and regardless of patients' numeracy levels. In Study 2, a sample from the UK adult population ( n = 203) reported that most GPs (60.6%) preferred to use "1-in-X" ratios compared with other formats. In Study 3, "1-in-X" ratios were the most commonly used format in a set of randomly sampled drug leaflets describing the risk of side effects (100%, n = 94). In Study 4, the "1-in-X" format was the most commonly used numerical expression of medical probabilities or frequencies on the UK's NHS website (45.7%, n = 2,469 sentences). The prevalent use of "1-in-X" ratios magnifies the chances of increased subjective probability. Further research should establish clinical significance of the "1-in-X" effect.

A DDDAS Framework for Volcanic Ash Propagation and Hazard Analysis

DTIC Science & Technology

2012-01-01

probability distribution for the input variables (for example, Hermite polynomials for normally distributed parameters, or Legendre for uniformly...parameters and windfields will drive our simulations. We will use uncertainty quantification methodology – polynomial chaos quadrature in combination...quantification methodology ? polynomial chaos quadrature in combination with data integration to complete the DDDAS loop. 15. SUBJECT TERMS 16. SECURITY

Global output feedback stabilisation of stochastic high-order feedforward nonlinear systems with time-delay

NASA Astrophysics Data System (ADS)

Zhang, Kemei; Zhao, Cong-Ran; Xie, Xue-Jun

2015-12-01

This paper considers the problem of output feedback stabilisation for stochastic high-order feedforward nonlinear systems with time-varying delay. By using the homogeneous domination theory and solving several troublesome obstacles in the design and analysis, an output feedback controller is constructed to drive the closed-loop system globally asymptotically stable in probability.

Constraints on cosmic strings using data from the first Advanced LIGO observing run

NASA Astrophysics Data System (ADS)

Abbott, B. P.; Abbott, R.; Abbott, T. D.; Acernese, F.; Ackley, K.; Adams, C.; Adams, T.; Addesso, P.; Adhikari, R. X.; Adya, V. B.; Affeldt, C.; Afrough, M.; Agarwal, B.; Agathos, M.; Agatsuma, K.; Aggarwal, N.; Aguiar, O. D.; Aiello, L.; Ain, A.; Ajith, P.; Allen, B.; Allen, G.; Allocca, A.; Altin, P. A.; Amato, A.; Ananyeva, A.; Anderson, S. B.; Anderson, W. G.; Antier, S.; Appert, S.; Arai, K.; Araya, M. C.; Areeda, J. S.; Arnaud, N.; Arun, K. G.; Ascenzi, S.; Ashton, G.; Ast, M.; Aston, S. M.; Astone, P.; Aufmuth, P.; Aulbert, C.; AultONeal, K.; Avila-Alvarez, A.; Babak, S.; Bacon, P.; Bader, M. K. M.; Bae, S.; Baker, P. T.; Baldaccini, F.; Ballardin, G.; Ballmer, S. W.; Banagiri, S.; Barayoga, J. C.; Barclay, S. E.; Barish, B. C.; Barker, D.; Barone, F.; Barr, B.; Barsotti, L.; Barsuglia, M.; Barta, D.; Bartlett, J.; Bartos, I.; Bassiri, R.; Basti, A.; Batch, J. C.; Baune, C.; Bawaj, M.; Bazzan, M.; Bécsy, B.; Beer, C.; Bejger, M.; Belahcene, I.; Bell, A. S.; Berger, B. K.; Bergmann, G.; Berry, C. P. L.; Bersanetti, D.; Bertolini, A.; Betzwieser, J.; Bhagwat, S.; Bhandare, R.; Bilenko, I. A.; Billingsley, G.; Billman, C. R.; Birch, J.; Birney, R.; Birnholtz, O.; Biscans, S.; Bisht, A.; Bitossi, M.; Biwer, C.; Bizouard, M. A.; Blackburn, J. K.; Blackman, J.; Blair, C. D.; Blair, D. G.; Blair, R. M.; Bloemen, S.; Bock, O.; Bode, N.; Boer, M.; Bogaert, G.; Bohe, A.; Bondu, F.; Bonnand, R.; Boom, B. A.; Bork, R.; Boschi, V.; Bose, S.; Bouffanais, Y.; Bozzi, A.; Bradaschia, C.; Brady, P. R.; Braginsky, V. B.; Branchesi, M.; Brau, J. E.; Briant, T.; Brillet, A.; Brinkmann, M.; Brisson, V.; Brockill, P.; Broida, J. E.; Brooks, A. F.; Brown, D. A.; Brown, D. D.; Brown, N. M.; Brunett, S.; Buchanan, C. C.; Buikema, A.; Bulik, T.; Bulten, H. J.; Buonanno, A.; Buskulic, D.; Buy, C.; Byer, R. L.; Cabero, M.; Cadonati, L.; Cagnoli, G.; Cahillane, C.; Calderón Bustillo, J.; Callister, T. A.; Calloni, E.; Camp, J. B.; Canepa, M.; Canizares, P.; Cannon, K. C.; Cao, H.; Cao, J.; Capano, C. D.; Capocasa, E.; Carbognani, F.; Caride, S.; Carney, M. F.; Casanueva Diaz, J.; Casentini, C.; Caudill, S.; Cavaglià, M.; Cavalier, F.; Cavalieri, R.; Cella, G.; Cepeda, C. B.; Cerboni Baiardi, L.; Cerretani, G.; Cesarini, E.; Chamberlin, S. J.; Chan, M.; Chao, S.; Charlton, P.; Chassande-Mottin, E.; Chatterjee, D.; Cheeseboro, B. D.; Chen, H. Y.; Chen, Y.; Cheng, H.-P.; Chincarini, A.; Chiummo, A.; Chmiel, T.; Cho, H. S.; Cho, M.; Chow, J. H.; Christensen, N.; Chu, Q.; Chua, A. J. K.; Chua, S.; Chung, A. K. W.; Chung, S.; Ciani, G.; Ciolfi, R.; Cirelli, C. E.; Cirone, A.; Clara, F.; Clark, J. A.; Cleva, F.; Cocchieri, C.; Coccia, E.; Cohadon, P.-F.; Colla, A.; Collette, C. G.; Cominsky, L. R.; Constancio, M.; Conti, L.; Cooper, S. J.; Corban, P.; Corbitt, T. R.; Corley, K. R.; Cornish, N.; Corsi, A.; Cortese, S.; Costa, C. A.; Coughlin, M. W.; Coughlin, S. B.; Coulon, J.-P.; Countryman, S. T.; Couvares, P.; Covas, P. B.; Cowan, E. E.; Coward, D. M.; Cowart, M. J.; Coyne, D. C.; Coyne, R.; Creighton, J. D. E.; Creighton, T. D.; Cripe, J.; Crowder, S. G.; Cullen, T. J.; Cumming, A.; Cunningham, L.; Cuoco, E.; Dal Canton, T.; Danilishin, S. L.; D'Antonio, S.; Danzmann, K.; Dasgupta, A.; Da Silva Costa, C. F.; Dattilo, V.; Dave, I.; Davier, M.; Davis, D.; Daw, E. J.; Day, B.; De, S.; DeBra, D.; Degallaix, J.; De Laurentis, M.; Deléglise, S.; Del Pozzo, W.; Denker, T.; Dent, T.; Dergachev, V.; De Rosa, R.; DeRosa, R. T.; DeSalvo, R.; Devenson, J.; Devine, R. C.; Dhurandhar, S.; Díaz, M. C.; Di Fiore, L.; Di Giovanni, M.; Di Girolamo, T.; Di Lieto, A.; Di Pace, S.; Di Palma, I.; Di Renzo, F.; Doctor, Z.; Dolique, V.; Donovan, F.; Dooley, K. L.; Doravari, S.; Dorrington, I.; Douglas, R.; Dovale Álvarez, M.; Downes, T. P.; Drago, M.; Drever, R. W. P.; Driggers, J. C.; Du, Z.; Ducrot, M.; Duncan, J.; Dwyer, S. E.; Edo, T. B.; Edwards, M. C.; Effler, A.; Eggenstein, H.-B.; Ehrens, P.; Eichholz, J.; Eikenberry, S. S.; Eisenstein, R. A.; Essick, R. C.; Etienne, Z. B.; Etzel, T.; Evans, M.; Evans, T. M.; Factourovich, M.; Fafone, V.; Fair, H.; Fairhurst, S.; Fan, X.; Farinon, S.; Farr, B.; Farr, W. M.; Fauchon-Jones, E. J.; Favata, M.; Fays, M.; Fehrmann, H.; Feicht, J.; Fejer, M. M.; Fernandez-Galiana, A.; Ferrante, I.; Ferreira, E. C.; Ferrini, F.; Fidecaro, F.; Fiori, I.; Fiorucci, D.; Fisher, R. P.; Fitz-Axen, M.; Flaminio, R.; Fletcher, M.; Fong, H.; Forsyth, P. W. F.; Forsyth, S. S.; Fournier, J.-D.; Frasca, S.; Frasconi, F.; Frei, Z.; Freise, A.; Frey, R.; Frey, V.; Fries, E. M.; Fritschel, P.; Frolov, V. V.; Fulda, P.; Fyffe, M.; Gabbard, H.; Gabel, M.; Gadre, B. U.; Gaebel, S. M.; Gair, J. R.; Gammaitoni, L.; Ganija, M. R.; Gaonkar, S. G.; Garufi, F.; Gaudio, S.; Gaur, G.; Gayathri, V.; Gehrels, N.; Gemme, G.; Genin, E.; Gennai, A.; George, D.; George, J.; Gergely, L.; Germain, V.; Ghonge, S.; Ghosh, Abhirup; Ghosh, Archisman; Ghosh, S.; Giaime, J. A.; Giardina, K. D.; Giazotto, A.; Gill, K.; Glover, L.; Goetz, E.; Goetz, R.; Gomes, S.; González, G.; Gonzalez Castro, J. M.; Gopakumar, A.; Gorodetsky, M. L.; Gossan, S. E.; Gosselin, M.; Gouaty, R.; Grado, A.; Graef, C.; Granata, M.; Grant, A.; Gras, S.; Gray, C.; Greco, G.; Green, A. C.; Groot, P.; Grote, H.; Grunewald, S.; Gruning, P.; Guidi, G. M.; Guo, X.; Gupta, A.; Gupta, M. K.; Gushwa, K. E.; Gustafson, E. K.; Gustafson, R.; Hall, B. R.; Hall, E. D.; Hammond, G.; Haney, M.; Hanke, M. M.; Hanks, J.; Hanna, C.; Hannam, M. D.; Hannuksela, O. A.; Hanson, J.; Hardwick, T.; Harms, J.; Harry, G. M.; Harry, I. W.; Hart, M. J.; Haster, C.-J.; Haughian, K.; Healy, J.; Heidmann, A.; Heintze, M. C.; Heitmann, H.; Hello, P.; Hemming, G.; Hendry, M.; Heng, I. S.; Hennig, J.; Henry, J.; Heptonstall, A. W.; Heurs, M.; Hild, S.; Hoak, D.; Hofman, D.; Holt, K.; Holz, D. E.; Hopkins, P.; Horst, C.; Hough, J.; Houston, E. A.; Howell, E. J.; Hu, Y. M.; Huerta, E. A.; Huet, D.; Hughey, B.; Husa, S.; Huttner, S. H.; Huynh-Dinh, T.; Indik, N.; Ingram, D. R.; Inta, R.; Intini, G.; Isa, H. N.; Isac, J.-M.; Isi, M.; Iyer, B. R.; Izumi, K.; Jacqmin, T.; Jani, K.; Jaranowski, P.; Jawahar, S.; Jiménez-Forteza, F.; Johnson, W. W.; Jones, D. I.; Jones, R.; Jonker, R. J. G.; Ju, L.; Junker, J.; Kalaghatgi, C. V.; Kalogera, V.; Kandhasamy, S.; Kang, G.; Kanner, J. B.; Karki, S.; Karvinen, K. S.; Kasprzack, M.; Katolik, M.; Katsavounidis, E.; Katzman, W.; Kaufer, S.; Kawabe, K.; Kéfélian, F.; Keitel, D.; Kemball, A. J.; Kennedy, R.; Kent, C.; Key, J. S.; Khalili, F. Y.; Khan, I.; Khan, S.; Khan, Z.; Khazanov, E. A.; Kijbunchoo, N.; Kim, Chunglee; Kim, J. C.; Kim, W.; Kim, W. S.; Kim, Y.-M.; Kimbrell, S. J.; King, E. J.; King, P. J.; Kirchhoff, R.; Kissel, J. S.; Kleybolte, L.; Klimenko, S.; Koch, P.; Koehlenbeck, S. M.; Koley, S.; Kondrashov, V.; Kontos, A.; Korobko, M.; Korth, W. Z.; Kowalska, I.; Kozak, D. B.; Krämer, C.; Kringel, V.; Krishnan, B.; Królak, A.; Kuehn, G.; Kumar, P.; Kumar, R.; Kumar, S.; Kuo, L.; Kutynia, A.; Kwang, S.; Lackey, B. D.; Lai, K. H.; Landry, M.; Lang, R. N.; Lange, J.; Lantz, B.; Lanza, R. K.; Lartaux-Vollard, A.; Lasky, P. D.; Laxen, M.; Lazzarini, A.; Lazzaro, C.; Leaci, P.; Leavey, S.; Lee, C. H.; Lee, H. K.; Lee, H. M.; Lee, H. W.; Lee, K.; Lehmann, J.; Lenon, A.; Leonardi, M.; Leroy, N.; Letendre, N.; Levin, Y.; Li, T. G. F.; Libson, A.; Littenberg, T. B.; Liu, J.; Lo, R. K. L.; Lockerbie, N. A.; London, L. T.; Lord, J. E.; Lorenzini, M.; Loriette, V.; Lormand, M.; Losurdo, G.; Lough, J. D.; Lousto, C. O.; Lovelace, G.; Lück, H.; Lumaca, D.; Lundgren, A. P.; Lynch, R.; Ma, Y.; Macfoy, S.; Machenschalk, B.; MacInnis, M.; Macleod, D. M.; Magaña Hernandez, I.; Magaña-Sandoval, F.; Magaña Zertuche, L.; Magee, R. M.; Majorana, E.; Maksimovic, I.; Man, N.; Mandic, V.; Mangano, V.; Mansell, G. L.; Manske, M.; Mantovani, M.; Marchesoni, F.; Marion, F.; Márka, S.; Márka, Z.; Markakis, C.; Markosyan, A. S.; Maros, E.; Martelli, F.; Martellini, L.; Martin, I. W.; Martynov, D. V.; Mason, K.; Masserot, A.; Massinger, T. J.; Masso-Reid, M.; Mastrogiovanni, S.; Matas, A.; Matichard, F.; Matone, L.; Mavalvala, N.; Mazumder, N.; McCarthy, R.; McClelland, D. E.; McCormick, S.; McCuller, L.; McGuire, S. C.; McIntyre, G.; McIver, J.; McManus, D. J.; McRae, T.; McWilliams, S. T.; Meacher, D.; Meadors, G. D.; Meidam, J.; Mejuto-Villa, E.; Melatos, A.; Mendell, G.; Mercer, R. A.; Merilh, E. L.; Merzougui, M.; Meshkov, S.; Messenger, C.; Messick, C.; Metzdorff, R.; Meyers, P. M.; Mezzani, F.; Miao, H.; Michel, C.; Middleton, H.; Mikhailov, E. E.; Milano, L.; Miller, A. L.; Miller, A.; Miller, B. B.; Miller, J.; Millhouse, M.; Minazzoli, O.; Minenkov, Y.; Ming, J.; Mishra, C.; Mitra, S.; Mitrofanov, V. P.; Mitselmakher, G.; Mittleman, R.; Moggi, A.; Mohan, M.; Mohapatra, S. R. P.; Montani, M.; Moore, B. C.; Moore, C. J.; Moraru, D.; Moreno, G.; Morriss, S. R.; Mours, B.; Mow-Lowry, C. M.; Mueller, G.; Muir, A. W.; Mukherjee, Arunava; Mukherjee, D.; Mukherjee, S.; Mukund, N.; Mullavey, A.; Munch, J.; Muniz, E. A. M.; Murray, P. G.; Napier, K.; Nardecchia, I.; Naticchioni, L.; Nayak, R. K.; Nelemans, G.; Nelson, T. J. N.; Neri, M.; Nery, M.; Neunzert, A.; Newport, J. M.; Newton, G.; Ng, K. K. Y.; Nguyen, T. T.; Nichols, D.; Nielsen, A. B.; Nissanke, S.; Nitz, A.; Noack, A.; Nocera, F.; Nolting, D.; Normandin, M. E. N.; Nuttall, L. K.; Oberling, J.; Ochsner, E.; Oelker, E.; Ogin, G. H.; Oh, J. J.; Oh, S. H.; Ohme, F.; Oliver, M.; Oppermann, P.; Oram, Richard J.; O'Reilly, B.; Ormiston, R.; Ortega, L. F.; O'Shaughnessy, R.; Ottaway, D. J.; Overmier, H.; Owen, B. J.; Pace, A. E.; Page, J.; Page, M. A.; Pai, A.; Pai, S. A.; Palamos, J. R.; Palashov, O.; Palomba, C.; Pal-Singh, A.; Pan, H.; Pang, B.; Pang, P. T. H.; Pankow, C.; Pannarale, F.; Pant, B. C.; Paoletti, F.; Paoli, A.; Papa, M. A.; Paris, H. R.; Parker, W.; Pascucci, D.; Pasqualetti, A.; Passaquieti, R.; Passuello, D.; Patricelli, B.; Pearlstone, B. L.; Pedraza, M.; Pedurand, R.; Pekowsky, L.; Pele, A.; Penn, S.; Perez, C. J.; Perreca, A.; Perri, L. M.; Pfeiffer, H. P.; Phelps, M.; Piccinni, O. J.; Pichot, M.; Piergiovanni, F.; Pierro, V.; Pillant, G.; Pinard, L.; Pinto, I. M.; Pitkin, M.; Poggiani, R.; Popolizio, P.; Porter, E. K.; Post, A.; Powell, J.; Prasad, J.; Pratt, J. W. W.; Predoi, V.; Prestegard, T.; Prijatelj, M.; Principe, M.; Privitera, S.; Prix, R.; Prodi, G. A.; Prokhorov, L. G.; Puncken, O.; Punturo, M.; Puppo, P.; Pürrer, M.; Qi, H.; Qin, J.; Qiu, S.; Quetschke, V.; Quintero, E. A.; Quitzow-James, R.; Raab, F. J.; Rabeling, D. S.; Radkins, H.; Raffai, P.; Raja, S.; Rajan, C.; Rakhmanov, M.; Ramirez, K. E.; Rapagnani, P.; Raymond, V.; Razzano, M.; Read, J.; Regimbau, T.; Rei, L.; Reid, S.; Reitze, D. H.; Rew, H.; Reyes, S. D.; Ricci, F.; Ricker, P. M.; Rieger, S.; Riles, K.; Rizzo, M.; Robertson, N. A.; Robie, R.; Robinet, F.; Rocchi, A.; Rolland, L.; Rollins, J. G.; Roma, V. J.; Romano, J. D.; Romano, R.; Romel, C. L.; Romie, J. H.; Rosińska, D.; Ross, M. P.; Rowan, S.; Rüdiger, A.; Ruggi, P.; Ryan, K.; Sachdev, S.; Sadecki, T.; Sadeghian, L.; Sakellariadou, M.; Salconi, L.; Saleem, M.; Salemi, F.; Samajdar, A.; Sammut, L.; Sampson, L. M.; Sanchez, E. J.; Sandberg, V.; Sandeen, B.; Sanders, J. R.; Sassolas, B.; Saulson, P. R.; Sauter, O.; Savage, R. L.; Sawadsky, A.; Schale, P.; Scheuer, J.; Schmidt, E.; Schmidt, J.; Schmidt, P.; Schnabel, R.; Schofield, R. M. S.; Schönbeck, A.; Schreiber, E.; Schuette, D.; Schulte, B. W.; Schutz, B. F.; Schwalbe, S. G.; Scott, J.; Scott, S. M.; Seidel, E.; Sellers, D.; Sengupta, A. S.; Sentenac, D.; Sequino, V.; Sergeev, A.; Shaddock, D. A.; Shaffer, T. J.; Shah, A. A.; Shahriar, M. S.; Shao, L.; Shapiro, B.; Shawhan, P.; Sheperd, A.; Shoemaker, D. H.; Shoemaker, D. M.; Siellez, K.; Siemens, X.; Sieniawska, M.; Sigg, D.; Silva, A. D.; Singer, A.; Singer, L. P.; Singh, A.; Singh, R.; Singhal, A.; Sintes, A. M.; Slagmolen, B. J. J.; Smith, B.; Smith, J. R.; Smith, R. J. E.; Son, E. J.; Sonnenberg, J. A.; Sorazu, B.; Sorrentino, F.; Souradeep, T.; Spencer, A. P.; Srivastava, A. K.; Staley, A.; Steer, D. A.; Steinke, M.; Steinlechner, J.; Steinlechner, S.; Steinmeyer, D.; Stephens, B. C.; Stone, R.; Strain, K. A.; Stratta, G.; Strigin, S. E.; Sturani, R.; Stuver, A. L.; Summerscales, T. Z.; Sun, L.; Sunil, S.; Sutton, P. J.; Swinkels, B. L.; Szczepańczyk, M. J.; Tacca, M.; Talukder, D.; Tanner, D. B.; Tápai, M.; Taracchini, A.; Taylor, J. A.; Taylor, R.; Theeg, T.; Thomas, E. G.; Thomas, M.; Thomas, P.; Thorne, K. A.; Thorne, K. S.; Thrane, E.; Tiwari, S.; Tiwari, V.; Tokmakov, K. V.; Toland, K.; Tonelli, M.; Tornasi, Z.; Torrie, C. I.; Töyrä, D.; Travasso, F.; Traylor, G.; Trifirò, D.; Trinastic, J.; Tringali, M. C.; Trozzo, L.; Tsang, K. W.; Tse, M.; Tso, R.; Tuyenbayev, D.; Ueno, K.; Ugolini, D.; Unnikrishnan, C. S.; Urban, A. L.; Usman, S. A.; Vahlbruch, H.; Vajente, G.; Valdes, G.; Vallisneri, M.; van Bakel, N.; van Beuzekom, M.; van den Brand, J. F. J.; Van Den Broeck, C.; Vander-Hyde, D. C.; van der Schaaf, L.; van Heijningen, J. V.; van Veggel, A. A.; Vardaro, M.; Varma, V.; Vass, S.; Vasúth, M.; Vecchio, A.; Vedovato, G.; Veitch, J.; Veitch, P. J.; Venkateswara, K.; Venugopalan, G.; Verkindt, D.; Vetrano, F.; Viceré, A.; Viets, A. D.; Vinciguerra, S.; Vine, D. J.; Vinet, J.-Y.; Vitale, S.; Vo, T.; Vocca, H.; Vorvick, C.; Voss, D. V.; Vousden, W. D.; Vyatchanin, S. P.; Wade, A. R.; Wade, L. E.; Wade, M.; Walet, R.; Walker, M.; Wallace, L.; Walsh, S.; Wang, G.; Wang, H.; Wang, J. Z.; Wang, M.; Wang, Y.-F.; Wang, Y.; Ward, R. L.; Warner, J.; Was, M.; Watchi, J.; Weaver, B.; Wei, L.-W.; Weinert, M.; Weinstein, A. J.; Weiss, R.; Wen, L.; Wessel, E. K.; Weßels, P.; Westphal, T.; Wette, K.; Whelan, J. T.; Whiting, B. F.; Whittle, C.; Williams, D.; Williams, R. D.; Williamson, A. R.; Willis, J. L.; Willke, B.; Wimmer, M. H.; Winkler, W.; Wipf, C. C.; Wittel, H.; Woan, G.; Woehler, J.; Wofford, J.; Wong, K. W. K.; Worden, J.; Wright, J. L.; Wu, D. S.; Wu, G.; Yam, W.; Yamamoto, H.; Yancey, C. C.; Yap, M. J.; Yu, Hang; Yu, Haocun; Yvert, M.; ZadroŻny, A.; Zanolin, M.; Zelenova, T.; Zendri, J.-P.; Zevin, M.; Zhang, L.; Zhang, M.; Zhang, T.; Zhang, Y.-H.; Zhao, C.; Zhou, M.; Zhou, Z.; Zhu, S. J.; Zhu, X. J.; Zucker, M. E.; Zweizig, J.; LIGO Scientific Collaboration; Virgo Collaboration

2018-05-01

Cosmic strings are topological defects which can be formed in grand unified theory scale phase transitions in the early universe. They are also predicted to form in the context of string theory. The main mechanism for a network of Nambu-Goto cosmic strings to lose energy is through the production of loops and the subsequent emission of gravitational waves, thus offering an experimental signature for the existence of cosmic strings. Here we report on the analysis conducted to specifically search for gravitational-wave bursts from cosmic string loops in the data of Advanced LIGO 2015-2016 observing run (O1). No evidence of such signals was found in the data, and as a result we set upper limits on the cosmic string parameters for three recent loop distribution models. In this paper, we initially derive constraints on the string tension G μ and the intercommutation probability, using not only the burst analysis performed on the O1 data set but also results from the previously published LIGO stochastic O1 analysis, pulsar timing arrays, cosmic microwave background and big-bang nucleosynthesis experiments. We show that these data sets are complementary in that they probe gravitational waves produced by cosmic string loops during very different epochs. Finally, we show that the data sets exclude large parts of the parameter space of the three loop distribution models we consider.

Data-dependence Profiling to Enable Safe Thread Level Speculation

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

Bhattacharyya, Arnamoy; Amaral, José Nelson; Finkel, Hal

Data-dependence profling is a technique that enables a com- piler to judiciously decide when the execution of a loop | which the compiler could not prove to be dependence free | should be speculated through the use of Thread Level Spec- ulation (TLS). The data collected by a data-dependence pro- fler can be used to predict if may dependencies reported by a compiler static analysis are likely to materialize at runtime. A cost analysis can then be used to decide that some loops with a lower probability of dependence should be specula- tively parallelized. This paper addresses the question asmore » to whether a loops' dependence behaviour changes when the in- put to the program changes | a study of 57 different bench- marks indicates that it usually does not change. Then the paper describes SpecEval, an automatic speculative paral- lelization framework that uses single-input data-dependence profles to find speculation candidates in the SPEC2006 and PolyBench/C benchmarks. This paper also presents a per- formance evaluation of TLS implementation in IBM's Blue- Gene/Q supercomputer and shows that the performance of TLS is affected by several factors, including the number of speculated loops, the execution-time coverage of speculated loops, the miss-speculation overhead, the L1 cache miss rate and the effect on dynamic instruction path length.« less

Binding of DNA hairpins to an assembler-strand as part of a primordial translation device

NASA Astrophysics Data System (ADS)

Baumann, Ulrich

1987-09-01

A crucial event in the process leading to the origin of life is the emergence of a simple translation device. To approach experimental realization of this device the binding ability of short DNA hairpins to complementary oligonucleotides fixed on a solid support was investigated. The binding is achieved by base pairing between the loop nucleotides of the hairpins containing different numbers of adenosine residues and oligothymidylates covalently linked to cellulose. The loop has to consist of at least five nucleotides to achieve binding. The exact number of established base pairs was determined in two ways. First, the elution temperatures of hairpins and those of oligoadenylates which had the length of the loop were compared. Secondly, the architecture of the loop was analyzed by means of the single-strand-specific nuclease from mung bean acting as structural probe. Onlyn-2 of n loop nucleotides of a hairpin are able to form base pairs. Therefore, a strong evidence for the formation of a triplet of base pairs between primeval tRNA and mRNA sufficient to stabilize the complex enzyme-free is given.

Coronal rain in magnetic bipolar weak fields

NASA Astrophysics Data System (ADS)

Xia, C.; Keppens, R.; Fang, X.

2017-07-01

Aims: We intend to investigate the underlying physics for the coronal rain phenomenon in a representative bipolar magnetic field, including the formation and the dynamics of coronal rain blobs. Methods: With the MPI-AMRVAC code, we performed three dimensional radiative magnetohydrodynamic (MHD) simulation with strong heating localized on footpoints of magnetic loops after a relaxation to quiet solar atmosphere. Results: Progressive cooling and in-situ condensation starts at the loop top due to radiative thermal instability. The first large-scale condensation on the loop top suffers Rayleigh-Taylor instability and becomes fragmented into smaller blobs. The blobs fall vertically dragging magnetic loops until they reach low-β regions and start to fall along the loops from loop top to loop footpoints. A statistic study of the coronal rain blobs finds that small blobs with masses of less than 1010 g dominate the population. When blobs fall to lower regions along the magnetic loops, they are stretched and develop a non-uniform velocity pattern with an anti-parallel shearing pattern seen to develop along the central axis of the blobs. Synthetic images of simulated coronal rain with Solar Dynamics Observatory Atmospheric Imaging Assembly well resemble real observations presenting dark falling clumps in hot channels and bright rain blobs in a cool channel. We also find density inhomogeneities during a coronal rain "shower", which reflects the observed multi-stranded nature of coronal rain. Movies associated to Figs. 3 and 7 are available at http://www.aanda.org

Prominence condensation and magnetic levitation in a coronal loop

NASA Technical Reports Server (NTRS)

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

1992-01-01

The results of a model dynamic simulation of the formation and support of a narrow prominence at the apex of a coronal magnetic loop or arcade are described. The condensation process proceeds via an initial radiative cooling and pressure drop, and a secondary siphon flow from the dense chromospheric ends. The antibuoyancy effect as the prominence forms causes a bending of the confining magnetic field, which propagates toward the semirigid ends of the magnetic loop. Thus, a wide magnetic 'hammock' or well (of the normal-polarity Kippenhahn-Schlueter-type) is formed, which supports the prominence at or near the field apex. The simplicity of this 1.5-dimensional model, with its accompanying diagnostics, elucidates the various contributions to the nonlinear dynamics of prominence condensation and levitation.

Funneled potential and flux landscapes dictate the stabilities of both the states and the flow: Fission yeast cell cycle.

PubMed

Luo, Xiaosheng; Xu, Liufang; Han, Bo; Wang, Jin

2017-09-01

Using fission yeast cell cycle as an example, we uncovered that the non-equilibrium network dynamics and global properties are determined by two essential features: the potential landscape and the flux landscape. These two landscapes can be quantified through the decomposition of the dynamics into the detailed balance preserving part and detailed balance breaking non-equilibrium part. While the funneled potential landscape is often crucial for the stability of the single attractor networks, we have uncovered that the funneled flux landscape is crucial for the emergence and maintenance of the stable limit cycle oscillation flow. This provides a new interpretation of the origin for the limit cycle oscillations: There are many cycles and loops existed flowing through the state space and forming the flux landscapes, each cycle with a probability flux going through the loop. The limit cycle emerges when a loop stands out and carries significantly more probability flux than other loops. We explore how robustness ratio (RR) as the gap or steepness versus averaged variations or roughness of the landscape, quantifying the degrees of the funneling of the underlying potential and flux landscapes. We state that these two landscapes complement each other with one crucial for stabilities of states on the cycle and the other crucial for the stability of the flow along the cycle. The flux is directly related to the speed of the cell cycle. This allows us to identify the key factors and structure elements of the networks in determining the stability, speed and robustness of the fission yeast cell cycle oscillations. We see that the non-equilibriumness characterized by the degree of detailed balance breaking from the energy pump quantified by the flux is the cause of the energy dissipation for initiating and sustaining the replications essential for the origin and evolution of life. Regulating the cell cycle speed is crucial for designing the prevention and curing strategy of cancer.

