NetTurnP--neural network prediction of beta-turns by use of evolutionary information and predicted protein sequence features.

PubMed

Petersen, Bent; Lundegaard, Claus; Petersen, Thomas Nordahl

2010-11-30

β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC=0.50, Qtotal=82.1%, sensitivity=75.6%, PPV=68.8% and AUC=0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17-0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences.

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project

DOE PAGES

Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A.; ...

2014-06-15

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project with the objective of sequencing 250 bacterial and archaeal genomes. The two major goals of that project were (a) to test the hypothesis that there are many benefits to the use the phylogenetic diversity of organisms in the tree of life as a primary criterion for generating their genome sequence and (b) to develop the necessary framework, technology and organization for large-scale sequencing of microbial isolate genomes. While the GEBA pilot project has not yet been entirely completed, both ofmore » the original goals have already been successfully accomplished, leading the way for the next phase of the project. Here we propose taking the GEBA project to the next level, by generating high quality draft genomes for 1,000 bacterial and archaeal strains. This represents a combined 16-fold increase in both scale and speed as compared to the GEBA pilot project (250 isolate genomes in 4+ years). We will follow a similar approach for organism selection and sequencing prioritization as was done for the GEBA pilot project (i.e. phylogenetic novelty, availability and growth of cultures of type strains and DNA extraction capability), focusing on type strains as this ensures reproducibility of our results and provides the strongest linkage between genome sequences and other knowledge about each strain. In turn, this project will constitute a pilot phase of a larger effort that will target the genome sequences of all available type strains of the Bacteria and Archaea.« less

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project

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

Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A.

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project with the objective of sequencing 250 bacterial and archaeal genomes. The two major goals of that project were (a) to test the hypothesis that there are many benefits to the use the phylogenetic diversity of organisms in the tree of life as a primary criterion for generating their genome sequence and (b) to develop the necessary framework, technology and organization for large-scale sequencing of microbial isolate genomes. While the GEBA pilot project has not yet been entirely completed, both ofmore » the original goals have already been successfully accomplished, leading the way for the next phase of the project. Here we propose taking the GEBA project to the next level, by generating high quality draft genomes for 1,000 bacterial and archaeal strains. This represents a combined 16-fold increase in both scale and speed as compared to the GEBA pilot project (250 isolate genomes in 4+ years). We will follow a similar approach for organism selection and sequencing prioritization as was done for the GEBA pilot project (i.e. phylogenetic novelty, availability and growth of cultures of type strains and DNA extraction capability), focusing on type strains as this ensures reproducibility of our results and provides the strongest linkage between genome sequences and other knowledge about each strain. In turn, this project will constitute a pilot phase of a larger effort that will target the genome sequences of all available type strains of the Bacteria and Archaea.« less

cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA.

PubMed

De Bruin, Lennart; Maddocks, John H

2018-06-14

The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to a few hundreds of bp, e.g. indirect read-out protein binding sites, nucleosome positioning sequences, phased A-tracts, etc. In turn, the equilibrium statistical mechanics behaviour of DNA depends upon its ground state configuration, or minimum free energy shape, as well as on its fluctuations as governed by its stiffness (in an appropriate sense). We here present cgDNAweb, which provides browser-based interactive visualization of the sequence-dependent ground states of double-stranded DNA molecules, as predicted by the underlying cgDNA coarse-grain rigid-base model of fragments with arbitrary sequence. The cgDNAweb interface is specifically designed to facilitate comparison between ground state shapes of different sequences. The server is freely available at cgDNAweb.epfl.ch with no login requirement.

Predicting turns in proteins with a unified model.

PubMed

Song, Qi; Li, Tonghua; Cong, Peisheng; Sun, Jiangming; Li, Dapeng; Tang, Shengnan

2012-01-01

Turns are a critical element of the structure of a protein; turns play a crucial role in loops, folds, and interactions. Current prediction methods are well developed for the prediction of individual turn types, including α-turn, β-turn, and γ-turn, etc. However, for further protein structure and function prediction it is necessary to develop a uniform model that can accurately predict all types of turns simultaneously. In this study, we present a novel approach, TurnP, which offers the ability to investigate all the turns in a protein based on a unified model. The main characteristics of TurnP are: (i) using newly exploited features of structural evolution information (secondary structure and shape string of protein) based on structure homologies, (ii) considering all types of turns in a unified model, and (iii) practical capability of accurate prediction of all turns simultaneously for a query. TurnP utilizes predicted secondary structures and predicted shape strings, both of which have greater accuracy, based on innovative technologies which were both developed by our group. Then, sequence and structural evolution features, which are profile of sequence, profile of secondary structures and profile of shape strings are generated by sequence and structure alignment. When TurnP was validated on a non-redundant dataset (4,107 entries) by five-fold cross-validation, we achieved an accuracy of 88.8% and a sensitivity of 71.8%, which exceeded the most state-of-the-art predictors of certain type of turn. Newly determined sequences, the EVA and CASP9 datasets were used as independent tests and the results we achieved were outstanding for turn predictions and confirmed the good performance of TurnP for practical applications.

Predicting Turns in Proteins with a Unified Model

PubMed Central

Song, Qi; Li, Tonghua; Cong, Peisheng; Sun, Jiangming; Li, Dapeng; Tang, Shengnan

2012-01-01

Motivation Turns are a critical element of the structure of a protein; turns play a crucial role in loops, folds, and interactions. Current prediction methods are well developed for the prediction of individual turn types, including α-turn, β-turn, and γ-turn, etc. However, for further protein structure and function prediction it is necessary to develop a uniform model that can accurately predict all types of turns simultaneously. Results In this study, we present a novel approach, TurnP, which offers the ability to investigate all the turns in a protein based on a unified model. The main characteristics of TurnP are: (i) using newly exploited features of structural evolution information (secondary structure and shape string of protein) based on structure homologies, (ii) considering all types of turns in a unified model, and (iii) practical capability of accurate prediction of all turns simultaneously for a query. TurnP utilizes predicted secondary structures and predicted shape strings, both of which have greater accuracy, based on innovative technologies which were both developed by our group. Then, sequence and structural evolution features, which are profile of sequence, profile of secondary structures and profile of shape strings are generated by sequence and structure alignment. When TurnP was validated on a non-redundant dataset (4,107 entries) by five-fold cross-validation, we achieved an accuracy of 88.8% and a sensitivity of 71.8%, which exceeded the most state-of-the-art predictors of certain type of turn. Newly determined sequences, the EVA and CASP9 datasets were used as independent tests and the results we achieved were outstanding for turn predictions and confirmed the good performance of TurnP for practical applications. PMID:23144872

Methods for magnetic resonance analysis using magic angle technique

DOEpatents

Hu, Jian Zhi [Richland, WA; Wind, Robert A [Kennewick, WA; Minard, Kevin R [Kennewick, WA; Majors, Paul D [Kennewick, WA

2011-11-22

Methods of performing a magnetic resonance analysis of a biological object are disclosed that include placing the object in a main magnetic field (that has a static field direction) and in a radio frequency field; rotating the object at a frequency of less than about 100 Hz around an axis positioned at an angle of about 54.degree.44' relative to the main magnetic static field direction; pulsing the radio frequency to provide a sequence that includes a phase-corrected magic angle turning pulse segment; and collecting data generated by the pulsed radio frequency. In particular embodiments the method includes pulsing the radio frequency to provide at least two of a spatially selective read pulse, a spatially selective phase pulse, and a spatially selective storage pulse. Further disclosed methods provide pulse sequences that provide extended imaging capabilities, such as chemical shift imaging or multiple-voxel data acquisition.

Redesigning the type II' β-turn in green fluorescent protein to type I': implications for folding kinetics and stability.

PubMed

Madan, Bharat; Sokalingam, Sriram; Raghunathan, Govindan; Lee, Sun-Gu

2014-10-01

Both Type I' and Type II' β-turns have the same sense of the β-turn twist that is compatible with the β-sheet twist. They occur predominantly in two residue β-hairpins, but the occurrence of Type I' β-turns is two times higher than Type II' β-turns. This suggests that Type I' β-turns may be more stable than Type II' β-turns, and Type I' β-turn sequence and structure can be more favorable for protein folding than Type II' β-turns. Here, we redesigned the native Type II' β-turn in GFP to Type I' β-turn, and investigated its effect on protein folding and stability. The Type I' β-turns were designed based on the statistical analysis of residues in natural Type I' β-turns. The substitution of the native "GD" sequence of i+1 and i+2 residues with Type I' preferred "(N/D)G" sequence motif increased the folding rate by 50% and slightly improved the thermodynamic stability. Despite the enhancement of in vitro refolding kinetics and stability of the redesigned mutants, they showed poor soluble expression level compared to wild type. To overcome this problem, i and i + 3 residues of the designed Type I' β-turn were further engineered. The mutation of Thr to Lys at i + 3 could restore the in vivo soluble expression of the Type I' mutant. This study indicates that Type II' β-turns in natural β-hairpins can be further optimized by converting the sequence to Type I'. © 2014 Wiley Periodicals, Inc.

Augmented brain function by coordinated reset stimulation with slowly varying sequences.

PubMed

Zeitler, Magteld; Tass, Peter A

2015-01-01

Several brain disorders are characterized by abnormally strong neuronal synchrony. Coordinated Reset (CR) stimulation was developed to selectively counteract abnormal neuronal synchrony by desynchronization. For this, phase resetting stimuli are delivered to different subpopulations in a timely coordinated way. In neural networks with spike timing-dependent plasticity CR stimulation may eventually lead to an anti-kindling, i.e., an unlearning of abnormal synaptic connectivity and abnormal synchrony. The spatiotemporal sequence by which all stimulation sites are stimulated exactly once is called the stimulation site sequence, or briefly sequence. So far, in simulations, pre-clinical and clinical applications CR was applied either with fixed sequences or rapidly varying sequences (RVS). In this computational study we show that appropriate repetition of the sequence with occasional random switching to the next sequence may significantly improve the anti-kindling effect of CR. To this end, a sequence is applied many times before randomly switching to the next sequence. This new method is called SVS CR stimulation, i.e., CR with slowly varying sequences. In a neuronal network with strong short-range excitatory and weak long-range inhibitory dynamic couplings SVS CR stimulation turns out to be superior to CR stimulation with fixed sequences or RVS.

Augmented brain function by coordinated reset stimulation with slowly varying sequences

PubMed Central

Zeitler, Magteld; Tass, Peter A.

2015-01-01

Several brain disorders are characterized by abnormally strong neuronal synchrony. Coordinated Reset (CR) stimulation was developed to selectively counteract abnormal neuronal synchrony by desynchronization. For this, phase resetting stimuli are delivered to different subpopulations in a timely coordinated way. In neural networks with spike timing-dependent plasticity CR stimulation may eventually lead to an anti-kindling, i.e., an unlearning of abnormal synaptic connectivity and abnormal synchrony. The spatiotemporal sequence by which all stimulation sites are stimulated exactly once is called the stimulation site sequence, or briefly sequence. So far, in simulations, pre-clinical and clinical applications CR was applied either with fixed sequences or rapidly varying sequences (RVS). In this computational study we show that appropriate repetition of the sequence with occasional random switching to the next sequence may significantly improve the anti-kindling effect of CR. To this end, a sequence is applied many times before randomly switching to the next sequence. This new method is called SVS CR stimulation, i.e., CR with slowly varying sequences. In a neuronal network with strong short-range excitatory and weak long-range inhibitory dynamic couplings SVS CR stimulation turns out to be superior to CR stimulation with fixed sequences or RVS. PMID:25873867

β oscillations are linked to the initiation of sensory-cued movement sequences and the internal guidance of regular tapping in the monkey.

PubMed

Bartolo, Ramón; Merchant, Hugo

2015-03-18

β oscillations in the basal ganglia have been associated with interval timing. We recorded the putaminal local field potentials (LFPs) from monkeys performing a synchronization-continuation task (SCT) and a serial reaction-time task (RTT), where the animals produced regularly and irregularly paced tapping sequences, respectively. We compared the activation profile of β oscillations between tasks and found transient bursts of β activity in both the RTT and SCT. During the RTT, β power was higher at the beginning of the task, especially when LFPs were aligned to the stimuli. During the SCT, β was higher during the internally driven continuation phase, especially for tap-aligned LFPs. Interestingly, a set of LFPs showed an initial burst of β at the beginning of the SCT, similar to the RTT, followed by a decrease in β oscillations during the synchronization phase, to finally rebound during the continuation phase. The rebound during the continuation phase of the SCT suggests that the corticostriatal circuit is involved in the control of internally driven motor sequences. In turn, the transient bursts of β activity at the beginning of both tasks suggest that the basal ganglia produce a general initiation signal that engages the motor system in different sequential behaviors. Copyright © 2015 the authors 0270-6474/15/354635-06$15.00/0.

Role of local sequence in the folding of cellular retinoic abinding protein I: structural propensities of reverse turns.

PubMed

Rotondi, Kenneth S; Gierasch, Lila M

2003-07-08

The experiments described here explore the role of local sequence in the folding of cellular retinoic acid binding protein I (CRABP I). This is a 136-residue, 10-stranded, antiparallel beta-barrel protein with seven beta-hairpins and is a member of the intracellular lipid binding protein (iLBP) family. The relative roles of local and global sequence information in governing the folding of this class of proteins are not well-understood. In question is whether the beta-turns are locally defined by short-range interactions within their sequences, and are thus able to play an active role in reducing the conformational space available to the folding chain, or whether the turns are passive, relying upon global forces to form. Short (six- and seven-residue) peptides corresponding to the seven CRABP I turns were analyzed by circular dichroism and NMR for their tendencies to take up the conformations they adopt in the context of the native protein. The results indicate that two of the peptides, encompassing turns III and IV in CRABP I, have a strong intrinsic bias to form native turns. Intriguingly, these turns are on linked hairpins in CRABP I and represent the best-conserved turns in the iLBP family. These results suggest that local sequence may play an important role in narrowing the conformational ensemble of CRABP I during folding.

A low-cost hierarchical nanostructured beta-titanium alloy with high strength

PubMed Central

Devaraj, Arun; Joshi, Vineet V.; Srivastava, Ankit; Manandhar, Sandeep; Moxson, Vladimir; Duz, Volodymyr A.; Lavender, Curt

2016-01-01

Lightweighting of automobiles by use of novel low-cost, high strength-to-weight ratio structural materials can reduce the consumption of fossil fuels and in turn CO2 emission. Working towards this goal we achieved high strength in a low cost β-titanium alloy, Ti–1Al–8V–5Fe (Ti185), by hierarchical nanostructure consisting of homogenous distribution of micron-scale and nanoscale α-phase precipitates within the β-phase matrix. The sequence of phase transformation leading to this hierarchical nanostructure is explored using electron microscopy and atom probe tomography. Our results suggest that the high number density of nanoscale α-phase precipitates in the β-phase matrix is due to ω assisted nucleation of α resulting in high tensile strength, greater than any current commercial titanium alloy. Thus hierarchical nanostructured Ti185 serves as an excellent candidate for replacing costlier titanium alloys and other structural alloys for cost-effective lightweighting applications. PMID:27034109

RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn

PubMed Central

Schroeder, Kersten T.; Daldrop, Peter; Lilley, David M.J.

2011-01-01

Summary The kink turn is a widespread RNA motif that introduces an acute kink into the axis of duplex RNA, typically comprising a bulge followed by a G⋅A and A⋅G pairs. The kinked conformation is stabilized by metal ions, or the binding of proteins including L7Ae. We now demonstrate a third mechanism for the stabilization of k-turn structure, involving tertiary interactions within a larger RNA structure. The SAM-I riboswitch contains an essential standard k-turn sequence that kinks a helix so that its terminal loop can make a long-range interaction. We find that some sequence variations in the k-turn within the riboswitch do not prevent SAM binding, despite preventing the folding of the k-turn in isolation. Furthermore, two crystal structures show that the sequence-variant k-turns are conventionally folded within the riboswitch. This study shows that the folded structure of the k-turn can be stabilized by tertiary interactions within a larger RNA structure. PMID:21893284

Guidelines for the use of protected/permissive left-turn phasing

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

Agent, K.R.

1987-07-01

Turning left across opposing traffic at a signalized intersection could result in a traffic accident, as well as create motorist delay. A solution to the left-turn problem may be the addition of a left-turn phase when certain guidelines are met. After a decision has been made to add a left-turn phase, one of two basic alternative phasing methods is . In a previous research study, the results of replacing protected-only (exclusive) with protected/permissive (permissive) phasing at four trial intersections were studied. The permissive phasing provided a substantial reduction in delay and was popular with local drivers. However, several left-turn relatedmore » accidents occurred at those locations. Since those initial trial installations, permissive phasing has been used at several intersections across the state. This created a larger data base that could be used to determine when permissive phasing could be used without causing an accident problem. The objective of this study was to develop guidelines to aid traffic engineers in deciding whether permissive left-turn phasing is appropriate for use at a given location.« less

Turn stability in beta-hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns.

PubMed

Blandl, Tamas; Cochran, Andrea G; Skelton, Nicholas J

2003-02-01

The turn-forming ability of a series of three-residue sequences was investigated by substituting them into a well-characterized beta-hairpin peptide. The starting scaffold, bhpW, is a disulfide-cyclized 10-residue peptide that folds into a stable beta-hairpin with two antiparallel strands connected by a two-residue reverse turn. Substitution of the central two residues with the three-residue test sequences leads to less stable hairpins, as judged by thiol-disulfide equilibrium measurements. However, analysis of NMR parameters indicated that each molecule retains a significant folded population, and that the type of turn adopted by the three-residue sequence is the same in all cases. The solution structure of a selected peptide with a PDG turn contained an antiparallel beta-hairpin with a 3:5 type I + G1 bulge turn. Analysis of the energetic contributions of individual turn residues in the series of peptides indicates that substitution effects have significant context dependence, limiting the predictive power of individual amino acid propensities for turn formation. The most stable and least stable sequences were also substituted into a more stable disulfide-cyclized scaffold and a linear beta-hairpin scaffold. The relative stabilities remained the same, suggesting that experimental measurements in the bhpW context are a useful way to evaluate turn stability for use in protein design projects. Moreover, these scaffolds are capable of displaying a diverse set of turns, which can be exploited for the mimicry of protein loops or for generating libraries of reverse turns.

On the determination of age and mass functions of stars in young open star clusters from the analysis of their luminosity functions

NASA Astrophysics Data System (ADS)

Piskunov, A. E.; Belikov, A. N.; Kharchenko, N. V.; Sagar, R.; Subramaniam, A.

2004-04-01

We construct the observed luminosity functions of the remote young open clusters NGC 2383, 2384, 4103, 4755, 7510 and Hogg 15 from CCD observations of them. The observed LFs are corrected for field star contamination determined with the help of a Galactic star count model. In the case of Hogg 15 and NGC 2383 we also consider the additional contamination from neighbouring clusters NGC 4609 and 2384, respectively. These corrections provide a realistic pattern of cluster LF in the vicinity of the main-sequence (MS) turn-on point and at fainter magnitudes reveal the so-called H-feature arising as a result of the transition of the pre-MS phase to the MS, which is dependent on the cluster age. The theoretical LFs are constructed representing a cluster population model with continuous star formation for a short time-scale and a power-law initial mass function (IMF), and these are fitted to the observed LF. As a result, we are able to determine for each cluster a set of parameters describing the cluster population (the age, duration of star formation, IMF slope and percentage of field star contamination). It is found that in spite of the non-monotonic behaviour of observed LFs, cluster IMFs can be described as power-law functions with slopes similar to Salpeter's value. The present main-sequence turn-on cluster ages are several times lower than those derived from the fitting of theoretical isochrones to the turn-off region of the upper main sequences.

The effects of processing and sequence organization on the timing of turn taking: a corpus study

PubMed Central

Roberts, Seán G.; Torreira, Francisco; Levinson, Stephen C.

2015-01-01

The timing of turn taking in conversation is extremely rapid given the cognitive demands on speakers to comprehend, plan and execute turns in real time. Findings from psycholinguistics predict that the timing of turn taking is influenced by demands on processing, such as word frequency or syntactic complexity. An alternative view comes from the field of conversation analysis, which predicts that the rules of turn-taking and sequence organization may dictate the variation in gap durations (e.g., the functional role of each turn in communication). In this paper, we estimate the role of these two different kinds of factors in determining the speed of turn-taking in conversation. We use the Switchboard corpus of English telephone conversation, already richly annotated for syntactic structure speech act sequences, and segmental alignment. To this we add further information including Floor Transfer Offset (the amount of time between the end of one turn and the beginning of the next), word frequency, concreteness, and surprisal values. We then apply a novel statistical framework (“random forests”) to show that these two dimensions are interwoven together with indexical properties of the speakers as explanatory factors determining the speed of response. We conclude that an explanation of the of the timing of turn taking will require insights from both processing and sequence organization. PMID:26029125

Approximation of a Brittle Fracture Energy with a Constraint of Non-interpenetration

NASA Astrophysics Data System (ADS)

Chambolle, Antonin; Conti, Sergio; Francfort, Gilles A.

2018-06-01

Linear fracture mechanics (or at least the initiation part of that theory) can be framed in a variational context as a minimization problem over an SBD type space. The corresponding functional can in turn be approximated in the sense of {Γ}-convergence by a sequence of functionals involving a phase field as well as the displacement field. We show that a similar approximation persists if additionally imposing a non-interpenetration constraint in the minimization, namely that only nonnegative normal jumps should be permissible.

A novel hybrid method of beta-turn identification in protein using binary logistic regression and neural network

PubMed Central

Asghari, Mehdi Poursheikhali; Hayatshahi, Sayyed Hamed Sadat; Abdolmaleki, Parviz

2012-01-01

From both the structural and functional points of view, β-turns play important biological roles in proteins. In the present study, a novel two-stage hybrid procedure has been developed to identify β-turns in proteins. Binary logistic regression was initially used for the first time to select significant sequence parameters in identification of β-turns due to a re-substitution test procedure. Sequence parameters were consisted of 80 amino acid positional occurrences and 20 amino acid percentages in sequence. Among these parameters, the most significant ones which were selected by binary logistic regression model, were percentages of Gly, Ser and the occurrence of Asn in position i+2, respectively, in sequence. These significant parameters have the highest effect on the constitution of a β-turn sequence. A neural network model was then constructed and fed by the parameters selected by binary logistic regression to build a hybrid predictor. The networks have been trained and tested on a non-homologous dataset of 565 protein chains. With applying a nine fold cross-validation test on the dataset, the network reached an overall accuracy (Qtotal) of 74, which is comparable with results of the other β-turn prediction methods. In conclusion, this study proves that the parameter selection ability of binary logistic regression together with the prediction capability of neural networks lead to the development of more precise models for identifying β-turns in proteins. PMID:27418910

A novel hybrid method of beta-turn identification in protein using binary logistic regression and neural network.

PubMed

Asghari, Mehdi Poursheikhali; Hayatshahi, Sayyed Hamed Sadat; Abdolmaleki, Parviz

2012-01-01

From both the structural and functional points of view, β-turns play important biological roles in proteins. In the present study, a novel two-stage hybrid procedure has been developed to identify β-turns in proteins. Binary logistic regression was initially used for the first time to select significant sequence parameters in identification of β-turns due to a re-substitution test procedure. Sequence parameters were consisted of 80 amino acid positional occurrences and 20 amino acid percentages in sequence. Among these parameters, the most significant ones which were selected by binary logistic regression model, were percentages of Gly, Ser and the occurrence of Asn in position i+2, respectively, in sequence. These significant parameters have the highest effect on the constitution of a β-turn sequence. A neural network model was then constructed and fed by the parameters selected by binary logistic regression to build a hybrid predictor. The networks have been trained and tested on a non-homologous dataset of 565 protein chains. With applying a nine fold cross-validation test on the dataset, the network reached an overall accuracy (Qtotal) of 74, which is comparable with results of the other β-turn prediction methods. In conclusion, this study proves that the parameter selection ability of binary logistic regression together with the prediction capability of neural networks lead to the development of more precise models for identifying β-turns in proteins.

Understanding the optics to aid microscopy image segmentation.

PubMed

Yin, Zhaozheng; Li, Kang; Kanade, Takeo; Chen, Mei

2010-01-01

Image segmentation is essential for many automated microscopy image analysis systems. Rather than treating microscopy images as general natural images and rushing into the image processing warehouse for solutions, we propose to study a microscope's optical properties to model its image formation process first using phase contrast microscopy as an exemplar. It turns out that the phase contrast imaging system can be relatively well explained by a linear imaging model. Using this model, we formulate a quadratic optimization function with sparseness and smoothness regularizations to restore the "authentic" phase contrast images that directly correspond to specimen's optical path length without phase contrast artifacts such as halo and shade-off. With artifacts removed, high quality segmentation can be achieved by simply thresholding the restored images. The imaging model and restoration method are quantitatively evaluated on two sequences with thousands of cells captured over several days.

Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA +H]+ and [YGPAA +H]+ Ions

NASA Astrophysics Data System (ADS)

Deblase, Andrew; Harrilal, Christopher; Lawler, John; Burke, Nicole; McLuckey, Scott; Timothy, Zwier

Incorporation of the unnatural D-proline stereoisomer into a peptide sequence is a typical strategy to synthesize model β-hairpin loops. Using conformation-specific IR and UV spectroscopy of cold ( 10 K) gas-phase ions, we unravel the inherent conformational preferences of the DP and LP diastereomers in the protonated peptide [YAPAA +H]+ because only intramolecular interactions are possible in this isolated regime. Consistent with the solution phase studies, one of the conformers of [YADPAA +H]+ is folded into a β-hairpin turn. However, a second predominant γ-turn conformer family is identified. The [YALPAA +H]+ stereoisomer discourages β-hairpin formation. We show that the trans(DP) ->cis (LP) isomerization is sterically driven and can be reversed by substituting [YGLPAA +H]+ for [YALPAA +H]+. Therefore, we provide a basis for understanding residue-specific alterations in the potential energy surface and reveal new insights into the origin of β-hairpin formation from the bottom-up. National Science Foundation (NSF CHE 1213289) and the U.S. Department of Energy (Office of Basic Energy Sciences under Award Number FG02-00ER15105).

Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion

PubMed Central

Dunn, Timothy W; Mu, Yu; Narayan, Sujatha; Randlett, Owen; Naumann, Eva A; Yang, Chao-Tsung; Schier, Alexander F

2016-01-01

In the absence of salient sensory cues to guide behavior, animals must still execute sequences of motor actions in order to forage and explore. How such successive motor actions are coordinated to form global locomotion trajectories is unknown. We mapped the structure of larval zebrafish swim trajectories in homogeneous environments and found that trajectories were characterized by alternating sequences of repeated turns to the left and to the right. Using whole-brain light-sheet imaging, we identified activity relating to the behavior in specific neural populations that we termed the anterior rhombencephalic turning region (ARTR). ARTR perturbations biased swim direction and reduced the dependence of turn direction on turn history, indicating that the ARTR is part of a network generating the temporal correlations in turn direction. We also find suggestive evidence for ARTR mutual inhibition and ARTR projections to premotor neurons. Finally, simulations suggest the observed turn sequences may underlie efficient exploration of local environments. DOI: http://dx.doi.org/10.7554/eLife.12741.001 PMID:27003593

Left-turn phase: permissive, protected, or both? A quasi-experimental design in New York City.

PubMed

Chen, Li; Chen, Cynthia; Ewing, Reid

2015-03-01

The practice of left-turn phasing selection (permissive, protected-only, or both) varies from one locality to another. The literature evidence on this issue is equally mixed and insufficient. In this study, we evaluate the safety impacts of changing left-turn signal phasing from permissive to protected/permissive or protected-only at 68 intersections in New York City using a rigorous quasi-experimental design accompanied with regression modeling. Changes in police reported crashes including total crashes, multiple-vehicle crashes, left-turn crashes, pedestrian crashes and bicyclist crashes were compared between before period and after period for the treatment group and comparison group by means of negative binomial regression using a Generalized Estimating Equations (GEE) technique. Confounding factors such as the built environment characteristics that were not controlled in comparison group selection are accounted for by this approach. The results show that the change of permissive left-turn signal phasing to protected/permissive or protected-only signal phasing does not result in a significant reduction in intersection crashes. Though the protected-only signal phasing does reduce the left-turn crashes and pedestrian crashes, this reduction was offset by a possible increase in over-taking crashes. These results suggest that left-turn phasing should not be treated as a universal solution that is always better than the permissive control for left-turn vehicles. The selection and implementation of left-turn signal phasing needs to be done carefully, considering potential trade-offs between safety and delay, and many other factors such as geometry, traffic flows and operations. Copyright © 2014 Elsevier Ltd. All rights reserved.

A low-cost hierarchical nanostructured beta-titanium alloy with high strength

DOE PAGES

Devaraj, Arun; Joshi, Vineet V.; Srivastava, Ankit; ...

2016-04-01

Lightweighting of automobiles by use of novel low-cost, high strength-to-weight ratio structural materials can reduce the consumption of fossil fuels and in turn CO 2 emission. Working towards this goal we achieved high strength in a low cost β-titanium alloy, Ti-1Al-8V-5Fe (Ti185), by hierarchical nanostructure consisting of homogenous distribution of micron-scale and nanoscale α-phase precipitates within the β-phase matrix. The sequence of phase transformation leading to this hierarchical nanostructure is explored using electron microscopy and atom probe tomography. Our results suggest that the high number density of nanoscale α-phase precipitates in the β-phase matrix is due to ω assisted nucleationmore » of α resulting in high tensile strength, greater than any current commercial titanium alloy. Furthermore hierarchical nanostructured Ti185 serves as an excellent candidate for replacing costlier titanium alloys and other structural alloys for cost-effective lightweighting applications.« less

A low-cost hierarchical nanostructured beta-titanium alloy with high strength

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

Devaraj, Arun; Joshi, Vineet V.; Srivastava, Ankit

Lightweighting of automobiles by use of novel low-cost, high strength-to-weight ratio structural materials can reduce the consumption of fossil fuels and in turn CO 2 emission. Working towards this goal we achieved high strength in a low cost β-titanium alloy, Ti-1Al-8V-5Fe (Ti185), by hierarchical nanostructure consisting of homogenous distribution of micron-scale and nanoscale α-phase precipitates within the β-phase matrix. The sequence of phase transformation leading to this hierarchical nanostructure is explored using electron microscopy and atom probe tomography. Our results suggest that the high number density of nanoscale α-phase precipitates in the β-phase matrix is due to ω assisted nucleationmore » of α resulting in high tensile strength, greater than any current commercial titanium alloy. Furthermore hierarchical nanostructured Ti185 serves as an excellent candidate for replacing costlier titanium alloys and other structural alloys for cost-effective lightweighting applications.« less

Information performances and illative sequences: Sequential organization of explanations of chemical phase equilibrium

NASA Astrophysics Data System (ADS)

Brown, Nathaniel James Swanton

While there is consensus that conceptual change is surprisingly difficult, many competing theories of conceptual change co-exist in the literature. This dissertation argues that this discord is partly the result of an inadequate account of the unwritten rules of human social interaction that underlie the field's preferred methodology---semi-structured interviewing. To better understand the contributions of interaction during explanations, I analyze eight undergraduate general chemistry students as they attempt to explain to various people, for various reasons, why phenomena involving chemical phase equilibrium occur. Using the methods of interaction analysis, I characterize the unwritten, but systematic, rules that these participants follow as they explain. The result is a description of the contributions of interaction to explaining. Each step in each explanation is a jointly performed expression of a subject-predicate relation, an interactive accomplishment I call an information performance (in-form, for short). Unlike clauses, in-forms need not have a coherent grammatical structure. Unlike speaker turns, in-forms have the clear function of expressing information. Unlike both clauses and speaker turns, in-forms are a co-construction, jointly performed by both the primary speaker and the other interlocutor. The other interlocutor strongly affects the form and content of each explanation by giving or withholding feedback at the end of each in-form, moments I call feedback-relevant places. While in-forms are the bricks out of which the explanation is constructed, they are secured by a series of inferential links I call an illative sequence. Illative sequences are forward-searching, starting with a remembered fact or observation and following a chain of inferences in the hope it leads to the target phenomenon. The participants treat an explanation as a success if the illative sequence generates an in-form that describes the phenomenon. If the illative sequence does not, it is partly or entirely scrubbed, a new in-form is introduced as a starting point, and the illative sequence begins anew. Knowledge of these interactional contributions to the production of explanations could allow researchers to better characterize conceptual understanding, be in a stronger position to support particular theories of conceptual change over others, improve assessments of conceptual understanding, and improve interviewing practices.

Influence of slope steepness, foot position and turn phase on plantar pressure distribution during giant slalom alpine ski racing

PubMed Central

Falda-Buscaiot, Thomas; Hintzy, Frédérique; Rougier, Patrice; Lacouture, Patrick; Coulmy, Nicolas

2017-01-01

The purpose of this study was to investigate the evolution of ground reaction force during alpine skiing turns. Specifically, this study investigated how turn phases and slope steepness affected the whole foot normal GRF pattern while performing giant slalom turns in a race-like setting. Moreover, the outside foot was divided into different plantar regions to see whether those parameters affected the plantar pressure distribution. Eleven skiers performed one giant slalom course at race intensity. Runs were recorded synchronously using a video camera in the frontal plane and pressure insoles under both feet’s plantar surface. Turns were divided according to kinematic criteria into four consecutive phases: initiation, steering1, steering2 and completion; both steering phases being separated by the gate passage. Component of the averaged Ground Reaction Force normal to the ski’s surface(nGRF¯, /BW), and Pressure Time Integral relative to the entire foot surface (relPTI, %) parameters were calculated for each turn phases based on plantar pressure data. Results indicated that nGRF¯ under the total foot surface differed significantly depending on the slope (higher in steep sections vs. flat sections), and the turn phase (higher during steering2 vs. three other phases), although such modifications were observable only on the outside foot. Moreover, nGRF¯ under the outside foot was significantly greater than under the inside foot.RelPTI under different foot regions of the outside foot revealed a global shift from forefoot loading during initiation phase, toward heel loading during steering2 phase, but this was dependent on the slope studied. These results suggest a differentiated role played by each foot in alpine skiing turns: the outside foot has an active role in the turning process, while the inside foot may only play a role in stability. PMID:28472092

Influence of slope steepness, foot position and turn phase on plantar pressure distribution during giant slalom alpine ski racing.

PubMed

Falda-Buscaiot, Thomas; Hintzy, Frédérique; Rougier, Patrice; Lacouture, Patrick; Coulmy, Nicolas

2017-01-01

The purpose of this study was to investigate the evolution of ground reaction force during alpine skiing turns. Specifically, this study investigated how turn phases and slope steepness affected the whole foot normal GRF pattern while performing giant slalom turns in a race-like setting. Moreover, the outside foot was divided into different plantar regions to see whether those parameters affected the plantar pressure distribution. Eleven skiers performed one giant slalom course at race intensity. Runs were recorded synchronously using a video camera in the frontal plane and pressure insoles under both feet's plantar surface. Turns were divided according to kinematic criteria into four consecutive phases: initiation, steering1, steering2 and completion; both steering phases being separated by the gate passage. Component of the averaged Ground Reaction Force normal to the ski's surface([Formula: see text], /BW), and Pressure Time Integral relative to the entire foot surface (relPTI, %) parameters were calculated for each turn phases based on plantar pressure data. Results indicated that [Formula: see text] under the total foot surface differed significantly depending on the slope (higher in steep sections vs. flat sections), and the turn phase (higher during steering2 vs. three other phases), although such modifications were observable only on the outside foot. Moreover, [Formula: see text] under the outside foot was significantly greater than under the inside foot.RelPTI under different foot regions of the outside foot revealed a global shift from forefoot loading during initiation phase, toward heel loading during steering2 phase, but this was dependent on the slope studied. These results suggest a differentiated role played by each foot in alpine skiing turns: the outside foot has an active role in the turning process, while the inside foot may only play a role in stability.

Proline Restricts Loop I Conformation of the High Affinity WW Domain from Human Nedd4-1 to a Ligand Binding-Competent Type I β-Turn.

PubMed

Schulte, Marianne; Panwalkar, Vineet; Freischem, Stefan; Willbold, Dieter; Dingley, Andrew J

2018-04-19

Sequence alignment of the four WW domains from human Nedd4-1 (neuronal precursor cell expressed developmentally down-regulated gene 4-1) reveals that the highest sequence diversity exists in loop I. Three residues in this type I β-turn interact with the PPxY motif of the human epithelial Na + channel (hENaC) subunits, indicating that peptide affinity is defined by the loop I sequence. The third WW domain (WW3*) has the highest ligand affinity and unlike the other three hNedd4-1 WW domains or other WW domains studied contains the highly statistically preferred proline at the ( i + 1) position found in β-turns. In this report, molecular dynamics simulations and experimental data were combined to characterize loop I stability and dynamics. Exchange of the proline to the equivalent residue in WW4 (Thr) results in the presence of a predominantly open seven residue Ω loop rather than the type I β-turn conformation for the wild-type apo-WW3*. In the presence of the ligand, the structure of the mutated loop I is locked into a type I β-turn. Thus, proline in loop I ensures a stable peptide binding-competent β-turn conformation, indicating that amino acid sequence modulates local flexibility to tune binding preferences and stability of dynamic interaction motifs.

Aircraft Evaluation Using Stochastic Duels

DTIC Science & Technology

2017-09-01

One of the more recent uses of Lanchester equations for modeling air-to-air combat was proposed by Gilbert (2011). His work studies the strategic...for the number of missiles fired on each side. C. PHASE 2—DOGFIGHT If neither aircraft is shot down in Phase 1, the duel will transit into Phase 2...become the Pursuer of B at the of the turn. On the other hand, in the case of a nose-to-tail turn, the impacts of the turn radius and turn rate are

Role of different β-turns in β-hairpin conformation and stability studied by optical spectroscopy.