Funneled potential and flux landscapes dictate the stabilities of both the states and the flow: Fission yeast cell cycle

PubMed Central

2017-01-01

Using fission yeast cell cycle as an example, we uncovered that the non-equilibrium network dynamics and global properties are determined by two essential features: the potential landscape and the flux landscape. These two landscapes can be quantified through the decomposition of the dynamics into the detailed balance preserving part and detailed balance breaking non-equilibrium part. While the funneled potential landscape is often crucial for the stability of the single attractor networks, we have uncovered that the funneled flux landscape is crucial for the emergence and maintenance of the stable limit cycle oscillation flow. This provides a new interpretation of the origin for the limit cycle oscillations: There are many cycles and loops existed flowing through the state space and forming the flux landscapes, each cycle with a probability flux going through the loop. The limit cycle emerges when a loop stands out and carries significantly more probability flux than other loops. We explore how robustness ratio (RR) as the gap or steepness versus averaged variations or roughness of the landscape, quantifying the degrees of the funneling of the underlying potential and flux landscapes. We state that these two landscapes complement each other with one crucial for stabilities of states on the cycle and the other crucial for the stability of the flow along the cycle. The flux is directly related to the speed of the cell cycle. This allows us to identify the key factors and structure elements of the networks in determining the stability, speed and robustness of the fission yeast cell cycle oscillations. We see that the non-equilibriumness characterized by the degree of detailed balance breaking from the energy pump quantified by the flux is the cause of the energy dissipation for initiating and sustaining the replications essential for the origin and evolution of life. Regulating the cell cycle speed is crucial for designing the prevention and curing strategy of cancer. PMID:28892489

Analysis of an Attenuator Artifact in an Experimental Attack by Gunn-Allison-Abbott Against the Kirchhoff-Law-Johnson-Noise (KLJN) Secure Key Exchange System

NASA Astrophysics Data System (ADS)

Kish, Laszlo B.; Gingl, Zoltan; Mingesz, Robert; Vadai, Gergely; Smulko, Janusz; Granqvist, Claes-Göran

2015-12-01

A recent paper by Gunn-Allison-Abbott (GAA) [L. J. Gunn et al., Scientific Reports 4 (2014) 6461] argued that the Kirchhoff-law-Johnson-noise (KLJN) secure key exchange system could experience a severe information leak. Here we refute their results and demonstrate that GAA's arguments ensue from a serious design flaw in their system. Specifically, an attenuator broke the single Kirchhoff-loop into two coupled loops, which is an incorrect operation since the single loop is essential for the security in the KLJN system, and hence GAA's asserted information leak is trivial. Another consequence is that a fully defended KLJN system would not be able to function due to its built-in current-comparison defense against active (invasive) attacks. In this paper we crack GAA's scheme via an elementary current-comparison attack which yields negligible error probability for Eve even without averaging over the correlation time of the noise.

An Iterative Information-Reduced Quadriphase-Shift-Keyed Carrier Synchronization Scheme Using Decision Feedback for Low Signal-to-Noise Ratio Applications

NASA Technical Reports Server (NTRS)

Simon, M.; Tkacenko, A.

2006-01-01

In a previous publication [1], an iterative closed-loop carrier synchronization scheme for binary phase-shift keyed (BPSK) modulation was proposed that was based on feeding back data decisions to the input of the loop, the purpose being to remove the modulation prior to carrier synchronization as opposed to the more conventional decision-feedback schemes that incorporate such feedback inside the loop. The idea there was that, with sufficient independence between the received data and the decisions on it that are fed back (as would occur in an error-correction coding environment with sufficient decoding delay), a pure tone in the presence of noise would ultimately be produced (after sufficient iteration and low enough error probability) and thus could be tracked without any squaring loss. This article demonstrates that, with some modification, the same idea of iterative information reduction through decision feedback can be applied to quadrature phase-shift keyed (QPSK) modulation, something that was mentioned in the previous publication but never pursued.

Conceptual model of sedimentation in the Sacramento-San Joaquin River Delta

USGS Publications Warehouse

Schoellhamer, David H.; Wright, Scott A.; Drexler, Judith Z.

2012-01-01

Sedimentation in the Sacramento–San Joaquin River Delta builds the Delta landscape, creates benthic and pelagic habitat, and transports sediment-associated contaminants. Here we present a conceptual model of sedimentation that includes submodels for river supply from the watershed to the Delta, regional transport within the Delta and seaward exchange, and local sedimentation in open water and marsh habitats. The model demonstrates feedback loops that affect the Delta ecosystem. Submerged and emergent marsh vegetation act as ecosystem engineers that can create a positive feedback loop by decreasing suspended sediment, increasing water column light, which in turn enables more vegetation. Sea-level rise in open water is partially countered by a negative feedback loop that increases deposition if there is a net decrease in hydrodynamic energy. Manipulation of regional sediment transport is probably the most feasible method to control suspended sediment and thus turbidity. The conceptual model is used to identify information gaps that need to be filled to develop an accurate sediment transport model.

Coherent 40-Hz Oscillation Characterizes Dream State in Humans

NASA Astrophysics Data System (ADS)

Llinas, Rodolfo; Ribary, Urs

1993-03-01

Magnetic recording from five normal human adults demonstrates large 40-Hz coherent magnetic activity in the awake and in rapid-eye-movement (REM) sleep states that is very reduced during delta sleep (deep sleep characterized by delta waves in the electroencephalogram). This 40-Hz magnetic oscillation has been shown to be reset by sensory stimuli in the awake state. Such resetting is not observed during REM or delta sleep. The 40 Hz in REM sleep is characterized, as is that in the awake state, by a fronto-occiptal phase shift over the head. This phase shift has a maximum duration of thickapprox12-13 msec. Because 40-Hz oscillation is seen in wakefulness and in dreaming, we propose it to be a correlate of cognition, probably resultant from coherent 40-Hz resonance between thalamocortical-specific and nonspecific loops. Moreover, we proposed that the specific loops give the content of cognition, and a nonspecific loop gives the temporal binding required for the unity of cognitive experience.

Geologic implications of the Apollo 14 Fra Mauro breccias and comparison with ejecta from the Ries Crater, Germany

USGS Publications Warehouse

Chao, E.C.T.

1973-01-01

On the basis of petrographic and laboratory and active seismic data for the Fra Mauro breccias, and by comparison with the nature and distribution of the ejecta from the Ries crater, Germany, some tentative conclusions regarding the geologic significance of the Fra Mauro Formation on the moon can be drawn. The Fra Mauro Formation, as a whole, consists of unwcldcd, porous ejecta, slightly less porous than the regolith. It contains hand-specimen and larger size clasts of strongly annealed complex breccias, partly to slightly annealed breccias, basalts, and perhaps spherule-rich breccias. These clasts are embedded in a matrix of porous aggregate dominated by mineral and breccia fragments and probably largely free of undevitrified glass. All strongly annealed hand-specimen-size breccias are clasts in the Fra Mauro Formation. To account for the porous, unwelded state of the Fra Mauro Formation, the ejecta must have been deposited at a temperature below that required for welding and annealing. Large boulders probably compacted by the Cone crater event occur near the rim of the crater. They probably consist of a similar suite of fragments, but are probably less porous than the formation. The geochronologic clocks of fragments in the Fra Mauro Formation, with textures ranging from unannealed to strongly annealed, were not reset or strongly modified by the Imbrian event. Strongly annealed breccia clasts and basalt clasts are pre-Imbrian, and probably existed as ejecta mixed with basalt flows in the Imbrium Basin prior to the Imbrian event. The Imbrian event probably occurred between 3.90 or 3.88 and 3.65 b.y. ago.

A Graphical Method for Estimation of Barometric Efficiency from Continuous Data - Concepts and Application to a Site in the Piedmont, Air Force Plant 6, Marietta, Georgia

USGS Publications Warehouse

Gonthier, Gerard

2007-01-01

A graphical method that uses continuous water-level and barometric-pressure data was developed to estimate barometric efficiency. A plot of nearly continuous water level (on the y-axis), as a function of nearly continuous barometric pressure (on the x-axis), will plot as a line curved into a series of connected elliptical loops. Each loop represents a barometric-pressure fluctuation. The negative of the slope of the major axis of an elliptical loop will be the ratio of water-level change to barometric-pressure change, which is the sum of the barometric efficiency plus the error. The negative of the slope of the preferred orientation of many elliptical loops is an estimate of the barometric efficiency. The slope of the preferred orientation of many elliptical loops is approximately the median of the slopes of the major axes of the elliptical loops. If water-level change that is not caused by barometric-pressure change does not correlate with barometric-pressure change, the probability that the error will be greater than zero will be the same as the probability that it will be less than zero. As a result, the negative of the median of the slopes for many loops will be close to the barometric efficiency. The graphical method provided a rapid assessment of whether a well was affected by barometric-pressure change and also provided a rapid estimate of barometric efficiency. The graphical method was used to assess which wells at Air Force Plant 6, Marietta, Georgia, had water levels affected by barometric-pressure changes during a 2003 constant-discharge aquifer test. The graphical method was also used to estimate barometric efficiency. Barometric-efficiency estimates from the graphical method were compared to those of four other methods: average of ratios, median of ratios, Clark, and slope. The two methods (the graphical and median-of-ratios methods) that used the median values of water-level change divided by barometric-pressure change appeared to be most resistant to error caused by barometric-pressure-independent water-level change. The graphical method was particularly resistant to large amounts of barometric-pressure-independent water-level change, having an average and standard deviation of error for control wells that was less than one-quarter that of the other four methods. When using the graphical method, it is advisable that more than one person select the slope or that the same person fits the same data several times to minimize the effect of subjectivity. Also, a long study period should be used (at least 60 days) to ensure that loops affected by large amounts of barometric-pressure-independent water-level change do not significantly contribute to error in the barometric-efficiency estimate.

Neural network disturbance observer-based distributed finite-time formation tracking control for multiple unmanned helicopters.

PubMed

Wang, Dandan; Zong, Qun; Tian, Bailing; Shao, Shikai; Zhang, Xiuyun; Zhao, Xinyi

2018-02-01

The distributed finite-time formation tracking control problem for multiple unmanned helicopters is investigated in this paper. The control object is to maintain the positions of follower helicopters in formation with external interferences. The helicopter model is divided into a second order outer-loop subsystem and a second order inner-loop subsystem based on multiple-time scale features. Using radial basis function neural network (RBFNN) technique, we first propose a novel finite-time multivariable neural network disturbance observer (FMNNDO) to estimate the external disturbance and model uncertainty, where the neural network (NN) approximation errors can be dynamically compensated by adaptive law. Next, based on FMNNDO, a distributed finite-time formation tracking controller and a finite-time attitude tracking controller are designed using the nonsingular fast terminal sliding mode (NFTSM) method. In order to estimate the second derivative of the virtual desired attitude signal, a novel finite-time sliding mode integral filter is designed. Finally, Lyapunov analysis and multiple-time scale principle ensure the realization of control goal in finite-time. The effectiveness of the proposed FMNNDO and controllers are then verified by numerical simulations. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

The role of synaptotagmin I C2A calcium-binding domain in synaptic vesicle clustering during synapse formation

PubMed Central

Gardzinski, Peter; Lee, David W K; Fei, Guang-He; Hui, Kwokyin; Huang, Guan J; Sun, Hong-Shuo; Feng, Zhong-Ping

2007-01-01

Synaptic vesicles aggregate at the presynaptic terminal during synapse formation via mechanisms that are poorly understood. Here we have investigated the role of the putative calcium sensor synaptotagmin I in vesicle aggregation during the formation of soma–soma synapses between identified partner cells using a simple in vitro synapse model in the mollusc Lymnaea stagnalis. Immunocytochemistry, optical imaging and electrophysiological recording techniques were used to monitor synapse formation and vesicle localization. Within 6 h, contact between appropriate synaptic partner cells up-regulated global synaptotagmin I expression, and induced a localized aggregation of synaptotagmin I at the contact site. Cell contacts between non-synaptic partner cells did not affect synaptotagmin I expression. Application of an human immunodeficiency virus type-1 transactivator (HIV-1 TAT)-tagged peptide corresponding to loop 3 of the synaptotagmin I C2A domain prevented synaptic vesicle aggregation and synapse formation. By contrast, a TAT-tagged peptide containing the calcium-binding motif of the C2B domain did not affect synaptic vesicle aggregation or synapse formation. Calcium imaging with Fura-2 demonstrated that TAT–C2 peptides did not alter either basal or evoked intracellular calcium levels. These results demonstrate that contact with an appropriate target cell is necessary to initiate synaptic vesicle aggregation during nascent synapse formation and that the initial aggregation of synaptic vesicles is dependent on loop 3 of the C2A domain of synaptotagmin I. PMID:17317745

Multiple roles of mobile active center loops in the E1 component of the Escherichia coli pyruvate dehydrogenase complex - Linkage of protein dynamics to catalysis

PubMed Central

Jordan, Frank; Arjunan, Palaniappa; Kale, Sachin; Nemeria, Natalia S.; Furey, William

2009-01-01

The region encompassing residues 401–413 on the E1 component of the pyruvate dehydrogenase multienzyme complex from Escherichia coli comprises a loop (the inner loop) which was not seen in the X-ray structure in the presence of thiamin diphosphate, the required cofactor for the enzyme. This loop is seen in the presence of a stable analogue of the pre-decarboxylation intermediate, the covalent adduct between the substrate analogue methyl acetylphosphonate and thiamin diphosphate, C2α-phosphonolactylthiamin diphosphate. It has been shown that the residue H407 and several other residues on this loop are required to reduce the mobility of the loop so electron density corresponding to it can be seen once the pre-decarboxylation intermediate is formed. Concomitantly, the loop encompassing residues 541–557 (the outer loop) appears to work in tandem with the inner loop and there is a hydrogen bond between the two loops ensuring their correlated motion. The inner loop was shown to: a) sequester the active center from carboligase side reactions; b) assist the interaction between the E1 and the E2 components, thereby affecting the overall reaction rate of the entire multienzyme complex; c) control substrate access to the active center. Using viscosity effects on kinetics it was shown that formation of the pre-decarboxylation intermediate is specifically affected by loop movement. A cysteine-less variant was created for the E1 component, onto which cysteines were substituted at selected loop positions. Introducing an electron spin resonance spin label and an 19F NMR label onto these engineered cysteines, the loop mobility was examined: a) both methods suggested that in the absence of ligand, the loop exists in two conformations; b) line-shape analysis of the NMR signal at different temperatures, enabled estimation of the rate constant for loop movement, and this rate constant was found to be of the same order of magnitude as the turnover number for the enzyme under the same conditions. Furthermore, this analysis gave important insights into rate-limiting thermal loop dynamics. Overall, the results suggest that the dynamic properties correlate with catalytic events on the E1 component of the pyruvate dehydrogenase complex. PMID:20160956

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

Michael, Alicia K.; Fribourgh, Jennifer L.; Chelliah, Yogarany

The basic helix-loop-helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ~24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here in this paper, we show that CRY1 binds directly to the PAS domain core of CLOCK: BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solutionmore » X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1.« less

DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation

PubMed Central

Boedicker, James Q.; Garcia, Hernan G.; Johnson, Stephanie; Phillips, Rob

2014-01-01

As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as through nucleosome positioning. Here we examine the sequence-dependent flexibility of DNA in bacterial transcription factor-mediated looping, a context for which the role of sequence remains poorly understood. Using a suite of synthetic constructs repressed by the Lac repressor and two well-known sequences that show large flexibility differences in vitro, we make precise statistical mechanical predictions as to how DNA sequence influences loop formation and test these predictions using in vivo transcription and in vitro single-molecule assays. Surprisingly, sequence-dependent flexibility does not affect in vivo gene regulation. By theoretically and experimentally quantifying the relative contributions of sequence and the DNA-bending protein HU to DNA mechanical properties, we reveal that bending by HU dominates DNA mechanics and masks intrinsic sequence-dependent flexibility. Such a quantitative understanding of how mechanical regulatory information is encoded in the genome will be a key step towards a predictive understanding of gene regulation at single-base pair resolution. PMID:24231252

Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake.

PubMed

Yildiz, Ozkan; Kalthoff, Christoph; Raunser, Stefan; Kühlbrandt, Werner

2007-01-24

A binary complex of the ammonia channel Amt1 from Methanococcus jannaschii and its cognate P(II) signalling protein GlnK1 has been produced and characterized. Complex formation is prevented specifically by the effector molecules Mg-ATP and 2-ketoglutarate. Single-particle electron microscopy of the complex shows that GlnK1 binds on the cytoplasmic side of Amt1. Three high-resolution X-ray structures of GlnK1 indicate that the functionally important T-loop has an extended, flexible conformation in the absence of Mg-ATP, but assumes a compact, tightly folded conformation upon Mg-ATP binding, which in turn creates a 2-ketoglutarate-binding site. We propose a regulatory mechanism by which nitrogen uptake is controlled by the binding of both effector molecules to GlnK1. At normal effector levels, a 2-ketoglutarate molecule binding at the apex of the compact T-loop would prevent complex formation, ensuring uninhibited ammonia uptake. At low levels of Mg-ATP, the extended loops would seal the ammonia channels in the complex. Binding of both effector molecules to P(II) signalling proteins may thus represent an effective feedback mechanism for regulating ammonium uptake through the membrane.

A numerical simulation of magnetic reconnection and radiative cooling in line-tied current sheets

NASA Technical Reports Server (NTRS)

Forbes, T. G.; Malherbe, J. M.

1991-01-01

Radiative MHD equations are used for an optically thin plasma to carry out a numerical experiment related to the formation of 'postflare' loops. The numerical experiment starts with a current sheet that is in mechanical and thermal equilibrium but is unstable to both tearing-mode and thermal-condensation instabilities. The current sheet is line-tied at one end to a photospheric-like boundary and evolves asymmetrically. The effects of thermal conduction, resistivity variation, and gravity are ignored. In general, reconnection in the nonlinear stage of the tearing-mode instability can strongly affect the onset of condensations unless the radiative-cooling time scale is much smaller than the tearing-mode time scale. When the ambient plasma is less than 0.2, the reconnection enters a regime where the outflow from the reconnection region is supermagnetosonic with respect to the fast-mode wave speed. In the supermagnetosonic regime the most rapidly condensing regions occur downstream of a fast-mode shock that forms where the outflow impinges on closed loops attached to the photospheric-like boundary. A similar shock-induced condensation might occur during the formation of 'postflare' loops.

Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment

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

Ling, Jiqiang; Peterson, Kaitlyn M.; Simonovic, Ivana

2014-03-12

Aminoacyl-tRNA synthetases (aaRSs) ensure faithful translation of mRNA into protein by coupling an amino acid to a set of tRNAs with conserved anticodon sequences. Here, we show that in mitochondria of Saccharomyces cerevisiae, a single aaRS (MST1) recognizes and aminoacylates two natural tRNAs that contain anticodon loops of different size and sequence. Besides a regular ?? with a threonine (Thr) anticodon, MST1 also recognizes an unusual ??, which contains an enlarged anticodon loop and an anticodon triplet that reassigns the CUN codons from leucine to threonine. Our data show that MST1 recognizes the anticodon loop in both tRNAs, but employsmore » distinct recognition mechanisms. The size but not the sequence of the anticodon loop is critical for ?? recognition, whereas the anticodon sequence is essential for aminoacylation of ??. The crystal structure of MST1 reveals that, while lacking the N-terminal editing domain, the enzyme closely resembles the bacterial threonyl-tRNA synthetase (ThrRS). A detailed structural comparison with Escherichia coli ThrRS, which is unable to aminoacylate ??, reveals differences in the anticodon-binding domain that probably allow recognition of the distinct anticodon loops. Finally, our mutational and modeling analyses identify the structural elements in MST1 (e.g., helix {alpha}11) that define tRNA selectivity. Thus, MTS1 exemplifies that a single aaRS can recognize completely divergent anticodon loops of natural isoacceptor tRNAs and that in doing so it facilitates the reassignment of the genetic code in yeast mitochondria.« less

Adsorptive behavior and solid-phase microextraction of bare stainless steel sample loop in high performance liquid chromatography.

PubMed

Zhang, Wenpeng; Zhang, Zixin; Meng, Jiawei; Zhou, Wei; Chen, Zilin

2014-10-24

In this work, we interestingly happened to observe the adsorption of stainless steel sample loop of HPLC. The adsorptive behaviors of the stainless steel loop toward different kinds of compounds were studied, including polycyclic aromatic hydrocarbons (PAHs), halogeno benzenes, aniline derivatives, benzoic acid derivatives, phenols, benzoic acid ethyl ester, benzaldehyde, 1-phenyl-ethanone and phenethyl alcohol. The adsorptive mechanism was probably related to hydrophobic interaction, electron-rich element-metal interaction and hydrogen bond. Universal adsorption of stainless steels was also testified. Inspired by its strong adsorptive capability, bare stainless steel loop was developed as a modification-free in-tube device for solid-phase microextraction (SPME), which served as both the substrate and sorbent and possessed ultra-high strength and stability. Great extraction efficiency toward PAHs was obtained by stainless steel loop without any modification, with enrichment factors of 651-834. By connecting the stainless steel loop onto a six-port valve, an online SPME-HPLC system was set up and an SPME-HPLC method has been validated for determination of PAHs. The method has exceptionally low limits of detection of 0.2-2pg/mL, which is significantly lower than that of reported methods with different kinds of sorbents. Wide linear range (0.5-500 and 2-1000pg/mL), good linearity (R(2)≥0.9987) and good reproducibility (RSD≤2.9%) were also obtained. The proposed method has been applied to determine PAHs in environmental samples. Good recoveries were obtained, ranging from 88.5% to 93.8%. Copyright © 2014 Elsevier B.V. All rights reserved.

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

PubMed Central

2017-01-01

Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult. Predictions of RNA tertiary structure tend to be least accurate in loop regions, where non-canonical pairs are important for determining the details of structure. Non-canonical pairs can be predicted using a knowledge-based model of structure that scores nucleotide cyclic motifs, or NCMs. In this work, a partition function algorithm is introduced that allows the estimation of base pairing probabilities for both canonical and non-canonical interactions. Pairs that are predicted to be probable are more likely to be found in the true structure than pairs of lower probability. Pair probability estimates can be further improved by predicting the structure conserved across multiple homologous sequences using the TurboFold algorithm. These pairing probabilities, used in concert with prior knowledge of the canonical secondary structure, allow accurate inference of non-canonical pairs, an important step towards accurate prediction of the full tertiary structure. Software to predict non-canonical base pairs and pairing probabilities is now provided as part of the RNAstructure software package. PMID:29107980

Disturbed P53-MDM2 Feedback Loop Contributes to Thoracic Aortic Dissection Formation and May be a Result of TRIM25 Overexpression.

PubMed

Gong, Bin; Wang, Zhiwei; Zhang, Min; Hu, Zhipeng; Ren, Zongli; Tang, Zheng; Jiang, Wanli; Cheng, Lianghao; Huang, Jun; Ren, Wei; Wang, Qingtao

2017-04-01

The development of thoracic aortic dissection (TAD) is attributed to a broad range of degenerative, genetic, structural, oxidative, apoptotic, and acquired disease states. In this study, we examined the role of the disturbed p53-MDM2 (murine double minute 2) feedback loop in the formation of TAD, and one of a potential feedback loop regulator, TRIM25 (tripartite motif protein-25). Surgical specimens of the aorta from TAD patients (n = 10) and controls (n = 10) were tested for α-smooth muscle actin (α-SMA), p53, MDM2, and TRIM25 by western blot, immunohistochemical staining, and quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR), respectively. When compared with controls, western blot shows that the protein levels of p53, MDM2, and TRIM25 were increased significantly in the aortic media of TAD patients. qRT-PCR further verified that the mRNA expression of MDM2 and TRIM25 was also increased 6- and 4-folds, respectively, in the TAD media of the aortic wall. Immunohistochemistry results showed significantly decreased staining of α-SMA, smooth muscle cells, and more collagen deposition in the media of the aortic wall from patients with TAD. This study provided a new insight into the disturbed p53-MDM2 feedback loop in the pathogenesis of TAD, and this may be because of the TRIM25 overexpression. Copyright © 2016 Elsevier Inc. All rights reserved.

Dynamics of quiescent prominences; Proceedings of the 117th Colloquium of IAU, Hvar, Yugoslavia, Sept. 25-29, 1989

NASA Technical Reports Server (NTRS)

Ruzdjak, Vladimir (Editor); Tandberg-Hanssen, Einar (Editor)

1990-01-01

Topics discussed include formation of a filament around a magnetic region, evolution of fine structures in a filament, the spatial distribution of prominence threads, high resolution analysis of quiescent prominences at NSO/Sacramento Peak Observatory, small-scale Doppler velocities in a quiescent prominence, Doppler velocity oscillations in quiescent prominences, oscillatory relaxation of an eruptive prominence, and matter flow velocities in an active region emission loop observed in H-alpha. Attention is also given to an automated procedure for measurement of prominence transverse velocities, the nonlinear evolution of magnetized filaments, thermal equilibrium of coronal loops and prominence formation, thermal instability in planar coronal strucutres, radiative transfer in cylindrical prominence threads, numerical simulation of a catastrophe model for prominence eruptions, and the law of evolution and destruction of solar prominences.

MHD Modelling of Coronal Loops: Injection of High-Speed Chromospheric Flows

NASA Technical Reports Server (NTRS)

Petralia, A.; Reale, F.; Orlando, S.; Klimchuk, J. A.

2014-01-01

Context. Observations reveal a correspondence between chromospheric type II spicules and bright upward-moving fronts in the corona observed in the extreme-ultraviolet (EUV) band. However, theoretical considerations suggest that these flows are probably not the main source of heating in coronal magnetic loops. Aims. We investigate the propagation of high-speed chromospheric flows into coronal magnetic flux tubes and the possible production of emission in the EUV band. Methods. We simulated the propagation of a dense 104 K chromospheric jet upward along a coronal loop by means of a 2D cylindrical MHD model that includes gravity, radiative losses, thermal conduction, and magnetic induction. The jet propagates in a complete atmosphere including the chromosphere and a tenuous cool (approximately 0.8 MK) corona, linked through a steep transition region. In our reference model, the jet initial speed is 70 km per second, its initial density is 10(exp 11) per cubic centimeter, and the ambient uniform magnetic field is 10 G. We also explored other values of jet speed and density in 1D and different magnetic field values in 2D, as well as the jet propagation in a hotter (approximately 1.5 MK) background loop. Results. While the initial speed of the jet does not allow it to reach the loop apex, a hot shock-front develops ahead of it and travels to the other extreme of the loop. The shock front compresses the coronal plasma and heats it to about 10(exp 6) K. As a result, a bright moving front becomes visible in the 171 Angstrom channel of the SDO/AIA mission. This result generally applies to all the other explored cases, except for the propagation in the hotter loop. Conclusions. For a cool, low-density initial coronal loop, the post-shock plasma ahead of upward chromospheric flows might explain at least part of the observed correspondence between type II spicules and EUV emission excess.

Association of a peptoid ligand with the apical loop of pri-miR-21 inhibits cleavage by Drosha

PubMed Central

Diaz, Jason P.; Chirayil, Rachel; Chirayil, Sara; Tom, Martin; Head, Katie J.; Luebke, Kevin J.

2014-01-01

We have found a small molecule that specifically inhibits cleavage of a precursor to the oncogenic miRNA, miR-21, by the microprocessor complex of Drosha and DGCR8. We identified novel ligands for the apical loop of this precursor from a screen of 14,024 N-substituted oligoglycines (peptoids) in a microarray format. Eight distinct compounds with specific affinity were obtained, three having affinities for the targeted loop in the low micromolar range and greater than 15-fold discrimination against a closely related hairpin. One of these compounds completely inhibits microprocessor cleavage of a miR-21 primary transcript at concentrations at which cleavage of another miRNA primary transcript, pri-miR-16, is little affected. The apical loop of pri-miR-21, placed in the context of pri-miR-16, is sufficient for inhibition of microprocessor cleavage by the peptoid. This compound also inhibits cleavage of pri-miR-21 containing the pri-miR-16 apical loop, suggesting an additional site of association within pri-miR-21. The reported peptoid is the first example of a small molecule that inhibits microprocessor cleavage by binding to the apical loop of a pri-miRNA. PMID:24497550

Damage structures in fission-neutron irradiated Ni-based alloys at high temperatures

NASA Astrophysics Data System (ADS)

Yamakawa, K.; Shimomura, Y.

1999-01-01

The defects formed in Ni based (Ni-Si, Ni-Cu and Ni-Fe) alloys which were irradiated with fission-neutrons were examined by electron microscopy. Irradiations were carried out at 473 K and 573 K. In the 473 K irradiated specimens, a high density of large interstitial loops and small vacancy clusters with stacking fault tetrahedra (SFT) were observed. The number densities of these two types of defects did not strongly depend on the amount of solute atoms in each alloy. The density of the loops in Ni-Si alloys was much higher than those in Ni-Cu and Ni-Fe alloys, while the density of SFT only slightly depended on the kind of solute. Also, the size of the loops depended on the kinds and amounts of solute. In 573 K irradiated Ni-Cu specimens, a high density of dislocation lines developed during the growth of interstitial loops. In Ni-Si alloys, the number density and size of the interstitial loops changed as a function of the amount of solute. Voids were formed in Ni-Cu alloys but scarcely formed in Ni-Si alloys. The number density of voids was one hundredth of that of SFT observed in 473 K irradiated Ni-Cu alloys. Possible formation processes of interstitial loops, SFT dislocation lines and voids are discussed.

Recombination and synaptic adjustment in oocytes of mice heterozygous for a large paracentric inversion.

PubMed

Torgasheva, Anna A; Rubtsov, Nikolai B; Borodin, Pavel M

2013-03-01

Homologous chromosome synapsis in inversion heterozygotes results in the formation of inversion loops. These loops might be transformed into straight, non-homologously paired bivalents via synaptic adjustment. Synaptic adjustment was discovered 30 years ago; however, its relationship with recombination has remained unclear. We analysed this relationship in female mouse embryos heterozygous for large paracentric inversion In(1)1Rk using immunolocalisation of the synaptonemal complex (SYCP3) and mature recombination nodules (MLH1) proteins. The frequency of cells containing bivalents with inversion loops decreased from 69 % to 28 % during pachytene. If an MLH1 focus was present in the non-homologously paired inverted region of the straight bivalent, it was always located in the middle of the inversion. Most of the small, incompletely adjusted loops contained MLH1 foci near the points at which pairing partners were switched. This observation indicates that the degree of synaptic adjustment depended on the crossover position. Complete synaptic adjustment was only possible if a crossover (CO) was located exactly in the middle of the inversion. If a CO was located at any other site, this interrupted synaptic adjustment and resulted in inversion loops of different sizes with an MLH1 focus at or near the edge of the remaining loop.