PubMed

Wu, Ling; McElheny, Dan; Setnicka, Vladimír; Hilario, Jovencio; Keiderling, Timothy A

2012-01-01

Model β-hairpin peptides based on variations in the turn sequence of Cochran's tryptophan zipper peptide, SWTWENGKWTWK, were studied using electronic circular dichroism (ECD), fluorescence, and infrared (IR) spectroscopies. The trpzip2 Asn-Gly turn sequence was substituted with Thr-Gly, Aib-Gly, (D)Pro-Gly, and Gly-Asn (trpzip1) to study the impact of turn stability on β-hairpin formation. Stability and conformational changes of these hairpins were monitored by thermodynamic analyses of the temperature variation of both FTIR (amide I') and ECD spectral intensities. These changes were fit to a two-state model which yielded different T(m) values, representing the folding/unfolding process, for hairpins with different β-turns. Different β-turns show systematic contributions to hairpin structure formation, and their inclusion in hairpin design can modify the folding pathways. Aib-Gly or (D)Pro-Gly sequences stabilize the turn resulting in residual Trp-Trp interaction at high temperatures, but at the same time the β-structure (cross strand H-bonds) can become less stable due to constraints of the turn, as seen for (D)Pro-Gly. The structure of the Aib-Gly turn containing hairpin was determined by NMR and was shown to be like trpzip2 (Asn-Gly turn) as regards turn and strand geometries, but to differ from trpzip1 (Gly-Asn turn). The Munoz and Eaton statistical mechanically derived multistate model, tested as an alternate point of view, represented contributions from H-bonds and hydrophobic interactions as well as conformational change as interdependent. Use of different spectral methods that vary in dependence on these physical interactions along with the structural variations provided insight to the complex folding pathways of these small, well-folded peptides. Copyright © 2011 Wiley Periodicals, Inc.

A limb action detector enabling people with multiple disabilities to control environmental stimulation through limb action with a Nintendo Wii Remote Controller.

PubMed

Shih, Ching-Hsiang; Chang, Man-Ling; Shih, Ching-Tien

2010-01-01

This study assessed whether two persons with multiple disabilities would be able to control environmental stimulation using limb action with a Nintendo Wii Remote Controller and a newly developed limb action detection program (LADP, i.e., a new software program that turns a Wii Remote Controller into a precise limb action detector). This study was carried out according to an ABAB sequence in which A represented baseline and B represented intervention phases. Data showed that both participants significantly increased their target response, thus increasing the level of environmental stimulation by activating the control system through limb action, during the intervention phases. Practical and developmental implications of the findings are discussed. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

A white dwarf cooling age of 8 Gyr for NGC 6791 from physical separation processes.

PubMed

García-Berro, Enrique; Torres, Santiago; Althaus, Leandro G; Renedo, Isabel; Lorén-Aguilar, Pablo; Córsico, Alejandro H; Rohrmann, René D; Salaris, Maurizio; Isern, Jordi

2010-05-13

NGC 6791 is a well studied open cluster that it is so close to us that can be imaged down to very faint luminosities. The main-sequence turn-off age ( approximately 8 Gyr) and the age derived from the termination of the white dwarf cooling sequence ( approximately 6 Gyr) are very different. One possible explanation is that as white dwarfs cool, one of the ashes of helium burning, (22)Ne, sinks in the deep interior of these stars. At lower temperatures, white dwarfs are expected to crystallize and phase separation of the main constituents of the core of a typical white dwarf ((12)C and (16)O) is expected to occur. This sequence of events is expected to introduce long delays in the cooling times, but has not hitherto been proven. Here we report that, as theoretically anticipated, physical separation processes occur in the cores of white dwarfs, resolving the age discrepancy for NGC 6791.

Prediction of beta-turns from amino acid sequences using the residue-coupled model.

PubMed

Guruprasad, K; Shukla, S

2003-04-01

We evaluated the prediction of beta-turns from amino acid sequences using the residue-coupled model with an enlarged representative protein data set selected from the Protein Data Bank. Our results show that the probability values derived from a data set comprising 425 protein chains yielded an overall beta-turn prediction accuracy 68.74%, compared with 94.7% reported earlier on a data set of 30 proteins using the same method. However, we noted that the overall beta-turn prediction accuracy using probability values derived from the 30-protein data set reduces to 40.74% when tested on the data set comprising 425 protein chains. In contrast, using probability values derived from the 425 data set used in this analysis, the overall beta-turn prediction accuracy yielded consistent results when tested on either the 30-protein data set (64.62%) used earlier or a more recent representative data set comprising 619 protein chains (64.66%) or on a jackknife data set comprising 476 representative protein chains (63.38%). We therefore recommend the use of probability values derived from the 425 representative protein chains data set reported here, which gives more realistic and consistent predictions of beta-turns from amino acid sequences.

Site-Specific Dynamics of β-Sheet Peptides with (D) Pro-Gly Turns Probed by Laser-Excited Temperature-Jump Infrared Spectroscopy.

PubMed

Popp, Alexander; Scheerer, David; Chi, Heng; Keiderling, Timothy A; Hauser, Karin

2016-05-04

Turn residues and side-chain interactions play an important role for the folding of β-sheets. We investigated the conformational dynamics of a three-stranded β-sheet peptide ((D) P(D) P) and a two-stranded β-hairpin (WVYY-(D) P) by time-resolved temperature-jump (T-jump) infrared spectroscopy. Both peptide sequences contain (D) Pro-Gly residues that favor a tight β-turn. The three-stranded β-sheet (Ac-VFITS(D) PGKTYTEV(D) PGOKILQ-NH2 ) is stabilized by the turn sequences, whereas the β-hairpin (SWTVE(D) PGKYTYK-NH2 ) folding is assisted by both the turn sequence and hydrophobic cross-strand interactions. Relaxation times after the T-jump were monitored as a function of temperature and occur on a sub-microsecond time scale, (D) P(D) P being faster than WVYY-(D) P. The Xxx-(D) Pro tertiary amide provides a detectable IR band, allowing us to probe the dynamics site-specifically. The relative importance of the turn versus the intrastrand stability in β-sheet formation is discussed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Magnetic and Structural Phase Transitions in Thulium under High Pressures and Low Temperatures

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

Vohra, Yogesh K.; Tsoi, Georgiy M.; Samudrala, Gopi K.

2017-10-01

The nature of 4f electrons in many rare earth metals and compounds may be broadly characterized as being either "localized" or "itinerant", and is held responsible for a wide range of physical and chemical properties. The pressure variable has a very dramatic effect on the electronic structure of rare earth metals which in turn drives a sequence of structural and magnetic transitions. We have carried out four-probe electrical resistance measurements on rare earth metal Thulium (Tm) under high pressures to 33 GPa and low temperatures to 10 K to monitor the magnetic ordering transition. These studies are complemented by anglemore » dispersive x-ray diffraction studies to monitor crystallographic phase transitions at high pressures and low temperatures. We observe an abrupt increase in magnetic ordering temperature in Tm at a pressure of 17 GPa on phase transition from ambient pressure hcp-phase to α-Sm phase transition. In addition, measured equation of state (EOS) at low temperatures show anomalously low thermal expansion coefficients likely linked to magnetic transitions.« less

Development of guidelines for permitted left-turn phasing using flashing yellow arrows : final report.

DOT National Transportation Integrated Search

2015-06-01

The objective of this project was to develop guidelines for time-of-day use of permitted left-turn phasing, : which can then be implemented using flashing yellow arrows (FYA). This required determining how the risk : for left-turn crashes varied as t...

The sigma factor SigD of Mycobacterium tuberculosis putatively enhances gene expression of the septum site determining protein under stressful environments.

PubMed

Ares, Miguel A; Rios-Sarabia, Nora; De la Cruz, Miguel A; Rivera-Gutiérrez, Sandra; García-Morales, Lázaro; León-Solís, Lizbel; Espitia, Clara; Pacheco, Sabino; Cerna-Cortés, Jorge F; Helguera-Repetto, Cecilia A; García, María Jesús; González-Y-Merchand, Jorge A

2017-07-01

This work examined the expression of the septum site determining gene (ssd) of Mycobacterium tuberculosis CDC1551 and its ∆sigD mutant under different growing conditions. The results showed an up-regulation of ssd during stationary phase and starvation conditions, but not during in vitro dormancy, suggesting a putative role for SigD in the control of ssd expression mainly under lack-of-nutrients environments. Furthermore, we elucidated a putative link between ssd expression and cell elongation of bacilli at stationary phase. In addition, a -35 sigD consensus sequence was found for the ssd promoter region, reinforcing the putative regulation of ssd by SigD, and in turn, supporting this protein role during the adaptation of M. tuberculosis to some stressful environments.

Tune Evaluation From Phased BPM Turn-By-Turn Data

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

Alexahin, Y.; Gianfelice-Wendt, E.; Marsh, W.

2010-05-18

In fast ramping synchrotrons like the Fermilab Booster the conventional methods of betatron tune evaluation from the turn-by-turn data may not work due to rapid changes of the tunes (sometimes in a course of a few dozens of turns) and a high level of noise. We propose a technique based on phasing of signals from a large number of BPMs which significantly increases the signal to noise ratio. Implementation of the method in the Fermilab Booster control system is described and some measurement results are presented.

Designing a Polymerase Chain Reaction Device Working with Radiation and Convection Heat Transfer

NASA Astrophysics Data System (ADS)

Madadelahi, M.; Kalan, K.; Shamloo, A.

2018-05-01

Gene proliferation is vital for infectious and genetic diseases diagnosis from a blood sample, even before birth. In addition, DNA sequencing, genetic finger-print analyzing, and genetic mutation detecting can be mentioned as other procedures requiring gene reproduction. Polymerase chain reaction, briefly known as PCR, is a convenient and effective way to accomplish this task; where the DNA containing sample faces three temperature phases alternatively. These phases are known as denaturation, annealing, and elongation/extension which in this study -regarding the type of the primers and the target DNA sequence- are set to occur at 95, 58, and 72 degrees of Celsius. In this study, a PCR device has been designed and fabricated which uses radiation and convection heat transfer at the same time to set and control the mentioned thermal sections. A 300W incandescent light bulb able to immediately turn off and on along with two 8×8 cm DC fans, controlled by a microcontroller as well as PID and PD controller codes are used to monitor the applied thermal cycles. In designing the controller codes it has been concerned that they not only control the temperature over the set-points as well as possible, but also increase the temperature variation rate between each two phases. The temperature data were plotted and DNA samples were used to assess the device function.

Unifying the microscopic picture of His-containing turns: from gas phase model peptides to crystallized proteins.

PubMed

Sohn, Woon Yong; Habka, Sana; Gloaguen, Eric; Mons, Michel

2017-07-14

The presence in crystallized proteins of a local anchoring between the side chain of a His residue, located in the central position of a γ- or β-turn, and its local main chain environment, was assessed by the comparison of protein structures with relevant isolated model peptides. Gas phase laser spectroscopy, combined with relevant quantum chemistry methods, was used to characterize the γ- and β-turn structures in these model peptides. A conformer-selective NH stretch infrared study provided evidence for the formation in vacuo of two types of short-range H-bonded motifs, labelled ε-6 δ and δ- δ 7/π H , bridging the His side chain (in its gauche+ rotamer) to the neighbouring NH(i) and CO(i) sites of the backbone; each side chain-backbone motif was found to be specific of the tautomer (ε or δ) adopted by the His side chain in its neutral form. A close comparison between β- and γ-turns, selected from the Protein Data Bank, and the gas phase models demonstrated that a significant proportion of the gauche+ His rotamer distribution of proteins was well described by the corresponding gas phase H-bonded structures. This is consistent with the persistence of local 6 δ and δ 7/π H intramolecular interactions in proteins, emphasizing the relevance of gas phase data to secondary structures that are poorly accessible to solvents, e.g., in the case of a specific compact topology (Xxx-His β-turns). Deviations from the gas phase structures were also observed, mainly in His-Xxx β-turns, and assigned to solvent accessible turn structures. They were well accounted for by theoretical models of microhydrated turns, in which a few solvent molecules take over the gas phase motifs, constituting a water-mediated local anchoring of the His side chain to the backbone. Finally, the present gas phase benchmark models also pinpointed weaknesses in the protein structure determination by X-ray diffraction analysis; in particular, besides the lack of tautomer information, inaccuracies in the description of imidazole ring flip rotamerism were identified.

Structure of a rare non-standard sequence k-turn bound by L7Ae protein

PubMed Central

Huang, Lin; Lilley, David M.J.

2014-01-01

Kt-23 from Thelohania solenopsae is a rare RNA kink turn (k-turn) where an adenine replaces the normal guanine at the 2n position. L7Ae is a member of a strongly conserved family of proteins that bind a range of k-turn structures in the ribosome, box C/D and H/ACA small nucleolar RNAs and U4 small nuclear RNA. We have solved the crystal structure of T. solenopsae Kt-23 RNA bound to Archeoglobus fulgidus L7Ae protein at a resolution of 2.95 Å. The protein binds in the major groove displayed on the outer face of the k-turn, in a manner similar to complexes with standard k-turn structures. The k-turn adopts a standard N3 class conformation, with a single hydrogen bond from A2b N6 to A2n N3. This contrasts with the structure of the same sequence located in the SAM-I riboswitch, where it adopts an N1 structure, showing the inherent plasticity of k-turn structure. This potentially can affect any tertiary interactions in which the RNA participates. PMID:24482444

Propensities of peptides containing the Asn-Gly segment to form β-turn and β-hairpin structures.

PubMed

Kang, Young Kee; Yoo, In Kee

2016-09-01

The propensities of peptides that contain the Asn-Gly segment to form β-turn and β-hairpin structures were explored using the density functional methods and the implicit solvation model in CH2 Cl2 and water. The populations of preferred β-turn structures varied depending on the sequence and solvent polarity. In solution, β-hairpin structures with βI' turn motifs were most preferred for the heptapeptides containing the Asn-Gly segment regardless of the sequence of the strands. These preferences in solution are consistent with the corresponding X-ray structures. The sequence, H-bond strengths, solvent polarity, and conformational flexibility appeared to interact to determine the preferred β-hairpin structure of each heptapeptide, although the β-turn segments played a role in promoting the formation of β-hairpin structures and the β-hairpin propensity varied. In the heptapeptides containing the Asn-Gly segment, the β-hairpin formation was enthalpically favored and entropically disfavored at 25°C in water. The calculated results for β-turns and β-hairpins containing the Asn-Gly segment imply that these structural preferences may be useful for the design of bioactive macrocyclic peptides containing β-hairpin mimics and the design of binding epitopes for protein-protein and protein-nucleic acid recognitions. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 653-664, 2016. © 2016 Wiley Periodicals, Inc.

Bosons with Synthetic Rashba Spin-Orbit Coupling at Finite Power

NASA Astrophysics Data System (ADS)

Anderson, Brandon; Clark, Charles

2013-05-01

Isotropic spin-orbit couplings, such as Rashba in two dimensions, have a continuous symmetry that produces a large degeneracy in the momentum-space dispersion. This degeneracy leads to an enhanced density-of-states, producing novel phases in systems of bosonic atoms. This model is idealistic, however, in that the symmetry of the lasers will weakly break the continuous symmetry to a discrete one in experimental manifestations. This perturbation typically scales inversely with the optical power, and only at infinite power will ideal symmetry be restored. In this talk, we consider the effects of this weak symmetry breaking in a system of bosons at finite power with synthetic Rashba coupling. We solve the mean-field equations and find new phases, such as a stripe phase with a larger symmetry group. We then consider the experimentally relevant scheme where the spin-orbit fields are turned on adiabatically from an initial spin-polarized state. At intermediate power, stripe phases are found, while at sufficiently high power it appears that the system quenches to phases similar to that of the ideal limit. Techniques for optimizing the adiabatic ramping sequence are discussed. NSF PFC Grant PHY-0822671 and by the ARO under the DARPA OLE program.

Dynamic flashing yellow arrow (FYA): a study on variable left-turn mode operational and safety impacts phase II - model expansion and testing.

DOT National Transportation Integrated Search

2016-06-01

The flashing yellow arrow (FYA) signal display creates an opportunity to enhance the left-turn phase with a : variable mode that can be changed on demand. The previously developed decision support system (DSS) in : phase I facilitated the selection o...

Roles of beta-turns in protein folding: from peptide models to protein engineering.

PubMed

Marcelino, Anna Marie C; Gierasch, Lila M

2008-05-01

Reverse turns are a major class of protein secondary structure; they represent sites of chain reversal and thus sites where the globular character of a protein is created. It has been speculated for many years that turns may nucleate the formation of structure in protein folding, as their propensity to occur will favor the approximation of their flanking regions and their general tendency to be hydrophilic will favor their disposition at the solvent-accessible surface. Reverse turns are local features, and it is therefore not surprising that their structural properties have been extensively studied using peptide models. In this article, we review research on peptide models of turns to test the hypothesis that the propensities of turns to form in short peptides will relate to the roles of corresponding sequences in protein folding. Turns with significant stability as isolated entities should actively promote the folding of a protein, and by contrast, turn sequences that merely allow the chain to adopt conformations required for chain reversal are predicted to be passive in the folding mechanism. We discuss results of protein engineering studies of the roles of turn residues in folding mechanisms. Factors that correlate with the importance of turns in folding indeed include their intrinsic stability, as well as their topological context and their participation in hydrophobic networks within the protein's structure.

Roles of β-Turns in Protein Folding: From Peptide Models to Protein Engineering

PubMed Central

Marcelino, Anna Marie C.; Gierasch, Lila M.

2010-01-01

Reverse turns are a major class of protein secondary structure; they represent sites of chain reversal and thus sites where the globular character of a protein is created. It has been speculated for many years that turns may nucleate the formation of structure in protein folding, as their propensity to occur will favor the approximation of their flanking regions and their general tendency to be hydrophilic will favor their disposition at the solvent-accessible surface. Reverse turns are local features, and it is therefore not surprising that their structural properties have been extensively studied using peptide models. In this article, we review research on peptide models of turns to test the hypothesis that the propensities of turns to form in short peptides will relate to the roles of corresponding sequences in protein folding. Turns with significant stability as isolated entities should actively promote the folding of a protein, and by contrast, turn sequences that merely allow the chain to adopt conformations required for chain reversal are predicted to be passive in the folding mechanism. We discuss results of protein engineering studies of the roles of turn residues in folding mechanisms. Factors that correlate with the importance of turns in folding indeed include their intrinsic stability, as well as their topological context and their participation in hydrophobic networks within the protein’s structure. PMID:18275088

Father's Day dike intrusion and eruption reveals interaction between magmatic and tectonic processes at Kilauea Volcano, Hawaii

NASA Astrophysics Data System (ADS)

Foster, J. H.; Brooks, B. A.; Sandwell, D. T.; Poland, M.; Miklius, A.; Myer, D.; Okubo, P. G.; Patrick, M.; Wolfe, C.

2007-12-01

The June 17-19, 2007, Father's Day dike intrusion and eruption at Kilauea volcano brought to an end a seven- year period of steady state lava effusion at the Pu'u 'O'o vent. The event was observed by an unprecedented number of geophysical instruments, with temporary arrays of GPS and tiltmeters augmenting the continuous monitoring network. Envisat and ALOS SAR scenes were also acquired during this event and provide further information on the surface deformation as the event progressed. Fortuitously, the Envisat acquisition was during a pause in the middle of the sequence, while the ALOS PALSAR scene was acquired at the end of the sequence, allowing us to model each phase separately. Analysis of these data sets indicates that, in addition to three phases of the dike intrusion, a slow earthquake also occurred on the south flank of Kilauea. The slow earthquake apparently began near the end of the second phase of the dike intrusion. It was still underway the following day, when the third phase of the intrusion began and culminated in a small eruption. This suggests the possibility that the slow earthquake was triggered by the initial diking, and then in turn influenced the progression of the intrusion. Two of the largest previous slow earthquakes also hint at a connection between slow earthquakes and eruptive activity on Kilauea. The range of observations of the Father's Day events provides us with a unique opportunity to investigate the complex interactions between the tectonic processes of the south flank and magmatic processes within the summit and rift zones.

Conformational dynamics of a short antigenic peptide in its free and antibody bound forms gives insight into the role of β-turns in peptide immunogenicity.

PubMed

Shukla, Rashmi Tambe; Sasidhar, Yellamraju U

2015-07-01

Earlier immunological experiments with a synthetic 36-residue peptide (75-110) from Influenza hemagglutinin have been shown to elicit anti-peptide antibodies (Ab) which could cross-react with the parent protein. In this article, we have studied the conformational features of a short antigenic (Ag) peptide ((98)YPYDVPDYASLRS(110)) from Influenza hemagglutinin in its free and antibody (Ab) bound forms with molecular dynamics simulations using GROMACS package and OPLS-AA/L all-atom force field at two different temperatures (293 K and 310 K). Multiple simulations for the free Ag peptide show sampling of ordered conformations and suggest different conformational preferences of the peptide at the two temperatures. The free Ag samples a conformation crucial for Ab binding (β-turn formed by "DYAS" sequence) with greater preference at 310 K while, it samples a native-like conformation with relatively greater propensity at 293 K. The sequence "DYAS" samples β-turn conformation with greater propensity at 310 K as part of the hemagglutinin protein also. The bound Ag too samples the β-turn involving "DYAS" sequence and in addition it also samples a β-turn formed by the sequence "YPYD" at its N-terminus, which seems to be induced upon binding to the Ab. Further, the bound Ag displays conformational flexibility at both 293 K and 310 K, particularly at terminal residues. The implications of these results for peptide immunogenicity and Ag-Ab recognition are discussed. © 2015 Wiley Periodicals, Inc.

Dynamic flashing yellow arrow (FYA) : a study on variable left turn model operational and safety impacts, [technical summary].

DOT National Transportation Integrated Search

2013-12-01

Traffic engineers use various left-turn signalization : methods to find an optimal balance of safety and : efficiency. While protected/permitted left-turn : configurations allow most left-turning traffic to : turn during the protected phase, the perm...

Prediction of β-turns in proteins from multiple alignment using neural network

PubMed Central

Kaur, Harpreet; Raghava, Gajendra Pal Singh

2003-01-01

A neural network-based method has been developed for the prediction of β-turns in proteins by using multiple sequence alignment. Two feed-forward back-propagation networks with a single hidden layer are used where the first-sequence structure network is trained with the multiple sequence alignment in the form of PSI-BLAST–generated position-specific scoring matrices. The initial predictions from the first network and PSIPRED-predicted secondary structure are used as input to the second structure-structure network to refine the predictions obtained from the first net. A significant improvement in prediction accuracy has been achieved by using evolutionary information contained in the multiple sequence alignment. The final network yields an overall prediction accuracy of 75.5% when tested by sevenfold cross-validation on a set of 426 nonhomologous protein chains. The corresponding Qpred, Qobs, and Matthews correlation coefficient values are 49.8%, 72.3%, and 0.43, respectively, and are the best among all the previously published β-turn prediction methods. The Web server BetaTPred2 (http://www.imtech.res.in/raghava/betatpred2/) has been developed based on this approach. PMID:12592033

[A turning point in the knowledge of the structure-function-activity relations of elastin].

PubMed

Alix, A J

2001-01-01

In this review are presented the last new results of our research group dealing with the molecular structures (atomic level) of tropoelastin, elastin and elastin derived peptides studied by using essentially methods of bioinformatics (theoretical predictions and molecular modelling) linked to experimental circular dichroism spectroscopic studies. We already had characterized both the local secondary structure and some parts of the tertiary structure of the tropoelastin and elastin molecules (human, bovine...), by using either theoretical predictions (local secondary structure, linear epitopes...) and/or experimental data (optical spectroscopic methods: Raman scattering, infrared absorption, circular dichroism). Except the cross-linking regions which are in helical conformations, the whole tropoelastin structure displays a lot of beta-reverse turns which usually belong to irregular structures in proteins. These turns play a key role in other regularly structures orientation (alpha-helix, beta-strand), thus they are very important in the native protein 3D architecture. It is particularly true for human tropoelastin, because its sequence is rich in glycines and prolines, and these residues are frequently met in beta-turns (a beta-turn is made of four consecutive residues which are stabilized by an hydrogen bond). Several types of beta-turns can be defined with the dihedral angles values phi and psi of the two central residues. Thus, by using a very recent updated set of propensities for the amino acid residues to belong to given types of reverse beta-turns (extracted from a reference set of known 3-D structures of globular proteins), we have determined, (by using our home made software COUDES), for all possible tetrapeptides of the human tropoelastin sequence, the distribution and the characterization of the possible type of turns. Thus, it is shown that the locations and/or the types of these reverse beta-turns reveal a regularity and are not all random. This confirms our hypothesis that intra-molecular elasticity of tropoelastin could be explained by the possibility of transitions between conformations involving short beta-strands and beta-turns. This result is of great interest in the construction (by using molecular biology) of elastic biomaterials derived from the elastin sequence (particularly, the elastin derived peptides corresponding to the sequence exon 21--(exon 24--exon 24...). Our study permit also to predict the conformations of specific elastin derived peptides which could have interesting biological activity. Peptides resulting from the degradation of elastin, the insoluble polymer of tropoelastin and responsible for the elasticity of vertebrate tissues, can induce biological effects and notably the regulation of matrix metalloproteinases (MMP-s) activity. Recently, it was proposed that some elastin derived hexapeptides resulting from circular permutations of VGVAPG (a three fold repetition sequence in exon 24 of human tropoelastin) possess MMP-1 production and activation regulation properties. This effect depends on the presence of the tropoelastin specific membraneous receptor 67 KDa EBP (Elastin Binding Protein). Our results obtained by using both circular dichroism spectroscopy and linear predictions confirmed the hypothesis of a structure dependent mechanism with a possibly occurring type VIII beta-turn on the first four residues of the GXXPG sequence consensus which is only present among all active peptides. Thus, we have performed extensive molecular dynamics studies, in both implicit and explicit solvent, on these active and inactive elastin derived hexapeptides. Using our own analysis method of pattern recognition of the types of the beta-reverse-turns followed during the molecular dynamics trajectory, we found that active and inactive peptides effectively form two well distinct conformational groups in which active peptides preferentially adopt conformation close to type VIII GXXP (beta-reverse-turn. The structural role of the C terminal G residue could also be explained. Additional molecular simulations on (VGVAPG)2 and (VGVAPG)3 show the formation of two or three GXXP tetrapeptides adopting a structure close to type VIII beta-reverse-turn, suggesting a local conformational preference for this motif. This observation of a specific structural single and/or repeated motif is in agreement with the circular dichroism spectra of the involved (VGVAPG)1, (VGVAPG)2 and (VGVAPG)3 peptides and then it can be proposed that their biological activities have to be linear. The final aim of this type of work is to understand more about the sequence/structure/function/activity relationships of those structured peptides in order to propose specific sequences (corresponding to specific structures) for best biological activity results.

Required coefficient of friction in the anteroposterior and mediolateral direction during turning at different walking speeds

PubMed Central

Yamaguchi, Takeshi; Suzuki, Akito; Hokkirigawa, Kazuo

2017-01-01

This study investigated the required coefficient of friction (RCOF) and the tangent of center of mass (COM)–center of pressure (COP) angle in the mediolateral (ML) and anteroposterior (AP) directions during turning at different walking speeds. Sixteen healthy young adults (8 males and 8 females) participated in this study. The participants were instructed to conduct trials of straight walking and 90° step and spin turns to the right at each of three self-selected speeds (slow, normal, and fast). The ML and AP directions during turning gait were defined using the orientation of the pelvis to construct a body-fixed reference frame. The RCOF values and COM–COP angle tangent in the ML direction during turning at weight acceptance phase were higher than those during straight walking, and those values increased with increasing walking speed. The ML component of the RCOF and COM–COP tangent values during weight acceptance for step turns were higher than those for spin turns. The mean centripetal force during turning tended to increase with an increase in walking speed and had a strong positive correlation with the RCOF values in the ML direction (R = 0.97 during the weight acceptance phase; R = 0.95 during the push-off phase). Therefore, turning, particularly step turn, is likely to cause lateral slip at weight acceptance because of the increased centripetal force compared with straight walking. Future work should test at-risk population and compare with the present results. PMID:28640853

Required coefficient of friction in the anteroposterior and mediolateral direction during turning at different walking speeds.

PubMed

Yamaguchi, Takeshi; Suzuki, Akito; Hokkirigawa, Kazuo

2017-01-01

This study investigated the required coefficient of friction (RCOF) and the tangent of center of mass (COM)-center of pressure (COP) angle in the mediolateral (ML) and anteroposterior (AP) directions during turning at different walking speeds. Sixteen healthy young adults (8 males and 8 females) participated in this study. The participants were instructed to conduct trials of straight walking and 90° step and spin turns to the right at each of three self-selected speeds (slow, normal, and fast). The ML and AP directions during turning gait were defined using the orientation of the pelvis to construct a body-fixed reference frame. The RCOF values and COM-COP angle tangent in the ML direction during turning at weight acceptance phase were higher than those during straight walking, and those values increased with increasing walking speed. The ML component of the RCOF and COM-COP tangent values during weight acceptance for step turns were higher than those for spin turns. The mean centripetal force during turning tended to increase with an increase in walking speed and had a strong positive correlation with the RCOF values in the ML direction (R = 0.97 during the weight acceptance phase; R = 0.95 during the push-off phase). Therefore, turning, particularly step turn, is likely to cause lateral slip at weight acceptance because of the increased centripetal force compared with straight walking. Future work should test at-risk population and compare with the present results.

Modulation of cyclobutane thymine photodimer formation in T11-tracts in rotationally phased nucleosome core particles and DNA minicircles.

PubMed

Wang, Kesai; Taylor, John-Stephen A

2017-07-07

Cyclobutane pyrimidine dimers (CPDs) are DNA photoproducts linked to skin cancer, whose mutagenicity depends in part on their frequency of formation and deamination. Nucleosomes modulate CPD formation, favoring outside facing sites and disfavoring inward facing sites. A similar pattern of CPD formation in protein-free DNA loops suggests that DNA bending causes the modulation in nucleosomes. To systematically study the cause and effect of nucleosome structure on CPD formation and deamination, we have developed a circular permutation synthesis strategy for positioning a target sequence at different superhelix locations (SHLs) across a nucleosome in which the DNA has been rotationally phased with respect to the histone octamer by TG motifs. We have used this system to show that the nucleosome dramatically modulates CPD formation in a T11-tract that covers one full turn of the nucleosome helix at seven different SHLs, and that the position of maximum CPD formation at all locations is shifted to the 5΄-side of that found in mixed-sequence nucleosomes. We also show that an 80-mer minicircle DNA using the same TG-motifs faithfully reproduces the CPD pattern in the nucleosome, indicating that it is a good model for protein-free rotationally phased bent DNA of the same curvature as in a nucleosome, and that bending is modulating CPD formation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Lattice modeling and calibration with turn-by-turn orbit data

NASA Astrophysics Data System (ADS)

Huang, Xiaobiao; Sebek, Jim; Martin, Don

2010-11-01

A new method that explores turn-by-turn beam position monitor (BPM) data to calibrate lattice models of accelerators is proposed. The turn-by-turn phase space coordinates at one location of the ring are first established using data from two BPMs separated by a simple section with a known transfer matrix, such as a drift space. The phase space coordinates are then tracked with the model to predict positions at other BPMs, which can be compared to measurements. The model is adjusted to minimize the difference between the measured and predicted orbit data. BPM gains and rolls are included as fitting variables. This technique can be applied to either the entire or a section of the ring. We have tested the method experimentally on a part of the SPEAR3 ring.

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.

Expanding the peptide beta-turn in alphagamma hybrid sequences: 12 atom hydrogen bonded helical and hairpin turns.

PubMed

Chatterjee, Sunanda; Vasudev, Prema G; Raghothama, Srinivasarao; Ramakrishnan, Chandrasekharan; Shamala, Narayanaswamy; Balaram, Padmanabhan

2009-04-29

Hybrid peptide segments containing contiguous alpha and gamma amino acid residues can form C(12) hydrogen bonded turns which may be considered as backbone expanded analogues of C(10) (beta-turns) found in alphaalpha segments. Exploration of the regular hydrogen bonded conformations accessible for hybrid alphagamma sequences is facilitated by the use of a stereochemically constrained gamma amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn), in which the two torsion angles about C(gamma)-C(beta) (theta(1)) and C(beta)-C(alpha) (theta(2)) are predominantly restricted to gauche conformations. The crystal structures of the octapeptides Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (1) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (2) reveal two distinct conformations for the Aib-Gpn segment. Peptide 1 forms a continuous helix over the Aib(2)-Aib(6) segment, while the peptide 2 forms a beta-hairpin structure stabilized by four cross-strand hydrogen bonds with the Aib-Gpn segment forming a nonhelical C(12) turn. The robustness of the helix in peptide 1 in solution is demonstrated by NMR methods. Peptide 2 is conformationally fragile in solution with evidence of beta-hairpin conformations being obtained in methanol. Theoretical calculations permit delineation of the various C(12) hydrogen bonded structures which are energetically feasible in alphagamma and gammaalpha sequences.

Beta-hairpin formation in aqueous solution and in the presence of trifluoroethanol: a (1)H and (13)C nuclear magnetic resonance conformational study of designed peptides.

PubMed

Santiveri, Clara M; Pantoja-Uceda, David; Rico, Manuel; Jiménez, M Angeles

2005-10-15

In order to check our current knowledge on the principles involved in beta-hairpin formation, we have modified the sequence of a 3:5 beta-hairpin forming peptide with two different purposes, first to increase the stability of the formed 3:5 beta-hairpin, and second to convert the 3:5 beta-hairpin into a 2:2 beta-hairpin. The conformational behavior of the designed peptides was investigated in aqueous solution and in 30% trifluoroethanol (TFE) by analysis of the following nuclear magnetic resonance (NMR) parameters: nuclear Overhauser effect (NOE) data, and C(alpha)H, (13)C(alpha), and (13)C(beta) conformational shifts. From the differences in the ability to adopt beta-hairpin structures in these peptides, we have arrived to the following conclusions: (i) beta-Hairpin population increases with the statistical propensity of residues to occupy each turn position. (ii) The loop length, and in turn, the beta-hairpin type, can be modified as a function of the type of turn favored by the loop sequence. These two conclusions reinforce previous results about the importance of beta-turn sequence in beta-hairpin folding. (iii) Side-chain packing on each face of the beta-sheet may play a major role in beta-hairpin stability; hence simplified analysis in terms of isolated pair interactions and intrinsic beta-sheet propensities is insufficient. (iv) Contributions to beta-hairpin stability of turn and strand sequences are not completely independent. (v) The burial of hydrophobic surface upon beta-hairpin formation that, in turn, depends on side-chain packing also contributes to beta-hairpin stability. (vi) As previously observed, TFE stabilizes beta-hairpin structures, but the extent of the contribution of different factors to beta-hairpin formation is sometimes different in aqueous solution and in 30% TFE. (c) 2005 Wiley Periodicals, Inc. Biopolymers 79: 150-162, 2005.

Phase Retrieval System for Assessing Diamond Turning and Optical Surface Defects

NASA Technical Reports Server (NTRS)

Dean, Bruce; Maldonado, Alex; Bolcar, Matthew

2011-01-01

An optical design is presented for a measurement system used to assess the impact of surface errors originating from diamond turning artifacts. Diamond turning artifacts are common by-products of optical surface shaping using the diamond turning process (a diamond-tipped cutting tool used in a lathe configuration). Assessing and evaluating the errors imparted by diamond turning (including other surface errors attributed to optical manufacturing techniques) can be problematic and generally requires the use of an optical interferometer. Commercial interferometers can be expensive when compared to the simple optical setup developed here, which is used in combination with an image-based sensing technique (phase retrieval). Phase retrieval is a general term used in optics to describe the estimation of optical imperfections or aberrations. This turnkey system uses only image-based data and has minimal hardware requirements. The system is straightforward to set up, easy to align, and can provide nanometer accuracy on the measurement of optical surface defects.

[Study of beta-turns in globular proteins].

PubMed

Amirova, S R; Milchevskiĭ, Iu V; Filatov, I V; Esipova, N G; Tumanian, V G

2005-01-01

The formation of beta-turns in globular proteins has been studied by the method of molecular mechanics. Statistical method of discriminant analysis was applied to calculate energy components and sequences of oligopeptide segments, and after this prediction of I type beta-turns has been drawn. The accuracy of true positive prediction is 65%. Components of conformational energy considerably affecting beta-turn formation were delineated. There are torsional energy, energy of hydrogen bonds, and van der Waals energy.

Structural mechanics of DNA wrapping in the nucleosome.

PubMed

Battistini, Federica; Hunter, Christopher A; Gardiner, Eleanor J; Packer, Martin J

2010-02-19

Experimental X-ray crystal structures and a database of calculated structural parameters of DNA octamers were used in combination to analyse the mechanics of DNA bending in the nucleosome core complex. The 1kx5 X-ray crystal structure of the nucleosome core complex was used to determine the relationship between local structure at the base-step level and the global superhelical conformation observed for nucleosome-bound DNA. The superhelix is characterised by a large curvature (597 degrees) in one plane and very little curvature (10 degrees) in the orthogonal plane. Analysis of the curvature at the level of 10-step segments shows that there is a uniform curvature of 30 degrees per helical turn throughout most of the structure but that there are two sharper kinks of 50 degrees at +/-2 helical turns from the central dyad base pair. The curvature is due almost entirely to the base-step parameter roll. There are large periodic variations in roll, which are in phase with the helical twist and account for 500 degrees of the total curvature. Although variations in the other base-step parameters perturb the local path of the DNA, they make minimal contributions to the total curvature. This implies that DNA bending in the nucleosome is achieved using the roll-slide-twist degree of freedom previously identified as the major degree of freedom in naked DNA oligomers. The energetics of bending into a nucleosome-bound conformation were therefore analysed using a database of structural parameters that we have previously developed for naked DNA oligomers. The minimum energy roll, the roll flexibility force constant and the maximum and minimum accessible roll values were obtained for each base step in the relevant octanucleotide context to account for the effects of conformational coupling that vary with sequence context. The distribution of base-step roll values and corresponding strain energy required to bend DNA into the nucleosome-bound conformation defined by the 1kx5 structure were obtained by applying a constant bending moment. When a single bending moment was applied to the entire sequence, the local details of the calculated structure did not match the experiment. However, when local 10-step bending moments were applied separately, the calculated structure showed excellent agreement with experiment. This implies that the protein applies variable bending forces along the DNA to maintain the superhelical path required for nucleosome wrapping. In particular, the 50 degrees kinks are constraints imposed by the protein rather than a feature of the 1kx5 DNA sequence. The kinks coincide with a relatively flexible region of the sequence, and this is probably a prerequisite for high-affinity nucleosome binding, but the bending strain energy is significantly higher at these points than for the rest of the sequence. In the most rigid regions of the sequence, a higher strain energy is also required to achieve the standard 30 degrees curvature per helical turn. We conclude that matching of the DNA sequence to the local roll periodicity required to achieve bending, together with the increased flexibility required at the kinks, determines the sequence selectivity of DNA wrapping in the nucleosome. 2009 Elsevier Ltd. All rights reserved.

Local sequence information in cellular retinoic acid-binding protein I: specific residue roles in beta-turns.