Identification of Bacillus thuringiensis Cry3Aa toxin domain II loop 1 as the binding site of Tenebrio molitor cadherin repeat CR12.

PubMed

Zúñiga-Navarrete, Fernando; Gómez, Isabel; Peña, Guadalupe; Amaro, Itzel; Ortíz, Ernesto; Becerril, Baltazar; Ibarra, Jorge E; Bravo, Alejandra; Soberón, Mario

2015-04-01

Bacillus thuringiensis Cry toxins exert their toxic effect by specific recognition of larval midgut proteins leading to oligomerization of the toxin, membrane insertion and pore formation. The exposed domain II loop regions of Cry toxins have been shown to be involved in receptor binding. Insect cadherins have shown to be functionally involved in toxin binding facilitating toxin oligomerization. Here, we isolated a VHH (VHHA5) antibody by phage display that binds Cry3Aa loop 1 and competed with the binding of Cry3Aa to Tenebrio molitor brush border membranes. VHHA5 also competed with the binding of Cry3Aa to a cadherin fragment (CR12) that was previously shown to be involved in binding and toxicity of Cry3Aa, indicating that Cry3Aa binds CR12 through domain II loop 1. Moreover, we show that a loop 1 mutant, previously characterized to have increased toxicity to T. molitor, displayed a correlative enhanced binding affinity to T. molitor CR12 and to VHHA5. These results show that Cry3Aa domain II loop 1 is a binding site of CR12 T. molitor cadherin. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

Wemmer, D.E.; Kumar, N.V.; Metrione, R.M.

Toxin II from Radianthus paumotensis (Rp/sub II/) has been investigated by high-resolution NMR and chemical sequencing methods. Resonance assignments have been obtained for this protein by the sequential approach. NMR assignments could not be made consistent with the previously reported primary sequence for this protein, and chemical methods have been used to determine a sequence with which the NMR data are consistent. Analysis of the 2D NOE spectra shows that the protein secondary structure is comprised of two sequences of ..beta..-sheet, probably joined into a distorted continuous sheet, connected by turns and extended loops, without any regular ..cap alpha..-helical segments.more » The residues previously implicated in activity in this class of proteins, D8 and R13, occur in a loop region.« less

Emergence of hysteresis loop in social contagions on complex networks.

PubMed

Su, Zhen; Wang, Wei; Li, Lixiang; Xiao, Jinghua; Stanley, H Eugene

2017-07-21

Understanding the spreading mechanisms of social contagions in complex network systems has attracted much attention in the physics community. Here we propose a generalized threshold model to describe social contagions. Using extensive numerical simulations and theoretical analyses, we find that a hysteresis loop emerges in the system. Specifically, the steady state of the system is sensitive to the initial conditions of the dynamics of the system. In the steady state, the adoption size increases discontinuously with the transmission probability of information about social contagions, and trial size exhibits a non-monotonic pattern, i.e., it first increases discontinuously then decreases continuously. Finally we study social contagions on heterogeneous networks and find that network topology does not qualitatively affect our results.

SL1 revisited: functional analysis of the structure and conformation of HIV-1 genome RNA.

PubMed

Sakuragi, Sayuri; Yokoyama, Masaru; Shioda, Tatsuo; Sato, Hironori; Sakuragi, Jun-Ichi

2016-11-11

The dimer initiation site/dimer linkage sequence (DIS/DLS) region of HIV is located on the 5' end of the viral genome and suggested to form complex secondary/tertiary structures. Within this structure, stem-loop 1 (SL1) is believed to be most important and an essential key to dimerization, since the sequence and predicted secondary structure of SL1 are highly stable and conserved among various virus subtypes. In particular, a six-base palindromic sequence is always present at the hairpin loop of SL1 and the formation of kissing-loop structure at this position between the two strands of genomic RNA is suggested to trigger dimerization. Although the higher-order structure model of SL1 is well accepted and perhaps even undoubted lately, there could be stillroom for consideration to depict the functional SL1 structure while in vivo (in virion or cell). In this study, we performed several analyses to identify the nucleotides and/or basepairing within SL1 which are necessary for HIV-1 genome dimerization, encapsidation, recombination and infectivity. We unexpectedly found that some nucleotides that are believed to contribute the formation of the stem do not impact dimerization or infectivity. On the other hand, we found that one G-C basepair involved in stem formation may serve as an alternative dimer interactive site. We also report on our further investigation of the roles of the palindromic sequences on viral replication. Collectively, we aim to assemble a more-comprehensive functional map of SL1 on the HIV-1 viral life cycle. We discovered several possibilities for a novel structure of SL1 in HIV-1 DLS. The newly proposed structure model suggested that the hairpin loop of SL1 appeared larger, and genome dimerization process might consist of more complicated mechanism than previously understood. Further investigations would be still required to fully understand the genome packaging and dimerization of HIV.

Residual stresses and vector hysteresis modeling

NASA Astrophysics Data System (ADS)

Ktena, Aphrodite

2016-04-01

Residual stresses in magnetic materials, whether the result of processing or intentional loading, leave their footprint on macroscopic data, such hysteresis loops and differential permeability measurements. A Preisach-type vector model is used to reproduce the phenomenology observed based on assumptions deduced from the data: internal stresses lead to smaller and misaligned grains, hence increased domain wall pinning and angular dispersion of local easy axes, favouring rotation as a magnetization reversal mechanism; misaligned grains contribute to magnetostatic fields opposing the direction of the applied field. The model is using a vector operator which accounts for both reversible and irreversible processes; the Preisach concept for interactions for the role of stress related demagnetizing fields; and a characteristic probability density function which is constructed as a weighed sum of constituent functions: the material is modeled as consisting of various subsystems, e.g. reversal mechanisms or areas subject to strong/weak long range interactions and each subsystem is represented by a constituent probability density function. Our assumptions are validated since the model reproduces the hysteresis loops and differential permeability curves observed experimentally and calculations involving rotating inputs at various residual stress levels are consistent and in agreement with experimental evidence.

EXPLAINING INVERTED-TEMPERATURE LOOPS IN THE QUIET SOLAR CORONA WITH MAGNETOHYDRODYNAMIC WAVE-MODE CONVERSION

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

Schiff, Avery J.; Cranmer, Steven R.

Coronal loops trace out bipolar, arch-like magnetic fields above the Sun’s surface. Recent measurements that combine rotational tomography, extreme-ultraviolet imaging, and potential-field extrapolation have shown the existence of large loops with inverted-temperature profiles, i.e., loops for which the apex temperature is a local minimum, not a maximum. These “down loops” appear to exist primarily in equatorial quiet regions near solar minimum. We simulate both these and the more prevalent large-scale “up loops” by modeling coronal heating as a time-steady superposition of (1) dissipation of incompressible Alfvén wave turbulence and (2) dissipation of compressive waves formed by mode conversion from themore » initial population of Alfvén waves. We found that when a large percentage (>99%) of the Alfvén waves undergo this conversion, heating is greatly concentrated at the footpoints and stable “down loops” are created. In some cases we found loops with three maxima that are also gravitationally stable. Models that agree with the tomographic temperature data exhibit higher gas pressures for “down loops” than for “up loops,” which is consistent with observations. These models also show a narrow range of Alfvén wave amplitudes: 3 to 6 km s{sup -1} at the coronal base. This is low in comparison to typical observed amplitudes of 20–30 km s{sup -1} in bright X-ray loops. However, the large-scale loops we model are believed to compose a weaker diffuse background that fills much of the volume of the corona. By constraining the physics of loops that underlie quiescent streamers, we hope to better understand the formation of the slow solar wind.« less

Active site CP-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins.

PubMed

Kamariah, Neelagandan; Eisenhaber, Birgit; Eisenhaber, Frank; Grüber, Gerhard

2018-04-01

Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (C P ) located in a conserved sequence Pxxx(T/S)xxC P motif known as C P -loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the C P -loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the C P -loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the C P -loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the C P -loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the C P -loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted C P -loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the C P -loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles. Copyright © 2018 Elsevier Inc. All rights reserved.

Emergence of self-sustained oscillations in excitable Erdös-Rényi random networks.

PubMed

Qian, Yu

2014-09-01

We investigate the emergence of self-sustained oscillations in excitable Erdös-Rényi random networks (EERRNs). Interestingly, periodical self-sustained oscillations have been found at a moderate connection probability P. For smaller or larger P, the system evolves into a homogeneous rest state with distinct mechanisms. One-dimensional Winfree loops are discovered as the sources to maintain the oscillations. Moreover, by analyzing these oscillation sources, we propose two criteria to explain the spatiotemporal dynamics obtained in EERRNs. Finally, the two critical connection probabilities for which self-sustained oscillations can emerge are approximately predicted based on these two criteria.

In situ heat treatment process utilizing a closed loop heating system

DOEpatents

Vinegar, Harold J.; Nguyen, Scott Vinh

2010-12-07

Systems and methods for an in situ heat treatment process that utilizes a circulation system to heat one or more treatment areas are described herein. The circulation system may use a heated liquid heat transfer fluid that passes through piping in the formation to transfer heat to the formation. In some embodiments, the piping may be positioned in at least two of the wellbores.

Synchrotron Protein Footprinting Supports Substrate Translocation by ClpA via ATP-Induced Movements of the D2 Loop

PubMed Central

Bohon, Jen; Jennings, Laura D.; Phillips, Christine M.; Licht, Stuart; Chance, Mark R.

2010-01-01

SUMMARY Synchrotron x-ray protein footprinting is used to study structural changes upon formation of the ClpA hexamer. Comparative solvent accessibilities between ClpA monomer and ClpA hexamer samples are in agreement throughout most of the sequence with calculations based on two previously proposed hexameric models. The data differ substantially from the proposed models in two parts of the structure: the D1 sensor 1 domain and the D2 loop region. The results suggest that these two regions can access alternate conformations in which their solvent protection is greater than in the structural models based on crystallographic data. In combination with previously reported structural data, the footprinting data provide support for a revised model in which the D2 loop contacts the D1 sensor 1 domain in the ATP-bound form of the complex. These data provide the first direct experimental support for the nucleotide-dependent D2 loop conformational change previously proposed to mediate substrate translocation. PMID:18682217

A mitosis-specific and R loop-driven ATR pathway promotes faithful chromosome segregation.

PubMed

Kabeche, Lilian; Nguyen, Hai Dang; Buisson, Rémi; Zou, Lee

2018-01-05

The ataxia telangiectasia mutated and Rad3-related (ATR) kinase is crucial for DNA damage and replication stress responses. Here, we describe an unexpected role of ATR in mitosis. Acute inhibition or degradation of ATR in mitosis induces whole-chromosome missegregation. The effect of ATR ablation is not due to altered cyclin-dependent kinase 1 (CDK1) activity, DNA damage responses, or unscheduled DNA synthesis but to loss of an ATR function at centromeres. In mitosis, ATR localizes to centromeres through Aurora A-regulated association with centromere protein F (CENP-F), allowing ATR to engage replication protein A (RPA)-coated centromeric R loops. As ATR is activated at centromeres, it stimulates Aurora B through Chk1, preventing formation of lagging chromosomes. Thus, a mitosis-specific and R loop-driven ATR pathway acts at centromeres to promote faithful chromosome segregation, revealing functions of R loops and ATR in suppressing chromosome instability. Copyright © 2018, American Association for the Advancement of Science.

Higher-order looping and nuclear organization of antigen receptor loci facilitate targeted RAG cleavage and regulated rearrangement in recombination centers

PubMed Central

Chaumeil, Julie; Micsinai, Mariann; Ntziachristos, Panagiotis; Deriano, Ludovic; Wang, Joy M-H; Ji, Yanhong; Nora, Elphege P.; Rodesch, Matthew J.; Jeddeloh, Jeffrey A.; Aifantis, Iannis; Kluger, Yuval; Schatz, David G.; Skok, Jane A.

2013-01-01

SUMMARY V(D)J recombination is essential for generating a diverse array of B and T cell receptors that can recognize and combat foreign antigen. As with any recombination event, tight control is essential to prevent the occurrence of genetic anomalies that drive cellular transformation. One important aspect of regulation is directed targeting of the RAG recombinase. Indeed, RAG accumulates at the 3’ end of individual antigen receptor loci poised for rearrangement, however, it is not known whether focal binding is involved in regulating cleavage, and what mechanisms lead to enrichment of RAG in this region. Here we show that mono-allelic looping out of the 3’ end of Tcra, coupled with transcription and increased chromatin/nuclear accessibility, are linked to focal RAG binding and ATM-mediated regulated mono-allelic cleavage on looped out 3’ regions. Our data identify higher order loop formation as a key determinant of directed RAG targeting and the maintenance of genome stability. PMID:23416051

High-throughput sample adaptive offset hardware architecture for high-efficiency video coding

NASA Astrophysics Data System (ADS)

Zhou, Wei; Yan, Chang; Zhang, Jingzhi; Zhou, Xin

2018-03-01

A high-throughput hardware architecture for a sample adaptive offset (SAO) filter in the high-efficiency video coding video coding standard is presented. First, an implementation-friendly and simplified bitrate estimation method of rate-distortion cost calculation is proposed to reduce the computational complexity in the mode decision of SAO. Then, a high-throughput VLSI architecture for SAO is presented based on the proposed bitrate estimation method. Furthermore, multiparallel VLSI architecture for in-loop filters, which integrates both deblocking filter and SAO filter, is proposed. Six parallel strategies are applied in the proposed in-loop filters architecture to improve the system throughput and filtering speed. Experimental results show that the proposed in-loop filters architecture can achieve up to 48% higher throughput in comparison with prior work. The proposed architecture can reach a high-operating clock frequency of 297 MHz with TSMC 65-nm library and meet the real-time requirement of the in-loop filters for 8 K × 4 K video format at 132 fps.

Non-topological cycloops

NASA Astrophysics Data System (ADS)

Lake, Matthew; Thomas, Steven; Ward, John

2010-01-01

We propose a mechanism for the creation of cosmic string loops with dynamically stabilised windings in the internal space. Assuming a velocity correlations regime in the post-inflationary epoch, such windings are seen to arise naturally in string networks prior to loop formation. The angular momentum of the string in the compact space may then be sufficient to ensure that the windings remain stable after the loop chops off from the network, even if the internal manifold is simply connected. For concreteness we embed our model in the Klebanov-Strassler geometry, which provides a natural mechanism for brane inflation, as well a being one of the best understood compactification schemes in type IIB string theory. We see that the interaction of angular momentum with the string tension causes the loop to oscillate between phases of expansion and contraction. This, in principle, should give rise to a distinct gravitational wave signature, the future detection of which could provide indirect evidence for the existence of extra dimensions.

OT2_wlanger_7: Dynamics of Giant Magnetic Gas Loops and Their Connection to the CMZ in the Galactic Center

NASA Astrophysics Data System (ADS)

Langer, W.

2011-09-01

Understanding the mass transfer and dynamics among the Galactic Center, the disk, and the halo of the Milky Way is fundamental to the study of the evolution of galaxies and star formation. Recently several giant loops of molecular gas (GML) have been found in the Galactic Center from CO maps, which are likely the result of the magnetic Parker instability. There is new evidence of a possible connection between these loops and the Central Molecular Zone as shown in a sparse [CII] sampling made by the Herschel Key Project GOT C+. Here we propose to map various features of the GMLs and the interface region in [CII] with HIFI. We will also map the foot points of the loop, which are thought to be highly shocked regions, in the ortho 110-101 line of water, which is a known shock tracer. With this data we will characterize different ISM components and their flow among these Galactic Center features.

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

PubMed Central

Hansen, Anders S; Pustova, Iryna; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier

2017-01-01

Folding of mammalian genomes into spatial domains is critical for gene regulation. The insulator protein CTCF and cohesin control domain location by folding domains into loop structures, which are widely thought to be stable. Combining genomic and biochemical approaches we show that CTCF and cohesin co-occupy the same sites and physically interact as a biochemically stable complex. However, using single-molecule imaging we find that CTCF binds chromatin much more dynamically than cohesin (~1–2 min vs. ~22 min residence time). Moreover, after unbinding, CTCF quickly rebinds another cognate site unlike cohesin for which the search process is long (~1 min vs. ~33 min). Thus, CTCF and cohesin form a rapidly exchanging 'dynamic complex' rather than a typical stable complex. Since CTCF and cohesin are required for loop domain formation, our results suggest that chromatin loops are dynamic and frequently break and reform throughout the cell cycle. DOI: http://dx.doi.org/10.7554/eLife.25776.001 PMID:28467304

Microwave detector

DOEpatents

Meldner, Heiner W.; Cusson, Ronald Y.; Johnson, Ray M.

1986-01-01

A microwave detector (10) is provided for measuring the envelope shape of a microwave pulse comprised of high-frequency oscillations. A biased ferrite (26, 28) produces a magnetization field flux that links a B-dot loop (16, 20). The magnetic field of the microwave pulse participates in the formation of the magnetization field flux. High-frequency insensitive means (18, 22) are provided for measuring electric voltage or current induced in the B-dot loop. The recorded output of the detector is proportional to the time derivative of the square of the envelope shape of the microwave pulse.

The m1A(58) modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI.

PubMed

Dégut, Clément; Ponchon, Luc; Folly-Klan, Marcia; Barraud, Pierre; Tisné, Carine

2016-03-01

The enzymes of the TrmI family catalyze the formation of the m(1)A58 modification in tRNA. We previously solved the crystal structure of the Thermus thermophilus enzyme and conducted a biophysical study to characterize the interaction between TrmI and tRNA. TrmI enzymes are active as a tetramer and up to two tRNAs can bind to TrmI simultaneously. In this paper, we present the structures of two TrmI mutants (D170A and Y78A). These residues are conserved in the active site of TrmIs and their mutations result in a dramatic alteration of TrmI activity. Both structures of TrmI mutants revealed the flexibility of the N-terminal domain that is probably important to bind tRNA. The structure of TrmI Y78A catalytic domain is unmodified regarding the binding of the SAM co-factor and the conformation of residues potentially interacting with the substrate adenine. This structure reinforces the previously proposed role of Y78, i.e. stabilize the conformation of the A58 ribose needed to hold the adenosine in the active site. The structure of the D170A mutant shows a flexible active site with one loop occupying in part the place of the co-factor and the second loop moving at the entrance to the active site. This structure and recent data confirms the central role of D170 residue binding the amino moiety of SAM and the exocyclic amino group of adenine. Possible mechanisms for methyl transfer are then discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

An integrated catch-and-hold mechanism activates nicotinic acetylcholine receptors.

PubMed

Jadey, Snehal; Auerbach, Anthony

2012-07-01

In neuromuscular acetylcholine (ACh) receptor channels (AChRs), agonist molecules bind with a low affinity (LA) to two sites that can switch to high affinity (HA) and increase the probability of channel opening. We measured (by using single-channel kinetic analysis) the rate and equilibrium constants for LA binding and channel gating for several different agonists of adult-type mouse AChRs. Almost all of the variation in the equilibrium constants for LA binding was from differences in the association rate constants. These were consistently below the limit set by diffusion and were substantially different even though the agonists had similar sizes and the same charge. This suggests that binding to resting receptors is not by diffusion alone and, hence, that each binding site can undergo two conformational changes ("catch" and "hold") that connect three different structures (apo-, LA-bound, and HA-bound). Analyses of ACh-binding protein structures suggest that this binding site, too, may adopt three discrete structures having different degrees of loop C displacement ("capping"). For the agonists we tested, the logarithms of the equilibrium constants for LA binding and LA↔HA gating were correlated. Although agonist binding and channel gating have long been considered to be separate processes in the activation of ligand-gated ion channels, this correlation implies that the catch-and-hold conformational changes are energetically linked and together comprise an integrated process having a common structural basis. We propose that loop C capping mainly reflects agonist binding, with its two stages corresponding to the formation of the LA and HA complexes. The catch-and-hold reaction coordinate is discussed in terms of preopening states and thermodynamic cycles of activation.

An integrated catch-and-hold mechanism activates nicotinic acetylcholine receptors

PubMed Central

Jadey, Snehal

2012-01-01

In neuromuscular acetylcholine (ACh) receptor channels (AChRs), agonist molecules bind with a low affinity (LA) to two sites that can switch to high affinity (HA) and increase the probability of channel opening. We measured (by using single-channel kinetic analysis) the rate and equilibrium constants for LA binding and channel gating for several different agonists of adult-type mouse AChRs. Almost all of the variation in the equilibrium constants for LA binding was from differences in the association rate constants. These were consistently below the limit set by diffusion and were substantially different even though the agonists had similar sizes and the same charge. This suggests that binding to resting receptors is not by diffusion alone and, hence, that each binding site can undergo two conformational changes (“catch” and “hold”) that connect three different structures (apo-, LA-bound, and HA-bound). Analyses of ACh-binding protein structures suggest that this binding site, too, may adopt three discrete structures having different degrees of loop C displacement (“capping”). For the agonists we tested, the logarithms of the equilibrium constants for LA binding and LA↔HA gating were correlated. Although agonist binding and channel gating have long been considered to be separate processes in the activation of ligand-gated ion channels, this correlation implies that the catch-and-hold conformational changes are energetically linked and together comprise an integrated process having a common structural basis. We propose that loop C capping mainly reflects agonist binding, with its two stages corresponding to the formation of the LA and HA complexes. The catch-and-hold reaction coordinate is discussed in terms of preopening states and thermodynamic cycles of activation. PMID:22732309

OBSERVATIONAL SIGNATURES OF CORONAL LOOP HEATING AND COOLING DRIVEN BY FOOTPOINT SHUFFLING

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

Dahlburg, R. B.; Taylor, B. D.; Einaudi, G.

The evolution of a coronal loop is studied by means of numerical simulations of the fully compressible three-dimensional magnetohydrodynamic equations using the HYPERION code. The footpoints of the loop magnetic field are advected by random motions. As a consequence, the magnetic field in the loop is energized and develops turbulent nonlinear dynamics characterized by the continuous formation and dissipation of field-aligned current sheets: energy is deposited at small scales where heating occurs. Dissipation is nonuniformly distributed so that only a fraction of the coronal mass and volume gets heated at any time. Temperature and density are highly structured at scalesmore » that, in the solar corona, remain observationally unresolved: the plasma of our simulated loop is multithermal, where highly dynamical hotter and cooler plasma strands are scattered throughout the loop at sub-observational scales. Numerical simulations of coronal loops of 50,000 km length and axial magnetic field intensities ranging from 0.01 to 0.04 T are presented. To connect these simulations to observations, we use the computed number densities and temperatures to synthesize the intensities expected in emission lines typically observed with the Extreme Ultraviolet Imaging Spectrometer on Hinode. These intensities are used to compute differential emission measure distributions using the Monte Carlo Markov Chain code, which are very similar to those derived from observations of solar active regions. We conclude that coronal heating is found to be strongly intermittent in space and time, with only small portions of the coronal loop being heated: in fact, at any given time, most of the corona is cooling down.« less

Point defect evolution in Ni, NiFe and NiCr alloys from atomistic simulations and irradiation experiments

DOE PAGES

Aidhy, Dilpuneet S.; Lu, Chenyang; Jin, Ke; ...

2015-08-08

Using molecular dynamics simulations, we elucidate irradiation-induced point defect evolution in fcc pure Ni, Ni 0.5Fe 0.5, and Ni 0.8Cr 0.2 solid solution alloys. We find that irradiation-induced interstitials form dislocation loops that are of 1/3 <111>{111}-type, consistent with our experimental results. While the loops are formed in all the three materials, the kinetics of formation is considerably slower in NiFe and NiCr than in pure Ni, indicating that defect migration barriers and extended defect formation energies could be higher in the alloys than pure Ni. As a result, while larger size clusters are formed in pure Ni, smaller andmore » more clusters are observed in the alloys. The vacancy diffusion occurs at relatively higher temperatures than interstitials, and their clustering leads to formation of stacking fault tetrahedra, also consistent with our experiments. The results also show that the surviving Frenkel pairs are composition-dependent and are largely Ni dominated.« less

Leader-follower formation control of underactuated surface vehicles based on sliding mode control and parameter estimation.

PubMed

Sun, Zhijian; Zhang, Guoqing; Lu, Yu; Zhang, Weidong

2018-01-01

This paper studies the leader-follower formation control of underactuated surface vehicles with model uncertainties and environmental disturbances. A parameter estimation and upper bound estimation based sliding mode control scheme is proposed to solve the problem of the unknown plant parameters and environmental disturbances. For each of these leader-follower formation systems, the dynamic equations of position and attitude are analyzed using coordinate transformation with the aid of the backstepping technique. All the variables are guaranteed to be uniformly ultimately bounded stable in the closed-loop system, which is proven by the distribution design Lyapunov function synthesis. The main advantages of this approach are that: first, parameter estimation based sliding mode control can enhance the robustness of the closed-loop system in presence of model uncertainties and environmental disturbances; second, a continuous function is developed to replace the signum function in the design of sliding mode scheme, which devotes to reduce the chattering of the control system. Finally, numerical simulations are given to demonstrate the effectiveness of the proposed method. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Etude par émission acoustique de la dynamique des dislocations pendant la déformation cyclique de polycristaux d'aluminium

NASA Astrophysics Data System (ADS)

Slimani, A.; Fleischmann, P.; Fougères, R.

1992-06-01

The cyclic plasticity of 5N polycrystalline aluminium have been studied at room temperature by measuring the continuous acoustic emission (A.E.) due to dislocations movements in the metal. In this study, original data have been obtained in the understanding of continuous A.E. sources. In comparison with classical interpretation given in the literature, the fact that dislocations are arranged according to a dislocation cell structure from the first cycle has been included in the analysis of the results. From this, it has been shown that the amplitude of the A.E. signal is not directly connected with the plastic strain rate prescribed to the fatigue sample and that the probability density function of dislocation loops created during the cycling can be determined. La plasticité cyclique de l'AI 5N polycristallin a été étudiée à la température ambiante à partir de mesures d'émission acoustique continue (E.A.). L'application de la technique de l'E.A. nous a permis d'obtenir des données originales quant aux mécanismes sources d'E.A. Par rapport aux interprétations classiques de la littérature, nous avons fait intervenir le fait que, dès les premiers cycles, une structure cellulaire de dislocations est établie. Nous montrons que l'amplitude du signal d'E.A. n'est plus liée directement à la vitesse de déformation plastique macroscopique. A partir de cette donnée, l'analyse des résultats d'E.A. permet d'obtenir des informations sur la fonction distribution des boucles de dislocations créées au cours de la déformation cyclique.

Integrated orbit and attitude hardware-in-the-loop simulations for autonomous satellite formation flying

NASA Astrophysics Data System (ADS)

Park, Han-Earl; Park, Sang-Young; Kim, Sung-Woo; Park, Chandeok

2013-12-01

Development and experiment of an integrated orbit and attitude hardware-in-the-loop (HIL) simulator for autonomous satellite formation flying are presented. The integrated simulator system consists of an orbit HIL simulator for orbit determination and control, and an attitude HIL simulator for attitude determination and control. The integrated simulator involves four processes (orbit determination, orbit control, attitude determination, and attitude control), which interact with each other in the same way as actual flight processes do. Orbit determination is conducted by a relative navigation algorithm using double-difference GPS measurements based on the extended Kalman filter (EKF). Orbit control is performed by a state-dependent Riccati equation (SDRE) technique that is utilized as a nonlinear controller for the formation control problem. Attitude is determined from an attitude heading reference system (AHRS) sensor, and a proportional-derivative (PD) feedback controller is used to control the attitude HIL simulator using three momentum wheel assemblies. Integrated orbit and attitude simulations are performed for a formation reconfiguration scenario. By performing the four processes adequately, the desired formation reconfiguration from a baseline of 500-1000 m was achieved with meter-level position error and millimeter-level relative position navigation. This HIL simulation demonstrates the performance of the integrated HIL simulator and the feasibility of the applied algorithms in a real-time environment. Furthermore, the integrated HIL simulator system developed in the current study can be used as a ground-based testing environment to reproduce possible actual satellite formation operations.

Structural variations of single and tandem mismatches in RNA duplexes: a joint MD simulation and crystal structure database analysis.

PubMed

Halder, Sukanya; Bhattacharyya, Dhananjay

2012-10-04

Internal loops within RNA duplex regions are formed by single or tandem basepairing mismatches with flanking canonical Watson-Crick basepairs on both sides. They are the most common motif observed in RNA secondary structures and play integral functional and structural roles. In this report, we have studied the structural features of 1 × 1, 2 × 2, and 3 × 3 internal loops using all-atom molecular dynamics (MD) simulation technique with explicit solvent model. As MD simulation is intricately dependent on the choice of force-field and these are often rather approximate, we have used both the most popular force-fields for nucleic acids-CHARMM27 and AMBER94-for a comparative analysis. We find that tandem noncanonical basepairs forming 2 × 2 and 3 × 3 internal loops are considerably more stable than the single mismatches forming 1 × 1 internal loops, irrespective of the force field. We have also analyzed crystal structure database to study the conservation of these helical fragments in the corresponding sets of RNA structures. We observe that the nature of stability in MD simulations mimic their fluctuating natures in crystal data sets also, probably indicating reliable natures of both the force fields to reproduce experimental results. We also notice significant structural changes in the wobble G:U basepairs present in these double helical stretches, leading to a biphasic stability for these wobble pairs to release the deformational strains introduced by internal loops within duplex regions.

Replication stress induces accumulation of FANCD2 at central region of large fragile genes

PubMed Central

Okamoto, Yusuke; Iwasaki, Watal M; Kugou, Kazuto; Takahashi, Kazuki K; Oda, Arisa; Sato, Koichi; Kobayashi, Wataru; Kawai, Hidehiko; Sakasai, Ryo; Takaori-Kondo, Akifumi; Yamamoto, Takashi; Kanemaki, Masato T; Taoka, Masato; Isobe, Toshiaki; Kurumizaka, Hitoshi; Innan, Hideki; Ohta, Kunihiro; Ishiai, Masamichi; Takata, Minoru

2018-01-01

Abstract During mild replication stress provoked by low dose aphidicolin (APH) treatment, the key Fanconi anemia protein FANCD2 accumulates on common fragile sites, observed as sister foci, and protects genome stability. To gain further insights into FANCD2 function and its regulatory mechanisms, we examined the genome-wide chromatin localization of FANCD2 in this setting by ChIP-seq analysis. We found that FANCD2 mostly accumulates in the central regions of a set of large transcribed genes that were extensively overlapped with known CFS. Consistent with previous studies, we found that this FANCD2 retention is R-loop-dependent. However, FANCD2 monoubiquitination and RPA foci formation were still induced in cells depleted of R-loops. Interestingly, we detected increased Proximal Ligation Assay dots between FANCD2 and R-loops following APH treatment, which was suppressed by transcriptional inhibition. Collectively, our data suggested that R-loops are required to retain FANCD2 in chromatin at the middle intronic region of large genes, while the replication stress-induced upstream events leading to the FA pathway activation are not triggered by R-loops. PMID:29394375

Shock heating in numerical simulations of kink-unstable coronal loops

PubMed Central

Bareford, M. R.; Hood, A. W.