PubMed

Rotondi, Kenneth S; Gierasch, Lila M

2003-01-01

We have recently shown that two of the beta-turns (III and IV) in the ten-stranded, beta-clam protein, cellular retinoic acid-binding protein I (CRABP I), are favored in short peptide fragments, arguing that they are encoded by local interactions (K. S. Rotondi and L. M. Gierasch, Biochemistry, 2003, Vol. 42, pp. 7976-7985). In this paper we examine these turns in greater detail to dissect the specific local interactions responsible for their observed native conformational biases. Conformations of peptides corresponding to the turn III and IV fragments were examined under conditions designed to selectively disrupt stabilizing interactions, using pH variation, chaotrope addition, or mutagenesis to probe specific side-chain influences. We find that steric constraints imposed by excluded volume effects between near neighbor residues (i,i+2), favorable polar (i,i+2) interactions, and steric permissiveness of glycines are the principal factors accounting for the observed native bias in these turns. Longer-range stabilizing interactions across the beta-turns do not appear to play a significant role in turn stability in these short peptides, in contrast to their importance in hairpins. Additionally, our data add to a growing number of examples of the 3:5 type I turn with a beta-bulge as a class of turns with high propensity to form locally defined structure. Current work is directed at the interplay between the local sequence information in the turns and more long-range influences in the mechanism of folding of this predominantly beta-sheet protein. Copyright 2004 Wiley Periodicals, Inc.

Not-so-simple stellar populations in the intermediate-age Large Magellanic Cloud star clusters NGC 1831 and NGC 1868

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

Li, Chengyuan; De Grijs, Richard; Deng, Licai, E-mail: joshuali@pku.edu.cn, E-mail: grijs@pku.edu.cn

2014-04-01

Using a combination of high-resolution Hubble Space Telescope/Wide-Field and Planetary Camera-2 observations, we explore the physical properties of the stellar populations in two intermediate-age star clusters, NGC 1831 and NGC 1868, in the Large Magellanic Cloud based on their color-magnitude diagrams. We show that both clusters exhibit extended main-sequence turn offs. To explain the observations, we consider variations in helium abundance, binarity, age dispersions, and the fast rotation of the clusters' member stars. The observed narrow main sequence excludes significant variations in helium abundance in both clusters. We first establish the clusters' main-sequence binary fractions using the bulk of themore » clusters' main-sequence stellar populations ≳ 1 mag below their turn-offs. The extent of the turn-off regions in color-magnitude space, corrected for the effects of binarity, implies that age spreads of order 300 Myr may be inferred for both clusters if the stellar distributions in color-magnitude space were entirely due to the presence of multiple populations characterized by an age range. Invoking rapid rotation of the population of cluster members characterized by a single age also allows us to match the observed data in detail. However, when taking into account the extent of the red clump in color-magnitude space, we encounter an apparent conflict for NGC 1831 between the age dispersion derived from that based on the extent of the main-sequence turn off and that implied by the compact red clump. We therefore conclude that, for this cluster, variations in stellar rotation rate are preferred over an age dispersion. For NGC 1868, both models perform equally well.« less

Comparison of the quality of different magnetic resonance image sequences of multiple myeloma.

PubMed

Sun, Zhao-yong; Zhang, Hai-bo; Li, Shuo; Wang, Yun; Xue, Hua-dan; Jin, Zheng-yu

2015-02-01

To compare the image quality of T1WI fat phase,T1WI water phase, short time inversion recovery (STIR) sequence, and diffusion weighted imaging (DWI) sequence in the evaluation of multiple myeloma (MM). Totally 20MM patients were enrolled in this study. All patients underwent scanning at coronal T1WI fat phase, coronal T1WI water phase, coronal STIR sequence, and axial DWI sequence. The image quality of the four different sequences was evaluated. The image was divided into seven sections(head and neck, chest, abdomen, pelvis, thigh, leg, and foot), and the signal-to-noise ratio (SNR) of each section was measured at 7 segments (skull, spine, pelvis, humerus, femur, tibia and fibula and ribs) were measured. In addition, 20 active MM lesions were selected, and the contrast-to-noise ratio (CNR) of each scan sequence was calculated. The average image quality scores of T1WI fat phase,T1WI water phase, STIR sequence, and DWI sequence were 4.19 ± 0.70,4.16 ± 0.73,3.89 ± 0.70, and 3.76 ± 0.68, respectively. The image quality at T1-fat phase and T1-water phase were significantly higher than those at STIR (P=0.000 and P=0.001) and DWI sequence (both P=0.000); however, there was no significant difference between T1-fat and T1-water phase (P=0.723)and between STIR and DWI sequence (P=0.167). The SNR of T1WI fat phase was significantly higher than those of the other three sequences (all P=0.000), and there was no significant difference among the other three sequences (all P>0.05). Although the CNR of DWI sequences was slightly higher than those of the other three sequences,there was no significant difference among all of them (all P>0.05). Imaging at T1WI fat phase,T1WI water phase, STIR sequence, and DWI sequence has certain advantages,and they should be combined in the diagnosis of MM.

Dynamic flashing yellow arrow (FYA): a study on variable left-turn mode operational and safety impacts phase II - model expansion and testing : [summary].

DOT National Transportation Integrated Search

2016-05-01

In phase two of this project, the UCF team further developed the DSS to automate selection of FYA left-turn modes based on traffic volumes at intersections acquired in real time from existing sensors.

pi-Turns: types, systematics and the context of their occurrence in protein structures

PubMed Central

Dasgupta, Bhaskar; Chakrabarti, Pinak

2008-01-01

Background For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue γ-turn to six-residue π-turn. The Schellman motif occurring at the C-terminal end of α-helices is a classical example of hydrogen bonded π-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded β- and α-turns have been identified previously; likewise, a systematic characterization of π-turns would provide valuable insight into turn structures. Results An analysis of protein structures indicates that at least 20% of π-turns occur independent of the Schellman motif. The two categories of π-turns, designated as π-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length β- and α-turns, π-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal Cα-atoms, and this resulted in a comparable number of non-hydrogen-bonded π-turns (π-NHB). The presence of shorter β- and α-turns within all categories of π-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied. Conclusion π-turns have been characterized, first using hydrogen bond and the distance between Cα atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the π-HB turns, being located on surface cavities, have functional role and there is also sequence conservation. PMID:18808671

pi-Turns: types, systematics and the context of their occurrence in protein structures.

PubMed

Dasgupta, Bhaskar; Chakrabarti, Pinak

2008-09-22

For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue gamma-turn to six-residue pi-turn. The Schellman motif occurring at the C-terminal end of alpha-helices is a classical example of hydrogen bonded pi-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded beta- and alpha-turns have been identified previously; likewise, a systematic characterization of pi-turns would provide valuable insight into turn structures. An analysis of protein structures indicates that at least 20% of pi-turns occur independent of the Schellman motif. The two categories of pi-turns, designated as pi-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length beta- and alpha-turns, pi-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal C alpha-atoms, and this resulted in a comparable number of non-hydrogen-bonded pi-turns (pi-NHB). The presence of shorter beta- and alpha-turns within all categories of pi-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied. pi-turns have been characterized, first using hydrogen bond and the distance between C alpha atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the pi-HB turns, being located on surface cavities, have functional role and there is also sequence conservation.

Class Identification Efficacy in Piecewise GMM with Unknown Turning Points

ERIC Educational Resources Information Center

Ning, Ling; Luo, Wen

2018-01-01

Piecewise GMM with unknown turning points is a new procedure to investigate heterogeneous subpopulations' growth trajectories consisting of distinct developmental phases. Unlike the conventional PGMM, which relies on theory or experiment design to specify turning points a priori, the new procedure allows for an optimal location of turning points…

Spatiotemporal and Kinematic Parameters Relating to Oriented Gait and Turn Performance in Patients with Chronic Stroke

PubMed Central

Bonnyaud, Céline; Pradon, Didier; Vuillerme, Nicolas; Bensmail, Djamel; Roche, Nicolas

2015-01-01

Background The timed up and go test (TUG) is a functional test which is increasingly used to evaluate patients with stroke. The outcome measured is usually global TUG performance-time. Assessment of spatiotemporal and kinematic parameters during the Oriented gait and Turn sub-tasks of the TUG would provide a better understanding of the mechanisms underlying patients’ performance and therefore may help to guide rehabilitation. The aim of this study was thus to determine the spatiotemporal and kinematic parameters which were most related to the walking and turning sub-tasks of TUG performance in stroke patients. Methods 29 stroke patients carried out the TUG test which was recorded using an optoelectronic system in two conditions: spontaneous and standardized condition (standardized foot position and instructed to turn towards the paretic side). They also underwent a clinical assessment. Stepwise regression was used to determine the parameters most related to Oriented gait and Turn sub-tasks. Relationships between explanatory parameters of Oriented gait and Turn performance and clinical scales were evaluated using Spearman correlations. Results Step length and cadence explained 82% to 95% of the variance for the walking sub-tasks in both conditions. Percentage single support phase and contralateral swing phase (depending on the condition) respectively explained 27% and 56% of the variance during the turning sub-task in the spontaneous and standardized conditions. Discussion and Conclusion Step length, cadence, percentage of paretic single support phase and non-paretic swing phase, as well as dynamic stability were the main parameters related to TUG performance and they should be targeted in rehabilitation. PMID:26091555

Four-phase or two-phase signal plan? A study on four-leg intersection by cellular automaton simulations

NASA Astrophysics Data System (ADS)

Jin, Cheng-Jie; Wang, Wei; Jiang, Rui

2016-08-01

The proper setting of traffic signals at signalized intersections is one of the most important tasks in traffic control and management. This paper has evaluated the four-phase traffic signal plans at a four-leg intersection via cellular automaton simulations. Each leg consists of three lanes, an exclusive left-turn lane, a through lane, and a through/right-turn lane. For a comparison, we also evaluate the two-phase signal plan. The diagram of the intersection states in the space of inflow rate versus turning ratio has been presented, which exhibits four regions: In region I/II/III, congestion will propagate upstream and laterally and result in queue spillover with both signal plans/two-phase signal plan/four-phase signal plan, respectively. Therefore, neither signal plan works in region I, and only the four-phase signal plan/two-phase signal plan works in region II/III. In region IV, both signal plans work, but two-phase signal plan performs better in terms of average delays of vehicles. Finally, we study the diagram of the intersection states and average delays in the asymmetrical configurations.

Pedestrian Safety Treatments for Signalized Intersections : Training Course Development

DOT National Transportation Integrated Search

2017-11-01

When drivers make left turns during a permissive turn phase, they must yield to pedestrians as well as oncoming through vehicles. Left-turning drivers sometimes overlook pedestrians in the crosswalk while watching the opposing intersection approach. ...

Spin-reorientation transitions in the Cairo pentagonal magnet Bi 4 Fe 5 O 13 F

DOE PAGES

Tsirlin, Alexander A.; Rousochatzakis, Ioannis; Filimonov, Dmitry; ...

2017-09-19

Here, we show that interlayer spins play a dual role in the Cairo pentagonal magnet Bi 4Fe 5O 13F, on one hand mediating the three-dimensional magnetic order, and on the other driving spin-reorientation transitions both within and between the planes. The corresponding sequence of magnetic orders unraveled by neutron diffraction and Mössbauer spectroscopy features two orthogonal magnetic structures described by opposite local vector chiralities, and an intermediate, partly disordered phase with nearly collinear spins. A similar collinear phase has been predicted theoretically to be stabilized by quantum fluctuations, but Bi 4Fe 5O 13F is very far from the relevant parametermore » regime. While the observed in-plane reorientation cannot be explained by any standard frustration mechanism, our ab initio band-structure calculations reveal strong single-ion anisotropy of the interlayer Fe 3+ spins that turns out to be instrumental in controlling the local vector chirality and the associated interlayer order.« less

Spin-reorientation transitions in the Cairo pentagonal magnet Bi4Fe5O13F

NASA Astrophysics Data System (ADS)

Tsirlin, Alexander A.; Rousochatzakis, Ioannis; Filimonov, Dmitry; Batuk, Dmitry; Frontzek, Matthias; Abakumov, Artem M.

2017-09-01

We show that interlayer spins play a dual role in the Cairo pentagonal magnet Bi4Fe5O13F , on one hand mediating the three-dimensional magnetic order, and on the other driving spin-reorientation transitions both within and between the planes. The corresponding sequence of magnetic orders unraveled by neutron diffraction and Mössbauer spectroscopy features two orthogonal magnetic structures described by opposite local vector chiralities, and an intermediate, partly disordered phase with nearly collinear spins. A similar collinear phase has been predicted theoretically to be stabilized by quantum fluctuations, but Bi4Fe5O13F is very far from the relevant parameter regime. While the observed in-plane reorientation cannot be explained by any standard frustration mechanism, our ab initio band-structure calculations reveal strong single-ion anisotropy of the interlayer Fe3 + spins that turns out to be instrumental in controlling the local vector chirality and the associated interlayer order.

The effect of continuous pressure monitoring on strategic shifting of medical inpatients at risk for PUs.

PubMed

Motamedi, S M; de Grood, J; Harman, S; Sargious, P; Baylis, B; Flemons, W; Ghali, W A

2012-11-01

To assess the impact of continuous pressure imaging technology on strategic turning of patients by health professionals. This pilot study of a newly-developed continuous pressure imaging technology (XSENSOR ForeSite PatientTurn System) involved two phases of videotaped observation of medical inpatients, with each patient serving as his/her own control: a control phase in which continuous pressure imaging was not available to health-care providers and an intervention phase where it was. The primary outcome was to determine whether access to the technology influenced the rate of patient turns/shifts by nursing staff. Secondary outcomes included a comparison of the rates of other care provider shifts, patient self-shifts, and family assisted shifts. Qualitative data regarding nurse and patient/family perspectives were also obtained. Complete control/intervention data were available for nine patients.The mean rate of two-person assisted turns was 0.274 +/- 0.087 turns per hour in the control phase versus 0.413 +/- 0.091 turns per hour in the intervention phase (p = 0.08). For the combined endpoint of two-person assisted turns or patient transfers off the bed into a wheelchair/chair, there was a statistically significant difference in the mean number of turns per hour: mean of 0.491 +/- 0.271 turns per hour for the intervention group versus 0.327 +/- 0.235 turns per hour for the control group (p = 0.04). Provider interviews confirmed that nurses used information from the technology to inform their patient shifting strategies and behaviours. This pilot study provides some initial data supporting the hypothesis that continuous pressure imaging technology could positively impact the frequency of patient turns by care providers, as well as provide impetus to inspect specific skin locations,thereby providing a potential targeted risk mitigation strategy for the development of pressure ulcers. Funding for the study was obtained from PreCarn Inc., an independent, nonprofit company supporting the pre-commercial development of new technologies, and from the Alberta Enterprise and Advanced Education (formally Alberta Advanced Education and Technology). The industry partner, XSENSOR, was involved in setup and maintenance of the technology, but was not involved in the evaluative research protocol. Specifically, XSENSOR personnel were not involved in the collection, coding, or analysis of outcome data, nor in the compilation and writing of this paper. None of the listed authors have any conflicts of interest, financial or otherwise, relating to the technology tested.

Describing-function analysis of a ripple regulator with slew-rate limits and time delays

NASA Technical Reports Server (NTRS)

Wester, Gene W.

1990-01-01

The effects of time delays and slew-rate limits on the steady-state operating points and performance of a free-running ripple regulator are evaluated using describing-function analysis. The describing function of an ideal comparator (no time delays or slew rate limits) has no phase shift and is independent of frequency. It is found that turn-on delay and turn-off delay have different effects on gain and phase and cannot be combined. Comparator hysteresis affects both gain and phase; likewise, time delays generally affect both gain and phase. It is found that the effective time delay around the feedback loop is one half the sum of turn-on and turn-off delays, regardless of whether the delays are caused by storage time or slew rate limits. Expressions are formulated for the switching frequency, switch duty ratio, dc output, and output ripple. For the case of no hysteresis, a simple, graphical solution for the switching frequency is possible, and the resulting switching frequency is independent of first-order variations of input or load.

A coordinated sequence of distinct flagellar waveforms enables a sharp flagellar turn mediated by squid sperm pH-taxis.

PubMed

Iida, Tomohiro; Iwata, Yoko; Mohri, Tatsuma; Baba, Shoji A; Hirohashi, Noritaka

2017-10-11

Animal spermatozoa navigate by sensing ambient chemicals to reach the site of fertilization. Generally, such chemicals derive from the female reproductive organs or cells. Exceptionally, squid spermatozoa mutually release and perceive carbon dioxide to form clusters after ejaculation. We previously identified the pH-taxis by which each spermatozoon can execute a sharp turn, but how flagellar dynamics enable this movement remains unknown. Here, we show that initiation of the turn motion requires a swim down a steep proton gradient (a theoretical estimation of ≥0.025 pH/s), crossing a threshold pH value of ~5.5. Time-resolved kinematic analysis revealed that the turn sequence results from the rhythmic exercise of two flagellar motions: a stereotypical flagellar 'bent-cane' shape followed by asymmetric wave propagation, which enables a sharp turn in the realm of low Reynolds numbers. This turning episode is terminated by an 'overshoot' trajectory that differs from either straight-line motility or turning. As with bidirectional pH-taxes in some bacteria, squid spermatozoa also showed repulsion from strong acid conditions with similar flagellar kinematics as in positive pH-taxis. These findings indicate that squid spermatozoa might have a unique reorientation mechanism, which could be dissimilar to that of classical egg-guided sperm chemotaxis in other marine invertebrates.

Engineering diverse changes in beta-turn propensities in the N-terminal beta-hairpin of ubiquitin reveals significant effects on stability and kinetics but a robust folding transition state.

PubMed

Simpson, Emma R; Meldrum, Jill K; Searle, Mark S

2006-04-04

Using the N-terminal 17-residue beta-hairpin of ubiquitin as a "host" for mutational studies, we have investigated the influence of the beta-turn sequence on protein stability and folding kinetics by replacing the native G-bulged turn (TLTGK) with more flexible analogues (TG3K and TG5K) and a series of four-residue type I' beta-turn sequences, commonly found in beta-hairpins. Although a statistical analysis of type I' turns demonstrates residue preferences at specific sites, the frequency of occurrence appears to only broadly correlate with experimentally determined protein stabilities. The subsequent engineering of context-dependent non-native tertiary contacts involving turn residues is shown to produce large changes in stability. Relatively few point mutations have been described that probe secondary structure formation in ubiquitin in a manner that is independent of tertiary contacts. To this end, we have used the more rigorous rate-equilibrium free energy relationship (Leffler analysis), rather than the two-point phi value analysis, to show for a family of engineered beta-turn mutants that stability (range of approximately 20 kJ/mol) and folding kinetics (190-fold variation in refolding rate) are linearly correlated (alpha(f) = 0.74 +/- 0.08). The data are consistent with a transition state that is robust with regard to a wide range of statistically favored and disfavored beta-turn mutations and implicate a loosely assembled beta-hairpin as a key template in transition state stabilization with the beta-turn playing a central role.

Repair Sequences in Dysarthric Conversational Speech: A Study in Interactional Phonetics

ERIC Educational Resources Information Center

Rutter, Ben

2009-01-01

This paper presents some findings from a case study of repair sequences in conversations between a dysarthric speaker, Chris, and her interactional partners. It adopts the methodology of interactional phonetics, where turn design, sequence organization, and variation in phonetic parameters are analysed in unison. The analysis focused on the use of…

Age-related modifications in steering behaviour: effects of base-of-support constraints at the turn point.

PubMed

Paquette, Maxime R; Fuller, Jason R; Adkin, Allan L; Vallis, Lori Ann

2008-09-01

This study investigated the effects of altering the base of support (BOS) at the turn point on anticipatory locomotor adjustments during voluntary changes in travel direction in healthy young and older adults. Participants were required to walk at their preferred pace along a 3-m straight travel path and continue to walk straight ahead or turn 40 degrees to the left or right for an additional 2-m. The starting foot and occasionally the gait starting point were adjusted so that participants had to execute the turn using a cross-over step with a narrow BOS or a lead-out step with a wide BOS. Spatial and temporal gait variables, magnitudes of angular segmental movement, and timing and sequencing of body segment reorientation were similar despite executing the turn with a narrow or wide BOS. A narrow BOS during turning generated an increased step width in the step prior to the turn for both young and older adults. Age-related changes when turning included reduced step velocity and step length for older compared to young adults. Age-related changes in the timing and sequencing of body segment reorientation prior to the turn point were also observed. A reduction in walking speed and an increase in step width just prior to the turn, combined with a delay in motion of the center of mass suggests that older adults used a more cautious combined foot placement and hip strategy to execute changes in travel direction compared to young adults. The results of this study provide insight into mobility constraints during a common locomotor task in older adults.

Automatic recovery of aftershock sequences at the International Data Centre: from concept to pipeline

NASA Astrophysics Data System (ADS)

Kitov, I.; Bobrov, D.; Rozhkov, M.

2016-12-01

Aftershocks of larger earthquakes represent an important source of information on the distribution and evolution of stresses and deformations in pre-seismic, co-seismic and post-seismic phases. For the International Data Centre (IDC) of the Comprehensive Nuclear-Test-Ban Organization (CTBTO) largest aftershocks sequences are also a challenge for automatic and interactive processing. The highest rate of events recorded by two and more seismic stations of the International Monitoring System from a relatively small aftershock area may reach hundreds per hour (e.g. Sumatra 2004 and Tohoku 2011). Moreover, there are thousands of reflected/refracted phases per hour with azimuth and slowness within the uncertainty limits of the first P-waves. Misassociation of these later phases, both regular and site specific, as the first P-wave results in creation of numerous wrong event hypotheses in automatic IDC pipeline. In turn, interactive review of such wrong hypotheses is direct waste of analysts' resources. Waveform cross correlation (WCC) is a powerful tool to separate coda phases from actual P-wave arrivals and to fully utilize the repeat character of waveforms generated by events close in space. Array seismic stations of the IMS enhance the performance of the WCC in two important aspects - they reduce detection threshold and effectively suppress arrivals from all sources except master events. An IDC specific aftershock tool has been developed and merged with standard IDC pipeline. The tool includes several procedures: creation of master events consisting of waveform templates at ten and more IMS stations; cross correlation (CC) of real-time waveforms with these templates, association of arrivals detected at CC-traces in event hypotheses; building events matching IDC quality criteria; and resolution of conflicts between events hypotheses created by neighboring master-events. The final cross correlation standard event lists (XSEL) is a start point of interactive analysis. Since global monitoring of underground nuclear tests is based on historical and synthetic data, each aftershock sequence can be tested for the CTBT violation with big earthquakes as an evasion scenario.

Phase retrieval from the phase-shift moiré fringe patterns in simultaneous dual-wavelength interferometry

NASA Astrophysics Data System (ADS)

Cheng, Jinlong; Gao, Zhishan; Bie, Shuyou; Dou, Yimeng; Ni, Ruihu; Yuan, Qun

2018-02-01

Simultaneous dual-wavelength interferometry (SDWI) could extend the measured range of each single-wavelength interferometry. The moiré fringe generated in SDWI indirectly represents the information of the measured long synthetic-wavelength ({λ }{{S}}) phase, thus the phase demodulation is rather arduous. To address this issue, we present a method to convert the moiré fringe pattern into a synthetic-wavelength interferogram (moiré to synthetic-wavelength, MTS). After the square of the moiré fringe pattern in the MTS method, the additive moiré pattern is turned into a multiplicative one. And the synthetic-wavelength interferogram could be obtained by a low-pass filtering in spectrum of the multiplicative moiré fringe pattern. Therefore, when the dual-wavelength interferometer is implemented with the π/2 phase shift at {λ }{{S}}, a sequence of synthetic-wavelength phase-shift interferograms with π/2 phase shift could be obtained after the MTS method processing on the captured moiré fringe patterns. And then the synthetic-wavelength phase could be retrieved by the conventional phase-shift algorithm. Compared with other methods in SDWI, the proposed MTS approach could reduce the restriction of the phase shift and frame numbers for the adoption of the conventional phase-shift algorithm. Following, numerical simulations are executed to evaluate the performance of the MTS method in processing time, frames of interferograms and the phase shift error compensation. And the necessary linear carrier for MTS method is less than 0.11 times of the traditional dual-wavelength spatial-domain Fourier transform method. Finally, the deviations for MTS method in experiment are 0.97% for a step with the height of 7.8 μm and 1.11% for a Fresnel lens with the step height of 6.2328 μm.

Project Apollo Flight Sequence

NASA Image and Video Library

1966-08-01

Lunar Orbiter's "Typical Flight sequence of Events" turned out to be quite typical indeed, as all five spacecraft performed exactly as planned. -- Published in James R. Hansen, Spaceflight Revolution: NASA Langley Research Center From Sputnik to Apollo, (Washington: NASA, 1995), p. 340.

Development of pedestrian safety based warrants for permissive left-turn control

DOT National Transportation Integrated Search

2010-12-01

At the intersections with permissive only signal control, pedestrians will move at the permissive phase with the parallel through vehicular movement and left-turn vehicles, the left-turn vehicles have to yield to both opposing through vehicles and pe...

Reduced vibration motor winding arrangement

DOEpatents

Slavik, C.J.; Rhudy, R.G.; Bushman, R.E.

1997-11-11

An individual phase winding arrangement having a sixty electrical degree phase belt width for use with a three phase motor armature includes a delta connected phase winding portion and a wye connected phase winding portion. Both the delta and wye connected phase winding portions have a thirty electrical degree phase belt width. The delta and wye connected phase winding portions are each formed from a preselected number of individual coils each formed, in turn, from an unequal number of electrical conductor turns in the approximate ratio of {radical}3. The individual coils of the delta and wye connected phase winding portions may either be connected in series or parallel. This arrangement provides an armature winding for a three phase motor which retains the benefits of the widely known and utilized thirty degree phase belt concept, including improved mmf waveform and fundamental distribution factor, with consequent reduced vibrations and improved efficiency. 4 figs.

Reduced vibration motor winding arrangement

DOEpatents

Slavik, Charles J.; Rhudy, Ralph G.; Bushman, Ralph E.

1997-01-01

An individual phase winding arrangement having a sixty electrical degree phase belt width for use with a three phase motor armature includes a delta connected phase winding portion and a wye connected phase winding portion. Both the delta and wye connected phase winding portions have a thirty electrical degree phase belt width. The delta and wye connected phase winding portions are each formed from a preselected number of individual coils each formed, in turn, from an unequal number of electrical conductor turns in the approximate ratio of .sqroot.3. The individual coils of the delta and wye connected phase winding portions may either be connected in series or parallel. This arrangement provides an armature winding for a three phase motor which retains the benefits of the widely known and utilized thirty degree phase belt concept, including improved mmf waveform and fundamental distribution factor, with consequent reduced vibrations and improved efficiency.

Co-Constructing Turns as Interactional Competence: Collaborative Turn Sequences in L1 and L2 Spanish

ERIC Educational Resources Information Center

Baxter, Robert Patrick

2017-01-01

"Interactional competence" is a theoretical construct that has only recently been tested empirically. Speakers contribute to an interaction with their individual resources; however, interactional competence is co-constructed by all participants. Interactional competence can be observed in spoken interaction as speakers' combined ability…

Circular permutation of a WW domain: Folding still occurs after excising the turn of the folding-nucleating hairpin

PubMed Central

Kier, Brandon L.; Anderson, Jordan M.; Andersen, Niels H.

2014-01-01

A hyperstable Pin1 WW domain has been circularly permuted via excision of the fold-nucleating turn; it still folds to form the native three-strand sheet and hydrophobic core features. Multiprobe folding dynamics studies of the normal and circularly permuted sequences, as well as their constituent hairpin fragments and comparable-length β-strand-loop-β-strand models, indicate 2-state folding for all topologies. N-terminal hairpin formation is the fold nucleating event for the wild-type sequence; the slower folding circular permutant has a more distributed folding transition state. PMID:24350581

SNMR pulse sequence phase cycling

DOEpatents

Walsh, David O; Grunewald, Elliot D

2013-11-12

Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

Prediction of beta-turns and beta-turn types by a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN).

PubMed

Kirschner, Andreas; Frishman, Dmitrij

2008-10-01

Prediction of beta-turns from amino acid sequences has long been recognized as an important problem in structural bioinformatics due to their frequent occurrence as well as their structural and functional significance. Because various structural features of proteins are intercorrelated, secondary structure information has been often employed as an additional input for machine learning algorithms while predicting beta-turns. Here we present a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN) capable of predicting multiple mutually dependent structural motifs and demonstrate its efficiency in recognizing three aspects of protein structure: beta-turns, beta-turn types, and secondary structure. The advantage of our method compared to other predictors is that it does not require any external input except for sequence profiles because interdependencies between different structural features are taken into account implicitly during the learning process. In a sevenfold cross-validation experiment on a standard test dataset our method exhibits the total prediction accuracy of 77.9% and the Mathew's Correlation Coefficient of 0.45, the highest performance reported so far. It also outperforms other known methods in delineating individual turn types. We demonstrate how simultaneous prediction of multiple targets influences prediction performance on single targets. The MOLEBRNN presented here is a generic method applicable in a variety of research fields where multiple mutually depending target classes need to be predicted. http://webclu.bio.wzw.tum.de/predator-web/.

Structure change of β-hairpin induced by turn optimization: an enhanced sampling molecular dynamics simulation study.

PubMed

Shao, Qiang; Yang, Lijiang; Gao, Yi Qin

2011-12-21

Our previous study showed that for the tested polypeptides which have similar β-hairpin structures but different sequences, their folding free energy pathways are dominantly determined by the turn conformational propensity. In this study, we study how the turn conformational propensity affects the structure of hairpins. The folding of two mutants of GB1p peptide (GB1m2 and GB1m3), which have the optimized turn sequence ((6)DDATK(11)T → (6)NPATG(11)K) with native structures unsolved, were simulated using integrated tempering sampling molecular dynamics simulations and the predicted stable structures were compared to wild-type GB1p. It was observed that the turn optimization of GB1p generates a more favored 5-residue type I(') turn in addition to the 6-residue type I turn in wild-type GB1p. As a result two distinctly different hairpin structures are formed corresponding to the "misfolded" (M) and the "folded" (F) states. M state is a one-residue-shifted asymmetric β-hairpin structure whereas F state has the similar symmetric hairpin structure as wild-type GB1p. The formation of the favored type I(') turn has a small free energy barrier and leads to the shifted β-hairpin structure, following the modified "zipping" model. The presence of disfavored type I turn structure makes the folding of a β-hairpin consistent with the "hydrophobic-core-centric" model. On the other hand, the folding simulations on other two GB1p mutants (GB1r1 and GBr2), which have the position of the hydrophobic core cluster further away from the turn compared to wild-type GB1p, showed that moving the hydrophobic core cluster away from the turn region destabilizes but does not change the hairpin structure. Therefore, the present study showed that the turn conformational propensity is a key factor in affecting not only the folding pathways but also the stable structure of β-hairpins, and the turn conformational change induced by the turn optimization leads to significant changes of β-hairpin structure.

Inhibitor profiling of the Pseudomonas aeruginosa virulence factor LasB using N-alpha mercaptoamide template-based inhibitors.

PubMed

Cathcart, George R; Gilmore, Brendan F; Greer, Brett; Harriott, Pat; Walker, Brian

2009-11-01

We report on the synthesis and biological evaluation of a focussed library of N-alpha mercaptoamide containing dipeptides as inhibitors of the zinc metallopeptidase Pseudomonas aeruginosa elastase (LasB, EC 3.4.24.26). The aim of the study was to derive an inhibitor profile for LasB with regard to mapping the S'1 binding site of the enzyme. Consequently, a focussed library of 160 members has been synthesised, using standard Fmoc-solid phase methods (on a Rink-amide resin), in which a subset of amino acids including examples of those with basic (Lys, Arg), aromatic (Phe, Trp), large aliphatic (Val, Leu) and acidic (Asp, Glu) side-chains populated the P'2 position of the inhibitor sequence and all 20 natural amino acids were incorporated, in turn, at the P'1 position. The study has revealed a preference for aromatic and/or large aliphatic amino acids at P'1 and a distinct bias against acidic residues at P'2. Ten inhibitor sequences were discovered that exhibited sub to low micromolar Ki values.

A case study of the response of the magnetosphere to changes in the interplanetary medium

NASA Technical Reports Server (NTRS)

Rostoker, G.; Baumjohann, W.; Russell, C. T.

1983-01-01

A detailed analysis of world-wide ground based magnetometer data is presented, together with information on the plasma and magnetic field properties of the interplanetary medium and magnetosheath obtained from the ISEE 1 and 2 and IMP 8 spacecraft. The event concerned exhibited an interval of relatively stable southward IMF followed by a sharp northward turning. It is pointed out that during the interval of southward IMF there were occasional transient northward turnings with significant substorm expansive phase activity appearing to be triggered by these transient northward turnings. The final northward turning of the IMF was linked with an episode of strong magnetospheric substorm expansive phase activity after which the level of high latitude magnetic activity declined to a low level. Evidence is presented indicating that the driven system auroral electrojets begin to decay at the time of the northward turning of the IMF, even as the substorm expansive phase activity is initiated in the midnight sector. The collapse of the substorm current wedge during the final decay of high latitude activity is described in some detail, and it is shown that this collapse occurs progressively from east to west in a series of impulsive episodes.

A High-Throughput Process for the Solid-Phase Purification of Synthetic DNA Sequences

PubMed Central

Grajkowski, Andrzej; Cieślak, Jacek; Beaucage, Serge L.

2017-01-01

An efficient process for the purification of synthetic phosphorothioate and native DNA sequences is presented. The process is based on the use of an aminopropylated silica gel support functionalized with aminooxyalkyl functions to enable capture of DNA sequences through an oximation reaction with the keto function of a linker conjugated to the 5′-terminus of DNA sequences. Deoxyribonucleoside phosphoramidites carrying this linker, as a 5′-hydroxyl protecting group, have been synthesized for incorporation into DNA sequences during the last coupling step of a standard solid-phase synthesis protocol executed on a controlled pore glass (CPG) support. Solid-phase capture of the nucleobase- and phosphate-deprotected DNA sequences released from the CPG support is demonstrated to proceed near quantitatively. Shorter than full-length DNA sequences are first washed away from the capture support; the solid-phase purified DNA sequences are then released from this support upon reaction with tetra-n-butylammonium fluoride in dry dimethylsulfoxide (DMSO) and precipitated in tetrahydrofuran (THF). The purity of solid-phase-purified DNA sequences exceeds 98%. The simulated high-throughput and scalability features of the solid-phase purification process are demonstrated without sacrificing purity of the DNA sequences. PMID:28628204

Spacecraft/Rover Hybrids for the Exploration of Small Solar System Bodies. [NASA NIAC Phase I Study

NASA Technical Reports Server (NTRS)

Pavone, Marco; Castillo-Rogez, Julie C.; Hoffman, Jeffrey A.; Nesnas, Issa A. D.

2012-01-01

This study investigated a novel mission architecture for the systematic and affordable in-situ exploration of small Solar System bodies. Specifically, a mother spacecraft would deploy over the surface of a small body one, or several, spacecraft/rover hybrids, which are small, multi-faceted enclosed robots with internal actuation and external spikes. They would be capable of 1) long excursions (by hopping), 2) short traverses to specific locations (through a sequence of controlled tumbles), and 3) high-altitude, attitude-controlled ballistic flight (akin to spacecraft flight). Their control would rely on synergistic operations with the mother spacecraft (where most of hybrids' perception and localization functionalities would be hosted), which would make the platforms minimalistic and, in turn, the entire mission architecture affordable.

History dependence in insect flight decisions during odor tracking.

PubMed

Pang, Rich; van Breugel, Floris; Dickinson, Michael; Riffell, Jeffrey A; Fairhall, Adrienne

2018-02-01

Natural decision-making often involves extended decision sequences in response to variable stimuli with complex structure. As an example, many animals follow odor plumes to locate food sources or mates, but turbulence breaks up the advected odor signal into intermittent filaments and puffs. This scenario provides an opportunity to ask how animals use sparse, instantaneous, and stochastic signal encounters to generate goal-oriented behavioral sequences. Here we examined the trajectories of flying fruit flies (Drosophila melanogaster) and mosquitoes (Aedes aegypti) navigating in controlled plumes of attractive odorants. While it is known that mean odor-triggered flight responses are dominated by upwind turns, individual responses are highly variable. We asked whether deviations from mean responses depended on specific features of odor encounters, and found that odor-triggered turns were slightly but significantly modulated by two features of odor encounters. First, encounters with higher concentrations triggered stronger upwind turns. Second, encounters occurring later in a sequence triggered weaker upwind turns. To contextualize the latter history dependence theoretically, we examined trajectories simulated from three normative tracking strategies. We found that neither a purely reactive strategy nor a strategy in which the tracker learned the plume centerline over time captured the observed history dependence. In contrast, "infotaxis", in which flight decisions maximized expected information gain about source location, exhibited a history dependence aligned in sign with the data, though much larger in magnitude. These findings suggest that while true plume tracking is dominated by a reactive odor response it might also involve a history-dependent modulation of responses consistent with the accumulation of information about a source over multi-encounter timescales. This suggests that short-term memory processes modulating decision sequences may play a role in natural plume tracking.

Salt-bridging effects on short amphiphilic helical structure and introducing sequence-based short beta-turn motifs.

PubMed

Guarracino, Danielle A; Gentile, Kayla; Grossman, Alec; Li, Evan; Refai, Nader; Mohnot, Joy; King, Daniel

2018-02-01

Determining the minimal sequence necessary to induce protein folding is beneficial in understanding the role of protein-protein interactions in biological systems, as their three-dimensional structures often dictate their activity. Proteins are generally comprised of discrete secondary structures, from α-helices to β-turns and larger β-sheets, each of which is influenced by its primary structure. Manipulating the sequence of short, moderately helical peptides can help elucidate the influences on folding. We created two new scaffolds based on a modestly helical eight-residue peptide, PT3, we previously published. Using circular dichroism (CD) spectroscopy and changing the possible salt-bridging residues to new combinations of Lys, Arg, Glu, and Asp, we found that our most helical improvements came from the Arg-Glu combination, whereas the Lys-Asp was not significantly different from the Lys-Glu of the parent scaffold, PT3. The marked 3 10 -helical contributions in PT3 were lessened in the Arg-Glu-containing peptide with the beginning of cooperative unfolding seen through a thermal denaturation. However, a unique and unexpected signature was seen for the denaturation of the Lys-Asp peptide which could help elucidate the stages of folding between the 3 10 and α-helix. In addition, we developed a short six-residue peptide with β-turn/sheet CD signature, again to help study minimal sequences needed for folding. Overall, the results indicate that improvements made to short peptide scaffolds by fine-tuning the salt-bridging residues can enhance scaffold structure. Likewise, with the results from the new, short β-turn motif, these can help impact future peptidomimetic designs in creating biologically useful, short, structured β-sheet-forming peptides.

History dependence in insect flight decisions during odor tracking

PubMed Central

van Breugel, Floris; Dickinson, Michael; Riffell, Jeffrey A.; Fairhall, Adrienne

2018-01-01

Natural decision-making often involves extended decision sequences in response to variable stimuli with complex structure. As an example, many animals follow odor plumes to locate food sources or mates, but turbulence breaks up the advected odor signal into intermittent filaments and puffs. This scenario provides an opportunity to ask how animals use sparse, instantaneous, and stochastic signal encounters to generate goal-oriented behavioral sequences. Here we examined the trajectories of flying fruit flies (Drosophila melanogaster) and mosquitoes (Aedes aegypti) navigating in controlled plumes of attractive odorants. While it is known that mean odor-triggered flight responses are dominated by upwind turns, individual responses are highly variable. We asked whether deviations from mean responses depended on specific features of odor encounters, and found that odor-triggered turns were slightly but significantly modulated by two features of odor encounters. First, encounters with higher concentrations triggered stronger upwind turns. Second, encounters occurring later in a sequence triggered weaker upwind turns. To contextualize the latter history dependence theoretically, we examined trajectories simulated from three normative tracking strategies. We found that neither a purely reactive strategy nor a strategy in which the tracker learned the plume centerline over time captured the observed history dependence. In contrast, “infotaxis”, in which flight decisions maximized expected information gain about source location, exhibited a history dependence aligned in sign with the data, though much larger in magnitude. These findings suggest that while true plume tracking is dominated by a reactive odor response it might also involve a history-dependent modulation of responses consistent with the accumulation of information about a source over multi-encounter timescales. This suggests that short-term memory processes modulating decision sequences may play a role in natural plume tracking. PMID:29432454

Sequence-Mandated, Distinct Assembly of Giant Molecules

DOE PAGES

Zhang, Wei; Lu, Xinlin; Mao, Jialin; ...

2017-10-24

Although controlling the primary structure of synthetic polymers is itself a great challenge, the potential of sequence control for tailoring hierarchical structures remains to be exploited, especially in the creation of new and unconventional phases. A series of model amphiphilic chain-like giant molecules was designed and synthesized by interconnecting both hydrophobic and hydrophilic molecular nanoparticles in precisely defined sequence and composition to investigate their sequence-dependent phase structures. Not only compositional variation changed the self-assembled supramolecular phases, but also specific sequences induce unconventional phase formation, including Frank-Kasper phases. The formation mechanism was attributed to the conformational change driven by the collectivemore » hydrogen bonding and the sequence-mandated topology of the molecules. Lastly, these results show that sequence control in synthetic polymers can have a dramatic impact on polymer properties and self-assembly.« less

Sequence-Mandated, Distinct Assembly of Giant Molecules

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

Zhang, Wei; Lu, Xinlin; Mao, Jialin

Although controlling the primary structure of synthetic polymers is itself a great challenge, the potential of sequence control for tailoring hierarchical structures remains to be exploited, especially in the creation of new and unconventional phases. A series of model amphiphilic chain-like giant molecules was designed and synthesized by interconnecting both hydrophobic and hydrophilic molecular nanoparticles in precisely defined sequence and composition to investigate their sequence-dependent phase structures. Not only compositional variation changed the self-assembled supramolecular phases, but also specific sequences induce unconventional phase formation, including Frank-Kasper phases. The formation mechanism was attributed to the conformational change driven by the collectivemore » hydrogen bonding and the sequence-mandated topology of the molecules. Lastly, these results show that sequence control in synthetic polymers can have a dramatic impact on polymer properties and self-assembly.« less

Code-Switching to Know a TL Equivalent of an L1 Word: Request-Provision-Acknowledgement (RPA) Sequence

ERIC Educational Resources Information Center

Lucero, Edgar

2011-01-01

This article focuses on the learner's use of Code-switching to learn the TL (Target Language) equivalent of an L1 word. The interactional pattern that this situation creates defines the Request-Provision-Acknowledgement (RPA) sequence. The article explains each of the turns of the sequence under the combination of the Ethnomethodological…

ELECTRONIC PULSE SCALING CIRCUITS

DOEpatents

Cooke-Yarborough, E.H.

1958-11-18

Electronic pulse scaling circults of the klnd comprlsing a serles of bi- stable elements connected ln sequence, usually in the form of a rlng so as to be cycllcally repetitive at the highest scallng factor, are described. The scaling circuit comprises a ring system of bi-stable elements each arranged on turn-off to cause, a succeeding element of the ring to be turned-on, and one being arranged on turn-off to cause a further element of the ring to be turned-on. In addition, separate means are provided for applying a turn-off pulse to all the elements simultaneously, and for resetting the elements to a starting condition at the end of each cycle.

Differences of Ballet Turns ("Pirouette") Performance between Experienced and Novice Ballet Dancers

ERIC Educational Resources Information Center

Lin, Chia-Wei; Chen, Shing-Jye; Su, Fong-Chin; Wu, Hong-Wen; Lin, Cheng-Feng

2014-01-01

Purpose: This study investigated the different postural control strategies exhibited by experienced and novice dancers in ballet turns ("pirouettes"). Method: Thirteen novice and 13 experienced dancers performed ballet turns with dominant-leg support. The peak push force was measured in the double-leg support phase. The inclination…

Negotiating towards a next turn: phonetic resources for 'doing the same'.

PubMed

Sikveland, Rein Ove

2012-03-01

This paper investigates hearers' use of response tokens (back-channels), in maintaining and differentiating their actions. Initial observations suggest that hearers produce a sequence of phonetically similar responses to disengage from the current topic, and dissimilar responses to engage with the current topic. This is studied systematically by combining detailed interactional and phonetic analysis in a collection of naturally-occurring talk in Norwegian. The interactional analysis forms the basis for labeling actions as maintained ('doing the same') and differentiated ('NOT doing the same'), which is then used as a basis for phonetic analysis. The phonetic analysis shows that certain phonetic characteristics, including pitch, loudness, voice quality and articulatory characteristics, are associated with 'doing the same', as different from 'NOT doing the same'. Interactional analysis gives further evidence of how this differentiation is of systematic relevance in the negotiations of a next turn. This paper addresses phonetic variation and variability by focusing on the relationship between sequence and phonetics in the turn-by-turn development of meaning. This has important implications for linguistic/phonetic research, and for the study of back-channels.

Support vector machines for prediction and analysis of beta and gamma-turns in proteins.

PubMed

Pham, Tho Hoan; Satou, Kenji; Ho, Tu Bao

2005-04-01

Tight turns have long been recognized as one of the three important features of proteins, together with alpha-helix and beta-sheet. Tight turns play an important role in globular proteins from both the structural and functional points of view. More than 90% tight turns are beta-turns and most of the rest are gamma-turns. Analysis and prediction of beta-turns and gamma-turns is very useful for design of new molecules such as drugs, pesticides, and antigens. In this paper we investigated two aspects of applying support vector machine (SVM), a promising machine learning method for bioinformatics, to prediction and analysis of beta-turns and gamma-turns. First, we developed two SVM-based methods, called BTSVM and GTSVM, which predict beta-turns and gamma-turns in a protein from its sequence. When compared with other methods, BTSVM has a superior performance and GTSVM is competitive. Second, we used SVMs with a linear kernel to estimate the support of amino acids for the formation of beta-turns and gamma-turns depending on their position in a protein. Our analysis results are more comprehensive and easier to use than the previous results in designing turns in proteins.

Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning

PubMed Central

Silberhorn, Elisabeth; Schwartz, Uwe; Symelka, Anne; de Koning-Ward, Tania; Längst, Gernot

2016-01-01

The packaging and organization of genomic DNA into chromatin represents an additional regulatory layer of gene expression, with specific nucleosome positions that restrict the accessibility of regulatory DNA elements. The mechanisms that position nucleosomes in vivo are thought to depend on the biophysical properties of the histones, sequence patterns, like phased di-nucleotide repeats and the architecture of the histone octamer that folds DNA in 1.65 tight turns. Comparative studies of human and P. falciparum histones reveal that the latter have a strongly reduced ability to recognize internal sequence dependent nucleosome positioning signals. In contrast, the nucleosomes are positioned by AT-repeat sequences flanking nucleosomes in vivo and in vitro. Further, the strong sequence variations in the plasmodium histones, compared to other mammalian histones, do not present adaptations to its AT-rich genome. Human and parasite histones bind with higher affinity to GC-rich DNA and with lower affinity to AT-rich DNA. However, the plasmodium nucleosomes are overall less stable, with increased temperature induced mobility, decreased salt stability of the histones H2A and H2B and considerable reduced binding affinity to GC-rich DNA, as compared with the human nucleosomes. In addition, we show that plasmodium histone octamers form the shortest known nucleosome repeat length (155bp) in vitro and in vivo. Our data suggest that the biochemical properties of the parasite histones are distinct from the typical characteristics of other eukaryotic histones and these properties reflect the increased accessibility of the P. falciparum genome. PMID:28033404

SEQ-REVIEW: A tool for reviewing and checking spacecraft sequences

NASA Astrophysics Data System (ADS)

Maldague, Pierre F.; El-Boushi, Mekki; Starbird, Thomas J.; Zawacki, Steven J.

1994-11-01

A key component of JPL's strategy to make space missions faster, better and cheaper is the Advanced Multi-Mission Operations System (AMMOS), a ground software intensive system currently in use and in further development. AMMOS intends to eliminate the cost of re-engineering a ground system for each new JPL mission. This paper discusses SEQ-REVIEW, a component of AMMOS that was designed to facilitate and automate the task of reviewing and checking spacecraft sequences. SEQ-REVIEW is a smart browser for inspecting files created by other sequence generation tools in the AMMOS system. It can parse sequence-related files according to a computer-readable version of a 'Software Interface Specification' (SIS), which is a standard document for defining file formats. It lets users display one or several linked files and check simple constraints using a Basic-like 'Little Language'. SEQ-REVIEW represents the first application of the Quality Function Development (QFD) method to sequence software development at JPL. The paper will show how the requirements for SEQ-REVIEW were defined and converted into a design based on object-oriented principles. The process starts with interviews of potential users, a small but diverse group that spans multiple disciplines and 'cultures'. It continues with the development of QFD matrices that related product functions and characteristics to user-demanded qualities. These matrices are then turned into a formal Software Requirements Document (SRD). The process concludes with the design phase, in which the CRC (Class, Responsibility, Collaboration) approach was used to convert requirements into a blueprint for the final product.

SEQ-REVIEW: A tool for reviewing and checking spacecraft sequences

NASA Technical Reports Server (NTRS)

Maldague, Pierre F.; El-Boushi, Mekki; Starbird, Thomas J.; Zawacki, Steven J.

1994-01-01

A key component of JPL's strategy to make space missions faster, better and cheaper is the Advanced Multi-Mission Operations System (AMMOS), a ground software intensive system currently in use and in further development. AMMOS intends to eliminate the cost of re-engineering a ground system for each new JPL mission. This paper discusses SEQ-REVIEW, a component of AMMOS that was designed to facilitate and automate the task of reviewing and checking spacecraft sequences. SEQ-REVIEW is a smart browser for inspecting files created by other sequence generation tools in the AMMOS system. It can parse sequence-related files according to a computer-readable version of a 'Software Interface Specification' (SIS), which is a standard document for defining file formats. It lets users display one or several linked files and check simple constraints using a Basic-like 'Little Language'. SEQ-REVIEW represents the first application of the Quality Function Development (QFD) method to sequence software development at JPL. The paper will show how the requirements for SEQ-REVIEW were defined and converted into a design based on object-oriented principles. The process starts with interviews of potential users, a small but diverse group that spans multiple disciplines and 'cultures'. It continues with the development of QFD matrices that related product functions and characteristics to user-demanded qualities. These matrices are then turned into a formal Software Requirements Document (SRD). The process concludes with the design phase, in which the CRC (Class, Responsibility, Collaboration) approach was used to convert requirements into a blueprint for the final product.

Molecular dynamics simulations of certain RGD-based peptides from Kistrin provide insight into the higher activity of REI-RGD34 protein at higher temperature.

PubMed

Upadhyay, Sanjay K

2014-05-01

To determine the bioactive conformation required to bind with receptor aIIbb3, the peptide sequence RIPRGDMP from Kistrin was inserted into CDR 1 loop region of REI protein, resulting in REI-RGD34. The activity of REI-RGD34 was observed to increase at higher temperature towards the receptor aIIbb3. It could be justified in either way: the modified complex forces the restricted peptide to adapt bioactive conformation or it unfolds the peptide in a way that opens its binding surface with high affinity for receptor. Here, we model the conformational preference of RGD sequence in RIPRGDMP at 25 and 42 °C using multiple MD simulations. Further, we model the peptide sequence RGD, PRGD and PRGDMP from kistrin to observe the effect of flanking residues on conformational sampling of RGD. The presence of flanking residues around RGD peptide greatly influenced the conformational sampling. A transition from bend to turn conformation was observed for RGD sequence at 42 °C. The turn conformation shows pharmacophoric parameters required to recognize the receptor aIIbb3. Thus, the temperaturedependent activity of RIPRGDMP when inserted into the loop region of REI can be explained by the presence of the turn conformation. This study will help in designing potential antagonist for the receptor aIIbb3.

Reinventing MaizeGDB

USDA-ARS?s Scientific Manuscript database

The Maize Database (MaizeDB) to the Maize Genetics and Genomics Database (MaizeGDB) turns 20 this year, and such a significant milestone must be celebrated! With the release of the B73 reference sequence and more sequenced genomes on the way, the maize community needs to address various opportunitie...

Prey Capture Behavior Evoked by Simple Visual Stimuli in Larval Zebrafish

PubMed Central

Bianco, Isaac H.; Kampff, Adam R.; Engert, Florian

2011-01-01

Understanding how the nervous system recognizes salient stimuli in the environment and selects and executes the appropriate behavioral responses is a fundamental question in systems neuroscience. To facilitate the neuroethological study of visually guided behavior in larval zebrafish, we developed “virtual reality” assays in which precisely controlled visual cues can be presented to larvae whilst their behavior is automatically monitored using machine vision algorithms. Freely swimming larvae responded to moving stimuli in a size-dependent manner: they directed multiple low amplitude orienting turns (∼20°) toward small moving spots (1°) but reacted to larger spots (10°) with high-amplitude aversive turns (∼60°). The tracking of small spots led us to examine how larvae respond to prey during hunting routines. By analyzing movie sequences of larvae hunting paramecia, we discovered that all prey capture routines commence with eye convergence and larvae maintain their eyes in a highly converged position for the duration of the prey-tracking and capture swim phases. We adapted our virtual reality assay to deliver artificial visual cues to partially restrained larvae and found that small moving spots evoked convergent eye movements and J-turns of the tail, which are defining features of natural hunting. We propose that eye convergence represents the engagement of a predatory mode of behavior in larval fish and serves to increase the region of binocular visual space to enable stereoscopic targeting of prey. PMID:22203793

Phase control and fast start-up of a magnetron using modulation of an addressable faceted cathode

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

Browning, J., E-mail: JimBrowning@BoiseState.edu; Fernandez-Gutierrez, S.; Lin, M. C.

The use of an addressable, faceted cathode has been proposed as a method of modulating current injection in a magnetron to improve performance and control phase. To implement the controllable electron emission, five-sided and ten-sided faceted planar cathodes employing gated field emitters are considered as these emitters could be fabricated on flat substrates. For demonstration, the conformal finite-difference time-domain particle-in-cell simulation, as implemented in VORPAL, has been used to model a ten-cavity, rising sun magnetron using the modulated current sources and benchmarked against a typical continuous current source. For the modulated, ten-sided faceted cathode case, the electrons are injected frommore » three emitter elements on each of the ten facets. Each emitter is turned ON and OFF in sequence at the oscillating frequency with five emitters ON at one time to drive the five electron spokes of the π-mode. The emitter duty cycle is then 1/6th the Radio-Frequency (RF) period. Simulations show a fast start-up time as low as 35 ns for the modulated case compared to 100 ns for the continuous current cases. Analysis of the RF phase using the electron spoke locations and the RF magnetic field components shows that the phase is controlled for the modulated case while it is random, as typical, for the continuous current case. Active phase control during oscillation was demonstrated by shifting the phase of the electron injection 180° after oscillations started. The 180° phase shift time was approximately 25 RF cycles.« less

Destination pluto: New horizons performance during the approach phase

NASA Astrophysics Data System (ADS)

Flanigan, Sarah H.; Rogers, Gabe D.; Guo, Yanping; Kirk, Madeline N.; Weaver, Harold A.; Owen, William M.; Jackman, Coralie D.; Bauman, Jeremy; Pelletier, Frederic; Nelson, Derek; Stanbridge, Dale; Dumont, Phillip J.; Williams, Bobby; Stern, S. Alan; Olkin, Cathy B.; Young, Leslie A.; Ennico, Kimberly

2016-11-01

The New Horizons spacecraft began its journey to the Pluto-Charon system on January 19, 2006 on-board an Atlas V rocket from Cape Canaveral, Florida. As the first mission in NASA's New Frontiers program, the objective of the New Horizons mission is to perform the first exploration of ice dwarfs in the Kuiper Belt, extending knowledge of the solar system to include the icy "third zone" for the first time. Arriving at the correct time and correct position relative to Pluto on July 14, 2015 depended on the successful execution of a carefully choreographed sequence of events. The Core command sequence, which was developed and optimized over multiple years and included the highest-priority science observations during the closest approach period, was contingent on precise navigation to the Pluto-Charon system and nominal performance of the guidance and control (G&C) subsystem. The flyby and gravity assist of Jupiter on February 28, 2007 was critical in placing New Horizons on the path to Pluto. Once past Jupiter, trajectory correction maneuvers (TCMs) became the sole source of trajectory control since the spacecraft did not encounter any other planetary bodies along its flight path prior to Pluto. During the Pluto approach phase, which formally began on January 15, 2015, optical navigation images were captured primarily with the Long Range Reconnaissance Imager to refine spacecraft and Pluto-Charon system trajectory knowledge, which in turn was used to design TCMs. Orbit determination solutions were also used to update the spacecraft's on-board trajectory knowledge throughout the approach phase. Nominal performance of the G&C subsystem, accurate TCM designs, and high-quality orbit determination solutions resulted in final Pluto-relative B-plane arrival conditions that facilitated a successful first reconnaissance of the Pluto-Charon system.

Training strategies and materials.

DOT National Transportation Integrated Search

2008-08-01

TxDOT project 0-5840 Development of Left-Turn Operations Guidelines at Signalized Intersections has developed : guidelines for recommending the most appropriate left-turn phasing treatments at signalized intersections by investigating all : asp...

Kinematics and muscle activity of the head, lumbar and knee joints during 180° turning and sitting down task in older adults.

PubMed

Kuo, Fang-Chuan; Hong, Chang-Zern; Liau, Ben-Yi

2014-01-01

The "180° turning and sitting down task" is a very conscious movement that requires focusing on turning at the exact moment, and very few studies address on this topic in older adults. The purpose of the study was to compare kinematics and electromyography of the head, lumbar and knee joints during 180°turning in older and young adults. Twenty older adults and 20 younger adults were assessed. A 16-channel telemetry electromyography system with electrogoniometers and an inclinometer were used to record the head, lumbar and knee joint kinematic and electromyography data during the 180° turning. This movement had been further divided into 4 phases (braking, mid-stance, swing, and terminal loading) for analysis. There were significant differences in the joint displacement and muscular activity among the different phases. Comparison between groups showed that the older adults group had less lateral lumbar flexion, less knee flexion and lower velocity of the head and knee flexion compared to young adults during turning. The electromyography data of the left biceps femoris, left gastrocnemius and left erector spinae muscles in the older adults group showed significantly higher levels than in the young adults. Older adults need to adjust velocities of moving joints and increase the extensor synergy muscles of the back and the stance leg to provide posture stability. Kinematics and neuromuscular modulations of the head, lumbar and knee are required according to the various phases of the turn movements and change with aging. © 2013.

Building a stable RNA U-turn with a protonated cytidine

PubMed Central

Gottstein-Schmidtke, Sina R.; Duchardt-Ferner, Elke; Groher, Florian; Weigand, Julia E.; Gottstein, Daniel; Suess, Beatrix; Wöhnert, Jens

2014-01-01

The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5′-UNR-3′ (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3′ phosphate group of the R residue as well as a hydrogen bond between the 2′-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3′ from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone. PMID:24951555

The Impact of Odor--Reward Memory on Chemotaxis in Larval "Drosophila"

ERIC Educational Resources Information Center

Schleyer, Michael; Reid, Samuel F.; Pamir, Evren; Saumweber, Timo; Paisios, Emmanouil; Davies, Alexander; Gerber, Bertram; Louis, Matthieu

2015-01-01

How do animals adaptively integrate innate with learned behavioral tendencies? We tackle this question using chemotaxis as a paradigm. Chemotaxis in the "Drosophila" larva largely results from a sequence of runs and oriented turns. Thus, the larvae minimally need to determine (i) how fast to run, (ii) when to initiate a turn, and (iii)…

Performance Analysis of a Static Synchronous Compensator (STATCOM)

NASA Astrophysics Data System (ADS)

Kambey, M. M.; Ticoh, J. D.

2018-02-01

Reactive power and voltage are some of the problems in electric power supply and A Gate Turn Off (GTO) Static Synchronous Compensator (STATCOM) is one of the type of FACTS with shunt which can supply variable reactive power and regulate the voltage of the bus where it is connected. This study only discuss about the performance characteristic of the three phase six-pulse STATCOM by analysing the current wave flowing through DC Capacitor which depend on switching current and capacitor voltage wave. Simulation methods used in this research is started with a mathematical analysis of the ac current, dc voltage and current equations that pass STATCOM from a literature. The result shows the presence of the capacitor voltage ripple also alters the ac current waveform, even though the errors to be not very significant and the constraint of the symmetry circuit is valid if the source voltages have no zero sequence components and the impedances in all the three phases are identical. There for to improve STATCOM performance it is necessary to use multi-pulse 12, 24, 36, 48 or more, and/or with a multilevel converter.

Droplet Digital™ PCR Next-Generation Sequencing Library QC Assay.

PubMed

Heredia, Nicholas J

2018-01-01

Digital PCR is a valuable tool to quantify next-generation sequencing (NGS) libraries precisely and accurately. Accurately quantifying NGS libraries enable accurate loading of the libraries on to the sequencer and thus improve sequencing performance by reducing under and overloading error. Accurate quantification also benefits users by enabling uniform loading of indexed/barcoded libraries which in turn greatly improves sequencing uniformity of the indexed/barcoded samples. The advantages gained by employing the Droplet Digital PCR (ddPCR™) library QC assay includes the precise and accurate quantification in addition to size quality assessment, enabling users to QC their sequencing libraries with confidence.

SNP-based genotyping in lentil: linking sequence information with phenotypes

USDA-ARS?s Scientific Manuscript database

Lentil (Lens culinaris) has been late to enter the world of high throughput molecular analysis due to a general lack of genomic resources. Using a 454 sequencing-based approach, SNPs have been identified in genes across the lentil genome. Several hundred have been turned into single SNP KASP assay...

BetaTPred: prediction of beta-TURNS in a protein using statistical algorithms.

PubMed

Kaur, Harpreet; Raghava, G P S

2002-03-01

beta-turns play an important role from a structural and functional point of view. beta-turns are the most common type of non-repetitive structures in proteins and comprise on average, 25% of the residues. In the past numerous methods have been developed to predict beta-turns in a protein. Most of these prediction methods are based on statistical approaches. In order to utilize the full potential of these methods, there is a need to develop a web server. This paper describes a web server called BetaTPred, developed for predicting beta-TURNS in a protein from its amino acid sequence. BetaTPred allows the user to predict turns in a protein using existing statistical algorithms. It also allows to predict different types of beta-TURNS e.g. type I, I', II, II', VI, VIII and non-specific. This server assists the users in predicting the consensus beta-TURNS in a protein. The server is accessible from http://imtech.res.in/raghava/betatpred/

Method for high resolution magnetic resonance analysis using magic angle technique

DOEpatents

Wind, Robert A.; Hu, Jian Zhi

2003-12-30

A method of performing a magnetic resonance analysis of a biological object that includes placing the object in a main magnetic field (that has a static field direction) and in a radio frequency field; rotating the object at a frequency of less than about 100 Hz around an axis positioned at an angle of about 54.degree.44' relative to the main magnetic static field direction; pulsing the radio frequency to provide a sequence that includes a phase-corrected magic angle turning pulse segment; and collecting data generated by the pulsed radio frequency. The object may be reoriented about the magic angle axis between three predetermined positions that are related to each other by 120.degree.. The main magnetic field may be rotated mechanically or electronically. Methods for magnetic resonance imaging of the object are also described.

Method for high resolution magnetic resonance analysis using magic angle technique

DOEpatents

Wind, Robert A.; Hu, Jian Zhi

2004-12-28

A method of performing a magnetic resonance analysis of a biological object that includes placing the object in a main magnetic field (that has a static field direction) and in a radio frequency field; rotating the object at a frequency of less than about 100 Hz around an axis positioned at an angle of about 54.degree.44' relative to the main magnetic static field direction; pulsing the radio frequency to provide a sequence that includes a phase-corrected magic angle turning pulse segment; and collecting data generated by the pulsed radio frequency. The object may be reoriented about the magic angle axis between three predetermined positions that are related to each other by 120.degree.. The main magnetic field may be rotated mechanically or electronically. Methods for magnetic resonance imaging of the object are also described.

The SLAC linac as used in the SLC collider

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

Seeman, J.T.; Abrams, G.; Adolphsen, C.

The linac of the SLAC Linear Collider (SLC) must accelerate three high intensity bunches on each linac pulse from 1.2 GeV to 50 GeV with minimal increase of the small transverse emittance. The procedures and adjustments used to obtain this goal are outlined. Some of the accelerator parameters and components which interact are the beam energy, transverse position, component alignment, RF manipulation, feedback systems, quadrupole lattice, BNS damping, energy spectra, phase space matching, collimation, instrumentation and modelling. The method to bring these interdependent parameters collectively into specification has evolved over several years. This review is ordered in the sequence whichmore » is used to turn on the linac from a cold start and produce acceptable beams for the final focus and collisions. Approximate time estimates for the various activities are given. 21 refs.« less

Magnetic particle imaging: from proof of principle to preclinical applications

NASA Astrophysics Data System (ADS)

Knopp, T.; Gdaniec, N.; Möddel, M.

2017-07-01

Tomographic imaging has become a mandatory tool for the diagnosis of a majority of diseases in clinical routine. Since each method has its pros and cons, a variety of them is regularly used in clinics to satisfy all application needs. Magnetic particle imaging (MPI) is a relatively new tomographic imaging technique that images magnetic nanoparticles with a high spatiotemporal resolution in a quantitative way, and in turn is highly suited for vascular and targeted imaging. MPI was introduced in 2005 and now enters the preclinical research phase, where medical researchers get access to this new technology and exploit its potential under physiological conditions. Within this paper, we review the development of MPI since its introduction in 2005. Besides an in-depth description of the basic principles, we provide detailed discussions on imaging sequences, reconstruction algorithms, scanner instrumentation and potential medical applications.

Design criteria for median turn lanes.

DOT National Transportation Integrated Search

1978-03-01

This study was initiated with an extensive literature review and survey of : left-turn median lane practices in Texas cities. The initial phase identified : characteristics of urban arterial accidents, basic design elements, current use of : left-tur...

Peer-Peer Interaction in a Speaking Test: The Case of the "First Certificate in English" Examination

ERIC Educational Resources Information Center

Galaczi, Evelina D.

2008-01-01

This discourse-based study turns its attention to paired test-taker discourse in the First Certificate in English speaking test. Its primary aim is to focus on fundamental conversation management concepts, such as overall structural organisation, turn-taking, sequencing, and topic organisation found in the dyadic test-taker interaction in 30 pairs…

Phase response of the Arabidopsis thaliana circadian clock to light pulses of different wavelengths.

PubMed

Ohara, Takayuki; Fukuda, Hirokazu; Tokuda, Isao T

2015-04-01

Light is known as one of the most powerful environmental time cues for the circadian system. The quality of light is characterized by its intensity and wavelength. We examined how the phase response of Arabidopsis thaliana depends on the wavelength of the stimulus light and the type of light perturbation. Using transgenic A. thaliana expressing a luciferase gene, we monitored the rhythm of the bioluminescence signal. We stimulated the plants under constant red light using 3 light perturbation treatments: (1) increasing the red light intensity, (2) turning on a blue light while turning off the red light, and (3) turning on a blue light while keeping the red light on. To examine the phase response properties, we generated a phase transition curve (PTC), which plots the phase after the perturbation as a function of the phase before the perturbation. To evaluate the effect of the 3 light perturbation treatments, we simulated PTCs using a mathematical model of the plant circadian clock and fitted the simulated PTCs to the experimentally measured PTCs. Among the 3 treatments, perturbation (3) provided the strongest stimulus. The results indicate that the color of the stimulus light and the type of pulse administration affect the phase response in a complex manner. Moreover, the results suggest the involvement of interaction between red and blue light signaling pathways in resetting of the plant circadian clock. © 2015 The Author(s).

Variable speed wind turbine generator with zero-sequence filter

DOEpatents

Muljadi, Eduard

1998-01-01

A variable speed wind turbine generator system to convert mechanical power into electrical power or energy and to recover the electrical power or energy in the form of three phase alternating current and return the power or energy to a utility or other load with single phase sinusoidal waveform at sixty (60) hertz and unity power factor includes an excitation controller for generating three phase commanded current, a generator, and a zero sequence filter. Each commanded current signal includes two components: a positive sequence variable frequency current signal to provide the balanced three phase excitation currents required in the stator windings of the generator to generate the rotating magnetic field needed to recover an optimum level of real power from the generator; and a zero frequency sixty (60) hertz current signal to allow the real power generated by the generator to be supplied to the utility. The positive sequence current signals are balanced three phase signals and are prevented from entering the utility by the zero sequence filter. The zero sequence current signals have zero phase displacement from each other and are prevented from entering the generator by the star connected stator windings. The zero sequence filter allows the zero sequence current signals to pass through to deliver power to the utility.

Variable Speed Wind Turbine Generator with Zero-sequence Filter

DOEpatents

Muljadi, Eduard

1998-08-25

A variable speed wind turbine generator system to convert mechanical power into electrical power or energy and to recover the electrical power or energy in the form of three phase alternating current and return the power or energy to a utility or other load with single phase sinusoidal waveform at sixty (60) hertz and unity power factor includes an excitation controller for generating three phase commanded current, a generator, and a zero sequence filter. Each commanded current signal includes two components: a positive sequence variable frequency current signal to provide the balanced three phase excitation currents required in the stator windings of the generator to generate the rotating magnetic field needed to recover an optimum level of real power from the generator; and a zero frequency sixty (60) hertz current signal to allow the real power generated by the generator to be supplied to the utility. The positive sequence current signals are balanced three phase signals and are prevented from entering the utility by the zero sequence filter. The zero sequence current signals have zero phase displacement from each other and are prevented from entering the generator by the star connected stator windings. The zero sequence filter allows the zero sequence current signals to pass through to deliver power to the utility.

Variable speed wind turbine generator with zero-sequence filter

DOEpatents

Muljadi, E.

1998-08-25

A variable speed wind turbine generator system to convert mechanical power into electrical power or energy and to recover the electrical power or energy in the form of three phase alternating current and return the power or energy to a utility or other load with single phase sinusoidal waveform at sixty (60) hertz and unity power factor includes an excitation controller for generating three phase commanded current, a generator, and a zero sequence filter. Each commanded current signal includes two components: a positive sequence variable frequency current signal to provide the balanced three phase excitation currents required in the stator windings of the generator to generate the rotating magnetic field needed to recover an optimum level of real power from the generator; and a zero frequency sixty (60) hertz current signal to allow the real power generated by the generator to be supplied to the utility. The positive sequence current signals are balanced three phase signals and are prevented from entering the utility by the zero sequence filter. The zero sequence current signals have zero phase displacement from each other and are prevented from entering the generator by the star connected stator windings. The zero sequence filter allows the zero sequence current signals to pass through to deliver power to the utility. 14 figs.

Building a stable RNA U-turn with a protonated cytidine.

PubMed

Gottstein-Schmidtke, Sina R; Duchardt-Ferner, Elke; Groher, Florian; Weigand, Julia E; Gottstein, Daniel; Suess, Beatrix; Wöhnert, Jens

2014-08-01

The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5'-UNR-3' (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3' phosphate group of the R residue as well as a hydrogen bond between the 2'-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3' from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone. © 2014 Gottstein-Schmidtke et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Model-independent analysis of the Fermilab Tevatron turn-by-turn beam position monitor measurements

NASA Astrophysics Data System (ADS)

Petrenko, A. V.; Valishev, A. A.; Lebedev, V. A.

2011-09-01

Coherent transverse beam oscillations in the Tevatron were analyzed with the model-independent analysis (MIA) technique. This allowed one to obtain the model-independent values of coupled betatron amplitudes, phase advances, and dispersion function around the ring from a single dipole kick measurement. In order to solve the MIA mode mixing problem which limits the accuracy of determination of the optical functions, we have developed a new technique of rotational MIA mode untangling. The basic idea is to treat each beam position monitor (BPM) as two BPMs separated in a ring by exactly one turn. This leads to a simple criterion of MIA mode separation: the betatron phase advance between any BPM and its counterpart shifted by one turn should be equal to the betatron tune and therefore should not depend on the BPM position in the ring. Furthermore, we describe a MIA-based technique to locate vibrating magnets in a storage ring.

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

Hachisu, Izumi; Kato, Mariko, E-mail: hachisu@ea.c.u-tokyo.ac.jp, E-mail: mariko@educ.cc.keio.ac.jp

We identified a general course of classical nova outbursts in the B – V versus U – B color-color diagram. It is reported that novae show spectra similar to those of A-F supergiants near optical light maximum. However, they do not follow the supergiant sequence in the color-color diagram, neither the blackbody nor the main-sequence sequence. Instead, we found that novae evolve along a new sequence in the pre-maximum and near-maximum phases, which we call 'the nova-giant sequence'. This sequence is parallel to but Δ(U – B) ≈ –0.2 mag bluer than the supergiant sequence. This is because the massmore » of a nova envelope is much (∼10{sup –4} times) less than that of a normal supergiant. After optical maximum, its color quickly evolves back blueward along the same nova-giant sequence and reaches the point of free-free emission (B – V = –0.03, U – B = –0.97), which coincides with the intersection of the blackbody sequence and the nova-giant sequence, and remains there for a while. Then the color evolves leftward (blueward in B – V but almost constant in U – B), owing mainly to the development of strong emission lines. This is the general course of nova outbursts in the color-color diagram, which was deduced from eight well-observed novae in various speed classes. For a nova with unknown extinction, we can determine a reliable value of the color excess by matching the observed track of the target nova with this general course. This is a new and convenient method for obtaining the color excesses of classical novae. Using this method, we redetermined the color excesses of 20 well-observed novae. The obtained color excesses are in reasonable agreement with the previous results, which in turn support the idea of our general track of nova outbursts. Additionally, we estimated the absolute V magnitudes of about 30 novae using a method for time-stretching nova light curves to analyze the distance-reddening relations of the novae.« less

Direct observation of the phase space footprint of a painting injection in the Rapid Cycling Synchrotron at the Japan Proton Accelerator Research Complex

NASA Astrophysics Data System (ADS)

Saha, P. K.; Shobuda, Y.; Hotchi, H.; Hayashi, N.; Takayanagi, T.; Harada, H.; Irie, Y.

2009-04-01

The 3 GeV Rapid Cycling Synchrotron (RCS) at Japan Proton Accelerator Research Complex is nearly at the operational stage with regard to the beam commissioning aspects. Recently, the design painting injection study has been commenced with the aim of high output beam power at the extraction. In order to observe the phase space footprint of the painting injection, a method was developed utilizing a beam position monitor (BPM) in the so-called single pass mode. The turn-by-turn phase space coordinates of the circulating beam directly measured using a pair of BPMs entirely positioned in drift space, and the calculated transfer matrices from the injection point to the pair of BPMs with several successive turns were used together in order to obtain the phase space footprint of the painting injection. There are two such pairs of BPMs placed in two different locations in the RCS, the results from which both agreed and were quite consistent with what was expected.

Advances in Understanding Stimulus Responsive Phase Behavior of Intrinsically Disordered Protein Polymers.

PubMed

Ruff, Kiersten M; Roberts, Stefan; Chilkoti, Ashutosh; Pappu, Rohit V

2018-06-24

Proteins and synthetic polymers can undergo phase transitions in response to changes to intensive solution parameters such as temperature, proton chemical potentials (pH), and hydrostatic pressure. For proteins and protein-based polymers, the information required for stimulus responsive phase transitions is encoded in their amino acid sequence. Here, we review some of the key physical principles that govern the phase transitions of archetypal intrinsically disordered protein polymers (IDPPs). These are disordered proteins with highly repetitive amino acid sequences. Advances in recombinant technologies have enabled the design and synthesis of protein sequences of a variety of sequence complexities and lengths. We summarize insights that have been gleaned from the design and characterization of IDPPs that undergo thermo-responsive phase transitions and build on these insights to present a general framework for IDPPs with pH and pressure responsive phase behavior. In doing so, we connect the stimulus responsive phase behavior of IDPPs with repetitive sequences to the coil-to-globule transitions that these sequences undergo at the single chain level in response to changes in stimuli. The proposed framework and ongoing studies of stimulus responsive phase behavior of designed IDPPs have direct implications in bioengineering, where designing sequences with bespoke material properties broadens the spectrum of applications, and in biology and medicine for understanding the sequence-specific driving forces for the formation of protein-based membraneless organelles as well as biological matrices that act as scaffolds for cells and mediators of cell-to-cell communication. Copyright © 2018. Published by Elsevier Ltd.

The Gaia-ESO Survey: evidence of atomic diffusion in M67?