2015-01-01

An analysis of the importance of shock heating within coronal magnetic fields has hitherto been a neglected area of study. We present new results obtained from nonlinear magnetohydrodynamic simulations of straight coronal loops. This work shows how the energy released from the magnetic field, following an ideal instability, can be converted into thermal energy, thereby heating the solar corona. Fast dissipation of magnetic energy is necessary for coronal heating and this requirement is compatible with the time scales associated with ideal instabilities. Therefore, we choose an initial loop configuration that is susceptible to the fast-growing kink, an instability that is likely to be created by convectively driven vortices, occurring where the loop field intersects the photosphere (i.e. the loop footpoints). The large-scale deformation of the field caused by the kinking creates the conditions for the formation of strong current sheets and magnetic reconnection, which have previously been considered as sites of heating, under the assumption of an enhanced resistivity. However, our simulations indicate that slow mode shocks are the primary heating mechanism, since, as well as creating current sheets, magnetic reconnection also generates plasma flows that are faster than the slow magnetoacoustic wave speed. PMID:25897092

Three-dimensional magnetohydrodynamics of the emerging magnetic flux in the solar atmosphere

NASA Technical Reports Server (NTRS)

Matsumoto, R.; Tajima, T.; Shibata, K.; Kaisig, M.

1993-01-01

The nonlinear evolution of an emerging magnetic flux tube or sheet in the solar atmosphere is studied through 3D MHD simulations. In the initial state, a horizontal magnetic flux sheet or tube is assumed to be embedded at the bottom of MHD two isothermal gas layers, which approximate the solar photosphere/chromosphere and the corona. The magnetic flux sheet or tube is unstable against the undular mode of the magnetic buoyancy instability. The magnetic loop rises due to the linear and then later nonlinear instabilities caused by the buoyancy enhanced by precipitating the gas along magnetic field lines. We find by 3D simulation that during the ascendance of loops the bundle of flux tubes or even the flux sheet develops into dense gas filaments pinched between magnetic loops. The interchange modes help produce a fine fiber flux structure perpendicular to the magnetic field direction in the linear stage, while the undular modes determine the overall buoyant loop structure. The expansion of such a bundle of magnetic loops follows the self-similar behavior observed in 2D cases studied earlier. Our study finds the threshold flux for arch filament system (AFS) formation to be about 0.3 x 10 exp 20 Mx.

RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination.

PubMed

Ribeiro de Almeida, Claudia; Dhir, Somdutta; Dhir, Ashish; Moghaddam, Amin E; Sattentau, Quentin; Meinhart, Anton; Proudfoot, Nicholas J

2018-05-17

Class switch recombination (CSR) at the immunoglobulin heavy-chain (IgH) locus is associated with the formation of R-loop structures over switch (S) regions. While these often occur co-transcriptionally between nascent RNA and template DNA, we now show that they also form as part of a post-transcriptional mechanism targeting AID to IgH S-regions. This depends on the RNA helicase DDX1 that is also required for CSR in vivo. DDX1 binds to G-quadruplex (G4) structures present in intronic switch transcripts and converts them into S-region R-loops. This in turn targets the cytidine deaminase enzyme AID to S-regions so promoting CSR. Notably R-loop levels over S-regions are diminished by chemical stabilization of G4 RNA or by the expression of a DDX1 ATPase-deficient mutant that acts as a dominant-negative protein to reduce CSR efficiency. In effect, we provide evidence for how S-region transcripts interconvert between G4 and R-loop structures to promote CSR in the IgH locus. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Numerical Simulation of DC Coronal Heating

NASA Astrophysics Data System (ADS)

Dahlburg, Russell B.; Einaudi, G.; Taylor, Brian D.; Ugarte-Urra, Ignacio; Warren, Harry; Rappazzo, A. F.; Velli, Marco

2016-05-01

Recent research on observational signatures of turbulent heating of a coronal loop will be discussed. The evolution of the loop is is studied by means of numerical simulations of the fully compressible three-dimensional magnetohydrodynamic equations using the HYPERION code. HYPERION calculates the full energy cycle involving footpoint convection, magnetic reconnection, nonlinear thermal conduction and optically thin radiation. The footpoints of the loop magnetic field are convected by random photospheric motions. As a consequence the magnetic field in the loop is energized and develops turbulent nonlinear dynamics characterized by the continuous formation and dissipation of field-aligned current sheets: energy is deposited at small scales where heating occurs. Dissipation is non-uniformly distributed so that only a fraction of thecoronal mass and volume gets heated at any time. Temperature and density are highly structured at scales which, in the solar corona, remain observationally unresolved: the plasma of the simulated loop is multi thermal, where highly dynamical hotter and cooler plasma strands are scattered throughout the loop at sub-observational scales. Typical simulated coronal loops are 50000 km length and have axial magnetic field intensities ranging from 0.01 to 0.04 Tesla. To connect these simulations to observations the computed number densities and temperatures are used to synthesize the intensities expected in emission lines typically observed with the Extreme ultraviolet Imaging Spectrometer (EIS) on Hinode. These intensities are then employed to compute differential emission measure distributions, which are found to be very similar to those derived from observations of solar active regions.

Observational Signatures of Coronal Heating

NASA Astrophysics Data System (ADS)

Dahlburg, R. B.; Einaudi, G.; Ugarte-Urra, I.; Warren, H. P.; Rappazzo, A. F.; Velli, M.; Taylor, B.

2016-12-01

Recent research on observational signatures of turbulent heating of a coronal loop will be discussed. The evolution of the loop is is studied by means of numericalsimulations of the fully compressible three-dimensionalmagnetohydrodynamic equations using the HYPERION code. HYPERION calculates the full energy cycle involving footpoint convection, magnetic reconnection,nonlinear thermal conduction and optically thin radiation.The footpoints of the loop magnetic field are convected by random photospheric motions. As a consequence the magnetic field in the loop is energized and develops turbulent nonlinear dynamics characterized by the continuous formation and dissipation of field-aligned current sheets: energy is deposited at small scales where heating occurs. Dissipation is non-uniformly distributed so that only a fraction of thecoronal mass and volume gets heated at any time. Temperature and density are highly structured at scales which, in the solar corona, remain observationally unresolved: the plasma of the simulated loop is multi-thermal, where highly dynamical hotter and cooler plasma strands arescattered throughout the loop at sub-observational scales. Typical simulated coronal loops are 50000 km length and have axial magnetic field intensities ranging from 0.01 to 0.04 Tesla.To connect these simulations to observations the computed numberdensities and temperatures are used to synthesize the intensities expected inemission lines typically observed with the Extreme ultraviolet Imaging Spectrometer(EIS) on Hinode. These intensities are then employed to compute differentialemission measure distributions, which are found to be very similar to those derivedfrom observations of solar active regions.

Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure.

PubMed

Takahashi, Shuntaro; Sugimoto, Naoki

2017-12-01

DNA guanine-quadruplexes (G-quadruplexes) are unique DNA structures formed by guanine-rich sequences. The loop regions of G-quadruplexes play key roles in stability and topology of G-quadruplexes. Here, we investigated volumetric changes induced by pressure in the folding of the G-quadruplex formed by the thrombin binding aptamer (TBA) with mutations within the loop regions. The change of partial molar volume in the transition from coil to G-quadruplex, ∆V tr , of TBA with a mutation from T to A in the 5' most loop (TBA T3A) was 75.5cm 3 mol -1 , which was larger than that of TBA (54.6cm 3 mol -1 ). TBA with a G to T mutation in the central loop (TBA G8T) had thermal stability similar to TBA T3A but a smaller ∆V tr of 41.1cm 3 mol -1 . In the presence of poly(ethylene)glycol 200 (PEG200), ∆V tr values were 14.7cm 3 mol -1 for TBA T3A and 13.2cm 3 mol -1 for TBA G8T. These results suggest that the two mutations destabilize the G-quadruplex structure differently. Thus, volumetric data obtained using pressure-based thermodynamic analyses provides information about the dynamics of the loop regions and the roles of loops in the stabilities and folding of G-quadruplex structures. Copyright © 2017 Elsevier B.V. All rights reserved.

Biostratigraphy and structural setting of the Permian Coyote Butte Formation of central Oregon.

USGS Publications Warehouse

Wardlaw, B.R.; Nestell, M.K.; Dutro, J.T.

1982-01-01

Larger isolated outcrops of the limestones of the Coyote Butte Formation consistently contain younger over older faunas that range through most of the Leonardian Series of the Early Permian. The outcrops of the Coyote Butte Formation are interpreted as right- side up blocks probably introduced into the area as one massive exotic unit. The Coyote Butte Formation is very similar to the Lower Permain limestone near Quinn River Crossing, Nevada, and both are suggested to have a similar origin. The Coyote Butte Formation was probably introduced during a late-stage event to deforming Mesozoic oceanic sediments in Mesozoic time. -Authors

Severe splenic rupture after colorectal endoscopic submucosal dissection

PubMed Central

Herreros de Tejada, Alberto; Giménez-Alvira, Luis; Van den Brule, Enrique; Sánchez-Yuste, Rosario; Matallanos, Pilar; Blázquez, Esther; Calleja, Jose L; Abreu, Luis E

2014-01-01

Splenic rupture (SR) after colonoscopy is a very rare but potentially serious complication. Delayed diagnosis is common, and may increase morbidity and mortality associated. There is no clear relation between SR and difficult diagnostic or therapeutic procedures, but it has been suggested that loop formation and excessive torquing might be risk factors. This is a case of a 65-year-old woman who underwent endoscopic submucosal dissection (ESD) for lateral spreading tumor in the descending colon, and 36 h afterwards presented symptoms and signs of severe hypotension due to SR. Standard splenectomy was completed and the patient recovered uneventfully. Colorectal ESD is usually a long and position-demanding technique, implying torquing and loop formation. To our knowledge this is the first case of SR after colorectal ESD reported in the literature. Endoscopists performing colorectal ESD in the left colon must be aware of this potential complication. PMID:25071360

The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability

PubMed Central

Hamperl, Stephan; Cimprich, Karlene A.

2014-01-01

Accurate DNA replication and DNA repair are crucial for the maintenance of genome stability, and it is generally accepted that failure of these processes is a major source of DNA damage in cells. Intriguingly, recent evidence suggests that DNA damage is more likely to occur at genomic loci with high transcriptional activity. Furthermore, loss of certain RNA processing factors in eukaryotic cells is associated with increased formation of co-transcriptional RNA:DNA hybrid structures known as R-loops, resulting in double-strand breaks (DSBs) and DNA damage. However, the molecular mechanisms by which R-loop structures ultimately lead to DNA breaks and genome instability is not well understood. In this review, we summarize the current knowledge about the formation, recognition and processing of RNA:DNA hybrids, and discuss possible mechanisms by which these structures contribute to DNA damage and genome instability in the cell. PMID:24746923

Verbal versus Numerical Probabilities: Does Format Presentation of Probabilistic Information regarding Breast Cancer Screening Affect Women's Comprehension?

ERIC Educational Resources Information Center

Vahabi, Mandana

2010-01-01

Objective: To test whether the format in which women receive probabilistic information about breast cancer and mammography affects their comprehension. Methods: A convenience sample of 180 women received pre-assembled randomized packages containing a breast health information brochure, with probabilities presented in either verbal or numeric…

Value of routine investigations to predict loop diuretic down-titration success in stable heart failure.

PubMed

Martens, Pieter; Verbrugge, Frederik H; Boonen, Levinia; Nijst, Petra; Dupont, Matthias; Mullens, Wilfried

2018-01-01

Guidelines advocate down-titration of loop diuretics in chronic heart failure (CHF) when patients have no signs of volume overload. Limited data are available on the expected success rate of this practice or how routine diagnostic tests might help steering this process. Fifty ambulatory CHF-patients on stable neurohumoral blocker/diuretic therapy for at least 3months without any clinical sign of volume overload were prospectively included to undergo loop diuretic down-titration. All patients underwent a similar pre-down-titration evaluation consisting of a dyspnea scoring, physical examination, transthoracic echocardiography (diastolic function, right ventricular function, cardiac filling pressures and valvular disease), blood sample (serum creatinine, plasma NT-pro-BNP and neurohormones). Loop diuretic maintenance dose was subsequently reduced by 50% or stopped if dose was ≤40mg furosemide equivalents. Successful down-titration was defined as a persistent dose reduction after 30days without weight increase >1.5kg or new-onset symptoms of worsening heart failure. At 30-day follow-up, down-titration was successful in 62% (n=31). In 12/19 patients exhibiting down-titration failure, this occurred within the first week. Physical examination, transthoracic echocardiography and laboratory analysis had limited predictive capability to detect patients with down-titration success/failure (positive likelihood-ratios below 1.5, or area under the curve [AUC] non-statically different from AUC=0.5). Loop diuretic down-titration is feasible in a majority of stable CHF patients in which the treating clinician felt continuation of loops was unnecessary to sustain euvolemia. Importantly, routine diagnostics which suggest euvolemia, have limited diagnostic impact on the post-test probability. Copyright © 2017 Elsevier B.V. All rights reserved.

HIV1 V3 loop hypermutability is enhanced by the guanine usage bias in the part of env gene coding for it.

PubMed

Khrustalev, Vladislav Victorovich

2009-01-01

Guanine is the most mutable nucleotide in HIV genes because of frequently occurring G to A transitions, which are caused by cytosine deamination in viral DNA minus strands catalyzed by APOBEC enzymes. Distribution of guanine between three codon positions should influence the probability for G to A mutation to be nonsynonymous (to occur in first or second codon position). We discovered that nucleotide sequences of env genes coding for third variable regions (V3 loops) of gp120 from HIV1 and HIV2 have different kinds of guanine usage biases. In the HIV1 reference strain and 100 additionally analyzed HIV1 strains the guanine usage bias in V3 loop coding regions (2G>1G>3G) should lead to elevated nonsynonymous G to A transitions occurrence rates. In the HIV2 reference strain and 100 other HIV2 strains guanine usage bias in V3 loop coding regions (3G>2G>1G) should protect V3 loops from hypermutability. According to the HIV1 and HIV2 V3 alignment, insertion of the sequence enriched with 2G (21 codons in length) occurred during the evolution of HIV1 predecessor, while insertion of the different sequence enriched with 3G (19 codons in length) occurred during the evolution of HIV2 predecessor. The higher is the level of 3G in the V3 coding region, the lower should be the immune escaping mutation occurrence rates. This hypothesis was tested in this study by comparing the guanine usage in V3 loop coding regions from HIV1 fast and slow progressors. All calculations have been performed by our algorithms "VVK In length", "VVK Dinucleotides" and "VVK Consensus" (www.barkovsky.hotmail.ru).

Survey of the vestibulum, and behavior of Xenopus laevis larvae developed during a 7-days space flight.

PubMed

Briegleb, W; Neubert, J; Schatz, A; Klein, T; Kruse, B

1986-01-01

Aquatic animals have almost no body weight related proprioception for spatial orientation. Xenopus larvae, like fish, maintain their attitude in water by continuous correction with their fin(s). For these reasons a special performance of the equilibrium system compared to terrestrial animals is necessary. Evidently fish therefore have more compact (dense) otoliths; Xenopus larvae have less dense otolith (membranes) similar to land vertebrates; but their sacculus-otoliths are vertically positioned, which also may lead to a higher g-sensitivity. For plausibility reasons gravity should influence the embryonic development of gravity receptors. Yet, evaluations of photographs taken from the surface of cut deep-frozen objects by incident light show no aberration of the shape of the whole vestibulum and of the shape, density, size and position of the otolith membrane in larvae developed under near-zero g (NEXPA-BW-STATEX in D-1-Mission). The further evaluation of the "weightless-larvae" revealed a probably not yet described statolith-like formation in the dorsal wall of the vestibulum. In the weightless larvae this formation outnumbers, also qualitatively, strongly the l-g controls. An extra result is the lack of striking effects of cosmic radiation on the embryonic development of the flown Xenopus eggs. The swimming behavior of the larvae which was observed about one hour after landing of the Space Shuttle showed a typical anomaly (loop swimming), which is known from larvae developed on the clinostat or from fish flown aboard Apollo capsules.

Survey of the vestibulum, and behavior of xenopus laevis larvae developed during a 7-days space flight

NASA Astrophysics Data System (ADS)

Briegleb, W.; Neubert, J.; Schatz, A.; Klein, T.; Kruse, B.

Aquatic animals have almost no body weight related proprioception for spatial orientation. Xenopus larvae, like fish, maintain their attitude in water by continuous correction with their fin(s). For these reasons a special performance of the equilibrium system compared to terrestrial animals is necessary. Evidently fish therefore have more compact (dense) otoliths; Xenopus larvae have less dense otolith (membranes) similar to land vertebrates; but their sacculus-otoliths are vertically positioned, which also may lead to a higher g-sensitivity. For plausibility reasons gravity should influence the embryonic development of gravity receptors. Yet, evaluations of photographs taken from the surface of cut deep-frozen objects by incident light show no aberration of the shape of the whole vestibulum and of the shape, density, size and position of the otolith membrane in larvae developed under near-zero g (NEXPA-BW-STATEX in D1-Mission). The further evaluation of the ``weightless-larvae'' revealed a probably not yet described statolith-like formation in the dorsal wall of the vestibulum. In the weightless larvae this formation outnumbers, also qualitatively, strongly the 1-g controls. An extra result is the lack of striking effects of cosmic radiation on the embryonic development of the flown Xenopus eggs. The swimming behavior of the larvae which was observed about one hour after landing of the Space Shuttle showed a typical anomaly (loop swimming), which is known from larvae developed on the clinostat or from fish flown aboard Apollo capsules.

Novel experimental surgical strategy to prevent traumatic neuroma formation by combining a 3D-printed Y-tube with an autograft.

PubMed

Bolleboom, Anne; de Ruiter, Godard C W; Coert, J Henk; Tuk, Bastiaan; Holstege, Jan C; van Neck, Johan W

2018-02-09

OBJECTIVE Traumatic neuromas may develop after nerve injury at the proximal nerve stump, which can lead to neuropathic pain. These neuromas are often resistant to therapy, and excision of the neuroma frequently leads to recurrence. In this study, the authors present a novel surgical strategy to prevent neuroma formation based on the principle of centro-central anastomosis (CCA), but rather than directly connecting the nerve ends to an autograft, they created a loop using a 3D-printed polyethylene Y-shaped conduit with an autograft in the distal outlets. METHODS The 3D-printed Y-tube with autograft was investigated in a model of rat sciatic nerve transection in which the Y-tube was placed on the proximal sciatic nerve stump and a peroneal graft was placed between the distal outlets of the Y-tube to form a closed loop. This model was compared with a CCA model, in which a loop was created between the proximal tibial and peroneal nerves with a peroneal autograft. Additional control groups consisted of the closed Y-tube and the extended-arm Y-tube. Results were analyzed at 12 weeks of survival using nerve morphometry for the occurrence of neuroma formation and axonal regeneration in plastic semi-thin sections. RESULTS Among the different surgical groups, the Y-tube with interposed autograft was the only model that did not result in neuroma formation at 12 weeks of survival. In addition, a 13% reduction in the number of myelinated axons regenerating through the interposed autograft was observed in the Y-tube with autograft model. In the CCA model, the authors also observed a decrease of 17% in the number of myelinated axons, but neuroma formation was present in this model. The closed Y-tube resulted in minimal nerve regeneration inside the tube together with extensive neuroma formation before the entrance of the tube. The extended-arm Y-tube model clearly showed that the majority of the regenerating axons merged into the Y-tube arm, which was connected to the autograft, leaving the extended plastic arm almost empty. CONCLUSIONS This pilot study shows that our novel 3D-printed Y-tube model with interposed autograft prevents neuroma formation, making this a promising surgical tool for the management of traumatic neuromas.

Simulations of Living Cell Origins Using a Cellular Automata Model

NASA Astrophysics Data System (ADS)

Ishida, Takeshi

2014-04-01

Understanding the generalized mechanisms of cell self-assembly is fundamental for applications in various fields, such as mass producing molecular machines in nanotechnology. Thus, the details of real cellular reaction networks and the necessary conditions for self-organized cells must be elucidated. We constructed a 2-dimensional cellular automata model to investigate the emergence of biological cell formation, which incorporated a looped membrane and a membrane-bound information system (akin to a genetic code and gene expression system). In particular, with an artificial reaction system coupled with a thermal system, the simultaneous formation of a looped membrane and an inner reaction process resulted in a more stable structure. These double structures inspired the primitive biological cell formation process from chemical evolution stage. With a model to simulate cellular self-organization in a 2-dimensional cellular automata model, 3 phenomena could be realized: (1) an inner reaction system developed as an information carrier precursor (akin to DNA); (2) a cell border emerged (akin to a cell membrane); and (3) these cell structures could divide into 2. This double-structured cell was considered to be a primary biological cell. The outer loop evolved toward a lipid bilayer membrane, and inner polymeric particles evolved toward precursor information carriers (evolved toward DNA). This model did not completely clarify all the necessary and sufficient conditions for biological cell self-organization. Further, our virtual cells remained unstable and fragile. However, the "garbage bag model" of Dyson proposed that the first living cells were deficient; thus, it would be reasonable that the earliest cells were more unstable and fragile than the simplest current unicellular organisms.

Simulations of living cell origins using a cellular automata model.

PubMed

Ishida, Takeshi

2014-04-01

Understanding the generalized mechanisms of cell self-assembly is fundamental for applications in various fields, such as mass producing molecular machines in nanotechnology. Thus, the details of real cellular reaction networks and the necessary conditions for self-organized cells must be elucidated. We constructed a 2-dimensional cellular automata model to investigate the emergence of biological cell formation, which incorporated a looped membrane and a membrane-bound information system (akin to a genetic code and gene expression system). In particular, with an artificial reaction system coupled with a thermal system, the simultaneous formation of a looped membrane and an inner reaction process resulted in a more stable structure. These double structures inspired the primitive biological cell formation process from chemical evolution stage. With a model to simulate cellular self-organization in a 2-dimensional cellular automata model, 3 phenomena could be realized: (1) an inner reaction system developed as an information carrier precursor (akin to DNA); (2) a cell border emerged (akin to a cell membrane); and (3) these cell structures could divide into 2. This double-structured cell was considered to be a primary biological cell. The outer loop evolved toward a lipid bilayer membrane, and inner polymeric particles evolved toward precursor information carriers (evolved toward DNA). This model did not completely clarify all the necessary and sufficient conditions for biological cell self-organization. Further, our virtual cells remained unstable and fragile. However, the "garbage bag model" of Dyson proposed that the first living cells were deficient; thus, it would be reasonable that the earliest cells were more unstable and fragile than the simplest current unicellular organisms.

Structural plasticity of 4-α-helical bundles exemplified by the puzzle-like molecular assembly of the Rop protein

PubMed Central

Amprazi, Maria; Kotsifaki, Dina; Providaki, Mary; Kapetaniou, Evangelia G.; Fellas, Georgios; Kyriazidis, Ioannis; Pérez, Javier; Kokkinidis, Michael

2014-01-01

The dimeric Repressor of Primer (Rop) protein, a widely used model system for the study of coiled-coil 4-α-helical bundles, is characterized by a remarkable structural plasticity. Loop region mutations lead to a wide range of topologies, folding states, and altered physicochemical properties. A protein-folding study of Rop and several loop variants has identified specific residues and sequences that are linked to the observed structural plasticity. Apart from the native state, native-like and molten-globule states have been identified; these states are sensitive to reducing agents due to the formation of nonnative disulfide bridges. Pro residues in the loop are critical for the establishment of new topologies and molten globule states; their effects, however, can be in part compensated by Gly residues. The extreme plasticity in the assembly of 4-α-helical bundles reflects the capacity of the Rop sequence to combine a specific set of hydrophobic residues into strikingly different hydrophobic cores. These cores include highly hydrated ones that are consistent with the formation of interchain, nonnative disulfide bridges and the establishment of molten globules. Potential applications of this structural plasticity are among others in the engineering of bio-inspired materials. PMID:25024213

Correlation between piezoresponse nonlinearity and hysteresis in ferroelectric crystals at nanoscale

DOE PAGES

Kalinin, Sergei V.; Jesse, Stephen; Yang, Yaodong; ...

2016-04-27

Here, the nonlinear response of a ferroic to external fields has been studied for decades, garnering interest for both understanding fundamental physics, as well as technological applications such as memory devices. Yet, the behavior of ferroelectrics at mesoscopic regimes remains poorly understood, and the scale limits of theories developed for macroscopic regimes are not well tested experimentally. Here, we test the link between piezo-nonlinearity and local piezoelectric strain hysteresis, via AC-field dependent measurements in conjunction with first order reversal curve (FORC) measurements on (K,Na)NbO 3 crystals with band-excitation piezoelectric force microscopy. The correlation coefficient between nonlinearity amplitude and the FORCmore » of the polarization switching shows a clear decrease in correlation with increasing AC bias, suggesting the impact of domain wall clamping on the DC measurement case. Further, correlation of polynomial fitting terms from the nonlinear measurements with the hysteresis loop area reveals that the largest correlations are reserved for the quadratic terms, which is expected for irreversible domain wall motion contributions that impact both piezoelectric behavior as well as minor loop formation. These confirm the link between local piezoelectric nonlinearity, domain wall motion and minor loop formation, and suggest that existing theories (such as Preisach) are applicable at these length scales, with associated implications for future nanoscale devices.« less

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

Kalinin, Sergei V.; Jesse, Stephen; Yang, Yaodong

Here, the nonlinear response of a ferroic to external fields has been studied for decades, garnering interest for both understanding fundamental physics, as well as technological applications such as memory devices. Yet, the behavior of ferroelectrics at mesoscopic regimes remains poorly understood, and the scale limits of theories developed for macroscopic regimes are not well tested experimentally. Here, we test the link between piezo-nonlinearity and local piezoelectric strain hysteresis, via AC-field dependent measurements in conjunction with first order reversal curve (FORC) measurements on (K,Na)NbO 3 crystals with band-excitation piezoelectric force microscopy. The correlation coefficient between nonlinearity amplitude and the FORCmore » of the polarization switching shows a clear decrease in correlation with increasing AC bias, suggesting the impact of domain wall clamping on the DC measurement case. Further, correlation of polynomial fitting terms from the nonlinear measurements with the hysteresis loop area reveals that the largest correlations are reserved for the quadratic terms, which is expected for irreversible domain wall motion contributions that impact both piezoelectric behavior as well as minor loop formation. These confirm the link between local piezoelectric nonlinearity, domain wall motion and minor loop formation, and suggest that existing theories (such as Preisach) are applicable at these length scales, with associated implications for future nanoscale devices.« less

Spectroscopic Study of a Dark Lane and a Cool Loop in a Solar Limb Active Region by Hinode/EIS

NASA Astrophysics Data System (ADS)

Lee, Kyoung-Sun; Imada, S.; Moon, Y.-J.; Lee, Jin-Yi

2014-01-01

We investigated a cool loop and a dark lane over a limb active region on 2007 March 14 using the Hinode/EUV Imaging Spectrometer. The cool loop is clearly seen in the spectral lines formed at the transition region temperature. The dark lane is characterized by an elongated faint structure in the coronal spectral lines and is rooted on a bright point. We examined their electron densities, Doppler velocities, and nonthermal velocities as a function of distance from the limb. We derived electron densities using the density sensitive line pairs of Mg VII, Si X, Fe XII, Fe XIII, and Fe XIV spectra. We also compared the observed density scale heights with the calculated scale heights from each peak formation temperatures of the spectral lines under the hydrostatic equilibrium. We noted that the observed density scale heights of the cool loop are consistent with the calculated heights, with the exception of one observed cooler temperature; we also found that the observed scale heights of the dark lane are much lower than their calculated scale heights. The nonthermal velocity in the cool loop slightly decreases along the loop, while nonthermal velocity in the dark lane sharply falls off with height. Such a decrease in the nonthermal velocity may be explained by wave damping near the solar surface or by turbulence due to magnetic reconnection near the bright point.

The 1/ N Expansion of Tensor Models Beyond Perturbation Theory

NASA Astrophysics Data System (ADS)

Gurau, Razvan

2014-09-01

We analyze in full mathematical rigor the most general quartically perturbed invariant probability measure for a random tensor. Using a version of the Loop Vertex Expansion (which we call the mixed expansion) we show that the cumulants write as explicit series in 1/ N plus bounded rest terms. The mixed expansion recasts the problem of determining the subleading corrections in 1/ N into a simple combinatorial problem of counting trees decorated by a finite number of loop edges. As an aside, we use the mixed expansion to show that the (divergent) perturbative expansion of the tensor models is Borel summable and to prove that the cumulants respect an uniform scaling bound. In particular the quartically perturbed measures fall, in the N→ ∞ limit, in the universality class of Gaussian tensor models.

Common and divergent roles of plant hormones in nodulation and arbuscular mycorrhizal symbioses.

PubMed

Foo, Eloise; Ferguson, Brett J; Reid, James B

2014-01-01

All of the classical plant hormones have been suggested to influence nodulation, including some that interact with the Autoregulation of Nodulation (AON) pathway. Leguminous plants strictly regulate the number of nodules formed through this AON pathway via a root-shoot-root loop that acts to suppress excessive nodulation. A related pathway, the Autoregulation of Mycorrhization (AOM) pathway controls the more ancient, arbuscular mycorrhizal (AM) symbiosis. A comparison of the published responses to the classical hormones in these 2 symbioses shows that most influence the symbioses in the same direction. This may be expected if they affect the symbioses via common components of these symbiotic regulatory pathways. However, some hormones influence these symbioses in opposite directions, suggesting a more complex relationship, and probably one that is not via the common components of these pathways. In a recent paper we showed, using a genetic approach, that strigolactones and brassinosteroids do not act downstream of the AON genes examined and argued that they probably act independently to promote nodule formation. Recently it has been shown that the control of nodulation via the AON pathway involves mobile CLE peptide signals. It is therefore suggested that a more direct avenue to determine if the classical hormones play a direct role in the autoregulatory pathways is to further examine whether CLE peptides and other components of these processes can influence, or be influenced by, the classical hormones. Such studies and other comparisons between the nodulation and mycorrhizal symbioses should allow the role of the classical hormones in these critical symbioses to be rapidly advanced.

Functional roles of H98 and W99 and β2α2 loop dynamics in the α-l-arabinofuranosidase from Thermobacillus xylanilyticus.