NASA Astrophysics Data System (ADS)

Bertelli Motta, C.; Pasquali, A.; Richer, J.; Michaud, G.; Salaris, M.; Bragaglia, A.; Magrini, L.; Randich, S.; Grebel, E. K.; Adibekyan, V.; Blanco-Cuaresma, S.; Drazdauskas, A.; Fu, X.; Martell, S.; Tautvaišienė, G.; Gilmore, G.; Alfaro, E. J.; Bensby, T.; Flaccomio, E.; Koposov, S. E.; Korn, A. J.; Lanzafame, A. C.; Smiljanic, R.; Bayo, A.; Carraro, G.; Casey, A. R.; Costado, M. T.; Damiani, F.; Franciosini, E.; Heiter, U.; Hourihane, A.; Jofré, P.; Lardo, C.; Lewis, J.; Monaco, L.; Morbidelli, L.; Sacco, G. G.; Sousa, S. G.; Worley, C. C.; Zaggia, S.

2018-07-01

Investigating the chemical homogeneity of stars born from the same molecular cloud at virtually the same time is very important for our understanding of the chemical enrichment of the interstellar medium and with it the chemical evolution of the Galaxy. One major cause of inhomogeneities in the abundances of open clusters is stellar evolution of the cluster members. In this work, we investigate variations in the surface chemical composition of member stars of the old open cluster M67 as a possible consequence of atomic diffusion effects taking place during the main-sequence phase. The abundances used are obtained from high-resolution UVES/FLAMES spectra within the framework of the Gaia-ESO Survey. We find that the surface abundances of stars on the main sequence decrease with increasing mass reaching a minimum at the turn-off. After deepening of the convective envelope in subgiant branch stars, the initial surface abundances are restored. We found the measured abundances to be consistent with the predictions of stellar evolutionary models for a cluster with the age and metallicity of M67. Our findings indicate that atomic diffusion poses a non-negligible constraint on the achievable precision of chemical tagging methods.

The Gaia-ESO Survey: Evidence of atomic diffusion in M67?

NASA Astrophysics Data System (ADS)

Motta, C. Bertelli; Pasquali, A.; Richer, J.; Michaud, G.; Salaris, M.; Bragaglia, A.; Magrini, L.; Randich, S.; Grebel, E. K.; Adibekyan, V.; Blanco-Cuaresma, S.; Drazdauskas, A.; Fu, X.; Martell, S.; TautvaišienÄ--, G.; Gilmore, G.; Alfaro, E. J.; Bensby, T.; Flaccomio, E.; Koposov, S. E.; Korn, A. J.; Lanzafame, A. C.; Smiljanic, R.; Bayo, A.; Carraro, G.; Casey, A. R.; Costado, M. T.; Damiani, F.; Franciosini, E.; Heiter, U.; Hourihane, A.; Jofré, P.; Lardo, C.; Lewis, J.; Monaco, L.; Morbidelli, L.; Sacco, G. G.; Sousa, S. G.; Worley, C. C.; Zaggia, S.

2018-04-01

Investigating the chemical homogeneity of stars born from the same molecular cloud at virtually the same time is very important for our understanding of the chemical enrichment of the interstellar medium and with it the chemical evolution of the Galaxy. One major cause of inhomogeneities in the abundances of open clusters is stellar evolution of the cluster members. In this work, we investigate variations in the surface chemical composition of member stars of the old open cluster M67 as a possible consequence of atomic diffusion effects taking place during the main-sequence phase. The abundances used are obtained from high-resolution UVES/FLAMES spectra within the framework of the Gaia-ESO Survey. We find that the surface abundances of stars on the main sequence decrease with increasing mass reaching a minimum at the turn-off. After deepening of the convective envelope in sub-giant branch stars, the initial surface abundances are restored. We found the measured abundances to be consistent with the predictions of stellar evolutionary models for a cluster with the age and metallicity of M67. Our findings indicate that atomic diffusion poses a non-negligible constraint on the achievable precision of chemical tagging methods.

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.

Power Supply Fault Tolerant Reliability Study

DTIC Science & Technology

1991-04-01

easier to design than for equivalent bipolar transistors. MCDONNELL DOUGLAS ELECTRONICS SYSTEMS COMPANY 9. Base circuitry should be designed to drive...SWITCHING REGULATORS (Ref. 28), SWITCHING AND LINEAR POWER SUPPLY DESIGN (Ref. 25) 6. Sequence the turn-off/turn-on logic in an orderly and controllable ...for equivalent bipolar transistors. MCDONNELL DOUGLAS ELECTRONICS SYSTEMS COMPANY 8. Base circuitry should be designed to drive the transistor into

On the nature of phase attraction in sensorimotor synchronization with interleaved auditory sequences.

PubMed

Repp, Bruno H

2004-10-01

In a task that requires in-phase synchronization of finger taps with an isochronous sequence of target tones that is interleaved with a sequence of distractor tones at various fixed phase relationships, the taps tend to be attracted to the distractor tones, especially when the distractor tones closely precede the target tones [Repp, B. H. (2003a). Phase attraction in sensorimotor synchronization with auditory sequences: Effects of single and periodic distractors on synchronization accuracy. Journal of Experimental Psychology: Human Perception and Performance, 29, 290-309]. The present research addressed two related questions about this distractor effect: (1) Is it a function of the absolute temporal separation or of the relative phase of the two stimulus sequences? (2) Is it the result of perceptual grouping (integration) of target and distractor tones or of simultaneous attraction to two independent sequences? In three experiments, distractor effects were compared across two different sequence rates. The results suggest that absolute temporal separation, not relative phase, is the critical variable. Experiment 3 also included an anti-phase tapping task that addressed the second question directly. The results suggest that the attraction of taps to distractor tones is caused mainly by temporal integration of target and distractor tones within a fixed window of 100-150 ms duration, with the earlier-occurring tone being weighted more strongly than the later-occurring one.

Extension of the classical classification of β-turns

PubMed Central

de Brevern, Alexandre G.

2016-01-01

The functional properties of a protein primarily depend on its three-dimensional (3D) structure. These properties have classically been assigned, visualized and analysed on the basis of protein secondary structures. The β-turn is the third most important secondary structure after helices and β-strands. β-turns have been classified according to the values of the dihedral angles φ and ψ of the central residue. Conventionally, eight different types of β-turns have been defined, whereas those that cannot be defined are classified as type IV β-turns. This classification remains the most widely used. Nonetheless, the miscellaneous type IV β-turns represent 1/3rd of β-turn residues. An unsupervised specific clustering approach was designed to search for recurrent new turns in the type IV category. The classical rules of β-turn type assignment were central to the approach. The four most frequently occurring clusters defined the new β-turn types. Unexpectedly, these types, designated IV1, IV2, IV3 and IV4, represent half of the type IV β-turns and occur more frequently than many of the previously established types. These types show convincing particularities, in terms of both structures and sequences that allow for the classical β-turn classification to be extended for the first time in 25 years. PMID:27627963

Extension of the classical classification of β-turns.

PubMed

de Brevern, Alexandre G

2016-09-15

The functional properties of a protein primarily depend on its three-dimensional (3D) structure. These properties have classically been assigned, visualized and analysed on the basis of protein secondary structures. The β-turn is the third most important secondary structure after helices and β-strands. β-turns have been classified according to the values of the dihedral angles φ and ψ of the central residue. Conventionally, eight different types of β-turns have been defined, whereas those that cannot be defined are classified as type IV β-turns. This classification remains the most widely used. Nonetheless, the miscellaneous type IV β-turns represent 1/3(rd) of β-turn residues. An unsupervised specific clustering approach was designed to search for recurrent new turns in the type IV category. The classical rules of β-turn type assignment were central to the approach. The four most frequently occurring clusters defined the new β-turn types. Unexpectedly, these types, designated IV1, IV2, IV3 and IV4, represent half of the type IV β-turns and occur more frequently than many of the previously established types. These types show convincing particularities, in terms of both structures and sequences that allow for the classical β-turn classification to be extended for the first time in 25 years.

Haplotype estimation using sequencing reads.

PubMed

Delaneau, Olivier; Howie, Bryan; Cox, Anthony J; Zagury, Jean-François; Marchini, Jonathan

2013-10-03

High-throughput sequencing technologies produce short sequence reads that can contain phase information if they span two or more heterozygote genotypes. This information is not routinely used by current methods that infer haplotypes from genotype data. We have extended the SHAPEIT2 method to use phase-informative sequencing reads to improve phasing accuracy. Our model incorporates the read information in a probabilistic model through base quality scores within each read. The method is primarily designed for high-coverage sequence data or data sets that already have genotypes called. One important application is phasing of single samples sequenced at high coverage for use in medical sequencing and studies of rare diseases. Our method can also use existing panels of reference haplotypes. We tested the method by using a mother-father-child trio sequenced at high-coverage by Illumina together with the low-coverage sequence data from the 1000 Genomes Project (1000GP). We found that use of phase-informative reads increases the mean distance between switch errors by 22% from 274.4 kb to 328.6 kb. We also used male chromosome X haplotypes from the 1000GP samples to simulate sequencing reads with varying insert size, read length, and base error rate. When using short 100 bp paired-end reads, we found that using mixtures of insert sizes produced the best results. When using longer reads with high error rates (5-20 kb read with 4%-15% error per base), phasing performance was substantially improved. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Improved pedestrian safety at signalized intersections operating the flashing yellow arrow.

DOT National Transportation Integrated Search

2013-04-01

In some jurisdictions, protected left-turn phasing has been replaced with the flashing yellow arrow (FYA) for : protected/permissive left turns (PPLTs) to reduce delay. However, it is important to have a thorough understanding of the : conflict betwe...

Machine learning Z2 quantum spin liquids with quasiparticle statistics

NASA Astrophysics Data System (ADS)

Zhang, Yi; Melko, Roger G.; Kim, Eun-Ah

2017-12-01

After decades of progress and effort, obtaining a phase diagram for a strongly correlated topological system still remains a challenge. Although in principle one could turn to Wilson loops and long-range entanglement, evaluating these nonlocal observables at many points in phase space can be prohibitively costly. With growing excitement over topological quantum computation comes the need for an efficient approach for obtaining topological phase diagrams. Here we turn to machine learning using quantum loop topography (QLT), a notion we have recently introduced. Specifically, we propose a construction of QLT that is sensitive to quasiparticle statistics. We then use mutual statistics between the spinons and visons to detect a Z2 quantum spin liquid in a multiparameter phase space. We successfully obtain the quantum phase boundary between the topological and trivial phases using a simple feed-forward neural network. Furthermore, we demonstrate advantages of our approach for the evaluation of phase diagrams relating to speed and storage. Such statistics-based machine learning of topological phases opens new efficient routes to studying topological phase diagrams in strongly correlated systems.

Timing of Visual Bodily Behavior in Repair Sequences: Evidence from Three Languages

ERIC Educational Resources Information Center

Floyd, Simeon; Manrique, Elizabeth; Rossi, Giovanni; Torreira, Francisco

2016-01-01

This article expands the study of other-initiated repair in conversation--when one party signals a problem with producing or perceiving another's turn at talk--into the domain of visual bodily behavior. It presents one primary cross-linguistic finding about the timing of visual bodily behavior in repair sequences: if the party who initiates repair…

On How "n" and "i" Turned out to Become Indices in Mathematical Sequences and Formulae

ERIC Educational Resources Information Center

Schubring, Gert

2011-01-01

The evolution of indexing sequences and series has been little studied so far, although this topic presents difficulties for students. This symbolisation signified, however, an important means for operating more generally with finite and infinite series. This paper investigates the first steps during the eighteenth century and then the different…

Random sequences generation through optical measurements by phase-shifting interferometry

NASA Astrophysics Data System (ADS)

François, M.; Grosges, T.; Barchiesi, D.; Erra, R.; Cornet, A.

2012-04-01

The development of new techniques for producing random sequences with a high level of security is a challenging topic of research in modern cryptographics. The proposed method is based on the measurement by phase-shifting interferometry of the speckle signals of the interaction between light and structures. We show how the combination of amplitude and phase distributions (maps) under a numerical process can produce random sequences. The produced sequences satisfy all the statistical requirements of randomness and can be used in cryptographic schemes.

Prediction and analysis of beta-turns in proteins by support vector machine.

PubMed

Pham, Tho Hoan; Satou, Kenji; Ho, Tu Bao

2003-01-01

Tight turn has long been recognized as one of the three important features of proteins after the alpha-helix and beta-sheet. Tight turns play an important role in globular proteins from both the structural and functional points of view. More than 90% tight turns are beta-turns. Analysis and prediction of beta-turns in particular and tight turns in general are very useful for the design of new molecules such as drugs, pesticides, and antigens. In this paper, we introduce a support vector machine (SVM) approach to prediction and analysis of beta-turns. We have investigated two aspects of applying SVM to the prediction and analysis of beta-turns. First, we developed a new SVM method, called BTSVM, which predicts beta-turns of a protein from its sequence. The prediction results on the dataset of 426 non-homologous protein chains by sevenfold cross-validation technique showed that our method is superior to the other previous methods. Second, we analyzed how amino acid positions support (or prevent) the formation of beta-turns based on the "multivariable" classification model of a linear SVM. This model is more general than the other ones of previous statistical methods. Our analysis results are more comprehensive and easier to use than previously published analysis results.

Defining the loop structures in proteins based on composite β-turn mimics.

PubMed

Dhar, Jesmita; Chakrabarti, Pinak

2015-06-01

Asx- and ω-turns are β-turn mimics, which replace the conventional main-chain hydrogen bonds seen in the latter by those involving the side chains, and both involve three residues. In this paper we analyzed the cases where these turns occur together--side by side, with or without any gap, overlapping and in any order. These composite turns (of length 3-15 residues), occurring at ∼1 per 100 residues, may constitute the full length of many loops, and when the residues in the two component turns overlap or are adjacent to each other, the composite may take well-defined shape. It is thus possible for non-regular regions in protein structure to form local structural motifs, akin to the regular geometrical features exhibited by secondary structures. Composites having the order ω-turns followed by Asx-turns can constitute N-terminal helix capping motif. Ternary composite turns (made up of ω-, Asx- and ST-turns), some with characteristic shape, have also been identified. Delineation of composite turns would help in characterizing loops in protein structures, which often have functional roles. Some sequence patterns seen in composites can be used for their incorporation in protein design. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Galaxies Collide to Create Hot, Huge Galaxy

NASA Technical Reports Server (NTRS)

2009-01-01

This image of a pair of colliding galaxies called NGC 6240 shows them in a rare, short-lived phase of their evolution just before they merge into a single, larger galaxy. The prolonged, violent collision has drastically altered the appearance of both galaxies and created huge amounts of heat turning NGC 6240 into an 'infrared luminous' active galaxy.

A rich variety of active galaxies, with different shapes, luminosities and radiation profiles exist. These galaxies may be related astronomers have suspected that they may represent an evolutionary sequence. By catching different galaxies in different stages of merging, a story emerges as one type of active galaxy changes into another. NGC 6240 provides an important 'missing link' in this process.

This image was created from combined data from the infrared array camera of NASA's Spitzer Space Telescope at 3.6 and 8.0 microns (red) and visible light from NASA's Hubble Space Telescope (green and blue).

Postural illusions experienced during Z-axis recumbent rotation and their dependence upon somatosensory stimulation of the body surface

NASA Technical Reports Server (NTRS)

Lackner, J. R.; Graybiel, A.

1978-01-01

A blindfolded recumbent subject experiences a variety of postural illusions when rotated about his Z axis. Initially, during the acceleratory phase of rotation, turning about his Z axis is experienced; but, as rotary velocity increases, a spiraling of the body outward in the direction opposite to true rotation is experienced as well. Above 15-20 rpm, only orbital motion of the body is experienced, with the subject feeling that he is always facing in the same direction. One cycle of the apparent orbit is completed each time the subject actually rotates 360 deg. The reverse sequence of illusory motion is experienced during deceleration. The illusory motion all subjects experience during Z-axis recumbent rotation is shown to depend upon the touch and pressure stimulation of the body surface generated by contact forces of support.

Phase correction, phase resetting, and phase shifts after subliminal timing perturbations in sensorimotor synchronization.

PubMed

Repp, B H

2001-06-01

Recent studies of synchronized finger tapping have shown that perceptually subliminal phase shifts in an auditory sequence are rapidly compensated for in the motor activity (B. H. Repp, 2000a). Experiment 1 used a continuation-tapping task to confirm that this compensation is indeed a phase correction, not an adjustment of the central timekeeper period. Experiments 2-5 revealed that this phase correction occurs even when there is no ordinary sensorimotor asynchrony--when the finger taps are in antiphase or arbitrary phase relative to the auditory sequence (Experiments 2 and 3) or when the tap coinciding with the sequence phase shift is withheld (Experiments 4 and 5). The phase correction observed in the latter conditions was instantaneous, which suggests that phase resetting occurs when the motor activity is discontinuous. A prolonged phase shift suggestive of overcompensation was observed in some conditions, which poses a challenge to pure phase correction models.

A new phase of activity of the Herbig Be star HD 200775 in 2001: Evidence for binarity

NASA Astrophysics Data System (ADS)

Pogodin, M. A.; Miroshnichenko, A. S.; Tarasov, A. E.; Mitskevich, M. P.; Chountonov, G. A.; Klochkova, V. G.; Yushkin, M. V.; Manset, N.; Bjorkman, K. S.; Morrison, N. D.; Wisniewski, J. P.

2004-04-01

The results of high-resolution spectroscopy of the Herbig Be star HD 200775 obtained within the framework of a cooperative observing programme in 2000-2002 are presented. A new high-activity phase of the object's Hα line occurred in the middle of 2001 in full agreement with a 3.68-year periodicity predicted by Miroshnichenko et al. (\\cite{mirosh}). A complicated picture of the Hα line profile variability near the activity maximum phase turned out to be very similar to that observed during the previous one in 1997. Variations of the radial velocity with the activity phase are detected in He I, Si II, and S II photospheric lines. The observed phenomena are interpreted in the framework of a model in which the star, together with its gaseous envelope, is a component of an eccentric binary system. A preliminary orbital solution is derived, and the system's parameters are estimated from the radial velocity curves of the Hα emission line. We find that the orbital eccentricity is e ˜0.3, the mean companion separation is ˜1000 R⊙, and the secondary companion is most likely to be a ˜3.5 M⊙ pre-main sequence object. We emphasize the importance of coordinated spectroscopic and interferometric observations at different phases of the object's activity for further understanding the properties of the system. Partially based on observations collected at the Canada-France-Hawaii telescope (CFHT), operated by the National Research Council of Canada, the Centre National de la Recherche Scientifique, and University of Hawaii.

Cosmic Accretion and Galaxy Co-Evolution: Lessons from the Extended Chandra Deep Field South

NASA Astrophysics Data System (ADS)

Urry, C. Megan

2011-05-01

The Chandra deep fields reveal that most cosmic accretion onto supermassive black holes is obscured by gas and dust. The GOODS and MUSYC multiwavelength data show that many X-ray-detected AGN are faint and red (or even undetectable) in the optical but bright in the infrared, as is characteristic of obscured sources. (N.B. The ECDFS is most sensitive to the AGN that constitute the X-ray background, namely, moderate luminosity AGN, with log Lx=43-44, at moderate redshifts, 0.5

Optimal aeroassisted orbital transfer with plane change using collocation and nonlinear programming

NASA Technical Reports Server (NTRS)

Shi, Yun. Y.; Nelson, R. L.; Young, D. H.

1990-01-01

The fuel optimal control problem arising in the non-planar orbital transfer employing aeroassisted technology is addressed. The mission involves the transfer from high energy orbit (HEO) to low energy orbit (LEO) with orbital plane change. The basic strategy here is to employ a combination of propulsive maneuvers in space and aerodynamic maneuvers in the atmosphere. The basic sequence of events for the aeroassisted HEO to LEO transfer consists of three phases. In the first phase, the orbital transfer begins with a deorbit impulse at HEO which injects the vehicle into an elliptic transfer orbit with perigee inside the atmosphere. In the second phase, the vehicle is optimally controlled by lift and bank angle modulations to perform the desired orbital plane change and to satisfy heating constraints. Because of the energy loss during the turn, an impulse is required to initiate the third phase to boost the vehicle back to the desired LEO orbital altitude. The third impulse is then used to circularize the orbit at LEO. The problem is solved by a direct optimization technique which uses piecewise polynomial representation for the state and control variables and collocation to satisfy the differential equations. This technique converts the optimal control problem into a nonlinear programming problem which is solved numerically. Solutions were obtained for cases with and without heat constraints and for cases of different orbital inclination changes. The method appears to be more powerful and robust than other optimization methods. In addition, the method can handle complex dynamical constraints.

Phase diagram of two-dimensional hard ellipses.

PubMed

Bautista-Carbajal, Gustavo; Odriozola, Gerardo

2014-05-28

We report the phase diagram of two-dimensional hard ellipses as obtained from replica exchange Monte Carlo simulations. The replica exchange is implemented by expanding the isobaric ensemble in pressure. The phase diagram shows four regions: isotropic, nematic, plastic, and solid (letting aside the hexatic phase at the isotropic-plastic two-step transition [E. P. Bernard and W. Krauth, Phys. Rev. Lett. 107, 155704 (2011)]). At low anisotropies, the isotropic fluid turns into a plastic phase which in turn yields a solid for increasing pressure (area fraction). Intermediate anisotropies lead to a single first order transition (isotropic-solid). Finally, large anisotropies yield an isotropic-nematic transition at low pressures and a high-pressure nematic-solid transition. We obtain continuous isotropic-nematic transitions. For the transitions involving quasi-long-range positional ordering, i.e., isotropic-plastic, isotropic-solid, and nematic-solid, we observe bimodal probability density functions. This supports first order transition scenarios.

The predicted secondary structures of class I fructose-bisphosphate aldolases.

PubMed Central

Sawyer, L; Fothergill-Gilmore, L A; Freemont, P S

1988-01-01

The results of several secondary-structure prediction programs were combined to produce an estimate of the regions of alpha-helix, beta-sheet and reverse turns for fructose-bisphosphate aldolases from human and rat muscle and liver, from Trypanosoma brucei and from Drosophila melanogaster. All the aldolase sequences gave essentially the same pattern of secondary-structure predictions despite having sequences up to 50% different. One exception to this pattern was an additional strongly predicted helix in the rat liver and Drosophila enzymes. Regions of relatively high sequence variation generally were predicted as reverse turns, and probably occur as surface loops. Most of the positions corresponding to exon boundaries are located between regions predicted to have secondary-structural elements consistent with a compact structure. The predominantly alternating alpha/beta structure predicted is consistent with the alpha/beta-barrel structure indicated by preliminary high-resolution X-ray diffraction studies on rabbit muscle aldolase [Sygusch, Beaudry & Allaire (1986) Biophys. J. 49, 287a]. Images Fig. 1. (cont.) Fig. 1. PMID:3128269

AutoGen Version 5.0

NASA Technical Reports Server (NTRS)

Gladden, Roy E.; Khanampornpan, Teerapat; Fisher, Forest W.

2010-01-01

Version 5.0 of the AutoGen software has been released. Previous versions, variously denoted Autogen and autogen, were reported in two articles: Automated Sequence Generation Process and Software (NPO-30746), Software Tech Briefs (Special Supplement to NASA Tech Briefs), September 2007, page 30, and Autogen Version 2.0 (NPO- 41501), NASA Tech Briefs, Vol. 31, No. 10 (October 2007), page 58. To recapitulate: AutoGen (now signifying automatic sequence generation ) automates the generation of sequences of commands in a standard format for uplink to spacecraft. AutoGen requires fewer workers than are needed for older manual sequence-generation processes, and greatly reduces sequence-generation times. The sequences are embodied in spacecraft activity sequence files (SASFs). AutoGen automates generation of SASFs by use of another previously reported program called APGEN. AutoGen encodes knowledge of different mission phases and of how the resultant commands must differ among the phases. AutoGen also provides means for customizing sequences through use of configuration files. The approach followed in developing AutoGen has involved encoding the behaviors of a system into a model and encoding algorithms for context-sensitive customizations of the modeled behaviors. This version of AutoGen addressed the MRO (Mars Reconnaissance Orbiter) primary science phase (PSP) mission phase. On previous Mars missions this phase has more commonly been referred to as mapping phase. This version addressed the unique aspects of sequencing orbital operations and specifically the mission specific adaptation of orbital operations for MRO. This version also includes capabilities for MRO s role in Mars relay support for UHF relay communications with the MER rovers and the Phoenix lander.

Magnetic flux density measurement with balanced steady state free precession pulse sequence for MREIT: a simulation study.

PubMed

Minhas, Atul S; Woo, Eung Je; Lee, Soo Yeol

2009-01-01

Magnetic Resonance Electrical Impedance Tomography (MREIT) utilizes the magnetic flux density B(z), generated due to current injection, to find conductivity distribution inside an object. This B(z) can be measured from MR phase images using spin echo pulse sequence. The SNR of B(z) and the sensitivity of phase produced by B(z) in MR phase image are critical in deciding the resolution of MREIT conductivity images. The conventional spin echo based data acquisition has poor phase sensitivity to current injection. Longer scan time is needed to acquire data with higher SNR. We propose a balanced steady state free precession (b-SSFP) based pulse sequence which is highly sensitive to small off-resonance phase changes. A procedure to reconstruct B(z) from MR signal obtained with b-SSFP sequence is described. Phases for b-SSFP signals for two conductivity phantoms of TX 151 and Gelatin are simulated from the mathematical models of b-SSFP signal. It was observed that the phase changes obtained from b-SSFP pulse sequence are highly sensitive to current injection and hence would produce higher magnetic flux density. However, the b-SSFP signal is dependent on magnetic field inhomogeneity and the signal deteriorated highly for small offset from resonance frequency. The simulation results show that the b-SSFP sequence can be utilized for conductivity imaging of a local region where magnetic field inhomogeneity is small. A proper shimming of magnet is recommended before using the b-SSFP sequence.

The validation of a swimming turn wall-contact-time measurement system: a touchpad application reliability study.

PubMed

Brackley, Victoria; Ball, Kevin; Tor, Elaine

2018-05-12

The effectiveness of the swimming turn is highly influential to overall performance in competitive swimming. The push-off or wall contact, within the turn phase, is directly involved in determining the speed the swimmer leaves the wall. Therefore, it is paramount to develop reliable methods to measure the wall-contact-time during the turn phase for training and research purposes. The aim of this study was to determine the concurrent validity and reliability of the Pool Pad App to measure wall-contact-time during the freestyle and backstroke tumble turn. The wall-contact-times of nine elite and sub-elite participants were recorded during their regular training sessions. Concurrent validity statistics included the standardised typical error estimate, linear analysis and effect sizes while the intraclass correlating coefficient (ICC) was used for the reliability statistics. The standardised typical error estimate resulted in a moderate Cohen's d effect size with an R 2 value of 0.80 and the ICC between the Pool Pad and 2D video footage was 0.89. Despite these measurement differences, the results from this concurrent validity and reliability analyses demonstrated that the Pool Pad is suitable for measuring wall-contact-time during the freestyle and backstroke tumble turn within a training environment.

Quantitative comparison between a multiecho sequence and a single-echo sequence for susceptibility-weighted phase imaging.

PubMed

Gilbert, Guillaume; Savard, Geneviève; Bard, Céline; Beaudoin, Gilles

2012-06-01

The aim of this study was to investigate the benefits arising from the use of a multiecho sequence for susceptibility-weighted phase imaging using a quantitative comparison with a standard single-echo acquisition. Four healthy adult volunteers were imaged on a clinical 3-T system using a protocol comprising two different three-dimensional susceptibility-weighted gradient-echo sequences: a standard single-echo sequence and a multiecho sequence. Both sequences were repeated twice in order to evaluate the local noise contribution by a subtraction of the two acquisitions. For the multiecho sequence, the phase information from each echo was independently unwrapped, and the background field contribution was removed using either homodyne filtering or the projection onto dipole fields method. The phase information from all echoes was then combined using a weighted linear regression. R2 maps were also calculated from the multiecho acquisitions. The noise standard deviation in the reconstructed phase images was evaluated for six manually segmented regions of interest (frontal white matter, posterior white matter, globus pallidus, putamen, caudate nucleus and lateral ventricle). The use of the multiecho sequence for susceptibility-weighted phase imaging led to a reduction of the noise standard deviation for all subjects and all regions of interest investigated in comparison to the reference single-echo acquisition. On average, the noise reduction ranged from 18.4% for the globus pallidus to 47.9% for the lateral ventricle. In addition, the amount of noise reduction was found to be strongly inversely correlated to the estimated R2 value (R=-0.92). In conclusion, the use of a multiecho sequence is an effective way to decrease the noise contribution in susceptibility-weighted phase images, while preserving both contrast and acquisition time. The proposed approach additionally permits the calculation of R2 maps. Copyright © 2012 Elsevier Inc. All rights reserved.

There's no ball without noise: cats' prediction of an object from noise.

PubMed

Takagi, Saho; Arahori, Minori; Chijiiwa, Hitomi; Tsuzuki, Mana; Hataji, Yuya; Fujita, Kazuo

2016-09-01

We used an expectancy violation procedure to ask whether cats could use a causal rule to infer the presence of an unseen object on hearing the noise it made inside a container and predict its appearance when the container was turned over. We presented cats with either an object dropping out of an opaque container or no object dropping out (turning-over phase) after producing either a rattling sound by shaking the container with the object inside, or no sound (shaking phase). The cats were then allowed to freely explore the experimental environment (exploration phase). The relation between the sound and the object matched with physical laws in half of the trials (congruent condition) and mismatched in the other half (incongruent condition). Inferring the presence of an unseen object from the noise was predicted to result in longer looking time in the incongruent condition. The prediction was supported by the cats' behavior during the turning-over phase. The results suggest that cats used a causal-logical understanding of auditory stimuli to predict the appearance of invisible objects. The ecology of cats' natural hunting style may favor the ability for inference on the basis of sounds.

A method for automatically abstracting visual documents

NASA Technical Reports Server (NTRS)

Rorvig, Mark E.

1994-01-01

Visual documents--motion sequences on film, videotape, and digital recording--constitute a major source of information for the Space Agency, as well as all other government and private sector entities. This article describes a method for automatically selecting key frames from visual documents. These frames may in turn be used to represent the total image sequence of visual documents in visual libraries, hypermedia systems, and training algorithm reduces 51 minutes of video sequences to 134 frames; a reduction of information in the range of 700:1.

Effects of leg dominance on performance of ballet turns (pirouettes) by experienced and novice dancers.

PubMed

Lin, Chia-Wei; Su, Fong-Chin; Wu, Hong-Wen; Lin, Cheng-Feng

2013-01-01

Turns (pirouettes) are an important movement in ballet and may be affected by "lateral bias". This study investigated physiological differences exhibited by experienced and novice dancers, respectively, when performing pirouette with dominant and non-dominant leg supports, respectively. Thirteen novice and 13 experienced dancers performed turns on dominant or non-dominant legs. The maximum ankle plantarflexion, knee extension and hip extension were measured during the single-leg support phase. The inclination angle of rotation axis is the angle between instantaneous rotation axis and global vertical axis in the early single-leg support phase. Both groups exhibited a greater hip extension, knee extension, and ankle plantarflexion when performing a turn on the non-dominant leg. For experienced dancers, the inclination angle of rotation axis during the pre-swing phase was generally smaller for dominant leg support than non-dominant leg. However, no significant difference was found in inclination angle of rotation axis of novice dancers. For experienced dancers, an improved performance is obtained when using the dominant leg for support. By contrast, for novice dancers, the performance is independent of choice of support leg. The significant lateral bias in experienced dancers indicates the possible influence of training. That is, repetitive rehearsal on the preferred leg strengthens the impact of side dominance in experienced dancers.

Gas phase electrodeposition: a programmable multimaterial deposition method for combinatorial nanostructured device discovery.

PubMed

Lin, En-Chiang; Cole, Jesse J; Jacobs, Heiko O

2010-11-10

This article reports and applies a recently discovered programmable multimaterial deposition process to the formation and combinatorial improvement of 3D nanostructured devices. The gas-phase deposition process produces charged <5 nm particles of silver, tungsten, and platinum and uses externally biased electrodes to control the material flux and to turn deposition ON/OFF in selected domains. Domains host nanostructured dielectrics to define arrays of electrodynamic 10 × nanolenses to further control the flux to form <100 nm resolution deposits. The unique feature of the process is that material type, amount, and sequence can be altered from one domain to the next leading to different types of nanostructures including multimaterial bridges, interconnects, or nanowire arrays with 20 nm positional accuracy. These features enable combinatorial nanostructured materials and device discovery. As a first demonstration, we produce and identify in a combinatorial way 3D nanostructured electrode designs that improve light scattering, absorption, and minority carrier extraction of bulk heterojunction photovoltaic cells. Photovoltaic cells from domains with long and dense nanowire arrays improve the relative power conversion efficiency by 47% when compared to flat domains on the same substrate.

Using support vector machine to predict beta- and gamma-turns in proteins.

PubMed

Hu, Xiuzhen; Li, Qianzhong

2008-09-01

By using the composite vector with increment of diversity, position conservation scoring function, and predictive secondary structures to express the information of sequence, a support vector machine (SVM) algorithm for predicting beta- and gamma-turns in the proteins is proposed. The 426 and 320 nonhomologous protein chains described by Guruprasad and Rajkumar (Guruprasad and Rajkumar J. Biosci 2000, 25,143) are used for training and testing the predictive model of the beta- and gamma-turns, respectively. The overall prediction accuracy and the Matthews correlation coefficient in 7-fold cross-validation are 79.8% and 0.47, respectively, for the beta-turns. The overall prediction accuracy in 5-fold cross-validation is 61.0% for the gamma-turns. These results are significantly higher than the other algorithms in the prediction of beta- and gamma-turns using the same datasets. In addition, the 547 and 823 nonhomologous protein chains described by Fuchs and Alix (Fuchs and Alix Proteins: Struct Funct Bioinform 2005, 59, 828) are used for training and testing the predictive model of the beta- and gamma-turns, and better results are obtained. This algorithm may be helpful to improve the performance of protein turns' prediction. To ensure the ability of the SVM method to correctly classify beta-turn and non-beta-turn (gamma-turn and non-gamma-turn), the receiver operating characteristic threshold independent measure curves are provided. (c) 2008 Wiley Periodicals, Inc.

Characteristic phasic evolution of convulsive seizure in PCDH19-related epilepsy.

PubMed

Ikeda, Hiroko; Imai, Katsumi; Ikeda, Hitoshi; Shigematsu, Hideo; Takahashi, Yukitoshi; Inoue, Yushi; Higurashi, Norimichi; Hirose, Shinichi

2016-03-01

PCDH19-related epilepsy is a genetic disorder that was first described in 1971, then referred to as "epilepsy and mental retardation limited to females". PCDH19 has recently been identified as the responsible gene, but a detailed characterization of the seizure manifestation based on video-EEG recording is still limited. The purpose of this study was to elucidate features of the seizure semiology in children with PCDH19-related epilepsy. To do this, ictal video-EEG recordings of 26 convulsive seizures in three girls with PCDH19-related epilepsy were analysed. All seizures occurred in clusters, mainly during sleep accompanied by fever. The motor manifestations consisted of six sequential phases: "jerk", "reactive", "mild tonic", "fluttering", "mild clonic", and "postictal". Some phases were brief or lacking in some seizures, whereas others were long or pronounced. In the reactive phase, the patients looked fearful or startled with sudden jerks and turned over reactively. The tonic and clonic components were less intense compared with those of typical tonic-clonic seizures in other types of epilepsy. The fluttering phase was characterised initially by asymmetric, less rhythmic, and less synchronous tremulous movement and was then followed by the subtle clonic phase. Subtle oral automatism was observed in the postictal phase. The reactive, mild tonic, fluttering and mild clonic phases were most characteristic of seizures of PCDH19-related epilepsy. Ictal EEG started bilaterally and was symmetric in some patients but asymmetric in others. It showed asymmetric rhythmic discharges in some seizures at later phases. The electroclinical pattern of the phasic evolution of convulsive seizure suggests a focal onset seizure with secondary generalisation. Based on our findings, we propose that the six unique sequential phases in convulsive seizures suggest the diagnosis of PCDH19-related epilepsy when occurring in clusters with or without high fever in girls. [Published with video sequences online].

Learning by observation: insights from Williams syndrome.

PubMed

Foti, Francesca; Menghini, Deny; Mandolesi, Laura; Federico, Francesca; Vicari, Stefano; Petrosini, Laura

2013-01-01

Observing another person performing a complex action accelerates the observer's acquisition of the same action and limits the time-consuming process of learning by trial and error. Observational learning makes an interesting and potentially important topic in the developmental domain, especially when disorders are considered. The implications of studies aimed at clarifying whether and how this form of learning is spared by pathology are manifold. We focused on a specific population with learning and intellectual disabilities, the individuals with Williams syndrome. The performance of twenty-eight individuals with Williams syndrome was compared with that of mental age- and gender-matched thirty-two typically developing children on tasks of learning of a visuo-motor sequence by observation or by trial and error. Regardless of the learning modality, acquiring the correct sequence involved three main phases: a detection phase, in which participants discovered the correct sequence and learned how to perform the task; an exercise phase, in which they reproduced the sequence until performance was error-free; an automatization phase, in which by repeating the error-free sequence they became accurate and speedy. Participants with Williams syndrome beneficiated of observational training (in which they observed an actor detecting the visuo-motor sequence) in the detection phase, while they performed worse than typically developing children in the exercise and automatization phases. Thus, by exploiting competencies learned by observation, individuals with Williams syndrome detected the visuo-motor sequence, putting into action the appropriate procedural strategies. Conversely, their impaired performances in the exercise phases appeared linked to impaired spatial working memory, while their deficits in automatization phases to deficits in processes increasing efficiency and speed of the response. Overall, observational experience was advantageous for acquiring competencies, since it primed subjects' interest in the actions to be performed and functioned as a catalyst for executed action.

Single phase four pole/six pole motor

DOEpatents

Kirschbaum, Herbert S.

1984-01-01

A single phase alternating current electric motor is provided with a main stator winding having two coil groups each including the series connection of three coils. These coil groups can be connected in series for six pole operation and in parallel for four pole operation. The coils are approximately equally spaced around the periphery of the machine but are not of equal numbers of turns. The two coil groups are identically wound and spaced 180 mechanical degrees apart. One coil of each group has more turns and a greater span than the other two coils.

Synchronized excitability in a network enables generation of internal neuronal sequences

PubMed Central

Wang, Yingxue; Roth, Zachary; Pastalkova, Eva

2016-01-01

Hippocampal place field sequences are supported by sensory cues and network internal mechanisms. In contrast, sharp-wave (SPW) sequences, theta sequences, and episode field sequences are internally generated. The relationship of these sequences to memory is unclear. SPW sequences have been shown to support learning and have been assumed to also support episodic memory. Conversely, we demonstrate these SPW sequences were present in trained rats even after episodic memory was impaired and after other internal sequences – episode field and theta sequences – were eliminated. SPW sequences did not support memory despite continuing to ‘replay’ all task-related sequences – place- field and episode field sequences. Sequence replay occurred selectively during synchronous increases of population excitability -- SPWs. Similarly, theta sequences depended on the presence of repeated synchronized waves of excitability – theta oscillations. Thus, we suggest that either intermittent or rhythmic synchronized changes of excitability trigger sequential firing of neurons, which in turn supports learning and/or memory. DOI: http://dx.doi.org/10.7554/eLife.20697.001 PMID:27677848

Automatic Command Sequence Generation

NASA Technical Reports Server (NTRS)

Fisher, Forest; Gladded, Roy; Khanampompan, Teerapat

2007-01-01

Automatic Sequence Generator (Autogen) Version 3.0 software automatically generates command sequences for the Mars Reconnaissance Orbiter (MRO) and several other JPL spacecraft operated by the multi-mission support team. Autogen uses standard JPL sequencing tools like APGEN, ASP, SEQGEN, and the DOM database to automate the generation of uplink command products, Spacecraft Command Message Format (SCMF) files, and the corresponding ground command products, DSN Keywords Files (DKF). Autogen supports all the major multi-mission mission phases including the cruise, aerobraking, mapping/science, and relay mission phases. Autogen is a Perl script, which functions within the mission operations UNIX environment. It consists of two parts: a set of model files and the autogen Perl script. Autogen encodes the behaviors of the system into a model and encodes algorithms for context sensitive customizations of the modeled behaviors. The model includes knowledge of different mission phases and how the resultant command products must differ for these phases. The executable software portion of Autogen, automates the setup and use of APGEN for constructing a spacecraft activity sequence file (SASF). The setup includes file retrieval through the DOM (Distributed Object Manager), an object database used to store project files. This step retrieves all the needed input files for generating the command products. Depending on the mission phase, Autogen also uses the ASP (Automated Sequence Processor) and SEQGEN to generate the command product sent to the spacecraft. Autogen also provides the means for customizing sequences through the use of configuration files. By automating the majority of the sequencing generation process, Autogen eliminates many sequence generation errors commonly introduced by manually constructing spacecraft command sequences. Through the layering of commands into the sequence by a series of scheduling algorithms, users are able to rapidly and reliably construct the desired uplink command products. With the aid of Autogen, sequences may be produced in a matter of hours instead of weeks, with a significant reduction in the number of people on the sequence team. As a result, the uplink product generation process is significantly streamlined and mission risk is significantly reduced. Autogen is used for operations of MRO, Mars Global Surveyor (MGS), Mars Exploration Rover (MER), Mars Odyssey, and will be used for operations of Phoenix. Autogen Version 3.0 is the operational version of Autogen including the MRO adaptation for the cruise mission phase, and was also used for development of the aerobraking and mapping mission phases for MRO.

Four quadrant control circuit for a brushless three-phase dc motor

NASA Technical Reports Server (NTRS)

Nola, Frank J. (Inventor)

1987-01-01

A control circuit is provided for a brushless three-phase dc motor which affords four quadrant control from a single command. The control circuit probes acceleration of the motor in both clockwise and counterclockwise directions and braking and generation in both clockwise and counterclockwise directions. In addition to turning on individual transistors of the transistor pairs connected to the phase windings of the motor for 120 deg periods while the other transistor of that pair is off, the control circuit also provides, in a future mode of operation, turning the two transistors of each pair on and off alternately at a phase modulation frequency during such a 120 deg period. A feedback signal is derived which is proportional to the motor current and which has a polarity consistent with the command signal, such that negative feedback results.

Robust sensorimotor representation to physical interaction changes in humanoid motion learning.

PubMed

Shimizu, Toshihiko; Saegusa, Ryo; Ikemoto, Shuhei; Ishiguro, Hiroshi; Metta, Giorgio

2015-05-01

This paper proposes a learning from demonstration system based on a motion feature, called phase transfer sequence. The system aims to synthesize the knowledge on humanoid whole body motions learned during teacher-supported interactions, and apply this knowledge during different physical interactions between a robot and its surroundings. The phase transfer sequence represents the temporal order of the changing points in multiple time sequences. It encodes the dynamical aspects of the sequences so as to absorb the gaps in timing and amplitude derived from interaction changes. The phase transfer sequence was evaluated in reinforcement learning of sitting-up and walking motions conducted by a real humanoid robot and compatible simulator. In both tasks, the robotic motions were less dependent on physical interactions when learned by the proposed feature than by conventional similarity measurements. Phase transfer sequence also enhanced the convergence speed of motion learning. Our proposed feature is original primarily because it absorbs the gaps caused by changes of the originally acquired physical interactions, thereby enhancing the learning speed in subsequent interactions.

Can We Improve Structured Sequence Processing? Exploring the Direct and Indirect Effects of Computerized Training Using a Mediational Model

PubMed Central

Smith, Gretchen N. L.; Conway, Christopher M.; Bauernschmidt, Althea; Pisoni, David B.

2015-01-01

Recent research suggests that language acquisition may rely on domain-general learning abilities, such as structured sequence processing, which is the ability to extract, encode, and represent structured patterns in a temporal sequence. If structured sequence processing supports language, then it may be possible to improve language function by enhancing this foundational learning ability. The goal of the present study was to use a novel computerized training task as a means to better understand the relationship between structured sequence processing and language function. Participants first were assessed on pre-training tasks to provide baseline behavioral measures of structured sequence processing and language abilities. Participants were then quasi-randomly assigned to either a treatment group involving adaptive structured visuospatial sequence training, a treatment group involving adaptive non-structured visuospatial sequence training, or a control group. Following four days of sequence training, all participants were assessed with the same pre-training measures. Overall comparison of the post-training means revealed no group differences. However, in order to examine the potential relations between sequence training, structured sequence processing, and language ability, we used a mediation analysis that showed two competing effects. In the indirect effect, adaptive sequence training with structural regularities had a positive impact on structured sequence processing performance, which in turn had a positive impact on language processing. This finding not only identifies a potential novel intervention to treat language impairments but also may be the first demonstration that structured sequence processing can be improved and that this, in turn, has an impact on language processing. However, in the direct effect, adaptive sequence training with structural regularities had a direct negative impact on language processing. This unexpected finding suggests that adaptive training with structural regularities might potentially interfere with language processing. Taken together, these findings underscore the importance of pursuing designs that promote a better understanding of the mechanisms underlying training-related changes, so that regimens can be developed that help reduce these types of negative effects while simultaneously maximizing the benefits to outcome measures of interest. PMID:25946222

Can we improve structured sequence processing? Exploring the direct and indirect effects of computerized training using a mediational model.

PubMed

Smith, Gretchen N L; Conway, Christopher M; Bauernschmidt, Althea; Pisoni, David B

2015-01-01

Recent research suggests that language acquisition may rely on domain-general learning abilities, such as structured sequence processing, which is the ability to extract, encode, and represent structured patterns in a temporal sequence. If structured sequence processing supports language, then it may be possible to improve language function by enhancing this foundational learning ability. The goal of the present study was to use a novel computerized training task as a means to better understand the relationship between structured sequence processing and language function. Participants first were assessed on pre-training tasks to provide baseline behavioral measures of structured sequence processing and language abilities. Participants were then quasi-randomly assigned to either a treatment group involving adaptive structured visuospatial sequence training, a treatment group involving adaptive non-structured visuospatial sequence training, or a control group. Following four days of sequence training, all participants were assessed with the same pre-training measures. Overall comparison of the post-training means revealed no group differences. However, in order to examine the potential relations between sequence training, structured sequence processing, and language ability, we used a mediation analysis that showed two competing effects. In the indirect effect, adaptive sequence training with structural regularities had a positive impact on structured sequence processing performance, which in turn had a positive impact on language processing. This finding not only identifies a potential novel intervention to treat language impairments but also may be the first demonstration that structured sequence processing can be improved and that this, in turn, has an impact on language processing. However, in the direct effect, adaptive sequence training with structural regularities had a direct negative impact on language processing. This unexpected finding suggests that adaptive training with structural regularities might potentially interfere with language processing. Taken together, these findings underscore the importance of pursuing designs that promote a better understanding of the mechanisms underlying training-related changes, so that regimens can be developed that help reduce these types of negative effects while simultaneously maximizing the benefits to outcome measures of interest.

25 Years of GenBank

MedlinePlus

... this page please turn Javascript on. Unique DNA database has helped advance scientific discoveries worldwide Since its origin 25 years ago, the database of nucleic acid sequences known as GenBank has ...

Exploring the Nuclear Phase Diagram with Beam Energy Scans

NASA Astrophysics Data System (ADS)

Horvat, Stephen

2017-04-01

The nuclear phase diagram is mapped using beam energy scans of relativistic heavy-ion collisions. This mapping is possible because different collision energies develop along different trajectories through the phase diagram. High energy collisions will evolve though a crossover phase transition according to lattice QCD, but lower collision energies may traverse a first order phase transition. There are hints for this first order phase transition and its critical endpoint, but further measurements and theoretical guidance is needed. In addition to mapping the phase transition, beam energy scans allow us to see if we can turn off the signatures of deconfinement. If an observable is a real signature for the formation of the deconfined state called quark-gluon plasma, then it should turn off at sufficiently low collision energies. In this summary talk I will show the current state of the field using beam energy scan results from RHIC and SPS, I will show where precise theoretical guidance is needed for understanding recent measurements, and I will motivate the need for more data and new measurements from FAIR, NICA, RHIC, and the SPS.

Targeted therapy by combined inhibition of the RAF and mTOR kinases in malignant spindle cell neoplasm harboring the KIAA1549-BRAF fusion protein.

PubMed

Subbiah, Vivek; Westin, Shannon N; Wang, Kai; Araujo, Dejka; Wang, Wei-Lien; Miller, Vincent A; Ross, Jeffrey S; Stephens, Phillip J; Palmer, Gary A; Ali, Siraj M

2014-01-14

Oncologic patients who are extreme responders to molecularly targeted therapy provide an important opportunity to better understand the biologic basis of response and, in turn, inform clinical decision making. Malignant neoplasms with an uncertain histologic and immunohistochemical characterization present challenges both on initial diagnostic workups and then later in management, as current treatment algorithms are based on a morphologic diagnosis. Herein, we report a case of a difficult to characterize sarcoma-like lesion for which genomic profiling with clinical next generation sequencing (NGS) identified the molecular underpinnings of arrested progression(stable disease) under combination targeted therapy within a phase I clinical trial. Genomic profiling with clinical next generation sequencing was performed on the FoundationOne™ platform (Foundation Medicine, Cambridge MA). Histopathology and immunohistochemical studies were performed in the Department of Pathology, MD Anderson Cancer Center (Houston, TX). Treatment was administered in the context of a phase I clinical trial ClinicalTrials.gov Identifier: (NCT01187199). The histology of the tumor was that of a spindle cell neoplasm, grade 2 by FNCLCC standards. Immunohistochemical staining was positive for S100 and CD34. Genomic profiling identified the following alterations: a KIAA1549-BRAF gene fusion resulting from a tandem duplication event, a homozygous deletion of PTEN, and frameshift insertion/deletions in CDKN2A A68fs*51, SUFU E283fs*3, and MAP3K1 N325fs*3. The patient had a 25% reduction in tumor (RECIST v1.1) following combination therapy consisting of sorafenib, temsirolimus, and bevazicumab within a phase I clinical trial. The patient responded to combination targeted therapy that fortuitously targeted KIAA1549-BRAF and PTEN loss within a spindle cell neoplasm, as revealed by genomic profiling based on NGS. This is the first report of a tumor driven by a KIAA1549-BRAF fusion responding to sorafenib-based combination therapy.

A Logical OR Redundancy within the Asx-Pro-Asx-Gly Type 1 {Beta}-Turn Motif

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

Lee, Jihun; Dubey, Vikash Kumar; Longo, Lian M.

2008-04-19

Turn secondary structure is essential to the formation of globular protein architecture. Turn structures are, however, much more complex than either {alpha}-helix or {beta}-sheet, and the thermodynamics and folding kinetics are poorly understood. Type I {beta}-turns are the most common type of reverse turn, and they exhibit a statistical consensus sequence of Asx-Pro-Asx-Gly (where Asx is Asp or Asn). A comprehensive series of individual and combined Asx mutations has been constructed within three separate type I 3:5 G1 bulge {beta}-turns in human fibroblast growth factor-1, and their effects on structure, stability, and folding have been determined. The results show amore » fundamental logical OR relationship between the Asx residues in the motif, involving H-bond interactions with main-chain amides within the turn. These interactions can be modulated by additional interactions with residues adjacent to the turn at positions i + 4 and i + 6. The results show that the Asx residues in the turn motif make a substantial contribution to the overall stability of the protein, and the Asx logical OR relationship defines a redundant system that can compensate for deleterious point mutations. The results also show that the stability of the turn is unlikely to be the prime determinant of formation of turn structure in the folding transition state.« less

Bacterial expression of self-assembling peptide hydrogelators

NASA Astrophysics Data System (ADS)

Sonmez, Cem

For tissue regeneration and drug delivery applications, various architectures are explored to serve as biomaterial tools. Via de novo design, functional peptide hydrogel materials have been developed as scaffolds for biomedical applications. The objective of this study is to investigate bacterial expression as an alternative method to chemical synthesis for the recombinant production of self-assembling peptides that can form rigid hydrogels under physiological conditions. The Schneider and Pochan Labs have designed and characterized a 20 amino acid beta-hairpin forming amphiphilic peptide containing a D-residue in its turn region (MAX1). As a result, this peptide must be prepared chemically. Peptide engineering, using the sequence of MAX1 as a template, afforded a small family of peptides for expression (EX peptides) that have different turn sequences consisting of natural amino acids and amenable to bacterial expression. Each sequence was initially chemically synthesized to quickly assess the material properties of its corresponding gel. One model peptide EX1, was chosen to start the bacterial expression studies. DNA constructs facilitating the expression of EX1 were designed in such that the peptide could be expressed with different fusion partners and subsequently cleaved by enzymatic or chemical means to afford the free peptide. Optimization studies were performed to increase the yield of pure peptide that ultimately allowed 50 mg of pure peptide to be harvested from one liter of culture, providing an alternate means to produce this hydrogel-forming peptide. Recombinant production of other self-assembling hairpins with different turn sequences was also successful using this optimized protocol. The studies demonstrate that new beta-hairpin self-assembling peptides that are amenable to bacterial production and form rigid hydrogels at physiological conditions can be designed and produced by fermentation in good yield at significantly reduced cost when compared to chemical synthesis.

In the Shadow of Three Mile Island.

ERIC Educational Resources Information Center

Blair-Clough, Ida; Wheeler, Brenda

1979-01-01

Describes how teachers turned the reality of the nuclear reactor incident at Three Mile Island into a learning experience for children by recreating the sequence of events through creative dramatics. (CM)

A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments.

PubMed

Quinn, Terrance; Sinkala, Zachariah

2014-01-01

We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature.

Family ties of WR to LBV nebulae yielding clues for stellar evolution

NASA Astrophysics Data System (ADS)

Weis, K.

Luminous Blue Variables (LBVs) are stars is a transitional phase massive stars may enter while evolving from main-sequence to Wolf-Rayet stars. The to LBVs intrinsic photometric variability is based on the modulation of the stellar spectrum. Within a few years the spectrum shifts from OB to AF type and back. During their cool phase LBVs are close to the Humphreys-Davidson (equivalent to Eddington/Omega-Gamma) limit. LBVs have a rather high mass loss rate, with stellar winds that are fast in the hot and slower in the cool phase of an LBV. These alternating wind velocities lead to the formation of LBV nebulae by wind-wind interactions. A nebula can also be formed in a spontaneous giant eruption in which larger amounts of mass are ejected. LBV nebulae are generally small (< 5 pc) mainly gaseous circumstellar nebulae, with a rather large fraction of LBV nebulae being bipolar. After the LBV phase the star will turn into a Wolf-Rayet star, but note that not all WR stars need to have passed the LBV phase. Some follow from the RSG and the most massive directly from the MS phase. In general WRs have a large mass loss and really fast stellar winds. The WR wind may interact with winds of earlier phases (MS, RSG) to form WR nebulae. As for WR with LBV progenitors the scenario might be different, here no older wind is present but an LBV nebula! The nature of WR nebulae are therefore manifold and in particular the connection (or family ties) of WR to LBV nebulae is important to understand the transition between these two phases, the evolution of massive stars, their winds, wind-wind and wind-nebula interactions. Looking at the similarities and differences of LBV and WR nebula, figuring what is a genuine LBV and WR nebula are the basic question addressed in the analysis presented here.

Charge pattern matching as a ‘fuzzy’ mode of molecular recognition for the functional phase separations of intrinsically disordered proteins

NASA Astrophysics Data System (ADS)

Lin, Yi-Hsuan; Brady, Jacob P.; Forman-Kay, Julie D.; Chan, Hue Sun

2017-11-01

Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is currently known about the molecular recognition mechanisms for distributing different IDP sequences into various cellular membraneless compartments. Pertinent physics was addressed recently by applying random-phase-approximation (RPA) polymer theory to electrostatics, which is a major energetic component governing IDP phase properties. RPA accounts for charge patterns and thus has advantages over Flory-Huggins (FH) and Overbeek-Voorn mean-field theories. To make progress toward deciphering the phase behaviors of multiple IDP sequences, the RPA formulation for one IDP species plus solvent is hereby extended to treat polyampholyte solutions containing two IDP species plus solvent. The new formulation generally allows for binary coexistence of two phases, each containing a different set of volume fractions ({φ }1,{φ }2) for the two different IDP sequences. The asymmetry between the two predicted coexisting phases with regard to their {φ }1/{φ }2 ratios for the two sequences increases with increasing mismatch between their charge patterns. This finding points to a multivalent, stochastic, ‘fuzzy’ mode of molecular recognition that helps populate various IDP sequences differentially into separate phase compartments. An intuitive illustration of this trend is provided by FH models, whereby a hypothetical case of ternary coexistence is also explored. Augmentations of the present RPA theory with a relative permittivity {ɛ }{{r}}(φ ) that depends on IDP volume fraction φ ={φ }1+{φ }2 lead to higher propensities to phase separate, in line with the case with one IDP species we studied previously. Notably, the cooperative, phase-separation-enhancing effects predicted by the prescriptions for {ɛ }{{r}}(φ ) we deem physically plausible are much more prominent than that entailed by common effective medium approximations based on Maxwell Garnett and Bruggeman mixing formulas. Ramifications of our findings on further theoretical development for IDP phase separation are discussed.

Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments.

PubMed

Zheng, Ce; Kurgan, Lukasz

2008-10-10

beta-turn is a secondary protein structure type that plays significant role in protein folding, stability, and molecular recognition. To date, several methods for prediction of beta-turns from protein sequences were developed, but they are characterized by relatively poor prediction quality. The novelty of the proposed sequence-based beta-turn predictor stems from the usage of a window based information extracted from four predicted three-state secondary structures, which together with a selected set of position specific scoring matrix (PSSM) values serve as an input to the support vector machine (SVM) predictor. We show that (1) all four predicted secondary structures are useful; (2) the most useful information extracted from the predicted secondary structure includes the structure of the predicted residue, secondary structure content in a window around the predicted residue, and features that indicate whether the predicted residue is inside a secondary structure segment; (3) the PSSM values of Asn, Asp, Gly, Ile, Leu, Met, Pro, and Val were among the top ranked features, which corroborates with recent studies. The Asn, Asp, Gly, and Pro indicate potential beta-turns, while the remaining four amino acids are useful to predict non-beta-turns. Empirical evaluation using three nonredundant datasets shows favorable Q total, Q predicted and MCC values when compared with over a dozen of modern competing methods. Our method is the first to break the 80% Q total barrier and achieves Q total = 80.9%, MCC = 0.47, and Q predicted higher by over 6% when compared with the second best method. We use feature selection to reduce the dimensionality of the feature vector used as the input for the proposed prediction method. The applied feature set is smaller by 86, 62 and 37% when compared with the second and two third-best (with respect to MCC) competing methods, respectively. Experiments show that the proposed method constitutes an improvement over the competing prediction methods. The proposed prediction model can better discriminate between beta-turns and non-beta-turns due to obtaining lower numbers of false positive predictions. The prediction model and datasets are freely available at http://biomine.ece.ualberta.ca/BTNpred/BTNpred.html.

Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments

PubMed Central

Zheng, Ce; Kurgan, Lukasz

2008-01-01

Background β-turn is a secondary protein structure type that plays significant role in protein folding, stability, and molecular recognition. To date, several methods for prediction of β-turns from protein sequences were developed, but they are characterized by relatively poor prediction quality. The novelty of the proposed sequence-based β-turn predictor stems from the usage of a window based information extracted from four predicted three-state secondary structures, which together with a selected set of position specific scoring matrix (PSSM) values serve as an input to the support vector machine (SVM) predictor. Results We show that (1) all four predicted secondary structures are useful; (2) the most useful information extracted from the predicted secondary structure includes the structure of the predicted residue, secondary structure content in a window around the predicted residue, and features that indicate whether the predicted residue is inside a secondary structure segment; (3) the PSSM values of Asn, Asp, Gly, Ile, Leu, Met, Pro, and Val were among the top ranked features, which corroborates with recent studies. The Asn, Asp, Gly, and Pro indicate potential β-turns, while the remaining four amino acids are useful to predict non-β-turns. Empirical evaluation using three nonredundant datasets shows favorable Qtotal, Qpredicted and MCC values when compared with over a dozen of modern competing methods. Our method is the first to break the 80% Qtotal barrier and achieves Qtotal = 80.9%, MCC = 0.47, and Qpredicted higher by over 6% when compared with the second best method. We use feature selection to reduce the dimensionality of the feature vector used as the input for the proposed prediction method. The applied feature set is smaller by 86, 62 and 37% when compared with the second and two third-best (with respect to MCC) competing methods, respectively. Conclusion Experiments show that the proposed method constitutes an improvement over the competing prediction methods. The proposed prediction model can better discriminate between β-turns and non-β-turns due to obtaining lower numbers of false positive predictions. The prediction model and datasets are freely available at . PMID:18847492

Workshop on the Design and Processing of Materials by Biomimicking Held in Seattle, Washington on 2-4 April 1991

DTIC Science & Technology

1991-11-01

These materials feature repeating stem-turn elements composed of 1-strands and amino acids predicted to participate in 1-hairpin formation. The...highly ordered crystalline material. Presently we are studying: (i) the effects of amino acid sequence on 1-turn formation, (ii) the influence of stem...length and amino acid composition on chain folding and materials properties, and (iii) the potential for biological incorporation of unnatural amino

Inertial oscillation of a vertical rotating draft with application to a supercell storm

NASA Technical Reports Server (NTRS)

Costen, Robert C.; Stock, Larry V.

1992-01-01

An analytic model (vertical rotating draft) which includes the gross features of a supercell storm on an f-plane, undergoes an inertial oscillation that appears to have been overlooked in previous analytic and numerical models. The oscillation is nonlinear and consists of a long quiescent phase and a short intense phase. During the intense phase, the rotating draft has the following features of a supercell: the diameter of the core contracts as it spins up and expands as it spins down; if vertical wind shear is included, the track of the rotating draft turns to the right (an anticyclonic rotating draft turns to the left); this turning point is followed by a predominantly upward flow; and the horizontal pressure gradient is very small (a property of most tornadoless supercells). The rapid spin-up during the intense phase and the high Rossby numbers obtainable establish the ability of the Coriolis force to spin up single cyclonic or anticyclonic supercells by means of this inertial oscillation. This surprising result has implications for numerical supercell simulations, which generally do not rely on the Coriolis force as a source of rotation. The physics and mathematics of the inertial oscillation are given, and the solution is applied to a documented supercell.

A 63 K phase change unit integrating with pulse tube cryocoolers

NASA Astrophysics Data System (ADS)

Chunhui, Kong; Liubiao, Chen; Sixue, Liu; Yuan, Zhou; Junjie, Wang

2017-02-01

This article presents the design and computer model results of an integrated cooler system which consists of a single stage pulse tube cryocooler integrated with a small amount of a phase change material. A cryogenic thermal switch was used to thermally connect the phase change unit to the cold end of the cryocooler. During heat load operation, the cryogenic thermal switch is turned off to avoid vibrations. The phase change unit absorbs heat loads by melting a substance in a constant pressure-temperature-volume process. Once the substance has been melted, the cryogenic thermal turned on, the cryocooler can then refreeze the material. Advantages of this type of cooler are no vibrations during sensor operations; the ability to absorb increased heat loads; potentially longer system lifetime; and a lower mass, volume and cost. A numerical model was constructed from derived thermodynamic relationships for the cooling/heating and freezing/melting processes.

Kinematics of swimming of the manta ray: three-dimensional analysis of open-water maneuverability.

PubMed

Fish, Frank E; Kolpas, Allison; Crossett, Andrew; Dudas, Michael A; Moored, Keith W; Bart-Smith, Hilary

2018-03-22

For aquatic animals, turning maneuvers represent a locomotor activity that may not be confined to a single coordinate plane, making analysis difficult, particularly in the field. To measure turning performance in a three-dimensional space for the manta ray ( Mobula birostris ), a large open-water swimmer, scaled stereo video recordings were collected. Movements of the cephalic lobes, eye and tail base were tracked to obtain three-dimensional coordinates. A mathematical analysis was performed on the coordinate data to calculate the turning rate and curvature (1/turning radius) as a function of time by numerically estimating the derivative of manta trajectories through three-dimensional space. Principal component analysis was used to project the three-dimensional trajectory onto the two-dimensional turn. Smoothing splines were applied to these turns. These are flexible models that minimize a cost function with a parameter controlling the balance between data fidelity and regularity of the derivative. Data for 30 sequences of rays performing slow, steady turns showed the highest 20% of values for the turning rate and smallest 20% of turn radii were 42.65±16.66 deg s -1 and 2.05±1.26 m, respectively. Such turning maneuvers fall within the range of performance exhibited by swimmers with rigid bodies. © 2018. Published by The Company of Biologists Ltd.

Measurement of 13C chemical shift tensor principal values with a magic-angle turning experiment.

PubMed

Hu, J Z; Orendt, A M; Alderman, D W; Pugmire, R J; Ye, C; Grant, D M

1994-08-01

The magic-angle turning (MAT) experiment introduced by Gan is developed into a powerful and routine method for measuring the principal values of 13C chemical shift tensors in powdered solids. A large-volume MAT probe with stable rotation frequencies down to 22 Hz is described. A triple-echo MAT pulse sequence is introduced to improve the quality of the two-dimensional baseplane. It is shown that measurements of the principal values of chemical shift tensors in complex compounds can be enhanced by using either short contact times or dipolar dephasing pulse sequences to isolate the powder patterns from protonated or non-protonated carbons, respectively. A model compound, 1,2,3-trimethoxybenzene, is used to demonstrate these techniques, and the 13C principal values in 2,3-dimethylnaphthalene and Pocahontas coal are reported as typical examples.

Deciding alternative left turn signal phases using expert systems

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

Chang, E.C.P.

1988-01-01

The Texas Transportation Institute (TTI) conducted a study to investigate the feasibility of applying artificial intelligence (AI) technology and expert systems (ES) design concepts to a traffic engineering problem. Prototype systems were developed to analyze user input, evaluate various reasoning, and suggest suitable left turn phase treatment. These systems were developed using AI programming tools on IBM PC/XT/AT-compatible microcomputers. Two slightly different systems were designed using AI languages; another was built with a knowledge engineering tool. These systems include the PD PROLOG and TURBO PROLOG AI programs, as well as the INSIGHT Production Rule Language.

Single phase four pole/six pole motor

DOEpatents

Kirschbaum, H.S.

1984-10-09

A single phase alternating current electric motor is provided with a main stator winding having two coil groups each including the series connection of three coils. These coil groups can be connected in series for six pole operation and in parallel for four pole operation. The coils are approximately equally spaced around the periphery of the machine but are not of equal numbers of turns. The two coil groups are identically wound and spaced 180 mechanical degrees apart. One coil of each group has more turns and a greater span than the other two coils. 10 figs.

THE QUENCHING TIMESCALE AND QUENCHING RATE OF GALAXIES

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

Lian, Jianhui; Kong, Xu; Yan, Renbin

2016-11-20

The average star formation rate (SFR) in galaxies has been declining since the redshift of 2. A fraction of galaxies quench and become quiescent. We constrain two key properties of the quenching process: the quenching timescale and the quenching rate among galaxies. We achieve this by analyzing the galaxy number density profile in NUV- u color space and the distribution in NUV- u versus u - i color–color diagram with a simple toy-model framework. We focus on galaxies in three mass bins between 10{sup 10} and 10{sup 10.6} M {sub ⊙}. In the NUV- u versus u - i color–colormore » diagram, the red u - i galaxies exhibit a different slope from the slope traced by the star-forming galaxies. This angled distribution and the number density profile of galaxies in NUV- u space strongly suggest that the decline of the SFR in galaxies has to accelerate before they turn quiescent. We model this color–color distribution with a two-phase exponential decline star formation history. The models with an e-folding time in the second phase (the quenching phase) of 0.5 Gyr best fit the data. We further use the NUV- u number density profile to constrain the quenching rate among star-forming galaxies as a function of mass. Adopting an e-folding time of 0.5 Gyr in the second phase (or the quenching phase), we found the quenching rate to be 19%/Gyr, 25%/Gyr and 33%/Gyr for the three mass bins. These are upper limits of the quenching rate as the transition zone could also be populated by rejuvenated red-sequence galaxies.« less

Using waveform cross correlation for automatic recovery of aftershock sequences

NASA Astrophysics Data System (ADS)

Bobrov, Dmitry; Kitov, Ivan; Rozhkov, Mikhail

2017-04-01

Aftershock sequences of the largest earthquakes are difficult to recover. There can be several hundred mid-sized aftershocks per hour within a few hundred km from each other recorded by the same stations. Moreover, these events generate thousands of reflected/refracted phases having azimuth and slowness close to those from the P-waves. Therefore, aftershock sequences with thousands of events represent a major challenge for automatic and interactive processing at the International Data Centre (IDC) of the Comprehensive Nuclear-Test-Ban Organization (CTBTO). Standard methods of detection and phase association do not use all information contained in signals. As a result, wrong association of the first and later phases, both regular and site specific, produces enormous number of wrong event hypotheses and destroys valid event hypotheses in automatic IDC processing. In turn, the IDC analysts have to reject false and recreate valid hypotheses wasting precious human resources. At the current level of the IDC catalogue completeness, the method of waveform cross correlation (WCC) can resolve most of detection and association problems fully utilizing the similarity of waveforms generated by aftershocks. Array seismic stations of the International monitoring system (IMS) can enhance the performance of the WCC method: reduce station-specific detection thresholds, allow accurate estimate of signal attributes, including relative magnitude, and effectively suppress irrelevant arrivals. We have developed and tested a prototype of an aftershock tool matching all IDC processing requirements and merged it with the current IDC pipeline. This tool includes creation of master events consisting of real or synthetic waveform templates at ten and more IMS stations; cross correlation (CC) of real-time waveforms with these templates, association of arrivals detected at CC-traces in event hypotheses; building events matching the IDC quality criteria; and resolution of conflicts between events hypotheses created by neighboring master-events. The final cross correlation standard event lists (XSEL) is a start point for interactive analysis with standard tools. We present select results for the biggest earthquakes, like Sumatra 2004 and Tohoku 2011, as well as for several smaller events with hundreds of aftershocks. The sensitivity and resolution of the aftershock tool is demonstrated on the example of mb=2.2 aftershock found after the September 9, 2016 DPRK test.

Molecular Structure and Sequence in Complex Coacervates

NASA Astrophysics Data System (ADS)

Sing, Charles; Lytle, Tyler; Madinya, Jason; Radhakrishna, Mithun

Oppositely-charged polyelectrolytes in aqueous solution can undergo associative phase separation, in a process known as complex coacervation. This results in a polyelectrolyte-dense phase (coacervate) and polyelectrolyte-dilute phase (supernatant). There remain challenges in understanding this process, despite a long history in polymer physics. We use Monte Carlo simulation to demonstrate that molecular features (charge spacing, size) play a crucial role in governing the equilibrium in coacervates. We show how these molecular features give rise to strong monomer sequence effects, due to a combination of counterion condensation and correlation effects. We distinguish between structural and sequence-based correlations, which can be designed to tune the phase diagram of coacervation. Sequence effects further inform the physical understanding of coacervation, and provide the basis for new coacervation models that take monomer-level features into account.

Quantized phase coding and connected region labeling for absolute phase retrieval.

PubMed

Chen, Xiangcheng; Wang, Yuwei; Wang, Yajun; Ma, Mengchao; Zeng, Chunnian

2016-12-12

This paper proposes an absolute phase retrieval method for complex object measurement based on quantized phase-coding and connected region labeling. A specific code sequence is embedded into quantized phase of three coded fringes. Connected regions of different codes are labeled and assigned with 3-digit-codes combining the current period and its neighbors. Wrapped phase, more than 36 periods, can be restored with reference to the code sequence. Experimental results verify the capability of the proposed method to measure multiple isolated objects.

Effects of Sequences of Cognitions on Group Performance Over Time

PubMed Central

Molenaar, Inge; Chiu, Ming Ming

2017-01-01

Extending past research showing that sequences of low cognitions (low-level processing of information) and high cognitions (high-level processing of information through questions and elaborations) influence the likelihoods of subsequent high and low cognitions, this study examines whether sequences of cognitions are related to group performance over time; 54 primary school students (18 triads) discussed and wrote an essay about living in another country (32,375 turns of talk). Content analysis and statistical discourse analysis showed that within each lesson, groups with more low cognitions or more sequences of low cognition followed by high cognition added more essay words. Groups with more high cognitions, sequences of low cognition followed by low cognition, or sequences of high cognition followed by an action followed by low cognition, showed different words and sequences, suggestive of new ideas. The links between cognition sequences and group performance over time can inform facilitation and assessment of student discussions. PMID:28490854

Effects of Sequences of Cognitions on Group Performance Over Time.

PubMed

Molenaar, Inge; Chiu, Ming Ming

2017-04-01

Extending past research showing that sequences of low cognitions (low-level processing of information) and high cognitions (high-level processing of information through questions and elaborations) influence the likelihoods of subsequent high and low cognitions, this study examines whether sequences of cognitions are related to group performance over time; 54 primary school students (18 triads) discussed and wrote an essay about living in another country (32,375 turns of talk). Content analysis and statistical discourse analysis showed that within each lesson, groups with more low cognitions or more sequences of low cognition followed by high cognition added more essay words. Groups with more high cognitions, sequences of low cognition followed by low cognition, or sequences of high cognition followed by an action followed by low cognition, showed different words and sequences, suggestive of new ideas. The links between cognition sequences and group performance over time can inform facilitation and assessment of student discussions.

A novel architecture of recovered data comparison for high speed clock and data recovery

NASA Astrophysics Data System (ADS)

Gao, Susan; Li, Fei; Wang, Zhigong; Cui, Hongliang

2005-05-01

A clock and data recovery (CDR) circuit is one of the crucial blocks in high-speed serial link communication systems. The data received in these systems are asynchronous and noisy, requiring that a clock be extracted to allow synchronous operations. Furthermore, the data must be "retimed" so that the jitter accumulated during transmission is removed. This paper presents a novel architecture of CDR, which is very tolerant to long sequences of serial ones or zeros and also robust to occasional long absence of transitions. The design is based on the fact that a basic clock recovery having a clock recovery circuit (CRC) and a data decision circuit separately would generate a high jitter clock when the received non-return-to-zero (NRZ) data with long sequences of ones or zeros. To eliminate this drawback, the proposed architecture incorporates a data circuit decision circuit within the phase-locked loop (PLL) CRC. Other than this, a new phase detector (PD) is also proposed, which was easy to accomplish and robust at high speed. This PD is functional with a random input and automatically turns to disable during both the locked state and long absence of transitions. The voltage-controlled oscillator (VCO) is also designed delicately to suppress the jitter. Due to the high stability, the jitter is highly reduced when the loop is locked. The simulation results of such CDR working at 1.25Gb/s particularly for 1000BASE-X Gigabit Ethernet by using TSMC 0.25μm technology are presented to prove the feasibility of this architecture. One more CDR based on edge detection architecture is also built in the circuit for performance comparisons.

Polysaccharide intercellular adhesin in biofilm: structural and regulatory aspects

PubMed Central

Arciola, Carla Renata; Campoccia, Davide; Ravaioli, Stefano; Montanaro, Lucio

2015-01-01

Staphylococcus aureus and Staphylococcus epidermidis are the leading etiologic agents of implant-related infections. Biofilm formation is the main pathogenetic mechanism leading to the chronicity and irreducibility of infections. The extracellular polymeric substances of staphylococcal biofilms are the polysaccharide intercellular adhesin (PIA), extracellular-DNA, proteins, and amyloid fibrils. PIA is a poly-β(1-6)-N-acetylglucosamine (PNAG), partially deacetylated, positively charged, whose synthesis is mediated by the icaADBC locus. DNA sequences homologous to ica locus are present in many coagulase-negative staphylococcal species, among which S. lugdunensis, however, produces a biofilm prevalently consisting of proteins. The product of icaA is an N-acetylglucosaminyltransferase that synthetizes PIA oligomers from UDP-N-acetylglucosamine. The product of icaD gives optimal efficiency to IcaA. The product of icaC is involved in the externalization of the nascent polysaccharide. The product of icaB is an N-deacetylase responsible for the partial deacetylation of PIA. The expression of ica locus is affected by environmental conditions. In S. aureus and S. epidermidis ica-independent alternative mechanisms of biofilm production have been described. S. epidermidis and S. aureus undergo to a phase variation for the biofilm production that has been ascribed, in turn, to the transposition of an insertion sequence in the icaC gene or to the expansion/contraction of a tandem repeat naturally harbored within icaC. A role is played by the quorum sensing system, which negatively regulates biofilm formation, favoring the dispersal phase that disseminates bacteria to new infection sites. Interfering with the QS system is a much debated strategy to combat biofilm-related infections. In the search of vaccines against staphylococcal infections deacetylated PNAG retained on the surface of S. aureus favors opsonophagocytosis and is a potential candidate for immune-protection. PMID:25713785

HUBBLE TARANTULA TREASURY PROJECT. V. THE STAR CLUSTER HODGE 301: THE OLD FACE OF 30 DORADUS

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

Cignoni, M.; Sabbi, E.; Marel, R. P. van der

Based on color–magnitude diagrams (CMDs) from the Hubble Space Telescope  Hubble Tarantula Treasury Project (HTTP) survey, we present the star formation history of Hodge 301, the oldest star cluster in the Tarantula Nebula. The HTTP photometry extends faint enough to reach, for the first time, the cluster pre-main sequence (PMS) turn-on, where the PMS joins the main sequence. Using the location of this feature, along with synthetic CMDs generated with the latest PARSEC models, we find that Hodge 301 is older than previously thought, with an age between 26.5 and 31.5 Myr. From this age, we also estimate that between 38 andmore » 61 Type II supernovae exploded in the region. The same age is derived from the main sequence turn-off, whereas the age derived from the post-main sequence stars is younger and between 20 and 25 Myr. Other relevant parameters are a total stellar mass of ≈8800 ± 800  M {sub ⊙} and average reddening E ( B − V ) ≈ 0.22–0.24 mag, with a differential reddening δE ( B − V ) ≈ 0.04 mag.« less

Hubble Tarantula Treasury Project V. The Star Cluster Hodge 301: The Old Face of 30 Doradus

NASA Astrophysics Data System (ADS)

Cignoni, M.; Sabbi, E.; van der Marel, R. P.; Lennon, D. J.; Tosi, M.; Grebel, E. K.; Gallagher, J. S., III; Aloisi, A.; de Marchi, G.; Gouliermis, D. A.; Larsen, S.; Panagia, N.; Smith, L. J.