PubMed

Arab-Jaziri, Faten; Bissaro, Bastien; Barbe, Sophie; Saurel, Olivier; Débat, Hélène; Dumon, Claire; Gervais, Virginie; Milon, Alain; André, Isabelle; Fauré, Régis; O'Donohue, Michael J

2012-10-01

This study is focused on the elucidation of the functional role of the mobile β2α2 loop in the α-L-arabinofuranosidase from Thermobacillus xylanilyticus, and particularly on the roles of loop residues H98 and W99. Using site-directed mutagenesis, coupled to characterization methods including isothermal titration calorimetry (ITC) and saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy, and molecular dynamics simulations, it has been possible to provide a molecular level view of interactions and the consequences of mutations. Binding of para-nitrophenyl α-L-arabinofuranoside (pNP-α-l-Araf) to the wild-type arabinofuranosidase was characterized by K(d) values (0.32 and 0.16 mm, from ITC and STD-NMR respectively) that highly resembled that of the arabinoxylo-oligosaccharide XA(3)XX (0.21 mm), and determination of the thermodynamic parameters of enzyme : pNP-α-L-Araf binding revealed that this process is driven by favourable entropy, which is linked to the movement of the β2α2 loop. Loop closure relocates the solvent-exposed W99 into a buried location, allowing its involvement in substrate binding and in the formation of a functional active site. Similarly, the data underline the role of H98 in the ‘dynamic’ formation and definition of a catalytically operational active site, which may be a specific feature of a subset of GH51 arabinofuranosidases. Substitution of H98 and W99 by alanine or phenylalanine revealed that mutations affected K(M) and/or k(cat). Molecular dynamics performed on W99A implied that this mutation causes the loss of a hydrogen bond and leads to an alternative binding mode that is detrimental for catalysis. STD-NMR experiments revealed altered binding of the aglycon motif in the active site, combined with reduced STD intensities of the α-L-arabinofuranosyl moiety for W99 substitutions. © 2012 The Authors Journal compilation © 2012 FEBS.

Timing performance of phased-locked loops in optical pulse position modulation communication systems

NASA Technical Reports Server (NTRS)

Lafaw, D. A.; Gardner, C. S.

1984-01-01

An optical digital communication system requires that an accurate clock signal be available at the receiver for proper synchronization with the transmitted signal. Phase synchronization is especially critical in M-ary pulse position modulation (PPM) systems where the optimum decision scheme is an energy detector which compares the energy in each of M time slots to decide which of M possible words was sent. Timing errors cause energy spillover into adjacent time slots (a form of intersymbol interference) so that only a portion of the signal energy may be attributed to the correct time slot. This effect decreases the effective signal, increases the effective noise, and increases the probability of error. A timing subsystem for a satellite-to-satellite optical PPM communication link is simulated. The receiver employs direct photodetection, preprocessing of the detected signal, and a phase-locked loop for timing synchronization. The variance of the relative phase error is examined under varying signal strength conditions as an indication of loop performance, and simulation results are compared to theoretical calculations.

Timing performance of phased-locked loops in optical pulse position modulation communication systems

NASA Astrophysics Data System (ADS)

Lafaw, D. A.; Gardner, C. S.

1984-08-01

An optical digital communication system requires that an accurate clock signal be available at the receiver for proper synchronization with the transmitted signal. Phase synchronization is especially critical in M-ary pulse position modulation (PPM) systems where the optimum decision scheme is an energy detector which compares the energy in each of M time slots to decide which of M possible words was sent. Timing errors cause energy spillover into adjacent time slots (a form of intersymbol interference) so that only a portion of the signal energy may be attributed to the correct time slot. This effect decreases the effective signal, increases the effective noise, and increases the probability of error. A timing subsystem for a satellite-to-satellite optical PPM communication link is simulated. The receiver employs direct photodetection, preprocessing of the detected signal, and a phase-locked loop for timing synchronization. The variance of the relative phase error is examined under varying signal strength conditions as an indication of loop performance, and simulation results are compared to theoretical calculations.

Dynamics of visual feedback in a laboratory simulation of a penalty kick.

PubMed

Morya, Edgard; Ranvaud, Ronald; Pinheiro, Walter Machado

2003-02-01

Sport scientists have devoted relatively little attention to soccer penalty kicks, despite their decisive role in important competitions such as the World Cup. Two possible kicker strategies have been described: ignoring the goalkeeper action (open loop) or trying to react to the goalkeeper action (closed loop). We used a paradigm simulating a penalty kick in the laboratory to investigate the dynamics of the closed-loop strategy in these controlled conditions. The probability of correctly responding to the simulated goalkeeper motion as a function of time available followed a logistic curve. Kickers on average reached perfect performance only if the goalkeeper committed him or herself to one side about 400 ms before ball contact and showed chance performance if the goalkeeper motion occurred less than 150 ms before ball contact. Interestingly, coincidence judgement--another aspect of the laboratory responses--appeared to be affected for a much longer time (> 500 ms) than was needed to correctly determine laterality. The present study is meant as groundwork for experiments in more ecological conditions applicable to kickers and goalkeepers.

Conformation Changes, N-terminal Involvement, and cGMP Signal Relay in the Phosphodiesterase-5 GAF Domain*

PubMed Central

Wang, Huanchen; Robinson, Howard; Ke, Hengming

2010-01-01

The activity of phosphodiesterase-5 (PDE5) is specific for cGMP and is regulated by cGMP binding to GAF-A in its regulatory domain. To better understand the regulatory mechanism, x-ray crystallographic and biochemical studies were performed on constructs of human PDE5A1 containing the N-terminal phosphorylation segment, GAF-A, and GAF-B. Superposition of this unliganded GAF-A with the previously reported NMR structure of cGMP-bound PDE5 revealed dramatic conformational differences and suggested that helix H4 and strand B3 probably serve as two lids to gate the cGMP-binding pocket in GAF-A. The structure also identified an interfacial region among GAF-A, GAF-B, and the N-terminal loop, which may serve as a relay of the cGMP signal from GAF-A to GAF-B. N-terminal loop 98–147 was physically associated with GAF-B domains of the dimer. Biochemical analyses showed an inhibitory effect of this loop on cGMP binding and its involvement in the cGMP-induced conformation changes. PMID:20861010

Conformation changes, N-terminal involvement and cGMP signal relay in phosphodiesterase-5 GAF domain

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

Wang, H.; Robinson, H.; Ke, H.

2010-12-03

The activity of phosphodiesterase-5 (PDE5) is specific for cGMP and is regulated by cGMP binding to GAF-A in its regulatory domain. To better understand the regulatory mechanism, x-ray crystallographic and biochemical studies were performed on constructs of human PDE5A1 containing the N-terminal phosphorylation segment, GAF-A, and GAF-B. Superposition of this unliganded GAF-A with the previously reported NMR structure of cGMP-bound PDE5 revealed dramatic conformational differences and suggested that helix H4 and strand B3 probably serve as two lids to gate the cGMP-binding pocket in GAF-A. The structure also identified an interfacial region among GAF-A, GAF-B, and the N-terminal loop, whichmore » may serve as a relay of the cGMP signal from GAF-A to GAF-B. N-terminal loop 98-147 was physically associated with GAF-B domains of the dimer. Biochemical analyses showed an inhibitory effect of this loop on cGMP binding and its involvement in the cGMP-induced conformation changes.« less

Conformation Changes N-terminal Involvement and cGMP Signal Relay in the Phosphodiesterase-5 GAF Domain

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

H Wang; H Robinson; H Ke

2011-12-31

The activity of phosphodiesterase-5 (PDE5) is specific for cGMP and is regulated by cGMP binding to GAF-A in its regulatory domain. To better understand the regulatory mechanism, x-ray crystallographic and biochemical studies were performed on constructs of human PDE5A1 containing the N-terminal phosphorylation segment, GAF-A, and GAF-B. Superposition of this unliganded GAF-A with the previously reported NMR structure of cGMP-bound PDE5 revealed dramatic conformational differences and suggested that helix H4 and strand B3 probably serve as two lids to gate the cGMP-binding pocket in GAF-A. The structure also identified an interfacial region among GAF-A, GAF-B, and the N-terminal loop, whichmore » may serve as a relay of the cGMP signal from GAF-A to GAF-B. N-terminal loop 98-147 was physically associated with GAF-B domains of the dimer. Biochemical analyses showed an inhibitory effect of this loop on cGMP binding and its involvement in the cGMP-induced conformation changes.« less

Cohesin organizes chromatin loops at DNA replication factories

PubMed Central

Guillou, Emmanuelle; Ibarra, Arkaitz; Coulon, Vincent; Casado-Vela, Juan; Rico, Daniel; Casal, Ignacio; Schwob, Etienne; Losada, Ana; Méndez, Juan

2010-01-01

Genomic DNA is packed in chromatin fibers organized in higher-order structures within the interphase nucleus. One level of organization involves the formation of chromatin loops that may provide a favorable environment to processes such as DNA replication, transcription, and repair. However, little is known about the mechanistic basis of this structuration. Here we demonstrate that cohesin participates in the spatial organization of DNA replication factories in human cells. Cohesin is enriched at replication origins and interacts with prereplication complex proteins. Down-regulation of cohesin slows down S-phase progression by limiting the number of active origins and increasing the length of chromatin loops that correspond with replicon units. These results give a new dimension to the role of cohesin in the architectural organization of interphase chromatin, by showing its participation in DNA replication. PMID:21159821

The size of coronal hard X-ray sources in solar flares: How big are they?

NASA Astrophysics Data System (ADS)

Effenberger, F.; Krucker, S.; Rubio da Costa, F.

2017-12-01

Coronal hard X-ray sources are considered to be one of the key signatures of non-thermal particle acceleration and heating during the energy release in solar flares. In some cases, X-ray observations reveal multiple components spatially located near and above the loop top and even further up in the corona. Here, we combine a detailed RHESSI imaging analysis of near-limb solar flares with occulted footpoints and a multi-wavelength study of the flare loop evolution in SDO/AIA. We connect our findings to different current sheet formation and magnetic break-out scenarios and relate it to particle acceleration theory. We find that the upper and usually fainter emission regions can be underestimated in their size due to the majority of flux originating from the lower loops.

Positronium formation studies in solid molecular complexes: Triphenylphosphine oxide-triphenylmethanol

NASA Astrophysics Data System (ADS)

Oliveira, F. C.; Denadai, A. M. L.; Fulgêncio, F. H.; Magalhães, W. F.; Alcântara, A. F. C.; Windmöller, D.; Machado, J. C.

2012-06-01

Positronium formation in triphenylphosphine oxide (TPPO), triphenylmethanol (TPM), and systems [TPPO(1-X)ṡTPMX] has been studied. The low probability of positronium formation in complex [TPPO0.5ṡTPM0.5] was attributed to strong hydrogen bond and sixfold phenyl embrace interactions. These strong interactions in complex reduce the possibility of the n- and π-electrons to interact with positrons on the spur and consequently, the probability of positronium formation is lower. The τ3 parameter and free volume (correlated to τ3) were also sensitive to the formation of hydrogen bonds and sixfold phenyl embrace interactions within the complex. For physical mixture the positron annihilation parameters remained unchanged throughout the composition range.

Photochemical method for generating superoxide radicals (O.sub.2.sup.-) in aqueous solutions

DOEpatents

Holroyd, Richard A.; Bielski, Benon H. J.

1980-01-01

A photochemical method and apparatus for generating superoxide radicals (ub.2.sup.-) in an aqueous solution by means of a vacuum-ultraviolet lamp of simple design. The lamp is a microwave powered rare gas device that emits far-ultraviolet light. The lamp includes an inner loop of high purity quartz tubing through which flows an oxygen-saturated sodium formate solution. The inner loop is designed so that the solution is subjected to an intense flux of far-ultraviolet light. This causes the solution to photodecompose and form the product radical (O.sub.2.sup.-).

MHD thermal instabilities in cool inhomogeneous atmospheres

NASA Technical Reports Server (NTRS)

Bodo, G.; Ferrari, A.; Massaglia, S.; Rosner, R.

1983-01-01

The formation of a coronal state in a stellar atmosphere is investigated. A numerical code is used to study the effects of atmospheric gradients and finite loop dimension on the scale of unstable perturbations, solving for oscillatory perturbations as eigenfunctions of a boundary value problem. The atmosphere is considered as initially isothermal, with density and pressure having scale heights fixed by the hydrostatic equations. Joule mode instability is found to be an efficient mechanism for current filamentation and subsequent heating in initially cool atmospheres. This instability is mainly effective at the top of magnetic loops and is not suppressed by thermal conduction.

Toluene stability Space Station Rankine power system

NASA Technical Reports Server (NTRS)

Havens, V. N.; Ragaller, D. R.; Sibert, L.; Miller, D.

1987-01-01

A dynamic test loop is designed to evaluate the thermal stability of an organic Rankine cycle working fluid, toluene, for potential application to the Space Station power conversion unit. Samples of the noncondensible gases and the liquid toluene were taken periodically during the 3410 hour test at 750 F peak temperature. The results obtained from the toluene stability loop verify that toluene degradation will not lead to a loss of performance over the 30-year Space Station mission life requirement. The identity of the degradation products and the low rates of formation were as expected from toluene capsule test data.

Characterization of a SAM-dependent fluorinase from a latent biosynthetic pathway for fluoroacetate and 4-fluorothreonine formation in Nocardia brasiliensis

PubMed Central

Qu, Xudong

2014-01-01

Fluorination has been widely used in chemical synthesis, but is rare in nature. The only known biological fluorination scope is represented by the fl pathway from Streptomyces cattleya that produces fluoroacetate (FAc) and 4-fluorothreonine (4-FT). Here we report the identification of a novel pathway for FAc and 4-FT biosynthesis from the actinomycetoma-causing pathogen Nocardia brasiliensis ATCC 700358. The new pathway shares overall conservation with the fl pathway in S. cattleya. Biochemical characterization of the conserved domains revealed a novel fluorinase NobA that can biosynthesize 5’-fluoro-5’-deoxyadenosine (5’-FDA) from inorganic fluoride and S-adenosyl-l-methionine (SAM). The NobA shows similar halide specificity and characteristics to the fluorination enzyme FlA of the fl pathway. Kinetic parameters for fluoride ( K m 4153 μM, k cat 0.073 min -1) and SAM ( K m 416 μM, k cat 0.139 min -1) have been determined, revealing that NobA is slightly (2.3 fold) slower than FlA. Upon sequence comparison, we finally identified a distinct loop region in the fluorinases that probably accounts for the disparity of fluorination activity. PMID:24795808

Structural and functional analyses of DM43, a snake venom metalloproteinase inhibitor from Didelphis marsupialis serum.

PubMed

Neves-Ferreira, Ana G C; Perales, Jonas; Fox, Jay W; Shannon, John D; Makino, Débora L; Garratt, Richard C; Domont, Gilberto B

2002-04-12

DM43, an opossum serum protein inhibitor of snake venom metalloproteinases, has been completely sequenced, and its disulfide bond pattern has been experimentally determined. It shows homology to human alpha(1)B-glycoprotein, a plasma protein of unknown function and a member of the immunoglobulin supergene family. Size exclusion and dynamic laser light scattering data indicated that two monomers of DM43, each composed of three immunoglobulin-like domains, associated to form a homodimer in solution. Analysis of its glycan moiety showed the presence of N-acetylglucosamine, mannose, galactose, and sialic acid, most probably forming four biantennary N-linked chains. DM43 inhibited the fibrinogenolytic activities of bothrolysin and jararhagin and formed 1:1 stoichiometric stable complexes with both metalloproteinases. DM43 was ineffective against atrolysin C or A. No complex formation was detected between DM43 and jararhagin C, indicating the essential role of the metalloproteinase domain for interaction. Homology modeling based on the crystal structure of a killer cell inhibitory receptor suggested the existence of an I-type Ig fold, a hydrophobic dimerization surface and six surface loops potentially forming the metalloproteinase-binding surface on DM43.

The closing behavior of mechanical aortic heart valve prostheses.

PubMed

Lu, Po-Chien; Liu, Jia-Shing; Huang, Ren-Hong; Lo, Chi-Wen; Lai, Ho-Cheng; Hwang, Ned H C

2004-01-01

Mechanical artificial heart valves rely on reverse flow to close their leaflets. This mechanism creates regurgitation and water hammer effects that may form cavitations, damage blood cells, and cause thromboembolism. This study analyzes closing mechanisms of monoleaflet (Medtronic Hall 27), bileaflet (Carbo-Medics 27; St. Jude Medical 27; Duromedics 29), and trileaflet valves in a circulatory mock loop, including an aortic root with three sinuses. Downstream flow field velocity was measured via digital particle image velocimetry (DPIV). A high speed camera (PIVCAM 10-30 CCD video camera) tracked leaflet movement at 1000 frames/s. All valves open in 40-50 msec, but monoleaflet and bileaflet valves close in much less time (< 35 msec) than the trileaflet valve (>75 msec). During acceleration phase of systole, the monoleaflet forms a major and minor flow, the bileaflet has three jet flows, and the trileaflet produces a single central flow like physiologic valves. In deceleration phase, the aortic sinus vortices hinder monoleaflet and bileaflet valve closure until reverse flows and high negative transvalvular pressure push the leaflets rapidly for a hard closure. Conversely, the vortices help close the trileaflet valve more softly, probably causing less damage, lessening back flow, and providing a washing effect that may prevent thrombosis formation.

Analytical expressions for the closure probability of a stiff wormlike chain for finite capture radius.

PubMed

Guérin, T

2017-08-01

Estimating the probability that two monomers of the same polymer chain are close together is a key ingredient to characterize intramolecular reactions and polymer looping. In the case of stiff wormlike polymers (rigid fluctuating elastic rods), for which end-to-end encounters are rare events, we derive an explicit analytical formula for the probability η(r_{c}) that the distance between the chain extremities is smaller than some capture radius r_{c}. The formula is asymptotically exact in the limit of stiff chains, and it leads to the identification of two distinct scaling regimes for the closure factor, originating from a strong variation of the fluctuations of the chain orientation at closure. Our theory is compatible with existing analytical results from the literature that cover the cases of a vanishing capture radius and of nearly fully extended chains.

EVIDENCE FOR EVAPORATION-INCOMPLETE CONDENSATION CYCLES IN WARM SOLAR CORONAL LOOPS

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

Froment, C.; Auchère, F.; Bocchialini, K.

2015-07-10

Quasi-constant heating at the footpoints of loops leads to evaporation and condensation cycles of the plasma: thermal non-equilibrium (TNE). This phenomenon is believed to play a role in the formation of prominences and coronal rain. However, it is often discounted as being involved in the heating of warm loops because the models do not reproduce observations. Recent simulations have shown that these inconsistencies with observations may be due to oversimplifications of the geometries of the models. In addition, our recent observations reveal that long-period intensity pulsations (several hours) are common in solar coronal loops. These periods are consistent with thosemore » expected from TNE. The aim of this paper is to derive characteristic physical properties of the plasma for some of these events to test the potential role of TNE in loop heating. We analyzed three events in detail using the six EUV coronal channels of the Solar Dynamics Observatory/Atmospheric Imaging Assembly. We performed both a differential emission measure (DEM) and a time-lag analysis, including a new method to isolate the relevant signal from the foreground and background emission. For the three events, the DEM undergoes long-period pulsations, which is a signature of periodic heating even though the loops are captured in their cooling phase, as is the bulk of the active regions. We link long-period intensity pulsations to new signatures of loop heating with strong evidence for evaporation and condensation cycles. We thus simultaneously witness widespread cooling and TNE. Finally, we discuss the implications of our new observations for both static and impulsive heating models.« less

LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length.

PubMed

Bao, Yu; Hayashida, Morihiro; Akutsu, Tatsuya

2016-11-25

Dicer is necessary for the process of mature microRNA (miRNA) formation because the Dicer enzyme cleaves pre-miRNA correctly to generate miRNA with correct seed regions. Nonetheless, the mechanism underlying the selection of a Dicer cleavage site is still not fully understood. To date, several studies have been conducted to solve this problem, for example, a recent discovery indicates that the loop/bulge structure plays a central role in the selection of Dicer cleavage sites. In accordance with this breakthrough, a support vector machine (SVM)-based method called PHDCleav was developed to predict Dicer cleavage sites which outperforms other methods based on random forest and naive Bayes. PHDCleav, however, tests only whether a position in the shift window belongs to a loop/bulge structure. In this paper, we used the length of loop/bulge structures (in addition to their presence or absence) to develop an improved method, LBSizeCleav, for predicting Dicer cleavage sites. To evaluate our method, we used 810 empirically validated sequences of human pre-miRNAs and performed fivefold cross-validation. In both 5p and 3p arms of pre-miRNAs, LBSizeCleav showed greater prediction accuracy than PHDCleav did. This result suggests that the length of loop/bulge structures is useful for prediction of Dicer cleavage sites. We developed a novel algorithm for feature space mapping based on the length of a loop/bulge for predicting Dicer cleavage sites. The better performance of our method indicates the usefulness of the length of loop/bulge structures for such predictions.

Design and implementation of satellite formations and constellations

NASA Technical Reports Server (NTRS)

Folta, David; Newman, Lauri Kraft; Quinn, David

1998-01-01

The direction to develop small low cost spacecraft has led many scientists to recognize the advantage of flying spacecraft in constellations and formations to achieve the correlated instrument measurements formerly possible only by flying many instruments on a single large platform. Yet, constellations and formation flying impose additional complications on orbit selection and orbit maintenance, especially when each spacecraft has its own orbit or science requirements. The purpose of this paper is to develop an operational control method for maintenance of these missions. Examples will be taken from the Earth Observing-1 (EO-1) spacecraft that is part of the New Millennium Program (NMP) and from proposed Earth System Science Program Office (ESSPO) constellations. Results can be used to determine the appropriateness of constellations and formation flying for a particular case as well as the operational impacts. Applications to the ESSPO and NMP are highly considered in analysis and applications. After constellation and formation analysis is completed, implementation of a maneuver maintenance strategy becomes the driver. Advances in technology and automation by GSFC's Guidance, Navigation, and Control Center allow more of the burden of the orbit selection and maneuver maintenance to be automated and ultimately placed onboard the spacecraft, mitigating most of the associated operational concerns. This paper presents the GSFC closed-loop control method to fly in either constellations or formations through the use of an autonomous closed loop three-axis navigation control and innovative orbit maintenance support. Simulation results using AutoCon(TM) and FreeFlyer(TM) with various fidelity levels of modeling and algorithms are presented.

Design and Implementation of Satellite Formations and Constellations

NASA Technical Reports Server (NTRS)

Folta, David; Newman, Lauri Kraft; Quinn, David

1998-01-01

The direction to develop small low cost spacecraft has led many scientists to recognize the advantage of flying spacecraft in constellations and formations to achieve the correlated instrument measurements formerly possible only by flying many instruments on a single large platform. Yet, constellations and formation flying impose additional complications on orbit selection and orbit maintenance, especially when each spacecraft has its own orbit or science requirements. The purpose of this paper is to develop an operational control method for maintenance of these missions. Examples will be taken from the Earth Observing-1 (EO-1) spacecraft that is part of the New Millennium Program (NMP) and from proposed Earth System Science Program Office (ESSPO) constellations. Results can be used to determine the appropriateness of constellations and formation flying for a particular case as well as the operational impacts. Applications to the ESSPO and NMP are highly considered in analysis and applications. After constellation and formation analysis is completed, implementation of a maneuver maintenance strategy becomes the driver. Advances in technology and automation by GSFC's Guidance, Navigation, and Control Center allow more of the burden of the orbit selection and maneuver maintenance to be automated and ultimately placed onboard the spacecraft, mitigating most of the associated operational concerns. This paper presents the GSFC closed-loop control method to fly in either constellations or formations through the use of an autonomous closed loop three-axis navigation control and innovative orbit maintenance support. Simulation results using AutoCon(Trademark) and FreeFlyer(Trademark) with various fidelity levels of modeling and algorithms are presented.

DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner.

PubMed

Wiedemann, Eva-Maria; Peycheva, Mihaela; Pavri, Rushad

2016-12-13

Class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) locus generates antibody isotypes. CSR depends on double-strand breaks (DSBs) induced by activation-induced cytidine deaminase (AID). Although DSB formation and repair machineries are active in G1 phase, efficient CSR is dependent on cell proliferation and S phase entry; however, the underlying mechanisms are obscure. Here, we show that efficient CSR requires the replicative helicase, the Mcm complex. Mcm proteins are enriched at IgH switch regions during CSR, leading to assembly of facultative replication origins that require Mcm helicase function for productive CSR. Assembly of CSR-associated origins is facilitated by R loops and promotes the physical proximity (synapsis) of recombining switch regions, which is reduced by R loop inhibition or Mcm complex depletion. Thus, R loops contribute to replication origin specification that promotes DSB resolution in CSR. This suggests a mechanism for the dependence of CSR on S phase and cell division. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Chemical Looping Autothermal Reforming at a 120 kW Pilot Rig

NASA Astrophysics Data System (ADS)

Bofhàr-Nordenkampf, Johannes; Pröll, Tobias; Kolbitsch, Philipp; Hofbauer, Hermann

Chemical looping with selective oxygen transport allows two step combustion or autothermal reforming without mixing of fuel and air. The reactor system consists of two reactors, an air reactor and a fuel reactor with a suitable oxygen carrier that transports the necessary oxygen for operation. In the present study, a highly active nickel based oxygen carrier is tested in a novel dual circulating fluidized bed (DCFB) system at a scale of 120 kW fuel power. The mean particle size of the oxygen carrier is 120 μm and the pilot rig is fueled with natural gas. For the investigated oxygen carrier high CH4 conversion is achieved. Air/fuel ratio is varied at three different fuel reactor temperatures. For chemical looping reforming one can observe synthesis gas composition close to thermodynamic equilibrium. In spite of the fact that no additional steam has been added to the fuel besides the one present through steam fluidization of the loop seals, coke formation does not occur at global stoichiometric air/fuel ratios above 0.46.

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

PubMed Central

Chen, Alan A.; García, Angel E.

2013-01-01

We report the de novo folding of three hyperstable RNA tetraloops to 1–3 Å rmsd from their experimentally determined structures using molecular dynamics simulations initialized in the unfolded state. RNA tetraloops with loop sequences UUCG, GCAA, or CUUG are hyperstable because of the formation of noncanonical loop-stabilizing interactions, and they are all faithfully reproduced to angstrom-level accuracy in replica exchange molecular dynamics simulations, including explicit solvent and ion molecules. This accuracy is accomplished using unique RNA parameters, in which biases that favor rigid, highly stacked conformations are corrected to accurately capture the inherent flexibility of ssRNA loops, accurate base stacking energetics, and purine syn-anti interconversions. In a departure from traditional quantum chemistrycentric approaches to force field optimization, our parameters are calibrated directly from thermodynamic and kinetic measurements of intra- and internucleotide structural transitions. The ability to recapitulate the signature noncanonical interactions of the three most abundant hyperstable stem loop motifs represents a significant milestone to the accurate prediction of RNA tertiary structure using unbiased all-atom molecular dynamics simulations. PMID:24043821

The irradiation-induced microstructural development and the role of γ' on void formation in Ni-based alloys

NASA Astrophysics Data System (ADS)

Kato, Takahiko; Nakata, Kiyotomo; Masaoka, Isao; Takahashi, Heishichiro; Takeyama, Taro; Ohnuki, Soumei; Osanai, Hisashi

1984-05-01

The microstructural development for Inconel X-750, N1-13 at%A1, and Ni-11.5 at%Si alloys during irradiation was investigated. These alloys were previously heat-treated at temperatures of 723-1073 K, and γ' precipitates were produced. Irradiation was performed in a high voltage electron microscope (1000 kV) in the temperature range 673-823 K. In the case of solution-treated Inconel, interstitial dislocation loops were formed initially, while voids were nucleated after longer times. When the Inconel specimen containing a high number density of small γ' was irradiated, dislocation loops were formed in both the matrix and precipitate-matrix interface. The loops formed on the interface scarcely grew during irradiation. On the other hand, for the Ni-Al alloy fine γ' nucleated during irradiation, the large γ' precipitated by pre-aging, dissolved. A similar resolution process was also observed in Ni-Si alloy. Furthermore, in the Ni-Si alloy precipitates of γ' formed preferentially at interstitial dislocation loops and both specimen surfaces.

RTEL1 dismantles T loops and counteracts telomeric G4-DNA to maintain telomere integrity.

PubMed

Vannier, Jean-Baptiste; Pavicic-Kaltenbrunner, Visnja; Petalcorin, Mark I R; Ding, Hao; Boulton, Simon J

2012-05-11

T loops and telomeric G-quadruplex (G4) DNA structures pose a potential threat to genome stability and must be dismantled to permit efficient telomere replication. Here we implicate the helicase RTEL1 in the removal of telomeric DNA secondary structures, which is essential for preventing telomere fragility and loss. In the absence of RTEL1, T loops are inappropriately resolved by the SLX4 nuclease complex, resulting in loss of the telomere as a circle. Depleting SLX4 or blocking DNA replication abolished telomere circles (TCs) and rescued telomere loss in RTEL1(-/-) cells but failed to suppress telomere fragility. Conversely, stabilization of telomeric G4-DNA or loss of BLM dramatically enhanced telomere fragility in RTEL1-deficient cells but had no impact on TC formation or telomere loss. We propose that RTEL1 performs two distinct functions at telomeres: it disassembles T loops and also counteracts telomeric G4-DNA structures, which together ensure the dynamics and stability of the telomere. Copyright © 2012 Elsevier Inc. All rights reserved.

The effects of intraparticle and interparticle interactions on the magnetic hysteresis loop of frozen suspensions of bionized nanoferrite particles

NASA Astrophysics Data System (ADS)

Boekelheide, Zoe; Gruettner, Cordula; Dennis, Cindi

Bionized nano-ferrite (iron oxide/dextran) nanoparticles have been shown to have a large heating response in an alternating magnetic field, making them very promising for applications in magnetic nanoparticle hyperthermia cancer treatment. Magnetic hysteresis loop measurements of these particles provide insight into the magnetic reversal behavior of these particles, and thus their heating response. Measurements have been performed on frozen suspensions of nanoparticles dispersed in H2O, which have been frozen in a range of applied fields in order to tune the interparticle dipolar interactions through formation of linear chains. These experimental results are compared with micromagnetic models of both monolithic (single-domain) and internally structured (multi-grain) particles. It is found that the internal structure of the nanoparticles, which are made up of parallelepiped-shaped grains, is important for describing the magnetic reversal behavior of the particles and the resulting shape of the hysteresis loops. In addition to this, interparticle interactions between particles in a linear chain modify the reversal behavior and thus the shape of the hysteresis loop.

Assisted closed-loop optimization of SSVEP-BCI efficiency

PubMed Central

Fernandez-Vargas, Jacobo; Pfaff, Hanns U.; Rodríguez, Francisco B.; Varona, Pablo

2012-01-01

We designed a novel assisted closed-loop optimization protocol to improve the efficiency of brain-computer interfaces (BCI) based on steady state visually evoked potentials (SSVEP). In traditional paradigms, the control over the BCI-performance completely depends on the subjects' ability to learn from the given feedback cues. By contrast, in the proposed protocol both the subject and the machine share information and control over the BCI goal. Generally, the innovative assistance consists in the delivery of online information together with the online adaptation of BCI stimuli properties. In our case, this adaptive optimization process is realized by (1) a closed-loop search for the best set of SSVEP flicker frequencies and (2) feedback of actual SSVEP magnitudes to both the subject and the machine. These closed-loop interactions between subject and machine are evaluated in real-time by continuous measurement of their efficiencies, which are used as online criteria to adapt the BCI control parameters. The proposed protocol aims to compensate for variability in possibly unknown subjects' state and trait dimensions. In a study with N = 18 subjects, we found significant evidence that our protocol outperformed classic SSVEP-BCI control paradigms. Evidence is presented that it takes indeed into account interindividual variabilities: e.g., under the new protocol, baseline resting state EEG measures predict subjects' BCI performances. This paper illustrates the promising potential of assisted closed-loop protocols in BCI systems. Probably their applicability might be expanded to innovative uses, e.g., as possible new diagnostic/therapeutic tools for clinical contexts and as new paradigms for basic research. PMID:23443214

Assisted closed-loop optimization of SSVEP-BCI efficiency.