2016-12-01

Based on color-magnitude diagrams (CMDs) from the Hubble Space Telescope Hubble Tarantula Treasury Project (HTTP) survey, we present the star formation history of Hodge 301, the oldest star cluster in the Tarantula Nebula. The HTTP photometry extends faint enough to reach, for the first time, the cluster pre-main sequence (PMS) turn-on, where the PMS joins the main sequence. Using the location of this feature, along with synthetic CMDs generated with the latest PARSEC models, we find that Hodge 301 is older than previously thought, with an age between 26.5 and 31.5 Myr. From this age, we also estimate that between 38 and 61 Type II supernovae exploded in the region. The same age is derived from the main sequence turn-off, whereas the age derived from the post-main sequence stars is younger and between 20 and 25 Myr. Other relevant parameters are a total stellar mass of ≈8800 ± 800 M ⊙ and average reddening E(B - V) ≈ 0.22-0.24 mag, with a differential reddening δE(B - V) ≈ 0.04 mag. Based on observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by AURA Inc., under NASA contract NAS 5-26555.

Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures

PubMed Central

2010-01-01

Background β-turns are secondary structure elements usually classified as coil. Their prediction is important, because of their role in protein folding and their frequent occurrence in protein chains. Results We have developed a novel method that predicts β-turns and their types using information from multiple sequence alignments, predicted secondary structures and, for the first time, predicted dihedral angles. Our method uses support vector machines, a supervised classification technique, and is trained and tested on three established datasets of 426, 547 and 823 protein chains. We achieve a Matthews correlation coefficient of up to 0.49, when predicting the location of β-turns, the highest reported value to date. Moreover, the additional dihedral information improves the prediction of β-turn types I, II, IV, VIII and "non-specific", achieving correlation coefficients up to 0.39, 0.33, 0.27, 0.14 and 0.38, respectively. Our results are more accurate than other methods. Conclusions We have created an accurate predictor of β-turns and their types. Our method, called DEBT, is available online at http://comp.chem.nottingham.ac.uk/debt/. PMID:20673368

Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures.

PubMed

Kountouris, Petros; Hirst, Jonathan D

2010-07-31

Beta-turns are secondary structure elements usually classified as coil. Their prediction is important, because of their role in protein folding and their frequent occurrence in protein chains. We have developed a novel method that predicts beta-turns and their types using information from multiple sequence alignments, predicted secondary structures and, for the first time, predicted dihedral angles. Our method uses support vector machines, a supervised classification technique, and is trained and tested on three established datasets of 426, 547 and 823 protein chains. We achieve a Matthews correlation coefficient of up to 0.49, when predicting the location of beta-turns, the highest reported value to date. Moreover, the additional dihedral information improves the prediction of beta-turn types I, II, IV, VIII and "non-specific", achieving correlation coefficients up to 0.39, 0.33, 0.27, 0.14 and 0.38, respectively. Our results are more accurate than other methods. We have created an accurate predictor of beta-turns and their types. Our method, called DEBT, is available online at http://comp.chem.nottingham.ac.uk/debt/.

Bodily-visual practices and turn continuation

PubMed Central

Ford, Cecilia E.; Thompson, Sandra A.; Drake, Veronika

2012-01-01

This paper considers points in turn construction where conversation researchers have shown that talk routinely continues beyond possible turn completion, but where we find bodily-visual behavior doing such turn extension work. The bodily-visual behaviors we examine share many features with verbal turn extensions, but we argue that embodied movements have distinct properties that make them well-suited for specific kinds of social action, including stance display and by-play in sequences framed as subsidiary to a simultaneous and related verbal exchange. Our study is in line with a research agenda taking seriously the point made by Goodwin (2000a, b, 2003), Hayashi (2003, 2005), Iwasaki (2009), and others that scholars seeking to account for practices in language and social interaction do themselves a disservice if they privilege the verbal dimension; rather, as suggested in Stivers/Sidnell (2005), each semiotic system/modality, while coordinated with others, has its own organization. With the current exploration of bodily-visual turn extensions, we hope to contribute to a growing understanding of how these different modes of organization are managed concurrently and in concert by interactants in carrying out their everyday social actions. PMID:23526861

Coupled Metagenomic and Chemical Analyses of Degrading Fungal Necromass and Implications for Fungal contributions to Stable Soil Organic Carbon

NASA Astrophysics Data System (ADS)

Egerton-Warburton, L. M.; Schreiner, K. M.; Morgan, B. S. T.; Schultz, J.; Blair, N. E.

2016-12-01

Fungi comprise a significant portion of total soil biomass, the turnover of which must represent a dominant flux within the soil carbon cycle. Fungal organic carbon (OC) can turn over on time scales of days to months, but this process is poorly understood. Here, we examined temporal changes in the chemical and microbial community composition of fungal necromass during a 2-month decomposition experiment in which Fusarium avenaceum (a common saprophyte) was exposed to a natural soil microbial community. Over the course of the experiment, residual fungal necromass was harvested and analyzed using FTIR and thermochemolysis-GCMS to examine chemical changes in the tissue. In addition, genomic DNA was extracted from tissues, amplified with barcoded ITS primers, and sequenced using the high-throughput Illumina platform to examine changes in microbial community composition. Up to 80% of the fungal necromass turned over in the first week. This rapid degradation phase corresponded to colonization of the necromass by known chitinolytic soil fungi including Mortierella species. Members of the Zygomycota and Ascomycota were among the dominant fungal groups involved in degradation with very small contributions from Basidiomycota. At the end of the 2-month degradation, only 15% of the original necromass remained. The residual material was rich in amide and C-O moieties which is consistent with previous work predicting that peptidoglycans are the main residual product from microbial tissue degradation. Straight-chain fatty acids exhibited varying degradation profiles, with some fatty acids (e.g. C16, C18:1) degrading more rapidly than bulk tissue while others maintained steady concentrations relative to bulk OC (C18) or increased in concentration throughout the degradation sequence (C24). These results indicate that the turnover of fungal necromass has the potential to rapidly and significantly influence a variety of soil OC properties including C/N ratios, lipid biomarker distributions, and OC turnover times.

Diamond turning machine controller implementation

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

Garrard, K.P.; Taylor, L.W.; Knight, B.F.

The standard controller for a Pnuemo ASG 2500 Diamond Turning Machine, an Allen Bradley 8200, has been replaced with a custom high-performance design. This controller consists of four major components. Axis position feedback information is provided by a Zygo Axiom 2/20 laser interferometer with 0.1 micro-inch resolution. Hardware interface logic couples the computers digital and analog I/O channels to the diamond turning machine`s analog motor controllers, the laser interferometer, and other machine status and control information. It also provides front panel switches for operator override of the computer controller and implement the emergency stop sequence. The remaining two components, themore » control computer hardware and software, are discussed in detail below.« less

Electromagnetic Gun With Commutated Coils

NASA Technical Reports Server (NTRS)

Elliott, David G.

1991-01-01

Proposed electromagnetic gun includes electromagnet coil, turns of which commutated in sequence along barrel. Electrical current fed to two armatures by brushes sliding on bus bars in barrel. Interaction between armature currents and magnetic field from coil produces force accelerating armature, which in turn, pushes on projectile. Commutation scheme chosen so magnetic field approximately coincides and moves with cylindrical region defined by armatures. Scheme has disadvantage of complexity, but in return, enables designer to increase driving magnetic field without increasing armature current. Attainable muzzle velocity increased substantially.

Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers

PubMed Central

Quiroz, Felipe García; Chilkoti, Ashutosh

2015-01-01

Proteins and synthetic polymers that undergo aqueous phase transitions mediate self-assembly in nature and in man-made material systems. Yet little is known about how the phase behaviour of a protein is encoded in its amino acid sequence. Here, by synthesizing intrinsically disordered, repeat proteins to test motifs that we hypothesized would encode phase behaviour, we show that the proteins can be designed to exhibit tunable lower or upper critical solution temperature (LCST and UCST, respectively) transitions in physiological solutions. We also show that mutation of key residues at the repeat level abolishes phase behaviour or encodes an orthogonal transition. Furthermore, we provide heuristics to identify, at the proteome level, proteins that might exhibit phase behaviour and to design novel protein polymers consisting of biologically active peptide repeats that exhibit LCST or UCST transitions. These findings set the foundation for the prediction and encoding of phase behaviour at the sequence level. PMID:26390327

Concatenated shift registers generating maximally spaced phase shifts of PN-sequences

NASA Technical Reports Server (NTRS)

Hurd, W. J.; Welch, L. R.

1977-01-01

A large class of linearly concatenated shift registers is shown to generate approximately maximally spaced phase shifts of pn-sequences, for use in pseudorandom number generation. A constructive method is presented for finding members of this class, for almost all degrees for which primitive trinomials exist. The sequences which result are not normally characterized by trinomial recursions, which is desirable since trinomial sequences can have some undesirable randomness properties.

Trunk-pelvis coordination during turning: A cross sectional study of young adults with and without a history of low back pain.

PubMed

Smith, Jo Armour; Kulig, Kornelia

2016-07-01

During steady-state locomotion, symptomatic individuals with low back pain demonstrate reduced ability to modulate coordination between the trunk and the pelvis in the axial plane. It is unclear if this is also true during functional locomotor perturbations such as changing direction, or if this change in coordination adaptability persists between symptomatic episodes. The purpose of this study was to compare trunk-pelvis coordination during walking turns in healthy individuals and asymptomatic individuals with a history of low back pain. Participants performed multiple ipsilateral turns. Axial plane inter-segmental coordination and stride-to-stride coordination variability were quantified using the vector coding technique. Frequency of coordination mode and amplitude of coordination variability was compared between groups using Wilcoxon signed-rank tests and paired t-tests respectively. During stance phase of the turn, there was no significant difference in either inter-segmental coordination or coordination variability between groups. Inter-segmental coordination between the trunk and the pelvis was predominantly inphase during this part of the turn. During swing phase, patterns of coordination were more diversified, and individuals with a history of low back pain had significantly greater trunk phase coordination than healthy controls. Coordination variability was the same in both groups. Changes in trunk-pelvis coordination are evident between symptomatic episodes in individuals with a history of low back pain. However, previously demonstrated decreases in coordination variability were not found between symptomatic episodes in individuals with recurrent low back pain and therefore may represent a response to concurrent pain rather than a persistent change in motor control. Copyright © 2016 Elsevier Ltd. All rights reserved.

Stability of monomeric Cro variants: Isoenergetic transformation of a type I' to a type II' beta-hairpin by single amino acid replacements.

PubMed

Mollah, A K M M; Stennis, Rhonda L; Mossing, Michael C

2003-05-01

The thermodynamic stabilities of three monomeric variants of the bacteriophage lambda Cro repressor that differ only in the sequence of two amino acids at the apex of an engineered beta-hairpin have been determined. The sequences of the turns are EVK-XX-EVK, where the two central residues are DG, GG, and GT, respectively. Standard-state unfolding free energies, determined from circular dichroism measurements as a function of urea concentration, range from 2.4 to 2.7 kcal/mole, while those determined from guanidine hydrochloride range from 2.8 to 3.3 kcal/mole for the three proteins. Thermal denaturation yields van't Hoff unfolding enthalpies of 36 to 40 kcal /mole at midpoint temperatures in the range of 53 to 58 degrees C. Extrapolation of the thermal denaturation free energies with heat capacities of 400 to 600 cal/mole deg gives good agreement with the parameters determined in denaturant titrations. As predicted from statistical surveys of amino acid replacements in beta-hairpins, energetic barriers to transformation from a type I' turn (DG) to a type II' turn (GT) can be quite small.

AC Resonant charger with charge rate unrelated to primary power frequency

DOEpatents

Watson, Harold

1982-01-01

An AC resonant charger for a capacitive load, such as a PFN, is provided with a variable repetition rate unrelated to the frequency of a multi-phase AC power source by using a control unit to select and couple the phase of the power source to the resonant charger in order to charge the capacitive load with a phase that is the next to begin a half cycle. For optimum range in repetition rate and increased charging voltage, the resonant charger includes a step-up transformer and full-wave rectifier. The next phase selected may then be of either polarity, but is always selected to be of a polarity opposite the polarity of the last phase selected so that the transformer core does not saturate. Thyristors are used to select and couple the correct phase just after its zero crossover in response to a sharp pulse generated by a zero-crossover detector. The thyristor that is turned on then automatically turns off after a full half cycle of its associated phase input. A full-wave rectifier couples the secondary winding of the transformer to the load so that the load capacitance is always charged with the same polarity.

Ac resonant charger with charge rate unrelated to preimary power requency

DOEpatents

Not Available

1979-12-07

An ac resonant charger for a capacitive load, such as a pulse forming network (PFN), is provided with a variable repetition rate unrelated to the frequency of a multi-phase ac power source by using a control unit to select and couple the phase of the power source to the resonant charger in order to charge the capacitive load with a phase that is the next to begin a half cycle. For optimum range in repetition rate and increased charging voltage, the resonant charger includes a step-up transformer and full-wave rectifier. The next phase selected may then be of either polarity, but is always selected to be of a polarity opposite the polarity of the last phase selected so that the transformer core does not saturate. Thyristors are used to select and couple the correct phase just after its zero crossover in response to a sharp pulse generated by a zero-crossover detector. The thyristor that is turned on then automatically turns off after a full half cycle of its associated phase input. A full-wave rectifier couples the secondary winding of the transformer to the load so that the load capacitance is always charged with the same polarity.

Sequence and onset of whole-body coordination when turning in response to a visual trigger: comparing people with Parkinson's disease and healthy adults.

PubMed

Ashburn, A; Kampshoff, C; Burnett, M; Stack, E; Pickering, R M; Verheyden, G

2014-01-01

Turning round is a routine everyday activity that can often lead to instability. The purpose of this study was to investigate abnormalities of turning among people with Parkinson's disease (PwPD) through the measurement of sequence of body segments and latency response. Participants were asked to turn 180° and whole-body movements were recorded using CODAmotion and Visio Fast eye tracking equipment. Thirty-one independently mobile PwPD and 15 age-matched healthy controls participated in the study. We found that contrary to common belief, the head preceded movement of all other body segments (eyes, shoulders, pelvis, first and second foot). We also found interaction between group and body segment (P=0.005), indicating that overall, PwPD took longer to move from head to second foot than age-matched healthy controls. For PwPD only, interactions were found between disease severity and body segment (P<0.0001), between age group and body segment (P<0.0001) and between gender and body segments (P<0.0001). For each interaction, longer time periods were noted between moving the first foot after the pelvis, and moving the second foot after the first, and this was noted for PwPD in Hoehn and Yahr stage III-IV (in comparison to Hoehn and Yahr stage I-II); for PwPD who were under 70 years (in comparison with 70 years or over); and for ladies (in comparison with men). Our results indicate that in PwPD and healthy elderly, turning-on-the-spot might not follow the top-to-bottom approach we know from previous research. Copyright © 2013. Published by Elsevier B.V.

An image processing study of a reentrant discotic cholesteric - biaxial cholesteric phase transition

NASA Astrophysics Data System (ADS)

Luders, D. D.; Zoner, G. A.; Santos, O. R.; Braga, W. S.; Sampaio, A. R.; Kimura, N. M.; Palangana, A. J.; Simões, M.

2018-04-01

In this work, we study and characterize the cholesteric sequence of phases (ChDr - ChB - ChD), where the first ChDr is the reentrant cholesteric discotic phase, ChB is the cholesteric biaxial phase and the second ChD is the cholesteric discotic phase. This sequence of phases is studied through polarized light microscopy and image processing technique, where, for the first time, the domains and borders of these transitions are established and characterized. They are also investigated and optically characterized throughout their textures.

Turtle Graphics of Morphic Sequences

NASA Astrophysics Data System (ADS)

Zantema, Hans

2016-02-01

The simplest infinite sequences that are not ultimately periodic are pure morphic sequences: fixed points of particular morphisms mapping single symbols to strings of symbols. A basic way to visualize a sequence is by a turtle curve: for every alphabet symbol fix an angle, and then consecutively for all sequence elements draw a unit segment and turn the drawing direction by the corresponding angle. This paper investigates turtle curves of pure morphic sequences. In particular, criteria are given for turtle curves being finite (consisting of finitely many segments), and for being fractal or self-similar: it contains an up-scaled copy of itself. Also space-filling turtle curves are considered, and a turtle curve that is dense in the plane. As a particular result we give an exact relationship between the Koch curve and a turtle curve for the Thue-Morse sequence, where until now for such a result only approximations were known.

An investigation of Hebbian phase sequences as assembly graphs

PubMed Central

Almeida-Filho, Daniel G.; Lopes-dos-Santos, Vitor; Vasconcelos, Nivaldo A. P.; Miranda, José G. V.; Tort, Adriano B. L.; Ribeiro, Sidarta

2014-01-01

Hebb proposed that synapses between neurons that fire synchronously are strengthened, forming cell assemblies and phase sequences. The former, on a shorter scale, are ensembles of synchronized cells that function transiently as a closed processing system; the latter, on a larger scale, correspond to the sequential activation of cell assemblies able to represent percepts and behaviors. Nowadays, the recording of large neuronal populations allows for the detection of multiple cell assemblies. Within Hebb's theory, the next logical step is the analysis of phase sequences. Here we detected phase sequences as consecutive assembly activation patterns, and then analyzed their graph attributes in relation to behavior. We investigated action potentials recorded from the adult rat hippocampus and neocortex before, during and after novel object exploration (experimental periods). Within assembly graphs, each assembly corresponded to a node, and each edge corresponded to the temporal sequence of consecutive node activations. The sum of all assembly activations was proportional to firing rates, but the activity of individual assemblies was not. Assembly repertoire was stable across experimental periods, suggesting that novel experience does not create new assemblies in the adult rat. Assembly graph attributes, on the other hand, varied significantly across behavioral states and experimental periods, and were separable enough to correctly classify experimental periods (Naïve Bayes classifier; maximum AUROCs ranging from 0.55 to 0.99) and behavioral states (waking, slow wave sleep, and rapid eye movement sleep; maximum AUROCs ranging from 0.64 to 0.98). Our findings agree with Hebb's view that assemblies correspond to primitive building blocks of representation, nearly unchanged in the adult, while phase sequences are labile across behavioral states and change after novel experience. The results are compatible with a role for phase sequences in behavior and cognition. PMID:24782715

High-speed optical phase-shifting apparatus

DOEpatents

Zortman, William A.

2016-11-08

An optical phase shifter includes an optical waveguide, a plurality of partial phase shifting elements arranged sequentially, and control circuitry electrically coupled to the partial phase shifting elements. The control circuitry is adapted to provide an activating signal to each of the N partial phase shifting elements such that the signal is delayed by a clock cycle between adjacent partial phase shifting elements in the sequence. The transit time for a guided optical pulse train between the input edges of consecutive partial phase shifting elements in the sequence is arranged to be equal to a clock cycle, thereby enabling pipelined processing of the optical pulses.

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on CPU+GPU.

PubMed

Zhang, Jing; Wang, Hao; Feng, Wu-Chun

2017-01-01

BLAST, short for Basic Local Alignment Search Tool, is a ubiquitous tool used in the life sciences for pairwise sequence search. However, with the advent of next-generation sequencing (NGS), whether at the outset or downstream from NGS, the exponential growth of sequence databases is outstripping our ability to analyze the data. While recent studies have utilized the graphics processing unit (GPU) to speedup the BLAST algorithm for searching protein sequences (i.e., BLASTP), these studies use coarse-grained parallelism, where one sequence alignment is mapped to only one thread. Such an approach does not efficiently utilize the capabilities of a GPU, particularly due to the irregularity of BLASTP in both execution paths and memory-access patterns. To address the above shortcomings, we present a fine-grained approach to parallelize BLASTP, where each individual phase of sequence search is mapped to many threads on a GPU. This approach, which we refer to as cuBLASTP, reorders data-access patterns and reduces divergent branches of the most time-consuming phases (i.e., hit detection and ungapped extension). In addition, cuBLASTP optimizes the remaining phases (i.e., gapped extension and alignment with trace back) on a multicore CPU and overlaps their execution with the phases running on the GPU.

Solving the crystal structure of human calcium-free S100Z: the siege and conquer of one of the last S100 family strongholds.

PubMed

Calderone, V; Fragai, M; Gallo, G; Luchinat, C

2017-06-01

The X-ray structure of human apo-S100Z has been solved and compared with that of the zebrafish calcium-bound S100Z, which is the closest in sequence. Human apo-S100A12, which shows only 43% sequence identity to human S100Z, has been used as template model to solve the crystallographic phase problem. Although a significant buried surface area between the two physiological dimers is present in the asymmetric unit of human apo-S100Z, the protein does not form the superhelical arrangement in the crystal as observed for the zebrafish calcium-bound S100Z and human calcium-bound S100A4. These findings further demonstrate that calcium plays a fundamental role in triggering quaternary structure formation in several S100s. Solving the X-ray structure of human apo-S100Z by standard molecular replacement procedures turned out to be a challenge and required trying different models and different software tools among which only one was successful. The model that allowed structure solution was that with one of the lowest sequence identity with the target protein among the S100 family in the apo state. Based on the previously solved zebrafish holo-S100Z, a putative human holo-S100Z structure has been then calculated through homology modeling; the differences between the experimental human apo and calculated holo structure have been compared to those existing for other members of the family.

Software framework for automatic learning of telescope operation

NASA Astrophysics Data System (ADS)

Rodríguez, Jose A.; Molgó, Jordi; Guerra, Dailos

2016-07-01

The "Gran Telescopio de Canarias" (GTC) is an optical-infrared 10-meter segmented mirror telescope at the ORM observatory in Canary Islands (Spain). The GTC Control System (GCS) is a distributed object and component oriented system based on RT-CORBA and it is responsible for the operation of the telescope, including its instrumentation. The current development state of GCS is mature and fully operational. On the one hand telescope users as PI's implement the sequences of observing modes of future scientific instruments that will be installed in the telescope and operators, in turn, design their own sequences for maintenance. On the other hand engineers develop new components that provide new functionality required by the system. This great work effort is possible to minimize so that costs are reduced, especially if one considers that software maintenance is the most expensive phase of the software life cycle. Could we design a system that allows the progressive assimilation of sequences of operation and maintenance of the telescope, through an automatic self-programming system, so that it can evolve from one Component oriented organization to a Service oriented organization? One possible way to achieve this is to use mechanisms of learning and knowledge consolidation to reduce to the minimum expression the effort to transform the specifications of the different telescope users to the operational deployments. This article proposes a framework for solving this problem based on the combination of the following tools: data mining, self-Adaptive software, code generation, refactoring based on metrics, Hierarchical Agglomerative Clustering and Service Oriented Architectures.

Sequence inversion and phenylalanine surrogates at the beta-turn enhance the antibiotic activity of gramicidin S.

PubMed

Solanas, Concepción; de la Torre, Beatriz G; Fernández-Reyes, María; Santiveri, Clara M; Jiménez, M Angeles; Rivas, Luis; Jiménez, Ana I; Andreu, David; Cativiela, Carlos

2010-05-27

A series of gramicidin S (GS) analogues have been synthesized where the Phe (i + 1) and Pro (i + 2) residues of the beta-turn have been swapped while the respective chiralities (D-, L-) at each position are preserved, and Phe is replaced by surrogates with aromatic side chains of diverse size, orientation, and flexibility. Although most analogues preserve the beta-sheet structure, as assessed by NMR, their antibiotic activities turn out to be highly dependent on the bulkiness and spatial arrangement of the aromatic side chain. Significant increases in microbicidal potency against both Gram-positive and Gram-negative pathogens are observed for several analogues, resulting in improved therapeutic profiles. Data indicate that seemingly minor replacements at the GS beta-turn can have significant impact on antibiotic activity, highlighting this region as a hot spot for modulating GS plasticity and activity.

Sequence inversion and phenylalanine surrogates at the β-turn enhance the antibiotic activity of gramicidin S

PubMed Central

Solanas, Concepción; de la Torre, Beatriz G.; Fernández-Reyes, María; Santiveri, Clara M.; Jiménez, M. Ángeles; Rivas, Luis; Jiménez, Ana I.; Andreu, David; Cativiela, Carlos

2010-01-01

A series of gramicidin S (GS) analogs have been synthesized where the Phe (i+1) and Pro (i+2) residues of the β-turn have been swapped while the respective chiralities (D-, L-) at each position are preserved, and Phe is replaced by surrogates with aromatic side chains of diverse size, orientation and flexibility. Although most analogs preserve the β-sheet structure, as assessed by NMR, their antibiotic activities turn out to be highly dependent on the bulkiness and spatial arrangement of the aromatic side chain. Significant increases in microbicidal potency against both Gram-positive and Gram-negative pathogens are observed for several analogs, resulting in improved therapeutic profiles. Data indicate that seemingly minor replacements at the GS β-turn can have significant impact on antibiotic activity, highlighting this region as a hot spot for modulating GS plasticity and activity. PMID:20411945

Metastable and equilibrium phase formation in sputter-deposited Ti/Al multilayer thin films

NASA Astrophysics Data System (ADS)

Lucadamo, G.; Barmak, K.; Lavoie, C.; Cabral, C., Jr.; Michaelsen, C.

2002-06-01

The sequence and kinetics of metastable and equilibrium phase formation in sputter deposited multilayer thin films was investigated by combining in situ synchrotron x-ray diffraction (XRD) with ex situ electron diffraction and differential scanning calorimetry (DSC). The sequence included both cubic and tetragonal modifications of the equilibrium TiAl3 crystal structure. Values for the formation activation energies of the various phases in the sequence were determined using the XRD and DSC data obtained here, as well as activation energy data reported in the literature.

Orbit Determination Strategy and Simulation Performance for OSIRIS-REx Proximity Operations

NASA Technical Reports Server (NTRS)

Leonard, Jason M.; Antreasian, Peter G.; Jackman, Coralie D.; Page, Brian; Wibben, Daniel R.; Moreau, Michael C.

2017-01-01

The Origins Spectral Interpretation Resource Identification Security Regolith Explorer (OSIRISREx)is a NASA New Frontiers mission to the near-earth asteroid Bennu that will rendez vousin 2018, create a comprehensive and detailed set of observations over several years, collect a regolith sample, and return the sample to Earth in 2023. The Orbit Determination (OD) team isa sub-section of the Flight Dynamics System responsible for generating precise reconstructions and predictions of the spacecraft trajectory. The OD team processes radiometric data, LIDAR, as well as center-finding and landmark-based Optical Navigation images throughout the proximity operations phase to estimate and predict the spacecraft location within several meters. Stringent knowledge requirements stress the OD teams concept of operations and procedures to produce verified and consistent high quality solutions for observation planning, maneuver planning, and onboard sequencing. This paper will provide insight into the OD concept of operations and summarize the OD performance expected during the approach and early proximity operation phases,based on our pre-encounter knowledge of Bennu. Strategies and methods used to compare and evaluate predicted and reconstructed solutions are detailed. The use of high fidelity operational tests during early 2017 will stress the teams concept of operations and ability to produce precise OD solutions with minimal turn-around delay.

Galileo probe battery system -- An update

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

Dagarin, B.P.; Taenaka, R.K.; Stofel, E.J.

NASA`s Galileo 6-year trip to Jupiter is in its final phase. The mission consists of a Jovian Orbiter and an atmospheric entry Probe. The Probe is designed to coast autonomously for up to 190 days and turn itself on 6 hours prior to entry. It will then descend through the upper atmosphere for 50 to 75 minutes with the aid of an 8-foot parachute. This paper discusses sources of electrical power for the Probe and battery testing at the systems level. Described are the final production phase, qualification, and systems testing prior to and following launch, as well as decisionsmore » made regarding the Probe separation Li/SO{sub 2} battery configuration. In addition, the paper briefly describes the thermal battery verification program. The main power source comprises three Li/SO{sub 2} battery modules containing 13 D-sized cell strings per module. These modules are required to retain capacity for 7.5 years and support a 150-day clock, ending with a 7-hour mission sequence of increasing loads from 0.15 A to 9.5 A during the last 30 minutes. The main power source is supplemented by two thermal batteries (CaCrO{sub 4}-Ca), which will be used for firing the pyrotechnic initiators during the atmospheric entry.« less

Testing resonating vector strength: Auditory system, electric fish, and noise

NASA Astrophysics Data System (ADS)

Leo van Hemmen, J.; Longtin, André; Vollmayr, Andreas N.

2011-12-01

Quite often a response to some input with a specific frequency ν○ can be described through a sequence of discrete events. Here, we study the synchrony vector, whose length stands for the vector strength, and in doing so focus on neuronal response in terms of spike times. The latter are supposed to be given by experiment. Instead of singling out the stimulus frequency ν○ we study the synchrony vector as a function of the real frequency variable ν. Its length turns out to be a resonating vector strength in that it shows clear maxima in the neighborhood of ν○ and multiples thereof, hence, allowing an easy way of determining response frequencies. We study this "resonating" vector strength for two concrete but rather different cases, viz., a specific midbrain neuron in the auditory system of cat and a primary detector neuron belonging to the electric sense of the wave-type electric fish Apteronotus leptorhynchus. We show that the resonating vector strength always performs a clear resonance correlated with the phase locking that it quantifies. We analyze the influence of noise and demonstrate how well the resonance associated with maximal vector strength indicates the dominant stimulus frequency. Furthermore, we exhibit how one can obtain a specific phase associated with, for instance, a delay in auditory analysis.

Expanded turn conformations: characterization and sequence-structure correspondence in alpha-turns with implications in helix folding.

PubMed

Dasgupta, Bhaskar; Pal, Lipika; Basu, Gautam; Chakrabarti, Pinak

2004-05-01

Like the beta-turns, which are characterized by a limiting distance between residues two positions apart (i, i+3), a distance criterion (involving residues at positions i and i+4) is used here to identify alpha-turns from a database of known protein structures. At least 15 classes of alpha-turns have been enumerated based on the location in the phi,psi space of the three central residues (i+1 to i+3)-one of the major being the class AAA, where the residues occupy the conventional helical backbone torsion angles. However, moving towards the C-terminal end of the turn, there is a shift in the phi,psi angles towards more negative phi, such that the electrostatic repulsion between two consecutive carbonyl oxygen atoms is reduced. Except for the last position (i+4), there is not much similarity in residue composition at different positions of hydrogen and non-hydrogen bonded AAA turns. The presence or absence of Pro at i+1 position of alpha- and beta-turns has a bearing on whether the turn is hydrogen-bonded or without a hydrogen bond. In the tertiary structure, alpha-turns are more likely to be found in beta-hairpin loops. The residue composition at the beginning of the hydrogen bonded AAA alpha-turn has similarity with type I beta-turn and N-terminal positions of helices, but the last position matches with the C-terminal capping position of helices, suggesting that the existence of a "helix cap signal" at i+4 position prevents alpha-turns from growing into helices. Our results also provide new insights into alpha-helix nucleation and folding. Copyright 2004 Wiley-Liss, Inc.

Folding and Stabilization of Native-Sequence-Reversed Proteins

PubMed Central

Zhang, Yuanzhao; Weber, Jeffrey K; Zhou, Ruhong

2016-01-01

Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we investigate how the reverse-sequences of native proteins might fold by examining a series of small proteins of increasing structural complexity (α-helix, β-hairpin, α-helix bundle, and α/β-protein). Employing a tandem protein structure prediction algorithmic and molecular dynamics simulation approach, we find that the ability of reverse sequences to adopt native-like folds is strongly influenced by protein size and the flexibility of the native hydrophobic core. For β-hairpins with reverse-sequences that fail to fold, we employ a simple mutational strategy for guiding stable hairpin formation that involves the insertion of amino acids into the β-turn region. This systematic look at reverse sequence duality sheds new light on the problem of protein sequence-structure mapping and may serve to inspire new protein design and protein structure prediction protocols. PMID:27113844

Folding and Stabilization of Native-Sequence-Reversed Proteins

NASA Astrophysics Data System (ADS)

Zhang, Yuanzhao; Weber, Jeffrey K.; Zhou, Ruhong

2016-04-01

Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we investigate how the reverse-sequences of native proteins might fold by examining a series of small proteins of increasing structural complexity (α-helix, β-hairpin, α-helix bundle, and α/β-protein). Employing a tandem protein structure prediction algorithmic and molecular dynamics simulation approach, we find that the ability of reverse sequences to adopt native-like folds is strongly influenced by protein size and the flexibility of the native hydrophobic core. For β-hairpins with reverse-sequences that fail to fold, we employ a simple mutational strategy for guiding stable hairpin formation that involves the insertion of amino acids into the β-turn region. This systematic look at reverse sequence duality sheds new light on the problem of protein sequence-structure mapping and may serve to inspire new protein design and protein structure prediction protocols.

Losing Something In Translation: Turning Requirements Into Specifications

DTIC Science & Technology

2016-06-01

specialized in Organizational Behavior. Perhaps the reader remembers the comedy routine in which a performer orates a lyrical, emotive passage in a deep...learned from the Technology Maturation and Risk Reduction phase and the Engineering and Manufacturing Development phase. These lessons learned, for

Development of a phase-sensitive Fourier domain optical coherence tomography system to measure mouse organ of Corti vibrations in two cochlear turns

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

Ramamoorthy, Sripriya; Zhang, Yuan; Jacques, Steven

In this study, we have developed a phase-sensitive Fourier-domain optical coherence tomography system to simultaneously measure the in vivo inner ear vibrations in the hook area and second turn of the mouse cochlea. This technical development will enable measurement of intra-cochlear distortion products at ideal locations such as the distortion product generation site and reflection site. This information is necessary to un-mix the complex mixture of intra-cochlear waves comprising the DPOAE and thus leads to the non-invasive identification of the local region of cochlear damage.

Gas-Phase Folding of Small Glutamine Containing Peptides: Sidechain Hydrogen Bonding Stabilizes β-turns

NASA Astrophysics Data System (ADS)

Walsh, Patrick S.; Blodgett, Karl N.; McBurney, Carl; Gellman, Samuel H.; Zwier, Timothy S.

Glutamine is vitally important to a class of neurodegenerative diseases called poly-glutamine (poly-Q) repeat diseases such as Huntington's Disease (HD). Recent studies have revealed a pathogenic pathway that proceeds through misfolding of poly-Q regions into characteristic β-turn/ β-hairpin structures that are highly correlated with toxicity. The inherent conformational preferences of small glutamine containing peptides (Ac-Q-Q-NHBn and Ac-A-Q-NHBn) were studied using conformation-specific IR and UV spectroscopies, with the goal of probing the delicate interplay between three competitive hydrogen bonding motifs: backbone-backbone, sidechain-backbone, and sidechain-sidechain hydrogen bonds. Laser desorption, coupled with a supersonic expansion, was used to introduce the non-thermally labile sample into the gas-phase. Resonant ion-dip infrared (RIDIR) spectroscopy is a powerful tool for recording the vibrational spectra of single conformational isomers and was used here to reveal the innate structural preferences of the glutamine containing peptides. Experimental results are compared against density functional calculations to arrive at firm conformational assignments. Our results demonstrate a striking preference for β-turn formation in the non-polar environment of the gas-phase. Previous Affiliation: Purdue University, Department of Chemistry.

How northward turnings of the IMF can lead to substorm expansion onsets

NASA Astrophysics Data System (ADS)

Russell, C. T.

2000-10-01

The frequent triggering of the expansion phase of substorms by northward turnings of the interplanetary magnetic field (IMF) can be understood in terms of the existence of two neutral points. The distant neutral point produces a plasma sheet on closed field lines that resupplies the magnetized plasma surrounding the near-Earth neutral point. As long as the near-Earth neutral point reconnects in moderately dense plasma, the reconnection rate is low. When the IMF turns northward, reconnection at the distant neutral point ceases but reconnection at the near-Earth neutral point continues and soon reaches open, low density magnetic field lines where the rate of reconnection is rapid, and a full expansion phase occurs. This model is consistent with the observations of substorms with two onsets: an initial one at low invariant latitudes when reconnection at the near Earth neutral point first begins and the second when reconnection reaches low density field lines at the edge of the plasma sheet and continues into the open flux of the tail lobes. It is also consistent with the occurrence of pseudo breakups in which reconnection at the near Earth neutral point begins but does not proceed to lobe field lines and a full expansion phase.

Navigational choice between reversal and curve during acidic pH avoidance behavior in Caenorhabditis elegans.