PubMed

Fernandez-Vargas, Jacobo; Pfaff, Hanns U; Rodríguez, Francisco B; Varona, Pablo

2013-01-01

We designed a novel assisted closed-loop optimization protocol to improve the efficiency of brain-computer interfaces (BCI) based on steady state visually evoked potentials (SSVEP). In traditional paradigms, the control over the BCI-performance completely depends on the subjects' ability to learn from the given feedback cues. By contrast, in the proposed protocol both the subject and the machine share information and control over the BCI goal. Generally, the innovative assistance consists in the delivery of online information together with the online adaptation of BCI stimuli properties. In our case, this adaptive optimization process is realized by (1) a closed-loop search for the best set of SSVEP flicker frequencies and (2) feedback of actual SSVEP magnitudes to both the subject and the machine. These closed-loop interactions between subject and machine are evaluated in real-time by continuous measurement of their efficiencies, which are used as online criteria to adapt the BCI control parameters. The proposed protocol aims to compensate for variability in possibly unknown subjects' state and trait dimensions. In a study with N = 18 subjects, we found significant evidence that our protocol outperformed classic SSVEP-BCI control paradigms. Evidence is presented that it takes indeed into account interindividual variabilities: e.g., under the new protocol, baseline resting state EEG measures predict subjects' BCI performances. This paper illustrates the promising potential of assisted closed-loop protocols in BCI systems. Probably their applicability might be expanded to innovative uses, e.g., as possible new diagnostic/therapeutic tools for clinical contexts and as new paradigms for basic research.

Worldline approach to helicity flip in plane waves

NASA Astrophysics Data System (ADS)

Ilderton, Anton; Torgrimsson, Greger

2016-04-01

We apply worldline methods to the study of vacuum polarization effects in plane wave backgrounds, in both scalar and spinor QED. We calculate helicity-flip probabilities to one loop order and treated exactly in the background field, and provide a toolkit of methods for use in investigations of higher-order processes. We also discuss the connections between the worldline, S-matrix, and lightfront approaches to vacuum polarization effects.

Imaging basal ganglia function

PubMed Central

BROOKS, DAVID J.

2000-01-01

In this review, the value of functional imaging for providing insight into the role of the basal ganglia in motor control is reviewed. Brain activation findings in normal subjects and Parkinson's disease patients are examined and evidence supporting the existence for functionally independent distributed basal ganglia-frontal loops is presented. It is argued that the basal ganglia probably act to focus and filter cortical output, optimising the running of motor programs. PMID:10923986

Topographic-baroclinic instability and formation of Kuroshio current loop

NASA Astrophysics Data System (ADS)

Guo, Jingsong; Zhang, Zhixin; Xia, Changshui; Guo, Binghuo; Yuan, Yeli

2018-03-01

Using time-series figures of sea-level anomaly and geostrophic currents from merged absolute dynamic topography, we analyzed the formation and evolution of the Kuroshio current loop (KCL). The main results are as follows. Perturbation origins of the KCLs are in three areas (eastern, western, and southern) surrounding the Hengchun Submarine Ridge. There are two basic types of KCL formation, i.e., "Kuroshio bend pushing" and "Kuroshio Branch rewinding", plus their combination. The KCLs propagate westward at 1.6-4.5 cm/s. There are two forms of KCL evolution into a shed eddy. The first is such that the northern KCL section initially divides to become an eddy joining the Kuroshio Branch current, which then separates from that current to become a shed eddy. The second form is such that the northern and southern sections of the KCL are separated almost simultaneously in westward elongated process. To understand the KCL formation mechanism, we derive linear equations in phase space from the governing equations in σ-coordinates, ultimately obtaining two groups of analytical solutions for interactions between waves, topography, and the basic current field. The solutions lead to the following results. The KCL propagates westward with the group velocity of the Kuroshio center region. The Kuroshio generally sweeps over the Hengchun Submarine Ridge, especially in winter, such that there is topographic-baroclinic instability. The analytical solutions effectively reveal the dynamic mechanism of the two basic types of KCL formation.

Diagnostic potential of multi-targeted LAMP (loop-mediated isothermal amplification) for osteoarticular tuberculosis.

PubMed

Sharma, Kusum; Sharma, Megha; Batra, Nitya; Sharma, Aman; Dhillon, Mandeep Singh

2017-02-01

Delay in diagnosing osteoarticular tuberculosis (OATB) contributes significantly to morbidity by causing disfiguration and neurological sequelae. The delay caused by conventional culture and the expertise and expense involved in other nucleic acid based tests, make LAMP (loop-mediated isothermal amplification) assay a favorable middle path. We evaluated LAMP assay using IS6110 and MPB64 for rapid diagnosis of OATB by comparing with IS6110 PCR and culture. LAMP assay was performed on 140 synovial fluid and pus samples (10 culture-positive proven cases, 80 culture-negative probable cases, and 50 negative controls) using three set of primer pairs each for IS6110 and MPB64. LAMP assay, using two-target approach, had an overall sensitivity and specificity of 90% and 100% in detecting OATB. Sensitivity of IS6110 PCR, IS6110 LAMP, and MPB64 LAMP was 80%, 100%, and 100%, respectively, for confirmed cases and 72.5%, 81.75%, and 86.25%, respectively, for probable cases. Six additional cases were picked using two-target approach. LAMP assay utilizing IS6110 and MPB64 is a cost-effective technique for an early and reliable diagnosis of OATB. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:361-365, 2017. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

GNSS Signal Tracking Performance Improvement for Highly Dynamic Receivers by Gyroscopic Mounting Crystal Oscillator.

PubMed

Abedi, Maryam; Jin, Tian; Sun, Kewen

2015-08-31

In this paper, the efficiency of the gyroscopic mounting method is studied for a highly dynamic GNSS receiver's reference oscillator for reducing signal loss. Analyses are performed separately in two phases, atmospheric and upper atmospheric flights. Results show that the proposed mounting reduces signal loss, especially in parts of the trajectory where its probability is the highest. This reduction effect appears especially for crystal oscillators with a low elevation angle g-sensitivity vector. The gyroscopic mounting influences frequency deviation or jitter caused by dynamic loads on replica carrier and affects the frequency locked loop (FLL) as the dominant tracking loop in highly dynamic GNSS receivers. In terms of steady-state load, the proposed mounting mostly reduces the frequency deviation below the one-sigma threshold of FLL (1σ(FLL)). The mounting method can also reduce the frequency jitter caused by sinusoidal vibrations and reduces the probability of signal loss in parts of the trajectory where the other error sources accompany this vibration load. In the case of random vibration, which is the main disturbance source of FLL, gyroscopic mounting is even able to suppress the disturbances greater than the three-sigma threshold of FLL (3σ(FLL)). In this way, signal tracking performance can be improved by the gyroscopic mounting method for highly dynamic GNSS receivers.

Development and testing of fiber-reinforced composite space maintainers.

PubMed

Kulkarni, Gajanan; Lau, Domenic; Hafezi, Sara

2009-01-01

The purpose of this study was to develop a clinically acceptable, cheaper, and more expedient alternative to standard stainless steel band and loop space maintainers. Loops of fiber-reinforced composites were constructed using polyethylene fiber (Ribbond) and glass fiber (Sticktech). The loops were bonded on extracted third molars and tested for flexural strength before and after thermocycling and following repair of the appliances after initial stress failure. Bacterial colonization on the appliances was also compared. Conventional stainless steel band and loop space maintainers cemented with Ketac were controls. Ribbond samples demonstrated higher flexural strength than Sticktech and the control (P<.05). No differences were noted among the other samples and the control. The repaired Ribbond samples were statistically comparable in flexural strength to the initial samples. Thermocycling resulted in decreased flexural strength of both Ribbond and Sticktech (P<.05). Thermocycled Ribbond samples were comparable to the control, but a lower flexural strength was noted for Sticktech samples (P<.05). While all space maintainers allowed some bacterial adhesion, Sticktech showed higher Streptococcus mutans counts than Ribbond (P=.06). Ribbond space-maintainers are comparable to the stainless steel in terms of physical strength and biofilm formation. The fiber-reinforced composite space maintainers may be a clinically acceptable and expedient alternative to the conventional band-loop appliance.

Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites

PubMed Central

Piazza, Aurèle; Adrian, Michael; Samazan, Frédéric; Heddi, Brahim; Hamon, Florian; Serero, Alexandre; Lopes, Judith; Teulade-Fichou, Marie-Paule; Phan, Anh Tuân; Nicolas, Alain

2015-01-01

G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids, with various biological roles. However, structural features dictating their formation and/or functionin vivo are unknown. InS. cerevisiae, the pathological persistency of G4 within the CEB1 minisatellite induces its rearrangement during leading-strand replication. We now show that several other G4-forming sequences remain stable. Extensive mutagenesis of the CEB25 minisatellite motif reveals that only variants with very short (≤ 4 nt) G4 loops preferentially containing pyrimidine bases trigger genomic instability. Parallel biophysical analyses demonstrate that shortening loop length does not change the monomorphic G4 structure of CEB25 variants but drastically increases its thermal stability, in correlation with thein vivo instability. Finally, bioinformatics analyses reveal that the threat for genomic stability posed by G4 bearing short pyrimidine loops is conserved inC. elegans and humans. This work provides a framework explanation for the heterogeneous instability behavior of G4-forming sequencesin vivo, highlights the importance of structure thermal stability, and questions the prevailing assumption that G4 structures with short or longer loops are as likely to formin vivo. PMID:25956747

Determination of Reaction Stoichiometries by Flow Injection Analysis.

ERIC Educational Resources Information Center

Rios, Angel; And Others

1986-01-01

Describes a method of flow injection analysis intended for calculation of complex-formation and redox reaction stoichiometries based on a closed-loop configuration. The technique is suitable for use in undergraduate laboratories. Information is provided for equipment, materials, procedures, and sample results. (JM)

NON-POTENTIAL FIELDS IN THE QUIET SUN NETWORK: EXTREME-ULTRAVIOLET AND MAGNETIC FOOTPOINT OBSERVATIONS

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

Chesny, D. L.; Oluseyi, H. M.; Orange, N. B.

The quiet Sun (QS) magnetic network is known to contain dynamics which are indicative of non-potential fields. Non-potential magnetic fields forming ''S-shaped'' loop arcades can lead to the breakdown of static activity and have only been observed in high temperature X-ray coronal structures—some of which show eruptive behavior. Thus, analysis of this type of atmospheric structuring has been restricted to large-scale coronal fields. Here we provide the first identification of non-potential loop arcades exclusive to the QS supergranulation network. High-resolution Atmospheric Imaging Assembly data from the Solar Dynamics Observatory have allowed for the first observations of fine-scale ''S-shaped'' loop arcadesmore » spanning the network. We have investigated the magnetic footpoint flux evolution of these arcades from Heliospheric and Magnetic Imager data and find evidence of evolving footpoint flux imbalances accompanying the formation of these non-potential fields. The existence of such non-potentiality confirms that magnetic field dynamics leading to the build up of helicity exist at small scales. QS non-potentiality also suggests a self-similar formation process between the QS network and high temperature corona and the existence of self-organized criticality (SOC) in the form of loop-pair reconnection and helicity dissipation. We argue that this type of behavior could lead to eruptive forms of SOC as seen in active region (AR) and X-ray sigmoids if sufficient free magnetic energy is available. QS magnetic network dynamics may be considered as a coronal proxy at supergranular scales, and events confined to the network can even mimic those in coronal ARs.« less

Mediator and Cohesin Connect Gene Expression and Chromatin Architecture

PubMed Central

Kagey, Michael H.; Newman, Jamie J.; Bilodeau, Steve; Zhan, Ye; Orlando, David A.; van Berkum, Nynke L.; Ebmeier, Christopher C.; Goossens, Jesse; Rahl, Peter B.; Levine, Stuart S.; Taatjes, Dylan J.; Dekker, Job; Young, Richard A.

2010-01-01

Summary Transcription factors control cell specific gene expression programs through interactions with diverse coactivators and the transcription apparatus. Gene activation may involve DNA loop formation between enhancer-bound transcription factors and the transcription apparatus at the core promoter, but this process is not well understood. We report here that Mediator and Cohesin physically and functionally connect the enhancers and core promoters of active genes in embryonic stem cells. Mediator, a transcriptional coactivator, forms a complex with Cohesin, which can form rings that connect two DNA segments. The Cohesin loading factor Nipbl is associated with Mediator/Cohesin complexes, providing a means to load Cohesin at promoters. DNA looping is observed between the enhancers and promoters occupied by Mediator and Cohesin. Mediator and Cohesin occupy different promoters in different cells, thus generating cell-type specific DNA loops linked to the gene expression program of each cell. PMID:20720539

Post Flare Giant Arches and Run-Away Reconnection

NASA Astrophysics Data System (ADS)

West, Matthew; Seaton, Daniel B.; Savage, Sabrina; Bryans, Paul

2016-05-01

The nature of post-flare giant arches and their relation to regular post flare loops has long been debated, especially in the context of how post-flare giant arches can sustain their growth for such long periods. In this presentation we discuss how magnetic reconnection can be sustained to such great heights, and the role the background corona plays in maintaining this growth. We use observations from 14 October 2014, when the SWAP EUV solar telescope on-board the PROBA2 spacecraft observed an eruption that led to the formation of perhaps the largest post-eruptive loop system seen in the solar corona in solar cycle 24. These loops grew to a height of approximately 400000 km (>0.5 solar-radii). We provide evidence of on-going reconnection, through observations spanning from the chromosphere to the middle corona, and discuss how only certain conditions can maintain prolonged growth.

Looped star polymers show conformational transition from spherical to flat toroidal shapes.

PubMed

Reiss, Pascal; Fritsche, Miriam; Heermann, Dieter W

2011-11-01

Inspired by the topological organization of the circular Escherichia coli chromosome, which is compacted by separate domains, we study a polymer architecture consisting of a central ring to which either looped or linear side chains are grafted. A shape change from a spherical to a toroidal organization takes place as soon as the inner ring becomes large enough for the attached arms to fit within its circumference. Building up a torus, the system flattens, depending on the effective bending rigidity of the chain induced by entropic repulsion of the attached loops and, to a lesser extent, linear arms. Our results suggest that the natural formation of a toroidal structure with a decreased amount of writhe induced by a specific underlying topology could be one driving force, among others, that nature exploits to ensure proper packaging of the genetic material within a rod-shaped, bacterial envelope.

Optimization of block-floating-point realizations for digital controllers with finite-word-length considerations.

PubMed

Wu, Jun; Hu, Xie-he; Chen, Sheng; Chu, Jian

2003-01-01

The closed-loop stability issue of finite-precision realizations was investigated for digital controllers implemented in block-floating-point format. The controller coefficient perturbation was analyzed resulting from using finite word length (FWL) block-floating-point representation scheme. A block-floating-point FWL closed-loop stability measure was derived which considers both the dynamic range and precision. To facilitate the design of optimal finite-precision controller realizations, a computationally tractable block-floating-point FWL closed-loop stability measure was then introduced and the method of computing the value of this measure for a given controller realization was developed. The optimal controller realization is defined as the solution that maximizes the corresponding measure, and a numerical optimization approach was adopted to solve the resulting optimal realization problem. A numerical example was used to illustrate the design procedure and to compare the optimal controller realization with the initial realization.

Space Shuttle program communication and tracking systems interface analysis

NASA Technical Reports Server (NTRS)

Dodds, J. G.; Holmes, J. K.; Huth, G. K.; Iwasaki, R. S.; Nilsen, P. W.; Polydoros, A.; Sampaio, D. R.; Udalov, S.

1984-01-01

The Space Shuttle Program Communications and Tracking Systems Interface Analysis began April 18, 1983. During this time, the shuttle communication and tracking systems began flight testing. Two areas of analysis documented were a result of observations made during flight tests. These analyses involved the Ku-band communication system. First, there was a detailed analysis of the interface between the solar max data format and the Ku-band communication system including the TDRSS ground station. The second analysis involving the Ku-band communication system was an analysis of the frequency lock loop of the Gunn oscillator used to generate the transmit frequency. The stability of the frequency lock loop was investigated and changes to the design were reviewed to alleviate the potential loss of data due the loop losing lock and entering the reacquisition mode. Other areas of investigation were the S-band antenna analysis and RF coverage analysis.

Adaptive PID formation control of nonholonomic robots without leader's velocity information.

PubMed

Shen, Dongbin; Sun, Weijie; Sun, Zhendong

2014-03-01

This paper proposes an adaptive proportional integral derivative (PID) algorithm to solve a formation control problem in the leader-follower framework where the leader robot's velocities are unknown for the follower robots. The main idea is first to design some proper ideal control law for the formation system to obtain a required performance, and then to propose the adaptive PID methodology to approach the ideal controller. As a result, the formation is achieved with much more enhanced robust formation performance. The stability of the closed-loop system is theoretically proved by Lyapunov method. Both numerical simulations and physical vehicle experiments are presented to verify the effectiveness of the proposed adaptive PID algorithm. Copyright © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

In situ conversion process utilizing a closed loop heating system

DOEpatents

Sandberg, Chester Ledlie [Palo Alto, CA; Fowler, Thomas David [Houston, TX; Vinegar, Harold J [Bellaire, TX; Schoeber, Willen Jan Antoon Henri

2009-08-18

An in situ conversion system for producing hydrocarbons from a subsurface formation is described. The system includes a plurality of u-shaped wellbores in the formation. Piping is positioned in at least two of the u-shaped wellbores. A fluid circulation system is coupled to the piping. The fluid circulation system is configured to circulate hot heat transfer fluid through at least a portion of the piping to form at least one heated portion of the formation. An electrical power supply is configured to provide electrical current to at least a portion of the piping located below an overburden in the formation to resistively heat at least a portion of the piping. Heat transfers from the piping to the formation.

Model of the Reticular Formation of the Brainstem Based on Glial-Neuronal Interactions.

PubMed

Mitterauer, Bernhard J

A new model of the reticular formation of the brainstem is proposed. It refers to the neuronal and glial cell systems. Thus, it is biomimetically founded. The reticular formation generates modes of behavior (sleeping, eating, etc.) and commands all behavior according to the most appropriate environmental information. The reticular formation works on an abductive logic and is dominated by a redundancy of potential command. Formally, a special mode of behavior is represented by a comprehensive cycle (Hamilton loop) located in the glial network (syncytium) and embodied in gap junctional plaques. Whereas for the neuronal network of the reticular formation, a computer simulation has already been presented; here, the necessary devices for computation in the whole network are outlined.

Vital Roles of the Second DNA-binding Site of Rad52 Protein in Yeast Homologous Recombination*

PubMed Central

Arai, Naoto; Kagawa, Wataru; Saito, Kengo; Shingu, Yoshinori; Mikawa, Tsutomu; Kurumizaka, Hitoshi; Shibata, Takehiko

2011-01-01

RecA/Rad51 proteins are essential in homologous DNA recombination and catalyze the ATP-dependent formation of D-loops from a single-stranded DNA and an internal homologous sequence in a double-stranded DNA. RecA and Rad51 require a “recombination mediator” to overcome the interference imposed by the prior binding of single-stranded binding protein/replication protein A to the single-stranded DNA. Rad52 is the prototype of recombination mediators, and the human Rad52 protein has two distinct DNA-binding sites: the first site binds to single-stranded DNA, and the second site binds to either double- or single-stranded DNA. We previously showed that yeast Rad52 extensively stimulates Rad51-catalyzed D-loop formation even in the absence of replication protein A, by forming a 2:1 stoichiometric complex with Rad51. However, the precise roles of Rad52 and Rad51 within the complex are unknown. In the present study, we constructed yeast Rad52 mutants in which the amino acid residues corresponding to the second DNA-binding site of the human Rad52 protein were replaced with either alanine or aspartic acid. We found that the second DNA-binding site is important for the yeast Rad52 function in vivo. Rad51-Rad52 complexes consisting of these Rad52 mutants were defective in promoting the formation of D-loops, and the ability of the complex to associate with double-stranded DNA was specifically impaired. Our studies suggest that Rad52 within the complex associates with double-stranded DNA to assist Rad51-mediated homologous pairing. PMID:21454474

Mechanisms of radiation embrittlement of VVER-1000 RPV steel at irradiation temperatures of (50-400)°C

NASA Astrophysics Data System (ADS)

Kuleshova, E. A.; Gurovich, B. A.; Bukina, Z. V.; Frolov, A. S.; Maltsev, D. A.; Krikun, E. V.; Zhurko, D. A.; Zhuchkov, G. M.

2017-07-01

This work summarizes and analyzes our recent research results on the effect of irradiation temperature within the range of (50-400)°C on microstructure and properties of 15Kh2NMFAA class 1 steel (VVER-1000 reactor pressure vessel (RPV) base metal). The paper considers the influence of accelerated irradiation with different temperature up to different fluences on the carbide and irradiation-induced phases, radiation defects, yield strength changes and critical brittleness temperature shift (ΔTK) as well as on changes of the fraction of brittle intergranular fracture and segregation processes in the steel. Low temperature irradiation resulted solely in formation of radiation defects - dislocation loops of high number density, the latter increased with increase in irradiation temperature while their size decreased. In this regard high embrittlement rate observed at low temperature irradiation is only due to the hardening mechanism of radiation embrittlement. Accelerated irradiation at VVER-1000 RPV operating temperature (∼300 °C) caused formation of radiation-induced precipitates and dislocation loops, as well as some increase in phosphorus grain boundary segregation. The observed ΔTK shift being within the regulatory curve for VVER-1000 RPV base metal is due to both hardening and non-hardening mechanisms of radiation embrittlement. Irradiation at elevated temperature caused more intense phosphorus grain boundary segregation, but no formation of radiation-induced precipitates or dislocation loops in contrast to irradiation at 300 °C. Carbide transformations observed only after irradiation at 400 °C caused increase in yield strength and, along with a contribution of the non-hardening mechanism, resulted in the lowest ΔTK shift in the studied range of irradiation temperature and fluence.

pH-induced conformational changes in human ABO(H) blood group glycosyltransferases confirm the importance of electrostatic interactions in the formation of the semi-closed state.

PubMed

Johal, Asha R; Blackler, Ryan J; Alfaro, Javier A; Schuman, Brock; Borisova, Svetlana; Evans, Stephen V

2014-03-01

The homologous human ABO(H) A and B blood group glycosyltransferases GTA and GTB have two mobile polypeptide loops surrounding their active sites that serve to allow substrate access and product egress and to recognize and sequester substrates for catalysis. Previous studies have established that these enzymes can move from the "open" state to the "semi-closed" then "closed" states in response to addition of a substrate. The contribution of electrostatic interactions to these conformational changes has now been demonstrated by the determination at various pH of the structures of GTA, GTB and the chimeric enzyme ABBA. At near-neutral pH, GTA displays the closed state in which both mobile loops order around the active site, whereas ABBA and GTB display the open state. At low pH, the apparent protonation of the DXD motif in GTA leads to the expulsion of the donor analog to yield the open state, whereas at high pH, both ABBA and GTB form the semi-closed state in which the first mobile loop becomes an ordered α-helix. Step-wise deprotonation of GTB in increments of 0.5 between pH 6.5 and 10.0 shows that helix ordering is gradual, which indicates that the formation of the semi-closed state is dependent on electrostatic forces consistent with the binding of substrate. Spectropolarimetric studies of the corresponding stand-alone peptide in solution reveal no tendency toward helix formation from pH 7.0 to 10.0, which shows that pH-dependent stability is a product of the larger protein environment and underlines the importance of substrate in active site ordering.

BMP signaling controls buckling forces to modulate looping morphogenesis of the gut.

PubMed

Nerurkar, Nandan L; Mahadevan, L; Tabin, Clifford J

2017-02-28

Looping of the initially straight embryonic gut tube is an essential aspect of intestinal morphogenesis, permitting proper placement of the lengthy small intestine within the confines of the body cavity. The formation of intestinal loops is highly stereotyped within a given species and results from differential-growth-driven mechanical buckling of the gut tube as it elongates against the constraint of a thin, elastic membranous tissue, the dorsal mesentery. Although the physics of this process has been studied, the underlying biology has not. Here, we show that BMP signaling plays a critical role in looping morphogenesis of the avian small intestine. We first exploited differences between chicken and zebra finch gut morphology to identify the BMP pathway as a promising candidate to regulate differential growth in the gut. Next, focusing on the developing chick small intestine, we determined that Bmp2 expressed in the dorsal mesentery establishes differential elongation rates between the gut tube and mesentery, thereby regulating the compressive forces that buckle the gut tube into loops. Consequently, the number and tightness of loops in the chick small intestine can be increased or decreased directly by modulation of BMP activity in the small intestine. In addition to providing insight into the molecular mechanisms underlying intestinal development, our findings provide an example of how biochemical signals act on tissue-level mechanics to drive organogenesis, and suggest a possible mechanism by which they can be modulated to achieve distinct morphologies through evolution.

BMP signaling controls buckling forces to modulate looping morphogenesis of the gut

PubMed Central

Nerurkar, Nandan L.; Mahadevan, L.; Tabin, Clifford J.

2017-01-01

Looping of the initially straight embryonic gut tube is an essential aspect of intestinal morphogenesis, permitting proper placement of the lengthy small intestine within the confines of the body cavity. The formation of intestinal loops is highly stereotyped within a given species and results from differential-growth–driven mechanical buckling of the gut tube as it elongates against the constraint of a thin, elastic membranous tissue, the dorsal mesentery. Although the physics of this process has been studied, the underlying biology has not. Here, we show that BMP signaling plays a critical role in looping morphogenesis of the avian small intestine. We first exploited differences between chicken and zebra finch gut morphology to identify the BMP pathway as a promising candidate to regulate differential growth in the gut. Next, focusing on the developing chick small intestine, we determined that Bmp2 expressed in the dorsal mesentery establishes differential elongation rates between the gut tube and mesentery, thereby regulating the compressive forces that buckle the gut tube into loops. Consequently, the number and tightness of loops in the chick small intestine can be increased or decreased directly by modulation of BMP activity in the small intestine. In addition to providing insight into the molecular mechanisms underlying intestinal development, our findings provide an example of how biochemical signals act on tissue-level mechanics to drive organogenesis, and suggest a possible mechanism by which they can be modulated to achieve distinct morphologies through evolution. PMID:28193855

Spectroscopic study of a dark lane and a cool loop in a solar limb active region by Hinode/EIS

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

Lee, Kyoung-Sun; Imada, S.; Moon, Y.-J.

2014-01-10

We investigated a cool loop and a dark lane over a limb active region on 2007 March 14 using the Hinode/EUV Imaging Spectrometer. The cool loop is clearly seen in the spectral lines formed at the transition region temperature. The dark lane is characterized by an elongated faint structure in the coronal spectral lines and is rooted on a bright point. We examined their electron densities, Doppler velocities, and nonthermal velocities as a function of distance from the limb. We derived electron densities using the density sensitive line pairs of Mg VII, Si X, Fe XII, Fe XIII, and Femore » XIV spectra. We also compared the observed density scale heights with the calculated scale heights from each peak formation temperatures of the spectral lines under the hydrostatic equilibrium. We noted that the observed density scale heights of the cool loop are consistent with the calculated heights, with the exception of one observed cooler temperature; we also found that the observed scale heights of the dark lane are much lower than their calculated scale heights. The nonthermal velocity in the cool loop slightly decreases along the loop, while nonthermal velocity in the dark lane sharply falls off with height. Such a decrease in the nonthermal velocity may be explained by wave damping near the solar surface or by turbulence due to magnetic reconnection near the bright point.« less

Application of Risk-Based Inspection method for gas compressor station

NASA Astrophysics Data System (ADS)

Zhang, Meng; Liang, Wei; Qiu, Zeyang; Lin, Yang

2017-05-01

According to the complex process and lots of equipment, there are risks in gas compressor station. At present, research on integrity management of gas compressor station is insufficient. In this paper, the basic principle of Risk Based Inspection (RBI) and the RBI methodology are studied; the process of RBI in the gas compressor station is developed. The corrosion loop and logistics loop of the gas compressor station are determined through the study of corrosion mechanism and process of the gas compressor station. The probability of failure is calculated by using the modified coefficient, and the consequence of failure is calculated by the quantitative method. In particular, we addressed the application of a RBI methodology in a gas compressor station. The risk ranking is helpful to find the best preventive plan for inspection in the case study.

Pulsed Thrust Method for Hover Formation Flying

NASA Technical Reports Server (NTRS)

Hope, Alan; Trask, Aaron

2003-01-01

A non-continuous thrust method for hover type formation flying has been developed. This method differs from a true hover which requires constant range and bearing from a reference vehicle. The new method uses a pulsed loop, or pogo, maneuver sequence that keeps the follower spacecraft within a defined box in a near hover situation. Equations are developed for the hover maintenance maneuvers. The constraints on the hover location, pulse interval, and maximum/minimum ranges are discussed.

Mechanism of the formation of the RecA-ssDNA nucleoprotein filament structure: a coarse-grained approach.

PubMed

Mukherjee, Goutam; Pal, Arumay; Levy, Yaakov

2017-11-21

In prokaryotes, the RecA protein catalyzes the repair and strand exchange of double-stranded DNA. RecA binds to single-stranded DNA (ssDNA) and forms a presynaptic complex in which the protein polymerizes around the ssDNA to form a right-handed helical nucleoprotein filament structure. In the present work, the mechanism for the formation of the RecA-ssDNA filament structure is modeled using coarse-grained molecular dynamics simulations. Information from the X-ray structure was used to model the protein itself but not its interactions; the interactions between the protein and the ssDNA were modeled solely by electrostatic, aromatic, and repulsive energies. For the present study, the monomeric, dimeric, and trimeric units of RecA and 4, 8, and 11 NT-long ssDNA, respectively, were studied. Our results indicate that monomeric RecA is not sufficient for nucleoprotein filament formation; rather, dimeric RecA is the elementary binding unit, with higher multimeric units of RecA facilitating filament formation. Our results reveal that loop region flexibility at the primary binding site of RecA is essential for it to bind the incoming ssDNA, that the aromatic residues present in the loop region play an important role in ssDNA binding, and that ATP may play a role in guiding the ssDNA by changing the electrostatic potential of the RecA protein.

Histone H3.3 promotes IgV gene diversification by enhancing formation of AID-accessible single-stranded DNA.

PubMed

Romanello, Marina; Schiavone, Davide; Frey, Alexander; Sale, Julian E

2016-07-01

Immunoglobulin diversification is driven by activation-induced deaminase (AID), which converts cytidine to uracil within the Ig variable (IgV) regions. Central to the recruitment of AID to the IgV genes are factors that regulate the generation of single-stranded DNA (ssDNA), the enzymatic substrate of AID Here, we report that chicken DT40 cells lacking variant histone H3.3 exhibit reduced IgV sequence diversification. We show that this results from impairment of the ability of AID to access the IgV genes due to reduced formation of ssDNA during IgV transcription. Loss of H3.3 also diminishes IgV R-loop formation. However, reducing IgV R-loops by RNase HI overexpression in wild-type cells does not affect IgV diversification, showing that these structures are not necessary intermediates for AID access. Importantly, the reduction in the formation of AID-accessible ssDNA in cells lacking H3.3 is independent of any effect on the level of transcription or the kinetics of RNAPII elongation, suggesting the presence of H3.3 in the nucleosomes of the IgV genes increases the chances of the IgV DNA becoming single-stranded, thereby creating an effective AID substrate. © 2016 MRC Laboratory of Molecular Biology. Published under the terms of the CC BY 4.0 license.

Global Identification of Disease Associated Genes in Fragile X Cells

DTIC Science & Technology

2016-08-01

for this study listed as follows: 1) Validate the co-localized R-loop formation and chromosome fragility in Fragile X cells, particularly at the brain ...retardation protein February 2016, NGS Data Analysis & Informatics Conference, San Diego, California (Poster presentation) Title: Global detection

Loop-Extended Symbolic Execution on Binary Programs

DTIC Science & Technology

2009-03-02

1434. Based on its speci- fication [35], one valid message format contains 2 fields: a header byte of value 4, followed by a string giving a database ...potentially become expensive. For instance the polyhedron technique [16] requires costly conversion operations on a multi-dimensional abstract representation

A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture

PubMed Central

Jégu, Teddy; Domenichini, Séverine; Blein, Thomas; Ariel, Federico; Christ, Aurélie; Kim, Soon-Kap; Crespi, Martin; Boutet-Mercey, Stéphanie; Mouille, Grégory; Bourge, Mickaël; Hirt, Heribert; Bergounioux, Catherine; Raynaud, Cécile; Benhamed, Moussa

2015-01-01

Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression. PMID:26457678

The BAF60 Subunit of the SWI/SNF Chromatin-Remodeling Complex Directly Controls the Formation of a Gene Loop at FLOWERING LOCUS C in Arabidopsis[W

PubMed Central

Jégu, Teddy; Latrasse, David; Delarue, Marianne; Hirt, Heribert; Domenichini, Séverine; Ariel, Federico; Crespi, Martin; Bergounioux, Catherine; Raynaud, Cécile; Benhamed, Moussa

2014-01-01

SWI/SNF complexes mediate ATP-dependent chromatin remodeling to regulate gene expression. Many components of these complexes are evolutionarily conserved, and several subunits of Arabidopsis thaliana SWI/SNF complexes are involved in the control of flowering, a process that depends on the floral repressor FLOWERING LOCUS C (FLC). BAF60 is a SWI/SNF subunit, and in this work, we show that BAF60, via a direct targeting of the floral repressor FLC, induces a change at the high-order chromatin level and represses the photoperiod flowering pathway in Arabidopsis. BAF60 accumulates in the nucleus and controls the formation of the FLC gene loop by modulation of histone density, composition, and posttranslational modification. Physiological analysis of BAF60 RNA interference mutant lines allowed us to propose that this chromatin-remodeling protein creates a repressive chromatin configuration at the FLC locus. PMID:24510722

Morphogengineering roots: comparing mechanisms of morphogen gradient formation

PubMed Central

2012-01-01

Background In developmental biology, there has been a recent focus on the robustness of morphogen gradients as possible providers of positional information. It was shown that functional morphogen gradients present strong biophysical constraints and lack of robustness to noise. Here we explore how the details of the mechanism which underlies the generation of a morphogen gradient can influence those properties. Results We contrast three gradient-generating mechanisms, (i) a source-decay mechanism; and (ii) a unidirectional transport mechanism; and (iii) a so-called reflux-loop mechanism. Focusing on the dynamics of the phytohormone auxin in the root, we show that only the reflux-loop mechanism can generate a gradient that would be adequate to supply functional positional information for the Arabidopsis root, for biophysically reasonable kinetic parameters. Conclusions We argue that traits that differ in spatial and temporal time-scales can impose complex selective pressures on the mechanism of morphogen gradient formation used for the development of the particular organism. PMID:22583698

Confined Electroconvective and Flexoelectric Instabilities Deep in the Freedericksz State of Nematic CB7CB.

PubMed

Krishnamurthy, Kanakapura S; Palakurthy, Nani Babu; Yelamaggad, Channabasaveshwar V

2017-06-01

We report wormlike flexoelectric structures evolving deep in the Freedericksz state of a nematic layer of the liquid crystal cyanobiphenyl-(CH2) 7 -cyanobiphenyl. They form in the predominantly splay-bend thin boundary layers and are built up of solitary flexoelectric domains of the Bobylev-Pikin type. Their formation is possibly triggered by the gradient flexoelectric surface instability that remains optically discernible up to unusually high frequencies. The threshold voltage at which the worms form scales as square root of the frequency; in their extended state, worms often appear as labyrinthine structures on a section of loops that separate regions of opposite director deviation. Such asymmetric loops are also derived through pincement-like dissociation of ring-shaped walls. Formation of isolated domains of bulk electroconvection precedes the onset of surface instabilities. In essence, far above the Freedericksz threshold, the twisted nematic layer behaves as a combination of two orthogonally oriented planar half-layers destabilized by localized flexoelectric distortion.

Existence of a regulatory loop between MCP-1 and TGF-beta in glomerular immune injury.

PubMed

Wolf, Gunter; Jocks, Thomas; Zahner, Gunther; Panzer, Ulf; Stahl, Rolf A K

2002-11-01

Glomerular upregulation of monocyte chemotactic protein-1 (MCP-1), followed by an influx of monocytes resulting eventually in extracellular matrix deposition is a common sequel of many types of glomerulonephritis. However, it is not entirely clear how early expression of MCP-1 is linked to the later development of glomerulosclerosis. Because transforming growth factor-beta (TGF-beta) is a key regulator of extracellular matrix proteins, we hypothesized that there might be a regulatory loop between early glomerular MCP-1 induction and subsequent TGF-beta expression. To avoid interference with other cytokines that may be released from infiltrating monocytes, isolated rat kidneys were perfused with a polyclonal anti-thymocyte-1 antiserum (ATS) and rat serum (RS) as a complement source to induce glomerular injury. Renal TGF-beta protein and mRNA expressions were strongly stimulated after perfusion with ATS-RS. This effect was attenuated by coperfusion with a neutralizing anti-MCP-1 but was partly mimicked by perfusion with recombinant MCP-1 protein. On the other hand, renal MCP-1 expression and production were stimulated by administration of ATS-RS. Additional perfusion with an anti-TGF-beta antibody further aggravated this increase, whereas application of recombinant TGF-beta protein reduced MCP-1 formation. Our data demonstrate an intrinsic regulatory loop in which increased MCP-1 levels stimulate TGF-beta formation in resident glomerular cells in the absence of infiltrating immune competent cells.

Structure and phase formation behavior and dielectric and magnetic properties of lead iron tantalate-lead zirconate titanate multiferroic ceramics

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

Wongmaneerung, R., E-mail: re_nok@yahoo.com; Tipakontitikul, R.; Jantaratana, P.

2016-03-15

Highlights: • The multiferroic ceramics consisted of PFT and PZT. • Crystal structure changed from cubic to mixedcubic and tetragonal with increasing PZT content. • Dielectric showed the samples underwent a typical relaxor ferroelectric behavior. • Magnetic properties showed very interesting behavior with square saturated magnetic hysteresis loops. - Abstract: Multiferroic (1 − x)Pb(Fe{sub 0.5}Ta{sub 0.5})O{sub 3}–xPb(Zr{sub 0.53}Ti{sub 0.47})O{sub 3} (or PFT–PZT) ceramics were synthesized by solid-state reaction method. The crystal structure and phase formation of the ceramics were examined by X-ray diffraction (XRD). The local structure surrounding Fe and Ti absorbing atoms was investigated by synchrotron X-ray Absorption Near-Edgemore » Structure (XANES) measurement. Dielectric properties were studied as a function of frequency and temperature using a LCR meter. A vibrating sample magnetometer (VSM) was used to determine the magnetic hysteresis loops. XRD study indicated that the crystal structure of the sample changed from pure cubic to mixed cubic and tetragonal with increasing PZT content. XANES measurements showed that the local structure surrounding Fe and Ti ions was similar. Dielectric study showed that the samples underwent a typical relaxor ferroelectric behavior while the magnetic properties showed very interesting behavior with square saturated magnetic hysteresis loops.« less

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

PubMed

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

2017-12-15

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

Adaptive Formation Control of Electrically Driven Nonholonomic Mobile Robots With Limited Information.

PubMed

Bong Seok Park; Jin Bae Park; Yoon Ho Choi

2011-08-01

We present a leader-follower-based adaptive formation control method for electrically driven nonholonomic mobile robots with limited information. First, an adaptive observer is developed under the condition that the velocity measurement is not available. With the proposed adaptive observer, the formation control part is designed to achieve the desired formation and guarantee the collision avoidance. In addition, neural network is employed to compensate the actuator saturation, and the projection algorithm is used to estimate the velocity information of the leader. It is shown, by using the Lyapunov theory, that all errors of the closed-loop system are uniformly ultimately bounded. Simulation results are presented to illustrate the performance of the proposed control system.

Laboratory formation of non-cementing, methane hydrate-bearing sands

USGS Publications Warehouse

Waite, William F.; Bratton, Peter M.; Mason, David H.

2011-01-01

Naturally occurring hydrate-bearing sands often behave as though methane hydrate is acting as a load-bearing member of the sediment. Mimicking this behavior in laboratory samples with methane hydrate likely requires forming hydrate from methane dissolved in water. To hasten this formation process, we initially form hydrate in a free-gas-limited system, then form additional hydrate by circulating methane-supersaturated water through the sample. Though the dissolved-phase formation process can theoretically be enhanced by increasing the pore pressure and flow rate and lowering the sample temperature, a more fundamental concern is preventing clogs resulting from inadvertent methane bubble formation in the circulation lines. Clog prevention requires careful temperature control throughout the circulation loop.

Observer enhanced control for spin-stabilized tethered formation in earth orbit

NASA Astrophysics Data System (ADS)

Guang, Zhai; Yuyang, Li; Liang, Bin

2018-04-01

This paper addresses the issues relevant to control of spin-stabilized tethered formation in circular orbit. Due to the dynamic complexities and nonlinear perturbations, it is challenging to promote the control precision for the formation deployment and maintenance. In this work, the formation dynamics are derived with considering the spinning rate of the central body, then major attention is dedicated to develop the nonlinear disturbance observer. To achieve better control performance, the observer-enhanced controller is designed by incorporating the disturbance observer into the control loop, benefits from the disturbance compensation are demonstrated, and also, the dependences of the disturbance observer performance on some important parameters are theoretically and numerically analyzed.

Left passage probability of Schramm-Loewner Evolution

NASA Astrophysics Data System (ADS)

Najafi, M. N.

2013-06-01

SLE(κ,ρ⃗) is a variant of Schramm-Loewner Evolution (SLE) which describes the curves which are not conformal invariant, but are self-similar due to the presence of some other preferred points on the boundary. In this paper we study the left passage probability (LPP) of SLE(κ,ρ⃗) through field theoretical framework and find the differential equation governing this probability. This equation is numerically solved for the special case κ=2 and hρ=0 in which hρ is the conformal weight of the boundary changing (bcc) operator. It may be referred to loop erased random walk (LERW) and Abelian sandpile model (ASM) with a sink on its boundary. For the curve which starts from ξ0 and conditioned by a change of boundary conditions at x0, we find that this probability depends significantly on the factor x0-ξ0. We also present the perturbative general solution for large x0. As a prototype, we apply this formalism to SLE(κ,κ-6) which governs the curves that start from and end on the real axis.

Left passage probability of Schramm-Loewner Evolution.

PubMed

Najafi, M N

2013-06-01

SLE(κ,ρ[over arrow]) is a variant of Schramm-Loewner Evolution (SLE) which describes the curves which are not conformal invariant, but are self-similar due to the presence of some other preferred points on the boundary. In this paper we study the left passage probability (LPP) of SLE(κ,ρ[over arrow]) through field theoretical framework and find the differential equation governing this probability. This equation is numerically solved for the special case κ=2 and h(ρ)=0 in which h(ρ) is the conformal weight of the boundary changing (bcc) operator. It may be referred to loop erased random walk (LERW) and Abelian sandpile model (ASM) with a sink on its boundary. For the curve which starts from ξ(0) and conditioned by a change of boundary conditions at x(0), we find that this probability depends significantly on the factor x(0)-ξ(0). We also present the perturbative general solution for large x(0). As a prototype, we apply this formalism to SLE(κ,κ-6) which governs the curves that start from and end on the real axis.

Loops formed by tidal tails as fossil records of a major merger

NASA Astrophysics Data System (ADS)

Wang, J.; Hammer, F.; Athanassoula, E.; Puech, M.; Yang, Y.; Flores, H.

2012-02-01

Context. Many haloes of nearby disc galaxies contain faint and extended features, including loops, which are often interpreted as relics of satellite infall in the main galaxy's potential well. In most cases, however, the residual nucleus of the satellite is not seen, although it is predicted by numerical simulations. Aims: We test whether such faint and extended features can be associated to gas-rich, major mergers, which may also lead to disc rebuilding and thus be a corner stone for the formation of spiral galaxies. Our goal is to test whether the major merger scenario can provide a good model for a particularly difficult case, that of NGC 5907, and to compare to the scenario of a satellite infall. Methods: Using the TreeSPH code GADGET-2, we model the formation of an almost bulge-less galaxy similar to NGC 5907 (B/T ≲ 0.2) after a gas-rich major merger. First, we trace tidal tail particles captured by the galaxy gravitational potential to verify whether they can form loops similar to those discovered in the galactic haloes. Results: We indeed find that 3:1 major mergers can form features similar to the loops found in many galactic haloes, including in NGC 5907, and can reproduce an extended thin disc, a bulge, as well as the pronounced warp of the gaseous disc. Relatively small bulge fractions can be reproduced by a large gas fraction in the progenitors, as well as appropriate orbital parameters. Conclusions: Even though it remains difficult to fully cover the large volume of free parameters, the present modelling of the loops in NGC 5907 proves that they could well be the result of a major merger. It has many advantages over the satellite infall scenario; e.g., it solves the problem of the visibility of the satellite remnant, and it may explain some additional features in the NGC 5907 halo, as well as some gas properties of this system. For orbital parameters derived from cosmological simulations, the loops in NGC 5907 can be reproduced by major mergers (3:1 to 5:1) and possibly by intermediate mergers (5:1 to 12:1). The major merger scenario thus challenges the minor merger one and could explain many properties that haloes of spiral galaxies have in common, including their red colours and the presence of faint extended features.

Three-Dimensional Printing of Vitrification Loop Prototypes for Aquatic Species.

PubMed

Tiersch, Nolan J; Childress, William M; Tiersch, Terrence R

2018-05-16

Vitrification is a method of cryopreservation that freezes samples rapidly, while forming an amorphous solid ("glass"), typically in small (μL) volumes. The goal of this project was to create, by three-dimensional (3D) printing, open vitrification devices based on an elliptical loop that could be efficiently used and stored. Vitrification efforts can benefit from the application of 3D printing, and to begin integration of this technology, we addressed four main variables: thermoplastic filament type, loop length, loop height, and method of loading. Our objectives were to: (1) design vitrification loops with varied dimensions; (2) print prototype loops for testing; (3) evaluate loading methods for the devices; and (4) classify vitrification responses to multiple device configurations. The various configurations were designed digitally using 3D CAD (Computer Aided Design) software, and prototype devices were produced with MakerBot ® 3D printers. The thermoplastic filaments used to produce devices were acrylonitrile butadiene styrene (ABS) and polylactic acid (PLA). Vitrification devices were characterized by the film volumes formed with different methods of loading (pipetting or submersion). Frozen films were classified to determine vitrification quality: zero (opaque, or abundant crystalline ice formation); one (translucent, or partial vitrification), or two (transparent, or substantial vitrification, glass). A published vitrification solution was used to conduct experiments. Loading by pipetting formed frozen films more reliably than by submersion, but submersion yielded fewer filling problems and was more rapid. The loop designs that yielded the highest levels of vitrification enabled rapid transfer of heat, and most often were characterized as being longer and consisting of fewer layers (height). 3D printing can assist standardization of vitrification methods and research, yet can also provide the ability to quickly design and fabricate custom devices when needed.

Slipping magnetic reconnection during an X-class solar flare observed by SDO/AIA

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

Dudík, J.; Del Zanna, G.; Mason, H. E.

2014-04-01

We present SDO/AIA observations of an eruptive X-class flare of 2012 July 12, and compare its evolution with the predictions of a three-dimensional (3D) numerical simulation. We focus on the dynamics of flare loops that are seen to undergo slipping reconnection during the flare. In the Atmospheric Imaging Assembly (AIA) 131 Å observations, lower parts of 10 MK flare loops exhibit an apparent motion with velocities of several tens of km s{sup –1} along the developing flare ribbons. In the early stages of the flare, flare ribbons consist of compact, localized bright transition-region emission from the footpoints of the flaremore » loops. A differential emission measure analysis shows that the flare loops have temperatures up to the formation of Fe XXIV. A series of very long, S-shaped loops erupt, leading to a coronal mass ejection observed by STEREO. The observed dynamics are compared with the evolution of magnetic structures in the 'standard solar flare model in 3D.' This model matches the observations well, reproducing the apparently slipping flare loops, S-shaped erupting loops, and the evolution of flare ribbons. All of these processes are explained via 3D reconnection mechanisms resulting from the expansion of a torus-unstable flux rope. The AIA observations and the numerical model are complemented by radio observations showing a noise storm in the metric range. Dm-drifting pulsation structures occurring during the eruption indicate plasmoid ejection and enhancement of the reconnection rate. The bursty nature of radio emission shows that the slipping reconnection is still intermittent, although it is observed to persist for more than an hour.« less

Testing anthropic reasoning for the cosmological constant with a realistic galaxy formation model

NASA Astrophysics Data System (ADS)

Sudoh, Takahiro; Totani, Tomonori; Makiya, Ryu; Nagashima, Masahiro

2017-01-01

The anthropic principle is one of the possible explanations for the cosmological constant (Λ) problem. In previous studies, a dark halo mass threshold comparable with our Galaxy must be assumed in galaxy formation to get a reasonably large probability of finding the observed small value, P(<Λobs), though stars are found in much smaller galaxies as well. Here we examine the anthropic argument by using a semi-analytic model of cosmological galaxy formation, which can reproduce many observations such as galaxy luminosity functions. We calculate the probability distribution of Λ by running the model code for a wide range of Λ, while other cosmological parameters and model parameters for baryonic processes of galaxy formation are kept constant. Assuming that the prior probability distribution is flat per unit Λ, and that the number of observers is proportional to stellar mass, we find P(<Λobs) = 6.7 per cent without introducing any galaxy mass threshold. We also investigate the effect of metallicity; we find P(<Λobs) = 9.0 per cent if observers exist only in galaxies whose metallicity is higher than the solar abundance. If the number of observers is proportional to metallicity, we find P(<Λobs) = 9.7 per cent. Since these probabilities are not extremely small, we conclude that the anthropic argument is a viable explanation, if the value of Λ observed in our Universe is determined by a probability distribution.

Reliability Assessment of a Robust Design Under Uncertainty for a 3-D Flexible Wing

NASA Technical Reports Server (NTRS)

Gumbert, Clyde R.; Hou, Gene J. -W.; Newman, Perry A.

2003-01-01

The paper presents reliability assessment results for the robust designs under uncertainty of a 3-D flexible wing previously reported by the authors. Reliability assessments (additional optimization problems) of the active constraints at the various probabilistic robust design points are obtained and compared with the constraint values or target constraint probabilities specified in the robust design. In addition, reliability-based sensitivity derivatives with respect to design variable mean values are also obtained and shown to agree with finite difference values. These derivatives allow one to perform reliability based design without having to obtain second-order sensitivity derivatives. However, an inner-loop optimization problem must be solved for each active constraint to find the most probable point on that constraint failure surface.

Finite-time state feedback stabilisation of stochastic high-order nonlinear feedforward systems

NASA Astrophysics Data System (ADS)

Xie, Xue-Jun; Zhang, Xing-Hui; Zhang, Kemei

2016-07-01

This paper studies the finite-time state feedback stabilisation of stochastic high-order nonlinear feedforward systems. Based on the stochastic Lyapunov theorem on finite-time stability, by using the homogeneous domination method, the adding one power integrator and sign function method, constructing a ? Lyapunov function and verifying the existence and uniqueness of solution, a continuous state feedback controller is designed to guarantee the closed-loop system finite-time stable in probability.

Mobile application MDDCS for modeling the expansion dynamics of a dislocation loop in FCC metals

NASA Astrophysics Data System (ADS)

Kirilyuk, Vasiliy; Petelin, Alexander; Eliseev, Andrey

2017-11-01

A mobile version of the software package Dynamic Dislocation of Crystallographic Slip (MDDCS) designed for modeling the expansion dynamics of dislocation loops and formation of a crystallographic slip zone in FCC-metals is examined. The paper describes the possibilities for using MDDCS, the application interface, and the database scheme. The software has a simple and intuitive interface and does not require special training. The user can set the initial parameters of the experiment, carry out computational experiments, export parameters and results of the experiment into separate text files, and display the experiment results on the device screen.

Auditory closed-loop stimulation of the sleep slow oscillation enhances memory.

PubMed

Ngo, Hong-Viet V; Martinetz, Thomas; Born, Jan; Mölle, Matthias

2013-05-08

Brain rhythms regulate information processing in different states to enable learning and memory formation. The <1 Hz sleep slow oscillation hallmarks slow-wave sleep and is critical to memory consolidation. Here we show in sleeping humans that auditory stimulation in phase with the ongoing rhythmic occurrence of slow oscillation up states profoundly enhances the slow oscillation rhythm, phase-coupled spindle activity, and, consequently, the consolidation of declarative memory. Stimulation out of phase with the ongoing slow oscillation rhythm remained ineffective. Closed-loop in-phase stimulation provides a straight-forward tool to enhance sleep rhythms and their functional efficacy. Copyright © 2013 Elsevier Inc. All rights reserved.

Radiation resistance of oxide dispersion strengthened alloys: Perspectives from in situ observations and rate theory calculations

DOE PAGES

Liu, Xiang; Miao, Yinbin; Li, Meimei; ...

2018-04-15

Here, in situ ion irradiation and rate theory calculations were employed to directly compare the radiation resistance of an oxide dispersion strengthened alloy with that of a conventional ferritic/martensitic alloy. Compared to the rapid buildup of dislocation loops, loop growth, and formation of network dislocations in the conventional ferritic/martensitic alloy, the superior radiation resistance of the oxide dispersion strengthened alloy is manifested by its stable dislocation structure under the same irradiation conditions. Thus, the results are consistent with rate theory calculations, which show that high-density nanoparticles can significantly reduce freely migrating defects and suppress the buildup of clustered defects.

Radiation resistance of oxide dispersion strengthened alloys: Perspectives from in situ observations and rate theory calculations

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

Liu, Xiang; Miao, Yinbin; Li, Meimei

Here, in situ ion irradiation and rate theory calculations were employed to directly compare the radiation resistance of an oxide dispersion strengthened alloy with that of a conventional ferritic/martensitic alloy. Compared to the rapid buildup of dislocation loops, loop growth, and formation of network dislocations in the conventional ferritic/martensitic alloy, the superior radiation resistance of the oxide dispersion strengthened alloy is manifested by its stable dislocation structure under the same irradiation conditions. Thus, the results are consistent with rate theory calculations, which show that high-density nanoparticles can significantly reduce freely migrating defects and suppress the buildup of clustered defects.

Vortex multiplication in applied flow: A precursor to superfluid turbulence.

PubMed

Finne, A P; Eltsov, V B; Eska, G; Hänninen, R; Kopu, J; Krusius, M; Thuneberg, E V; Tsubota, M

2006-03-03

A surface-mediated process is identified in 3He-B which generates vortices at a roughly constant rate. It precedes a faster form of turbulence where intervortex interactions dominate. This precursor becomes observable when vortex loops are introduced in low-velocity rotating flow at sufficiently low mutual friction dissipation at temperatures below 0.5Tc. Our measurements indicate that the formation of new loops is associated with a single vortex interacting in the applied flow with the sample boundary. Numerical calculations show that the single-vortex instability arises when a helical Kelvin wave expands from a reconnection kink at the wall and then intersects again with the wall.

Multiferroic properties in NdFeO3-PbTiO3 solid solutions

NASA Astrophysics Data System (ADS)

Kumar, Sunil; Pal, Jaswinder; Kaur, Shubhpreet; Agrawal, P.; Singh, Mandeep; Singh, Anupinder

2018-05-01

The x(NdFeO3) - 1-x(PbTiO3) where x = 0.2 solid solution was prepared using solid state reaction route. The X-ray diffraction (XRD) data reveals the single phase formation. The microstructure shows grain growth with lesser porosity. The energy dispersive analysis confirms the presence of elements in stochiometric proportion. The polarization vs. Electric field loop estabilished a ferroelectric type behavior but lossy in nature. This lossy nature may be due to the presence of large leakage current in solid solution. The Magnetization vs. Magnetic field plot exhibits a unsaturated hysteriss loop indicates that the sample is not purely ferromagnetic.

Three-dimensional characterization of tethered microspheres by total internal reflection fluorescence microscopy

NASA Technical Reports Server (NTRS)

Blumberg, Seth; Gajraj, Arivalagan; Pennington, Matthew W.; Meiners, Jens-Christian

2005-01-01

Tethered particle microscopy is a powerful tool to study the dynamics of DNA molecules and DNA-protein complexes in single-molecule experiments. We demonstrate that stroboscopic total internal reflection microscopy can be used to characterize the three-dimensional spatiotemporal motion of DNA-tethered particles. By calculating characteristic measures such as symmetry and time constants of the motion, well-formed tethers can be distinguished from defective ones for which the motion is dominated by aberrant surface effects. This improves the reliability of measurements on tether dynamics. For instance, in observations of protein-mediated DNA looping, loop formation is distinguished from adsorption and other nonspecific events.

Pd/Cu-Oxide Nanoconjugate at Zeolite-Y Crystallite Crafting the Mesoporous Channels for Selective Oxidation of Benzyl-Alcohols.

PubMed

Sharma, Mukesh; Das, Biraj; Sharma, Mitu; Deka, Biplab K; Park, Young-Bin; Bhargava, Suresh K; Bania, Kusum K

2017-10-11

Solid-state grinding of palladium and copper salts allowed the growth of palladium/copper oxide interface at the zeolite-Y surface. The hybrid nanostructured material was used as reusable heterogeneous catalyst for selective oxidation of various benzyl alcohols. The large surface area provided by the zeolite-Y matrix highly influenced the catalytic activity, as well as the recyclability of the synthesized catalyst. Impregnation of PdO-CuO nanoparticles on zeolite crystallite leads to the generation of mesoporous channel that probably prevented the leaching of the metal-oxide nanoparticles and endorsed high mass transfer. Formation of mesoporous channel at the external surface of zeolite-Y was evident from transmission electron microscopy and surface area analysis. PdO-CuO nanoparticles were found to be within the range of 2-5 nm. The surface area of PdO-CuO-Y catalyst was found to be much lower than parent zeolite-Y. The decrease in surface area as well as the presence of hysteresis loop in the N 2 -adsoprtion isotherm further suggested successful encapsulation of PdO-CuO nanoparticles via the mesoporous channel formation. The high positive shifting in binding energy in both Pd and Cu was attributed to the influence of zeolite-Y framework on lattice contraction of metal oxides via confinement effect. PdO-CuO-Y catalyst was found to oxidize benzyl alcohol with 99% selectivity. On subjecting to microwave irradiation the same oxidation reaction was found to occur at ambient condition giving same conversion and selectivity.

An IP-Based Software System for Real-time, Closed Loop, Multi-Spacecraft Mission Simulations

NASA Technical Reports Server (NTRS)

Cary, Everett; Davis, George; Higinbotham, John; Burns, Richard; Hogie, Keith; Hallahan, Francis

2003-01-01

This viewgraph presentation provides information on the architecture of a computerized testbest for simulating Distributed Space Systems (DSS) for controlling spacecraft flying in formation. The presentation also discusses and diagrams the Distributed Synthesis Environment (DSE) for simulating and planning DSS missions.

Cambium

NASA Technical Reports Server (NTRS)

Savidge, Rodney

2009-01-01

The Cambium investigation is one in a pair of investigations which utilizes the Advanced Biological Research System (ABRS). Cambium seeks definitive evidence that gravity has a direct effect on cambial cells (cells located under the inner bark where secondary growth occurs) in willow, Salix babylonica. The Cambium investigation uses willow plants flown on the International Space Station to better understand the fundamental processes by which plants produce cellulose and lignin, the two main structural materials found in plant matter. On Earth, the nature of wood within tree stems varies depending on position, and that within-tree variation includes differences in cell types and chemistry including lignin and cellulose, two major components of wood influencing wood strength, usefulness and carbon content. Reaction wood is an extreme example of such variation, and it is believed that reaction wood develops as a reaction to the influence of gravity. For the Cambium experiment, young willow plants will be launched to the ISS where their stems will be looped in an attempt to induce reaction wood formation. After on-orbit growth, the plants will be preserved and returned to Earth for analysis. Understanding the role of gravity in wood formation is expected to enable wiser management of forests for carbon sequestration as well as better utilization of trees for wood products. Detailed Research Description: The Cambium experiment will provide an understanding of physiological processes such as gene expression, metabolism and general plant development that are affected in plant systems exposed to space flight. Cambium seeks definitive evidence that gravity has a direct effect on the cambial cells (cells located under the inner bark where secondary growth occurs) that contribute to xylogenesis (reaction wood formation) in willow plants, Salix babylonica. Tension wood fibers differentiate on the upper sides of stems when the stem is altered from its normal (vertical) growth position by looping. This reaction wood response does not occur if the orientation of the plant stem with respect to gravity is not altered. If a localized zone of tension wood should be formed in looped stems under microgravity conditions, this would be the first conclusive evidence that gravity is not required. On the other hand, if a zone of tension wood is not produced in looped stems (subjected to tension on one side, compression on the other) in microgravity, this would be the first definitive evidence that gravity has a direct effect on the cambial cells which contribute to reaction wood formation. Following return to Earth the plants will be analyzed by microscopy and chemical methods.

Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase.

PubMed

Ouedraogo, Daniel; Souffrant, Michael; Vasquez, Sheena; Hamelberg, Donald; Gadda, Giovanni

2017-05-16

Mobile loops located at the active site entrance in enzymes often participate in conformational changes required to shield the reaction from bulk solvent, to control the access of the substrate to the active site, and to position residues for substrate binding and catalysis. In d-arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH), previous crystallographic data suggested that residues 45-47 in the FAD-binding domain and residues 50-56 in the substrate-binding domain in loop L1 could adopt two distinct conformations. In this study, we have used molecular dynamics, kinetics, and fluorescence spectroscopy on the S45A and A46G enzyme variants of PaDADH to investigate the impact of mutations in loop L1 on the catalytic function of the enzyme. Molecular dynamics showed that the mutant enzymes have probabilities of being in open conformations that are higher than that of wild-type PaDADH of loop L1, yielding an increased level of solvent exposure of the active site. In agreement, the flavin fluorescence intensity was ∼2-fold higher in the S45A and A46G enzymes than in wild-type PaDADH, with a 9 nm bathochromic shift of the emission band. In the variant enzymes, the k cat /K m values with d-arginine were ∼13-fold lower than in wild-type PaDADH. Moreover, the pH profiles for the k cat value with d-arginine showed a hollow, consistent with restricted proton movements in catalysis, and no saturation was achieved with the alternate substrate d-leucine in the reductive half-reaction of the variant enzymes. Taken together, the computational and experimental data are consistent with the dynamics of loop L1 being important for substrate capture and catalysis in PaDADH.

Timing performance of phase-locked loops in optical pulse position modulation communication systems

NASA Astrophysics Data System (ADS)

Lafaw, D. A.

In an optical digital communication system, an accurate clock signal must be available at the receiver to provide proper synchronization with the transmitted signal. Phase synchronization is especially critical in M-ary pulse position modulation (PPM) systems where the optimum decision scheme is an energy detector which compares the energy in each of M time slots to decide which of M possible words was sent. A timing error causes energy spillover into adjacent time slots (a form of intersymbol interference) so that only a portion of the signal energy may be attributed to the correct time slot. This effect decreases the effective signal, increases the effective noise, and increases the probability of error. This report simulates a timing subsystem for a satellite-to-satellite optical PPM communication link. The receiver employs direct photodetection, preprocessing of the optical signal, and a phase-locked loop for timing synchronization. The photodetector output is modeled as a filtered, doubly stochastic Poisson shot noise process. The variance of the relative phase error is examined under varying signal strength conditions as an indication of loop performance, and simulation results are compared to theoretical relations.

Comparison of Damping Mechanisms for Transverse Waves in Solar Coronal Loops

NASA Astrophysics Data System (ADS)

Montes-Solís, María; Arregui, Iñigo

2017-09-01

We present a method to assess the plausibility of alternative mechanisms to explain the damping of magnetohydrodynamic transverse waves in solar coronal loops. The considered mechanisms are resonant absorption of kink waves in the Alfvén continuum, phase mixing of Alfvén waves, and wave leakage. Our methods make use of Bayesian inference and model comparison techniques. We first infer the values for the physical parameters that control the wave damping, under the assumption of a particular mechanism, for typically observed damping timescales. Then, the computation of marginal likelihoods and Bayes factors enable us to quantify the relative plausibility between the alternative mechanisms. We find that, in general, the evidence is not large enough to support a single particular damping mechanism as the most plausible one. Resonant absorption and wave leakage offer the most probable explanations in strong damping regimes, while phase mixing is the best candidate for weak/moderate damping. When applied to a selection of 89 observed transverse loop oscillations, with their corresponding measurements of damping timescales and taking into account data uncertainties, we find that positive evidence for a given damping mechanism is only available in a few cases.

Incorporating parametric uncertainty into population viability analysis models

USGS Publications Warehouse

McGowan, Conor P.; Runge, Michael C.; Larson, Michael A.

2011-01-01

Uncertainty in parameter estimates from sampling variation or expert judgment can introduce substantial uncertainty into ecological predictions based on those estimates. However, in standard population viability analyses, one of the most widely used tools for managing plant, fish and wildlife populations, parametric uncertainty is often ignored in or discarded from model projections. We present a method for explicitly incorporating this source of uncertainty into population models to fully account for risk in management and decision contexts. Our method involves a two-step simulation process where parametric uncertainty is incorporated into the replication loop of the model and temporal variance is incorporated into the loop for time steps in the model. Using the piping plover, a federally threatened shorebird in the USA and Canada, as an example, we compare abundance projections and extinction probabilities from simulations that exclude and include parametric uncertainty. Although final abundance was very low for all sets of simulations, estimated extinction risk was much greater for the simulation that incorporated parametric uncertainty in the replication loop. Decisions about species conservation (e.g., listing, delisting, and jeopardy) might differ greatly depending on the treatment of parametric uncertainty in population models.

Between giant oscillations and uniform distribution of droplets: The role of varying lumen of channels in microfluidic networks.

PubMed

Cybulski, Olgierd; Jakiela, Slawomir; Garstecki, Piotr

2015-12-01

The simplest microfluidic network (a loop) comprises two parallel channels with a common inlet and a common outlet. Recent studies that assumed a constant cross section of the channels along their length have shown that the sequence of droplets entering the left (L) or right (R) arm of the loop can present either a uniform distribution of choices (e.g., RLRLRL...) or long sequences of repeated choices (RRR...LLL), with all the intermediate permutations being dynamically equivalent and virtually equally probable to be observed. We use experiments and computer simulations to show that even small variation of the cross section along channels completely shifts the dynamics either into the strong preference for highly grouped patterns (RRR...LLL) that generate system-size oscillations in flow or just the opposite-to patterns that distribute the droplets homogeneously between the arms of the loop. We also show the importance of noise in the process of self-organization of the spatiotemporal patterns of droplets. Our results provide guidelines for rational design of systems that reproducibly produce either grouped or homogeneous sequences of droplets flowing in microfluidic networks.

Comparison of Damping Mechanisms for Transverse Waves in Solar Coronal Loops

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

Montes-Solís, María; Arregui, Iñigo, E-mail: mmsolis@iac.es

We present a method to assess the plausibility of alternative mechanisms to explain the damping of magnetohydrodynamic transverse waves in solar coronal loops. The considered mechanisms are resonant absorption of kink waves in the Alfvén continuum, phase mixing of Alfvén waves, and wave leakage. Our methods make use of Bayesian inference and model comparison techniques. We first infer the values for the physical parameters that control the wave damping, under the assumption of a particular mechanism, for typically observed damping timescales. Then, the computation of marginal likelihoods and Bayes factors enable us to quantify the relative plausibility between the alternativemore » mechanisms. We find that, in general, the evidence is not large enough to support a single particular damping mechanism as the most plausible one. Resonant absorption and wave leakage offer the most probable explanations in strong damping regimes, while phase mixing is the best candidate for weak/moderate damping. When applied to a selection of 89 observed transverse loop oscillations, with their corresponding measurements of damping timescales and taking into account data uncertainties, we find that positive evidence for a given damping mechanism is only available in a few cases.« less

Unusual presentation of obscure Meckel diverticulum treated with robot-assisted diverticulectomy: A case report.

PubMed

Pandey, Sagar; Fan, Miao; Xu, Zhe; Yan, Chaogui; Zhu, Junfeng; Li, Xiuhong

2016-10-01

Meckel diverticulum (MD) is the most common congenital abnormality of gastrointestinal tract. Tough believed to occur in 2% of population, most of them remain veiled because majority are clinically asymptomatic and remain obscure in radiological examination. A 26-year-old male with episodic black colored stool since last 10 years. Tough symptomatic, diagnosis of pathological lesion, and the bleeding site could not be established with any of the sophisticated diagnostic technique. After 10 years, it was finally diagnosed as MD with careful observation of bowel loops on computed tomography enterography (CTE) where remnant of vitelline vessel and hyper-enhancing nodule are seen along the wall of diverticular loop. The patient underwent robot assisted laparoscopic surgery with excision of diverticular loop. To the best of our knowledge, this robot-assistant Meckel diverculectomy is probably the first reported surgical procedure in PubMed. Follow-up for 3 month showed no complication or recurrence. Every case is unique and we must be aware and remain alert in tracing the possible morphological variation of the case. Here, we present one unique but rare feature of MD, which helped us in making diagnosis.

Structure of force networks in tapped particulate systems of disks and pentagons. II. Persistence analysis.

PubMed

Kondic, L; Kramár, M; Pugnaloni, Luis A; Carlevaro, C Manuel; Mischaikow, K

2016-06-01

In the companion paper [Pugnaloni et al., Phys. Rev. E 93, 062902 (2016)10.1103/PhysRevE.93.062902], we use classical measures based on force probability density functions (PDFs), as well as Betti numbers (quantifying the number of components, related to force chains, and loops), to describe the force networks in tapped systems of disks and pentagons. In the present work, we focus on the use of persistence analysis, which allows us to describe these networks in much more detail. This approach allows us not only to describe but also to quantify the differences between the force networks in different realizations of a system, in different parts of the considered domain, or in different systems. We show that persistence analysis clearly distinguishes the systems that are very difficult or impossible to differentiate using other means. One important finding is that the differences in force networks between disks and pentagons are most apparent when loops are considered: the quantities describing properties of the loops may differ significantly even if other measures (properties of components, Betti numbers, force PDFs, or the stress tensor) do not distinguish clearly or at all the investigated systems.

Conservative Analytical Collision Probabilities for Orbital Formation Flying

NASA Technical Reports Server (NTRS)

Carpenter, J. Russell

2004-01-01

The literature offers a number of approximations for analytically and/or efficiently computing the probability of collision between two space objects. However, only one of these techniques is a completely analytical approximation that is suitable for use in the preliminary design phase, when it is more important to quickly analyze a large segment of the trade space than it is to precisely compute collision probabilities. Unfortunately, among the types of formations that one might consider, some combine a range of conditions for which this analytical method is less suitable. This work proposes a simple, conservative approximation that produces reasonable upper bounds on the collision probability in such conditions. Although its estimates are much too conservative under other conditions, such conditions are typically well suited for use of the existing method.

Conservative Analytical Collision Probability for Design of Orbital Formations

NASA Technical Reports Server (NTRS)

Carpenter, J. Russell

2004-01-01

The literature offers a number of approximations for analytically and/or efficiently computing the probability of collision between two space objects. However, only one of these techniques is a completely analytical approximation that is suitable for use in the preliminary design phase, when it is more important to quickly analyze a large segment of the trade space than it is to precisely compute collision probabilities. Unfortunately, among the types of formations that one might consider, some combine a range of conditions for which this analytical method is less suitable. This work proposes a simple, conservative approximation that produces reasonable upper bounds on the collision probability in such conditions. Although its estimates are much too conservative under other conditions, such conditions are typically well suited for use of the existing method.

Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.

PubMed

Nakashima, T; Yao, M; Kawamura, S; Iwasaki, K; Kimura, M; Tanaka, I

2001-05-01

Ribosomal protein L5 is a 5S rRNA binding protein in the large subunit and plays an essential role in the promotion of a particular conformation of 5S rRNA. The crystal structure of the ribosomal protein L5 from Bacillus stearothermophilus has been determined at 1.8 A resolution. The molecule consists of a five-stranded antiparallel beta-sheet and four alpha-helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. The molecular shape and electrostatic representation suggest that the concave surface and loop regions are involved in 5S rRNA binding. To identify amino acid residues responsible for 5S rRNA binding, we made use of Ala-scanning mutagenesis of evolutionarily conserved amino acids occurring in the beta-strands and loop regions. The mutations of Asn37 at the beta1-strand and Gln63 at the loop between helix 2 and beta3-strand as well as that of Phe77 at the tip of the loop structure between the beta2- and beta3-strands caused a significant reduction in 5S rRNA binding. In addition, the mutations of Thr90 on the beta3-strand and Ile141 and Asp144 at the loop between beta4- and beta5-strands moderately reduced the 5S rRNA-binding affinity. Comparison of these results with the more recently analyzed structure of the 50S subunit from Haloarcula marismortui suggests that there are significant differences in the structure at N- and C-terminal regions and probably in the 5S rRNA binding.

Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.

PubMed Central

Nakashima, T; Yao, M; Kawamura, S; Iwasaki, K; Kimura, M; Tanaka, I

2001-01-01

Ribosomal protein L5 is a 5S rRNA binding protein in the large subunit and plays an essential role in the promotion of a particular conformation of 5S rRNA. The crystal structure of the ribosomal protein L5 from Bacillus stearothermophilus has been determined at 1.8 A resolution. The molecule consists of a five-stranded antiparallel beta-sheet and four alpha-helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. The molecular shape and electrostatic representation suggest that the concave surface and loop regions are involved in 5S rRNA binding. To identify amino acid residues responsible for 5S rRNA binding, we made use of Ala-scanning mutagenesis of evolutionarily conserved amino acids occurring in the beta-strands and loop regions. The mutations of Asn37 at the beta1-strand and Gln63 at the loop between helix 2 and beta3-strand as well as that of Phe77 at the tip of the loop structure between the beta2- and beta3-strands caused a significant reduction in 5S rRNA binding. In addition, the mutations of Thr90 on the beta3-strand and Ile141 and Asp144 at the loop between beta4- and beta5-strands moderately reduced the 5S rRNA-binding affinity. Comparison of these results with the more recently analyzed structure of the 50S subunit from Haloarcula marismortui suggests that there are significant differences in the structure at N- and C-terminal regions and probably in the 5S rRNA binding. PMID:11350033

Reverse Transcription of a Self-Primed Retrotransposon Requires an RNA Structure Similar to the U5-IR Stem-Loop of Retroviruses

PubMed Central

Lin, Jia-Hwei; Levin, Henry L.

1998-01-01

An inverted repeat (IR) within the U5 region of the Rous sarcoma virus (RSV) mRNA forms a structure composed of a 7-bp stem and a 5-nucleotide (nt) loop. This U5-IR structure has been shown to be required for the initiation of reverse transcription. The mRNA of Tf1, long terminal repeat-containing retrotransposon from fission yeast (Schizosaccharomyces pombe) contains nucleotides with the potential to form a U5-IR stem-loop that is strikingly similar to that of RSV. The putative U5-IR stem-loop of Tf1 consists of a 7-bp stem and a 25-nt loop. Results from mutagenesis studies indicate that the U5-IR stem-loop in the mRNA of Tf1 does form and that it is required for Tf1 transposition. Although the loop is required for transposition, we were surprised that the specific sequence of the nucleotides within the loop was unimportant for function. Additional investigation indicates that the loss of transposition activity due to a reduction in the loop size to 6 nt could be rescued by increasing the GC content of the stem. This result indicates that the large loop in the Tf1 mRNA relative to that of the RSV allows the formation of the relatively weak U5-IR stem. The levels of Tf1 proteins expressed and the amounts of Tf1 RNA packaged into the virus-like particles were not affected by mutations in the U5-IR structure. However, all of the mutations in the U5-IR structure that caused defects in transposition produced low amounts of reverse transcripts. A unique feature in the initiation of Tf1 reverse transcription is that, instead of a tRNA, the first 11 nt of the Tf1 mRNA serve as the minus-strand primer. Analysis of the 5′ end of Tf1 mRNA revealed that the mutations in the U5-IR stem-loop that resulted in defects in reverse transcription caused a reduction in the cleavage activity required to generate the Tf1 primer. Our results indicate that the U5-IR stems of Tf1 and RSV are conserved in size, position, and function. PMID:9774699

MacA is a second cytochrome c peroxidase of Geobacter sulfurreducens.

PubMed

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

2012-04-03

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

MacA is a Second Cytochrome c Peroxidase of Geobacter sulfurreducens

PubMed Central

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

2012-01-01

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

Velocity Measurements for a Solar Active Region Fan Loop from Hinode/EIS Observations

NASA Astrophysics Data System (ADS)

Young, P. R.; O'Dwyer, B.; Mason, H. E.

2012-01-01

The velocity pattern of a fan loop structure within a solar active region over the temperature range 0.15-1.5 MK is derived using data from the EUV Imaging Spectrometer (EIS) on board the Hinode satellite. The loop is aligned toward the observer's line of sight and shows downflows (redshifts) of around 15 km s-1 up to a temperature of 0.8 MK, but for temperatures of 1.0 MK and above the measured velocity shifts are consistent with no net flow. This velocity result applies over a projected spatial distance of 9 Mm and demonstrates that the cooler, redshifted plasma is physically disconnected from the hotter, stationary plasma. A scenario in which the fan loops consist of at least two groups of "strands"—one cooler and downflowing, the other hotter and stationary—is suggested. The cooler strands may represent a later evolutionary stage of the hotter strands. A density diagnostic of Mg VII was used to show that the electron density at around 0.8 MK falls from 3.2 × 109 cm-3 at the loop base, to 5.0 × 108 cm-3 at a projected height of 15 Mm. A filling factor of 0.2 is found at temperatures close to the formation temperature of Mg VII (0.8 MK), confirming that the cooler, downflowing plasma occupies only a fraction of the apparent loop volume. The fan loop is rooted within a so-called outflow region that displays low intensity and blueshifts of up to 25 km s-1 in Fe XII λ195.12 (formed at 1.5 MK), in contrast to the loop's redshifts of 15 km s-1 at 0.8 MK. A new technique for obtaining an absolute wavelength calibration for the EIS instrument is presented and an instrumental effect, possibly related to a distorted point-spread function, that affects velocity measurements is identified.

VELOCITY MEASUREMENTS FOR A SOLAR ACTIVE REGION FAN LOOP FROM HINODE/EIS OBSERVATIONS

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

Young, P. R.; O'Dwyer, B.; Mason, H. E.

2012-01-01

The velocity pattern of a fan loop structure within a solar active region over the temperature range 0.15-1.5 MK is derived using data from the EUV Imaging Spectrometer (EIS) on board the Hinode satellite. The loop is aligned toward the observer's line of sight and shows downflows (redshifts) of around 15 km s{sup -1} up to a temperature of 0.8 MK, but for temperatures of 1.0 MK and above the measured velocity shifts are consistent with no net flow. This velocity result applies over a projected spatial distance of 9 Mm and demonstrates that the cooler, redshifted plasma is physicallymore » disconnected from the hotter, stationary plasma. A scenario in which the fan loops consist of at least two groups of 'strands'-one cooler and downflowing, the other hotter and stationary-is suggested. The cooler strands may represent a later evolutionary stage of the hotter strands. A density diagnostic of Mg VII was used to show that the electron density at around 0.8 MK falls from 3.2 Multiplication-Sign 10{sup 9} cm{sup -3} at the loop base, to 5.0 Multiplication-Sign 10{sup 8} cm{sup -3} at a projected height of 15 Mm. A filling factor of 0.2 is found at temperatures close to the formation temperature of Mg VII (0.8 MK), confirming that the cooler, downflowing plasma occupies only a fraction of the apparent loop volume. The fan loop is rooted within a so-called outflow region that displays low intensity and blueshifts of up to 25 km s{sup -1} in Fe XII {lambda}195.12 (formed at 1.5 MK), in contrast to the loop's redshifts of 15 km s{sup -1} at 0.8 MK. A new technique for obtaining an absolute wavelength calibration for the EIS instrument is presented and an instrumental effect, possibly related to a distorted point-spread function, that affects velocity measurements is identified.« less

HRD Motif as the Central Hub of the Signaling Network for Activation Loop Autophosphorylation in Abl Kinase.

PubMed

La Sala, Giuseppina; Riccardi, Laura; Gaspari, Roberto; Cavalli, Andrea; Hantschel, Oliver; De Vivo, Marco

2016-11-08

A number of structural factors modulate the activity of Abelson (Abl) tyrosine kinase, whose deregulation is often related to oncogenic processes. First, only the open conformation of the Abl kinase domain's activation loop (A-loop) favors ATP binding to the catalytic cleft. In this regard, the trans-autophosphorylation of the Y412 residue, which is located along the A-loop, favors the stability of the open conformation, in turn enhancing Abl activity. Another key factor for full Abl activity is the formation of active conformations of the catalytic DFG motif in the Abl kinase domain. Furthermore, binding of the SH2 domain to the N-lobe of the Abl kinase was recently demonstrated to have a long-range allosteric effect on the stabilization of the A-loop open state. Intriguingly, these distinct structural factors imply a complex signal transmission network for controlling the A-loop's flexibility and conformational preference for optimal Abl function. However, the exact dynamical features of this signal transmission network structure remain unclear. Here, we report on microsecond-long molecular dynamics coupled with enhanced sampling simulations of multiple Abl model systems, in the presence or absence of the SH2 domain and with the DFG motif flipped in two ways (in or out conformation). Through comparative analysis, our simulations augment the interpretation of the existing Abl experimental data, revealing a dynamical network of interactions that interconnect SH2 domain binding with A-loop plasticity and Y412 autophosphorylation in Abl. This signaling network engages the DFG motif and, importantly, other conserved structural elements of the kinase domain, namely, the EPK-ELK H-bond network and the HRD motif. Our results show that the signal propagation for modulating the A-loop spatial localization is highly dependent on the HRD motif conformation, which thus acts as the central hub of this (allosteric) signaling network controlling Abl activation and function.

Using coronal seismology to estimate the magnetic field strength in a realistic coronal model

NASA Astrophysics Data System (ADS)

Chen, F.; Peter, H.

2015-09-01

Aims: Coronal seismology is used extensively to estimate properties of the corona, e.g. the coronal magnetic field strength is derived from oscillations observed in coronal loops. We present a three-dimensional coronal simulation, including a realistic energy balance in which we observe oscillations of a loop in synthesised coronal emission. We use these results to test the inversions based on coronal seismology. Methods: From the simulation of the corona above an active region, we synthesise extreme ultraviolet emission from the model corona. From this, we derive maps of line intensity and Doppler shift providing synthetic data in the same format as obtained from observations. We fit the (Doppler) oscillation of the loop in the same fashion as done for observations to derive the oscillation period and damping time. Results: The loop oscillation seen in our model is similar to imaging and spectroscopic observations of the Sun. The velocity disturbance of the kink oscillation shows an oscillation period of 52.5 s and a damping time of 125 s, which are both consistent with the ranges of periods and damping times found in observations. Using standard coronal seismology techniques, we find an average magnetic field strength of Bkink = 79 G for our loop in the simulation, while in the loop the field strength drops from roughly 300 G at the coronal base to 50 G at the apex. Using the data from our simulation, we can infer what the average magnetic field derived from coronal seismology actually means. It is close to the magnetic field strength in a constant cross-section flux tube, which would give the same wave travel time through the loop. Conclusions: Our model produced a realistic looking loop-dominated corona, and provides realistic information on the oscillation properties that can be used to calibrate and better understand the result from coronal seismology. A movie associated with Fig. 1 is available in electronic form at http://www.aanda.org

Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor

PubMed Central

Sarker, Muzaddid; de Antueno, Roberto; Langelaan, David N.; Parmar, Hiren B.; Shin, Kyungsoo; Rainey, Jan K.; Duncan, Roy

2015-01-01

Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS) in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST) protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS) but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation. PMID:26061049

Comparison of Five System Identification Algorithms for Rotorcraft Higher Harmonic Control

NASA Technical Reports Server (NTRS)

Jacklin, Stephen A.

1998-01-01

This report presents an analysis and performance comparison of five system identification algorithms. The methods are presented in the context of identifying a frequency-domain transfer matrix for the higher harmonic control (HHC) of helicopter vibration. The five system identification algorithms include three previously proposed methods: (1) the weighted-least- squares-error approach (in moving-block format), (2) the Kalman filter method, and (3) the least-mean-squares (LMS) filter method. In addition there are two new ones: (4) a generalized Kalman filter method and (5) a generalized LMS filter method. The generalized Kalman filter method and the generalized LMS filter method were derived as extensions of the classic methods to permit identification by using more than one measurement per identification cycle. Simulation results are presented for conditions ranging from the ideal case of a stationary transfer matrix and no measurement noise to the more complex cases involving both measurement noise and transfer-matrix variation. Both open-loop identification and closed- loop identification were simulated. Closed-loop mode identification was more challenging than open-loop identification because of the decreasing signal-to-noise ratio as the vibration became reduced. The closed-loop simulation considered both local-model identification, with measured vibration feedback and global-model identification with feedback of the identified uncontrolled vibration. The algorithms were evaluated in terms of their accuracy, stability, convergence properties, computation speeds, and relative ease of implementation.

Utilization of municipal wastewater for cooling in thermoelectric power plants

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

Safari, Iman; Walker, Michael E.; Hsieh, Ming-Kai

2013-09-01

A process simulation model has been developed using Aspen Plus® with the OLI (OLI System, Inc.) water chemistry model to predict water quality in the recirculating cooling loop utilizing secondary- and tertiary-treated municipal wastewater as the source of makeup water. Simulation results were compared with pilot-scale experimental data on makeup water alkalinity, loop pH, and ammonia evaporation. The effects of various parameters including makeup water quality, salt formation, NH 3 and CO 2 evaporation mass transfer coefficients, heat load, and operating temperatures were investigated. The results indicate that, although the simulation model can capture the general trends in the loopmore » pH, experimental data on the rates of salt precipitation in the system are needed for more accurate prediction of the loop pH. It was also found that stripping of ammonia and carbon dioxide in the cooling tower can influence the cooling loop pH significantly. The effects of the NH 3 mass transfer coefficient on cooling loop pH appear to be more significant at lower values (e.g., k NH3 < 4×10 -3 m/s) when the makeup water alkalinity is low (e.g., <90 mg/L as CaCO 3). The effect of the CO2 mass transfer coefficient was found to be significant only at lower alkalinity values (e.g., k CO2<4×10 -6 m/s).« less

Ponderomotive Acceleration in Coronal Loops

NASA Astrophysics Data System (ADS)

Dahlburg, Russell B.; Laming, J. Martin; Taylor, Brian; Obenschain, Keith

2017-08-01

Ponderomotive acceleration has been asserted to be a cause of the First Ionization Potential (FIP) effect, the by now well known enhancement in abundance by a factor of 3-4 over photospheric values of elements in the solar corona with FIP less than about 10 eV. It is shown here by means of numerical simulations that ponderomotive acceleration occurs in solar coronal loops, with the appropriate magnitude and direction, as a ``byproduct'' of coronal heating. The numerical simulations are performed with the HYPERION code, which solves the fully compressible three-dimensional magnetohydrodynamic equations including nonlinear thermal conduction and optically thin radiation. Numerical simulations of a coronal loops with an axial magnetic field from 0.005 Teslas to 0.02 Teslas and lengths from 25000 km to 75000 km are presented. In the simulations the footpoints of the axial loop magnetic field are convected by random, large-scale motions. There is a continuous formation and dissipation of field-aligned current sheets which act to heat the loop. As a consequence of coronal magnetic reconnection, small scale, high speed jets form. The familiar vortex quadrupoles form at reconnection sites. Between the magnetic footpoints and the corona the reconnection flow merges with the boundary flow. It is in this region that the ponderomotive acceleration occurs. Mirroring the character of the coronal reconnection, the ponderomotive acceleration is also found to be intermittent.

Reduced Moment-Based Models for Oxygen Precipitates and Dislocation Loops in Silicon

NASA Astrophysics Data System (ADS)

Trzynadlowski, Bart

The demand for ever smaller, higher-performance integrated circuits and more efficient, cost-effective solar cells continues to push the frontiers of process technology. Fabrication of silicon devices requires extremely precise control of impurities and crystallographic defects. Failure to do so not only reduces performance, efficiency, and yield, it threatens the very survival of commercial enterprises in today's fiercely competitive and price-sensitive global market. The presence of oxygen in silicon is an unavoidable consequence of the Czochralski process, which remains the most popular method for large-scale production of single-crystal silicon. Oxygen precipitates that form during thermal processing cause distortion of the surrounding silicon lattice and can lead to the formation of dislocation loops. Localized deformation caused by both of these defects introduces potential wells that trap diffusing impurities such as metal atoms, which is highly desirable if done far away from sensitive device regions. Unfortunately, dislocations also reduce the mechanical strength of silicon, which can cause wafer warpage and breakage. Engineers must negotiate this and other complex tradeoffs when designing fabrication processes. Accomplishing this in a complex, modern process involving a large number of thermal steps is impossible without the aid of computational models. In this dissertation, new models for oxygen precipitation and dislocation loop evolution are described. An oxygen model using kinetic rate equations to evolve the complete precipitate size distribution was developed first. This was then used to create a reduced model tracking only the moments of the size distribution. The moment-based model was found to run significantly faster than its full counterpart while accurately capturing the evolution of oxygen precipitates. The reduced model was fitted to experimental data and a sensitivity analysis was performed to assess the robustness of the results. Source code for both models is included. A moment-based model for dislocation loop formation from {311} defects in ion-implanted silicon was also developed and validated against experimental data. Ab initio density functional theory calculations of stacking faults and edge dislocations were performed to extract energies and elastic properties. This allowed the effect of applied stress on the evolution of {311} defects and dislocation loops to be investigated.

Genetic instability associated with loop or stem–loop structures within transcription units can be independent of nucleotide excision repair

PubMed Central

Burns, John A; Chowdhury, Moinuddin A; Cartularo, Laura; Berens, Christian; Scicchitano, David A

2018-01-01

Abstract Simple sequence repeats (SSRs) are found throughout the genome, and under some conditions can change in length over time. Germline and somatic expansions of trinucleotide repeats are associated with a series of severely disabling illnesses, including Huntington's disease. The underlying mechanisms that effect SSR expansions and contractions have been experimentally elusive, but models suggesting a role for DNA repair have been proposed, in particular the involvement of transcription-coupled nucleotide excision repair (TCNER) that removes transcription-blocking DNA damage from the transcribed strand of actively expressed genes. If the formation of secondary DNA structures that are associated with SSRs were to block RNA polymerase progression, TCNER could be activated, resulting in the removal of the aberrant structure and a concomitant change in the region's length. To test this, TCNER activity in primary human fibroblasts was assessed on defined DNA substrates containing extrahelical DNA loops that lack discernible internal base pairs or DNA stem–loops that contain base pairs within the stem. The results show that both structures impede transcription elongation, but there is no corresponding evidence that nucleotide excision repair (NER) or TCNER operates to remove them. PMID:29474673

Detection of low tension cosmic superstrings

NASA Astrophysics Data System (ADS)

Chernoff, David F.; Tye, S.-H. Henry

2018-05-01

Cosmic superstrings of string theory differ from conventional cosmic strings of field theory. We review how the physical and cosmological properties of the macroscopic string loops influence experimental searches for these relics from the epoch of inflation. The universe's average density of cosmic superstrings can easily exceed that of conventional cosmic strings having the same tension by two or more orders of magnitude. The cosmological behavior of the remnant superstring loops is qualitatively distinct because the string tension is exponentially smaller than the string scale in flux compactifications in string theory. Low tension superstring loops live longer, experience less recoil (rocket effect from the emission of gravitational radiation) and tend to cluster like dark matter in galaxies. Clustering enhances the string loop density with respect to the cosmological average in collapsed structures in the universe. The enhancement at the Sun's position is ~ 105. We develop a model encapsulating the leading order string theory effects, the current understanding of the string network loop production and the influence of cosmological structure formation suitable for forecasting the detection of superstring loops via optical microlensing, gravitational wave bursts and fast radio bursts. We evaluate the detection rate of bursts from cusps and kinks by LIGO- and LISA-like experiments. Clustering dominates rates for G μ < 10‑11.9 (LIGO cusp), G μ<10‑11.2 (LISA cusp), G μ < 10‑10.6 (LISA kink); we forecast experimentally accessible gravitational wave bursts for G μ>10‑14.2 (LIGO cusp), G μ>10‑15 (LISA cusp) and G μ>10‑ 14.1 (LISA kink).

Pre-Lingual Communication and Attachment Behavior.

ERIC Educational Resources Information Center

Modarressi, Taghi; McCulloch, Duncan

Infant's crying may have an important mediating role in the formation of attachment behavior. The earliest vocalizations are discussed in terms of an acoustic communications model in which the baby's vocal repertoire becomes incorporated into a closed-loop, feedback system with his mother. Certain pre-lingual "signals" may be associated with those…