PubMed

Wakabayashi, Tokumitsu; Sakata, Kazumi; Togashi, Takuya; Itoi, Hiroaki; Shinohe, Sayaka; Watanabe, Miwa; Shingai, Ryuzo

2015-11-19

Under experimental conditions, virtually all behaviors of Caenorhabditis elegans are achieved by combinations of simple locomotion, including forward, reversal movement, turning by deep body bending, and gradual shallow turning. To study how worms regulate these locomotion in response to sensory information, acidic pH avoidance behavior was analyzed by using worm tracking system. In the acidic pH avoidance, we characterized two types of behavioral maneuvers that have similar behavioral sequences in chemotaxis and thermotaxis. A stereotypic reversal-turn-forward sequence of reversal avoidance caused an abrupt random reorientation, and a shallow gradual turn in curve avoidance caused non-random reorientation in a less acidic direction to avoid the acidic pH. Our results suggest that these two maneuvers were each triggered by a distinct threshold pH. A simulation study using the two-distinct-threshold model reproduced the avoidance behavior of the real worm, supporting the presence of the threshold. Threshold pH for both reversal and curve avoidance was altered in mutants with reduced or enhanced glutamatergic signaling from acid-sensing neurons. C. elegans employ two behavioral maneuvers, reversal (klinokinesis) and curve (klinotaxis) to avoid acidic pH. Unlike the chemotaxis in C. elegans, reversal and curve avoidances were triggered by absolute pH rather than temporal derivative of stimulus concentration in this behavior. The pH threshold is different between reversal and curve avoidance. Mutant studies suggested that the difference results from a differential amount of glutamate released from ASH and ASK chemosensory neurons.

Analysis of the lateral push-off in the freestyle flip turn.

PubMed

Araujo, Luciana; Pereira, Suzana; Gatti, Roberta; Freitas, Elinai; Jacomel, Gabriel; Roesler, Helio; Villas-Boas, Joao

2010-09-01

The aim of this study was to examine the contact phase during the lateral push-off in the turn of front crawl swimming to determine which biomechanical variables (maximum normalized peak force, contact time, impulse, angle of knee flexion, and total turn time within 15 m) contribute to the performance of this turn technique. Thirty-four swimmers of state, national, and international competitive standard participated in the study. For data collection, the following equipment was used: an underwater force platform, a 30-Hz VHS video camera, and a MiniDv digital camera within an underwater box. Data are expressed as descriptive statistics. Inferential analyses were performed using Pearson's correlation and multiple linear regressions. All variables studied had a significant relationship with turn performance. We conclude that a turn executed with a knee flexion angle of between 100° and 120° provides optimum peak forces to generate impulses that allow the swimmer to lose less time in the turn without the need for an excessive force application and with less energy lost.

Searching for Criteria in Evaluating the Monofin Swimming Turn from the Perspective of Coaching and Improving Technique

PubMed Central

Rejman, Marek; Borowska, Grażyna

2008-01-01

This study aims to analysise the selected kinematic parameters of the monofin swimming turn. The high complexity of performing turns is hindered by the large surface of the monofin, which disturbs control and sense of the body in water. A lack of objective data available on monofin swimming turns has resulted in field research connected with the specification of parameters needed for the evaluation of the technique. Therefore, turns observed in elite swimmers contain underlying conclusions for objective criteria, ensuring the highest level of coaching and the improving of turns in young swimmers. Six, high level, male swimmers participated in the study. The subject of the analysis was the fastest turn, from one out of three trial turns made after swimming a distance of 25 m. Images of the turns were collected from two cameras located under water in accordance with the procedures of the previous analyses of freestyle turns. The images were digitized and analysed by the SIMI®- Movement Analysis System. The interdependency of the total turn time and the remaining recorded parameters, constituted the basis for analysis of the kinematic parameters of five turn phases. The interdependency was measured using r- Pearson’s correlation coefficients. The novel character of the subject covered in this study, forced interpretation of the results on the basis of turn analyses in freestyle swimming. The results allow for the creation of a diagram outlinig area of search for an effective and efficient monofin swimming turn mechanism. The activities performed from the moment of wall contact until the commencement of stroking seem to be crucial for turn improvement. A strong belief has resulted that, the correct monofin swimming turn, is more than just a simple consequence of the fastest performance of all its components. The most important criteria in evaluating the quality of the monofin swimming turn are: striving for the optimal extension of wall contact time, push-off time and glide time. Key pointsShort time and large surface of the monofin additionally hinders complexity of the turn performance by disturbance in sensing and controlling body in water. Availability of no objective data on monofin swimming turns resulted in research in the field connected with specifying parameters needed for the technique evaluation.Correct turn technique may help to improve swimming race results.The diagram constructed on the basis of the interdependency of the total turn time and the remaining recorded kinematic parameters should establish the areas of searching for mechanism of effective and efficient monofin swimming turn.The most crucial, from the coaching and improving point of view, seem to be activities which take place from the moment of feet wall contact till the first propulsive movements. Therefore, the high quality of the monofin swimming turn technique is not just a simple consequence of the fastest performance of all its component parts.The most important criteria of the quality in the monofin swimming turn technique are: striving for extending in the optimum scope of wall contact time, the time of the push-off phase and the glide time. PMID:24150136

Decreased Load on General Motor Preparation and Visual-Working Memory while Preparing Familiar as Compared to Unfamiliar Movement Sequences

ERIC Educational Resources Information Center

De Kleine, Elian; Van der Lubbe, Rob H. J.

2011-01-01

Learning movement sequences is thought to develop from an initial controlled attentive phase to a more automatic inattentive phase. Furthermore, execution of sequences becomes faster with practice, which may result from changes at a general motor processing level rather than at an effector specific motor processing level. In the current study, we…

Early Events in the Folding of an Amphipathic Peptide A Multi- Nanosecond Molecular Dynamics Study

NASA Technical Reports Server (NTRS)

Chipot, Christophe; Maigret, Bernard; Pohorille, Andrew

1999-01-01

Folding of the capped LQQLLQQLLQL peptide is investigated at the water-hexane interface by molecular dynamics simulations over 161.5 nanoseconds. Initially placed in the aqueous phase as a beta-strand, the peptide rapidly adsorbs to the interface, where it adopts an amphipathic conformation. The marginal presence of non-amphipathic structures throughout the complete trajectory indicate- that the corresponding conformations are strongly disfavored at the interface. It is further suggestive that folding in an interfacial environment proceeds through a pathway of successive amphipathic intermediates. The energetic and entropic penalties involved in the conformational changes along this pathway markedly increase the folding time-scales of LQQLLQQLLQL, explaining why the alpha-helix, the hypothesized lowest free energy structure for a sequence with a hydrophobic periodicity of 3.6, has not been reached yet. The formation of a type I beta-turn at the end of the simulation confirms the importance of such motifs as initiation sites allowing the peptide to coalesce towards a secondary structure.

Photoluminescent carbon dots based on a rare 3D inorganic-organic hybrid cadmium borate crystal.

PubMed

Zhou, Kang; Zhang, Wen-Jin; Luo, Yuan-Zhang; Pan, Chun-Yang

2018-05-17

A 3D inorganic-organic hybridized skeleton cadmium borate [Cden][B5O8(OH)] (1) (en = ethylenediamine) has been solvothermally synthesized. By calcining it, specific shape carbon dots (C-dots) with abundant free radicals were observed. In addition, C-dots in the ethanol phase exhibited variable photoluminescence and showed rare turn on or off effects to Cr3+ ions and CdSe/ZnS quantum dots, but only a turn on effect to Cs+ ions and a turn off effect to CsPbBr3 quantum dots.

The barium iron ruthenium oxide system

NASA Technical Reports Server (NTRS)

Kemmler-Sack, S.; Ehmann, A.

1986-01-01

In the system BaFe(1-x)Ru(x)O(3-y), three phases, separated by immiscibility gaps, are present: an Fe-rich phase (x = 0 to 0.75) with hexagonal BaTiO3 structure (6H; sequence (hcc)2), a Ru-rich phase (x = 0.9) of hexagonal 4H-type (sequence (hc)2), and the pure Ru compounds BaRuO3 with rhombohedral 9R structure (sequence (hhc)3). By vibrational spectroscopic investigations in the 6H phase a transition from n-type semiconduction (Fe-rich compounds with complete O lattice) can be detected. The 4H and 9R stacking polytypes are good, metal-like conductors. The lattice parameters are given.

A method for simultaneous linear optics and coupling correction for storage rings with turn-by-turn beam position monitor data

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

Yang, Xi; Huang, Xiaobiao

2016-05-13

Here, we propose a method to simultaneously correct linear optics errors and linear coupling for storage rings using turn-by-turn (TbT) beam position monitor (BPM) data. The independent component analysis (ICA) method is used to isolate the betatron normal modes from the measured TbT BPM data. The betatron amplitudes and phase advances of the projections of the normal modes on the horizontal and vertical planes are then extracted, which, combined with dispersion measurement, are used to fit the lattice model. The fitting results are used for lattice correction. Finally, the method has been successfully demonstrated on the NSLS-II storage ring.

A method for simultaneous linear optics and coupling correction for storage rings with turn-by-turn beam position monitor data

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

Yang, Xi; Huang, Xiaobiao

2016-08-01

We propose a method to simultaneously correct linear optics errors and linear coupling for storage rings using turn-by-turn (TbT) beam position monitor (BPM) data. The independent component analysis (ICA) method is used to isolate the betatron normal modes from the measured TbT BPM data. The betatron amplitudes and phase advances of the projections of the normal modes on the horizontal and vertical planes are then extracted, which, combined with dispersion measurement, are used to fit the lattice model. Furthermore, the fitting results are used for lattice correction. Our method has been successfully demonstrated on the NSLS-II storage ring.

A method for simultaneous linear optics and coupling correction for storage rings with turn-by-turn beam position monitor data

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

Yang, Xi; Huang, Xiaobiao

2016-08-01

We propose a method to simultaneously correct linear optics errors and linear coupling for storage rings using turn-by-turn (TbT) beam position monitor (BPM) data. The independent component analysis (ICA) method is used to isolate the betatron normal modes from the measured TbT BPM data. The betatron amplitudes and phase advances of the projections of the normal modes on the horizontal and vertical planes are then extracted, which, combined with dispersion measurement, are used to fit the lattice model. The fitting results are used for lattice correction. The method has been successfully demonstrated on the NSLS-II storage ring.

Autonomous Circuitry for Substrate Exploration in Freely Moving Drosophila Larvae

PubMed Central

Berni, Jimena; Pulver, Stefan R.; Griffith, Leslie C.; Bate, Michael

2014-01-01

Summary Background Many organisms, from bacteria to human hunter-gatherers, use specialized random walk strategies to explore their environment. Such behaviors are an efficient stratagem for sampling the environment and usually consist of an alternation between straight runs and turns that redirect these runs. Drosophila larvae execute an exploratory routine of this kind that consists of sequences of straight crawls, pauses, turns, and redirected crawls. Central pattern generating networks underlying rhythmic movements are distributed along the anteroposterior axis of the nervous system. The way in which the operation of these networks is incorporated into extended behavioral routines such as substrate exploration has not yet been explored. In particular, the part played by the brain in dictating the sequence of movements required is unknown. Results We report the use of a genetic method to block synaptic activity acutely in the brain and subesophageal ganglia (SOG) of larvae during active exploratory behavior. We show that the brain and SOG are not required for the normal performance of an exploratory routine. Alternation between crawls and turns is an intrinsic property of the abdominal and/or thoracic networks. The brain modifies this autonomous routine during goal-directed movements such as those of chemotaxis. Nonetheless, light avoidance behavior can be mediated in the absence of brain activity solely by the sensorimotor system of the abdomen and thorax. Conclusions The sequence of movements for substrate exploration is an autonomous capacity of the thoracic and abdominal nervous system. The brain modulates this exploratory routine in response to environmental cues. PMID:22940472

Relationship between linear velocity and tangential push force while turning to change the direction of the manual wheelchair.

PubMed

Hwang, Seonhong; Lin, Yen-Sheng; Hogaboom, Nathan S; Wang, Lin-Hwa; Koontz, Alicia M

2017-08-28

Wheelchair propulsion is a major cause of upper limb pain and injuries for manual wheelchair users with spinal cord injuries (SCIs). Few studies have investigated wheelchair turning biomechanics on natural ground surfaces. The purpose of this study was to investigate the relationship between tangential push force and linear velocity of the wheelchair during the turning portions of propulsion. Using an instrumented handrim, velocity and push force data were recorded for 25 subjects while they propel their own wheelchairs on a concrete floor along a figure-eight-shaped course at a maximum velocity. The braking force (1.03 N) of the inside wheel while turning was the largest of all other push forces (p<0.05). Larger changes in squared velocity while turning were significantly correlated with higher propulsive and braking forces used at the pre-turning, turning, and post-turning phases (p<0.05). Subjects with less change of velocity while turning needed less braking force to maneuver themselves successfully and safely around the turns. Considering the magnitude and direction of tangential force applied to the wheel, it seems that there are higher risks of injury and instability for upper limb joints when braking the inside wheel to turn. The results provide insight into wheelchair setup and mobility skills training for wheelchair users.

Accuracy of magnetic resonance imaging in differentiating between benign and malignant vertebral lesions: role of diffusion-weighted imaging, in-phase/opposed-phase imaging and apparent diffusion coefficient.

PubMed

Martel Villagrán, J; Bueno Horcajadas, Á; Pérez Fernández, E; Martín Martín, S

2015-01-01

To determine the ability of MRI to distinguish between benign and malignant vertebral lesions. We included 85 patients and studied a total of 213 vertebrae (both pathologic and normal). For each vertebra, we determined whether the lesion was hypointense in T1-weighted sequences and whether it was hyperintense in STIR and in diffusion-weighted sequences. We calculated the in-phase/out-of-phase quotient and the apparent diffusion coefficient for each vertebra. We combined parameters from T1-weighted, diffusion-weighted, and STIR sequences to devise a formula to distinguish benign from malignant lesions. The group comprised 60 (70.6%) women and 25 (29.4%) men with a mean age of 67±13.5 years (range, 33-90 y). Of the 85 patients, 26 (30.6%) had a known primary tumor. When the lesion was hypointense on T1-weighted sequences, hyperintense on STIR and diffusion-weighted sequences, and had a signal intensity quotient greater than 0.8, the sensitivity was 97.2%, the specificity was 90%, and the diagnostic accuracy was 91.2%. If the patient had a known primary tumor, these values increased to 97.2%, 99.4%, and 99%, respectively. Benign lesions can be distinguished from malignant lesions if we combine the information from T1-weighted, STIR, and diffusion-weighted sequences together with the in-phase/out-of-phase quotient of the lesion detected in the vertebral body on MRI. Copyright © 2013 SERAM. Published by Elsevier España, S.L.U. All rights reserved.

Comparison of phasing strategies for whole human genomes

PubMed Central

Kirkness, Ewen; Schork, Nicholas J.

2018-01-01

Humans are a diploid species that inherit one set of chromosomes paternally and one homologous set of chromosomes maternally. Unfortunately, most human sequencing initiatives ignore this fact in that they do not directly delineate the nucleotide content of the maternal and paternal copies of the 23 chromosomes individuals possess (i.e., they do not ‘phase’ the genome) often because of the costs and complexities of doing so. We compared 11 different widely-used approaches to phasing human genomes using the publicly available ‘Genome-In-A-Bottle’ (GIAB) phased version of the NA12878 genome as a gold standard. The phasing strategies we compared included laboratory-based assays that prepare DNA in unique ways to facilitate phasing as well as purely computational approaches that seek to reconstruct phase information from general sequencing reads and constructs or population-level haplotype frequency information obtained through a reference panel of haplotypes. To assess the performance of the 11 approaches, we used metrics that included, among others, switch error rates, haplotype block lengths, the proportion of fully phase-resolved genes, phasing accuracy and yield between pairs of SNVs. Our comparisons suggest that a hybrid or combined approach that leverages: 1. population-based phasing using the SHAPEIT software suite, 2. either genome-wide sequencing read data or parental genotypes, and 3. a large reference panel of variant and haplotype frequencies, provides a fast and efficient way to produce highly accurate phase-resolved individual human genomes. We found that for population-based approaches, phasing performance is enhanced with the addition of genome-wide read data; e.g., whole genome shotgun and/or RNA sequencing reads. Further, we found that the inclusion of parental genotype data within a population-based phasing strategy can provide as much as a ten-fold reduction in phasing errors. We also considered a majority voting scheme for the construction of a consensus haplotype combining multiple predictions for enhanced performance and site coverage. Finally, we also identified DNA sequence signatures associated with the genomic regions harboring phasing switch errors, which included regions of low polymorphism or SNV density. PMID:29621242

Extracting flat-field images from scene-based image sequences using phase correlation

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

Caron, James N., E-mail: Caron@RSImd.com; Montes, Marcos J.; Obermark, Jerome L.

Flat-field image processing is an essential step in producing high-quality and radiometrically calibrated images. Flat-fielding corrects for variations in the gain of focal plane array electronics and unequal illumination from the system optics. Typically, a flat-field image is captured by imaging a radiometrically uniform surface. The flat-field image is normalized and removed from the images. There are circumstances, such as with remote sensing, where a flat-field image cannot be acquired in this manner. For these cases, we developed a phase-correlation method that allows the extraction of an effective flat-field image from a sequence of scene-based displaced images. The method usesmore » sub-pixel phase correlation image registration to align the sequence to estimate the static scene. The scene is removed from sequence producing a sequence of misaligned flat-field images. An average flat-field image is derived from the realigned flat-field sequence.« less

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.

PubMed

Cretu Stancu, Mircea; van Roosmalen, Markus J; Renkens, Ivo; Nieboer, Marleen M; Middelkamp, Sjors; de Ligt, Joep; Pregno, Giulia; Giachino, Daniela; Mandrile, Giorgia; Espejo Valle-Inclan, Jose; Korzelius, Jerome; de Bruijn, Ewart; Cuppen, Edwin; Talkowski, Michael E; Marschall, Tobias; de Ridder, Jeroen; Kloosterman, Wigard P

2017-11-06

Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline-NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications.

The impact of odor–reward memory on chemotaxis in larval Drosophila

PubMed Central

Schleyer, Michael; Reid, Samuel F.; Pamir, Evren; Saumweber, Timo; Paisios, Emmanouil; Davies, Alexander

2015-01-01

How do animals adaptively integrate innate with learned behavioral tendencies? We tackle this question using chemotaxis as a paradigm. Chemotaxis in the Drosophila larva largely results from a sequence of runs and oriented turns. Thus, the larvae minimally need to determine (i) how fast to run, (ii) when to initiate a turn, and (iii) where to direct a turn. We first report how odor-source intensities modulate these decisions to bring about higher levels of chemotactic performance for higher odor-source intensities during innate chemotaxis. We then examine whether the same modulations are responsible for alterations of chemotactic performance by learned odor “valence” (understood throughout as level of attractiveness). We find that run speed (i) is neither modulated by the innate nor by the learned valence of an odor. Turn rate (ii), however, is modulated by both: the higher the innate or learned valence of the odor, the less often larvae turn whenever heading toward the odor source, and the more often they turn when heading away. Likewise, turning direction (iii) is modulated concordantly by innate and learned valence: turning is biased more strongly toward the odor source when either innate or learned valence is high. Using numerical simulations, we show that a modulation of both turn rate and of turning direction is sufficient to account for the empirically found differences in preference scores across experimental conditions. Our results suggest that innate and learned valence organize adaptive olfactory search behavior by their summed effects on turn rate and turning direction, but not on run speed. This work should aid studies into the neural mechanisms by which memory impacts specific aspects of behavior. PMID:25887280

Frequency-locked pulse sequencer for high-frame-rate monochromatic tissue motion imaging.

PubMed

Azar, Reza Zahiri; Baghani, Ali; Salcudean, Septimiu E; Rohling, Robert

2011-04-01

To overcome the inherent low frame rate of conventional ultrasound, we have previously presented a system that can be implemented on conventional ultrasound scanners for high-frame-rate imaging of monochromatic tissue motion. The system employs a sector subdivision technique in the sequencer to increase the acquisition rate. To eliminate the delays introduced during data acquisition, a motion phase correction algorithm has also been introduced to create in-phase displacement images. Previous experimental results from tissue- mimicking phantoms showed that the system can achieve effective frame rates of up to a few kilohertz on conventional ultrasound systems. In this short communication, we present a new pulse sequencing strategy that facilitates high-frame-rate imaging of monochromatic motion such that the acquired echo signals are inherently in-phase. The sequencer uses the knowledge of the excitation frequency to synchronize the acquisition of the entire imaging plane to that of an external exciter. This sequencing approach eliminates any need for synchronization or phase correction and has applications in tissue elastography, which we demonstrate with tissue-mimicking phantoms. © 2011 IEEE

How many hydrogen-bonded α-turns are possible?

PubMed

Schreiber, Anette; Schramm, Peter; Hofmann, Hans-Jörg

2011-06-01

The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employing the methods of ab initio MO theory in vacuum (HF/6-31G*, B3LYP/6-311 + G*) and in solution (CPCM/HF/6-31G*). Only few α-turn structures with glycine and alanine backbones fulfill the geometry criteria for the i←(i + 4) hydrogen bond satisfactorily. The most stable representatives agree with structures found in the Protein Data Bank. There is a general tendency to form additional hydrogen bonds for smaller pseudocycles corresponding to β- and γ-turns with better hydrogen bond geometries. Sometimes, this competition weakens or even destroys the i←(i + 4) hydrogen bond leading to very stable double β-turn structures. This is also the reason why an "ideal" α-turn with three central amino acids having the perfect backbone angle values of an α-helix could not be localized. There are numerous hints for stable α-turns with a distance between the C(α)-atoms of the first and fifth amino acid smaller than 6-7 Å, but without an i←(i + 4) hydrogen bond.

Technical Note: MR-visualization of interventional devices using transient field alterations and balanced steady-state free precession imaging.

PubMed

Eibofner, Frank; Martirosian, Petros; Würslin, Christian; Graf, Hansjörg; Syha, Roland; Clasen, Stephan

2015-11-01

In interventional magnetic resonance imaging, instruments can be equipped with conducting wires for visualization by current application. The potential of sequence triggered application of transient direct currents in balanced steady-state free precession (bSSFP) imaging is demonstrated. A conductor and a modified catheter were examined in water phantoms and in an ex vivo porcine liver. The current was switched by a trigger pulse in the bSSFP sequence in an interval between radiofrequency pulse and signal acquisition. Magnitude and phase images were recorded. Regions with transient field alterations were evaluated by a postprocessing algorithm. A phase mask was computed and overlaid with the magnitude image. Transient field alterations caused continuous phase shifts, which were separated by the postprocessing algorithm from phase jumps due to persistent field alterations. The overlaid images revealed the position of the conductor. The modified catheter generated visible phase offset in all orientations toward the static magnetic field and could be unambiguously localized in the ex vivo porcine liver. The application of a sequence triggered, direct current in combination with phase imaging allows conspicuous localization of interventional devices with a bSSFP sequence.

ChIP-Seq Analysis for Identifying Genome-Wide Histone Modifications Associated with Stress-Responsive Genes in Plants.

PubMed

Li, Guosheng; Jagadeeswaran, Guru; Mort, Andrew; Sunkar, Ramanjulu

2017-01-01

Histone modifications represent the crux of epigenetic gene regulation essential for most biological processes including abiotic stress responses in plants. Thus, identification of histone modifications at the genome-scale can provide clues for how some genes are 'turned-on' while some others are "turned-off" in response to stress. This chapter details a step-by-step protocol for identifying genome-wide histone modifications associated with stress-responsive gene regulation using chromatin immunoprecipitation (ChIP) followed by sequencing of the DNA (ChIP-seq).

MinION Analysis and Reference Consortium: Phase 1 data release and analysis

PubMed Central

Eccles, David A.; Zalunin, Vadim; Urban, John M.; Piazza, Paolo; Bowden, Rory J.; Paten, Benedict; Mwaigwisya, Solomon; Batty, Elizabeth M.; Simpson, Jared T.; Snutch, Terrance P.

2015-01-01

The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance. PMID:26834992

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

A Homologue of an Operon Required for DNA Transfer in Agrobacterium Is Required in Brucella abortus for Virulence and Intracellular Multiplication

PubMed Central

Sieira, Rodrigo; Comerci, Diego J.; Sánchez, Daniel O.; Ugalde, Rodolfo A.

2000-01-01

As part of a Brucella abortus 2308 genome project carried out in our laboratory, we identified, cloned, and sequenced a genomic DNA fragment containing a locus (virB) highly homologous to bacterial type IV secretion systems. The B. abortus virB locus is a collinear arrangement of 13 open reading frames (ORFs). Between virB1 and virB2 and downstream of ORF12, two degenerated, palindromic repeat sequences characteristic of Brucella intergenic regions were found. Gene reporter studies demonstrated that the B. abortus virB locus constitutes an operon transcribed from virB1 which is turned on during the stationary phase of growth. A B. abortus polar virB1 mutant failed to replicate in HeLa cells, indicating that the virB operon plays a critical role in intracellular multiplication. Mutants with polar and nonpolar mutations introduced in virB10 showed different behaviors in mice and in the HeLa cell infection assay, suggesting that virB10 per se is necessary for the correct function of this type IV secretion apparatus. Mouse infection assays demonstrated that the virB operon constitutes a major determinant of B. abortus virulence. It is suggested that putative effector molecules secreted by this type IV secretion system determine routing of B. abortus to an endoplasmic reticulum-related replication compartment. PMID:10940027

A comprehensively molecular haplotype-resolved genome of a European individual

PubMed Central

Suk, Eun-Kyung; McEwen, Gayle K.; Duitama, Jorge; Nowick, Katja; Schulz, Sabrina; Palczewski, Stefanie; Schreiber, Stefan; Holloway, Dustin T.; McLaughlin, Stephen; Peckham, Heather; Lee, Clarence; Huebsch, Thomas; Hoehe, Margret R.

2011-01-01

Independent determination of both haplotype sequences of an individual genome is essential to relate genetic variation to genome function, phenotype, and disease. To address the importance of phase, we have generated the most complete haplotype-resolved genome to date, “Max Planck One” (MP1), by fosmid pool-based next generation sequencing. Virtually all SNPs (>99%) and 80,000 indels were phased into haploid sequences of up to 6.3 Mb (N50 ∼1 Mb). The completeness of phasing allowed determination of the concrete molecular haplotype pairs for the vast majority of genes (81%) including potential regulatory sequences, of which >90% were found to be constituted by two different molecular forms. A subset of 159 genes with potentially severe mutations in either cis or trans configurations exemplified in particular the role of phase for gene function, disease, and clinical interpretation of personal genomes (e.g., BRCA1). Extended genomic regions harboring manifold combinations of physically and/or functionally related genes and regulatory elements were resolved into their underlying “haploid landscapes,” which may define the functional genome. Moreover, the majority of genes and functional sequences were found to contain individual or rare SNPs, which cannot be phased from population data alone, emphasizing the importance of molecular phasing for characterizing a genome in its molecular individuality. Our work provides the foundation to understand that the distinction of molecular haplotypes is essential to resolve the (inherently individual) biology of genes, genomes, and disease, establishing a reference point for “phase-sensitive” personal genomics. MP1's annotated haploid genomes are available as a public resource. PMID:21813624

Evolution dynamics of a model for gene duplication under adaptive conflict

NASA Astrophysics Data System (ADS)

Ancliff, Mark; Park, Jeong-Man

2014-06-01

We present and solve the dynamics of a model for gene duplication showing escape from adaptive conflict. We use a Crow-Kimura quasispecies model of evolution where the fitness landscape is a function of Hamming distances from two reference sequences, which are assumed to optimize two different gene functions, to describe the dynamics of a mixed population of individuals with single and double copies of a pleiotropic gene. The evolution equations are solved through a spin coherent state path integral, and we find two phases: one is an escape from an adaptive conflict phase, where each copy of a duplicated gene evolves toward subfunctionalization, and the other is a duplication loss of function phase, where one copy maintains its pleiotropic form and the other copy undergoes neutral mutation. The phase is determined by a competition between the fitness benefits of subfunctionalization and the greater mutational load associated with maintaining two gene copies. In the escape phase, we find a dynamics of an initial population of single gene sequences only which escape adaptive conflict through gene duplication and find that there are two time regimes: until a time t* single gene sequences dominate, and after t* double gene sequences outgrow single gene sequences. The time t* is identified as the time necessary for subfunctionalization to evolve and spread throughout the double gene sequences, and we show that there is an optimum mutation rate which minimizes this time scale.

Evaluating the protein coding potential of exonized transposable element sequences

PubMed Central

Piriyapongsa, Jittima; Rutledge, Mark T; Patel, Sanil; Borodovsky, Mark; Jordan, I King

2007-01-01

Background Transposable element (TE) sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes. Analysis of complete genome sequences have turned up numerous cases where TE sequences have been incorporated as exons into mRNAs, and it is widely assumed that such 'exonized' TEs encode protein sequences. However, the extent to which TE-derived sequences actually encode proteins is unknown and a matter of some controversy. We have tried to address this outstanding issue from two perspectives: i-by evaluating ascertainment biases related to the search methods used to uncover TE-derived protein coding sequences (CDS) and ii-through a probabilistic codon-frequency based analysis of the protein coding potential of TE-derived exons. Results We compared the ability of three classes of sequence similarity search methods to detect TE-derived sequences among data sets of experimentally characterized proteins: 1-a profile-based hidden Markov model (HMM) approach, 2-BLAST methods and 3-RepeatMasker. Profile based methods are more sensitive and more selective than the other methods evaluated. However, the application of profile-based search methods to the detection of TE-derived sequences among well-curated experimentally characterized protein data sets did not turn up many more cases than had been previously detected and nowhere near as many cases as recent genome-wide searches have. We observed that the different search methods used were complementary in the sense that they yielded largely non-overlapping sets of hits and differed in their ability to recover known cases of TE-derived CDS. The probabilistic analysis of TE-derived exon sequences indicates that these sequences have low protein coding potential on average. In particular, non-autonomous TEs that do not encode protein sequences, such as Alu elements, are frequently exonized but unlikely to encode protein sequences. Conclusion The exaptation of the numerous TE sequences found in exons as bona fide protein coding sequences may prove to be far less common than has been suggested by the analysis of complete genomes. We hypothesize that many exonized TE sequences actually function as post-transcriptional regulators of gene expression, rather than coding sequences, which may act through a variety of double stranded RNA related regulatory pathways. Indeed, their relatively high copy numbers and similarity to sequences dispersed throughout the genome suggests that exonized TE sequences could serve as master regulators with a wide scope of regulatory influence. Reviewers: This article was reviewed by Itai Yanai, Kateryna D. Makova, Melissa Wilson (nominated by Kateryna D. Makova) and Cedric Feschotte (nominated by John M. Logsdon Jr.). PMID:18036258

Quantification of turbulence and velocity in stenotic flow using spiral three-dimensional phase-contrast MRI.

PubMed

Petersson, Sven; Dyverfeldt, Petter; Sigfridsson, Andreas; Lantz, Jonas; Carlhäll, Carl-Johan; Ebbers, Tino

2016-03-01

Evaluate spiral three-dimensional (3D) phase contrast MRI for the assessment of turbulence and velocity in stenotic flow. A-stack-of-spirals 3D phase contrast MRI sequence was evaluated in vitro against a conventional Cartesian sequence. Measurements were made in a flow phantom with a 75% stenosis. Both spiral and Cartesian imaging were performed using different scan orientations and flow rates. Volume flow rate, maximum velocity and turbulent kinetic energy (TKE) were computed for both methods. Moreover, the estimated TKE was compared with computational fluid dynamics (CFD) data. There was good agreement between the turbulent kinetic energy from the spiral, Cartesian and CFD data. Flow rate and maximum velocity from the spiral data agreed well with Cartesian data. As expected, the short echo time of the spiral sequence resulted in less prominent displacement artifacts compared with the Cartesian sequence. However, both spiral and Cartesian flow rate estimates were sensitive to displacement when the flow was oblique to the encoding directions. Spiral 3D phase contrast MRI appears favorable for the assessment of stenotic flow. The spiral sequence was more than three times faster and less sensitive to displacement artifacts when compared with a conventional Cartesian sequence. © 2015 Wiley Periodicals, Inc.

Early-Time Solution of the Horizontal Unconfined Aquifer in the Buildup Phase

NASA Astrophysics Data System (ADS)

Gravanis, Elias; Akylas, Evangelos

2017-10-01

We derive the early-time solution of the Boussinesq equation for the horizontal unconfined aquifer in the buildup phase under constant recharge and zero inflow. The solution is expressed as a power series of a suitable similarity variable, which is constructed so that to satisfy the boundary conditions at both ends of the aquifer, that is, it is a polynomial approximation of the exact solution. The series turns out to be asymptotic and it is regularized by resummation techniques that are used to define divergent series. The outflow rate in this regime is linear in time, and the (dimensionless) coefficient is calculated to eight significant figures. The local error of the series is quantified by its deviation from satisfying the self-similar Boussinesq equation at every point. The local error turns out to be everywhere positive, hence, so is the integrated error, which in turn quantifies the degree of convergence of the series to the exact solution.

Sequence-specific unusual (1-->2)-type helical turns in alpha/beta-hybrid peptides.

PubMed

Prabhakaran, Panchami; Kale, Sangram S; Puranik, Vedavati G; Rajamohanan, P R; Chetina, Olga; Howard, Judith A K; Hofmann, Hans-Jörg; Sanjayan, Gangadhar J

2008-12-31

This article describes novel conformationally ordered alpha/beta-hybrid peptides consisting of repeating l-proline-anthranilic acid building blocks. These oligomers adopt a compact, right-handed helical architecture determined by the intrinsic conformational preferences of the individual amino acid residues. The striking feature of these oligomers is their ability to display an unusual periodic pseudo beta-turn network of nine-membered hydrogen-bonded rings formed in the forward direction of the sequence by 1-->2 amino acid interactions both in solid-state and in solution. Conformational investigations of several of these oligomers by single-crystal X-ray diffraction, solution-state NMR, and ab initio MO theory suggest that the characteristic steric and dihedral angle restraints exerted by proline are essential for stabilizing the unusual pseudo beta-turn network found in these oligomers. Replacing proline by the conformationally flexible analogue alanine (Ala) or by the conformationally more constrained alpha-amino isobutyric acid (Aib) had an adverse effect on the stabilization of this structural architecture. These findings increase the potential to design novel secondary structure elements profiting from the steric and dihedral angle constraints of the amino acid constituents and help to augment the conformational space available for synthetic oligomer design with diverse backbone structures.

On the stability and maximum mass of differentially rotating relativistic stars

NASA Astrophysics Data System (ADS)

Weih, Lukas R.; Most, Elias R.; Rezzolla, Luciano

2018-01-01

The stability properties of rotating relativistic stars against prompt gravitational collapse to a black hole are rather well understood for uniformly rotating models. This is not the case for differentially rotating neutron stars, which are expected to be produced in catastrophic events such as the merger of binary system of neutron stars or the collapse of a massive stellar core. We consider sequences of differentially rotating equilibrium models using the j-constant law and by combining them with their dynamical evolution, we show that a sufficient stability criterion for differentially rotating neutron stars exists similar to the one of their uniformly rotating counterparts. Namely: along a sequence of constant angular momentum, a dynamical instability sets in for central rest-mass densities slightly below the one of the equilibrium solution at the turning point. In addition, following Breu & Rezzolla, we show that `quasi-universal' relations can be found when calculating the turning-point mass. In turn, this allows us to compute the maximum mass allowed by differential rotation, Mmax,dr, in terms of the maximum mass of the non-rotating configuration, M_{_TOV}, finding that M_{max, dr} ˜eq (1.54 ± 0.05) M_{_TOV} for all the equations of state we have considered.

Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology.

PubMed

Sharma, Archana; Satyanarayana, T

2013-01-01

With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Today, genome sequences of several Bacillus species are available, and comparative genomics of this genus helps in understanding their physiology, biochemistry, and genetics. The genomes of these bacterial species are the sources of many industrially important enzymes and antibiotics and, therefore, provide an opportunity to tailor enzymes with desired properties to suit a wide range of applications. A comparative account of strengths and weaknesses of the different sequencing platforms are also highlighted in the review.

Kinematics of center of mass and center of pressure predict friction requirement at shoe-floor interface during walking.

PubMed

Yamaguchi, Takeshi; Yano, Masaru; Onodera, Hiroshi; Hokkirigawa, Kazuo

2013-06-01

We aimed to determine whether inclination angles of the line connecting the whole body center of mass (COM) to the center of pressure (COP) (COM-COP angle) help predict the required coefficient of friction (RCOF) in young adult males during the weight acceptance and push-off phases in transient movements such as turning, gait termination and initiation, and steady-state movements such as straight walking. Seventeen healthy young adult males were asked to (1) walk in a straight line, (2) turn 60° with either foot (step and spin turns), and (3) initiate and terminate walking on a dry level floor. Peak absolute values of the ratio between resultant horizontal and vertical ground reaction forces during the weight acceptance and push-off phases (RCOFh and RCOFt, respectively) were calculated. COM-COP angles θh and θt at the instant of RCOFh and RCOFt, respectively, were also calculated. Bivariate regression analysis demonstrated that the |θh| and |θt| tangents were significant predictors of RCOFh (R = 0.878; R(2) = 0.770; p<0.001) and RCOFt (R = 0.918; R(2) = 0.843; p<0.001), respectively. The results suggest that COM and COP kinematics (i.e., the COM-COP angle) serve as a predictor of friction requirement during the weight acceptance and push-off phases in steady-state movements such as straight walking and transient movements such as turning as well as gait termination and initiation. Copyright © 2012 Elsevier B.V. All rights reserved.

Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis.

PubMed

Han, S; Arvai, A S; Clancy, S B; Tainer, J A

2001-01-05

Clostridium botulinum C3 exoenzyme inactivates the small GTP-binding protein family Rho by ADP-ribosylating asparagine 41, which depolymerizes the actin cytoskeleton. C3 thus represents a major family of the bacterial toxins that transfer the ADP-ribose moiety of NAD to specific amino acids in acceptor proteins to modify key biological activities in eukaryotic cells, including protein synthesis, differentiation, transformation, and intracellular signaling. The 1.7 A resolution C3 exoenzyme structure establishes the conserved features of the core NAD-binding beta-sandwich fold with other ADP-ribosylating toxins despite little sequence conservation. Importantly, the central core of the C3 exoenzyme structure is distinguished by the absence of an active site loop observed in many other ADP-ribosylating toxins. Unlike the ADP-ribosylating toxins that possess the active site loop near the central core, the C3 exoenzyme replaces the active site loop with an alpha-helix, alpha3. Moreover, structural and sequence similarities with the catalytic domain of vegetative insecticidal protein 2 (VIP2), an actin ADP-ribosyltransferase, unexpectedly implicates two adjacent, protruding turns, which join beta5 and beta6 of the toxin core fold, as a novel recognition specificity motif for this newly defined toxin family. Turn 1 evidently positions the solvent-exposed, aromatic side-chain of Phe209 to interact with the hydrophobic region of Rho adjacent to its GTP-binding site. Turn 2 evidently both places the Gln212 side-chain for hydrogen bonding to recognize Rho Asn41 for nucleophilic attack on the anomeric carbon of NAD ribose and holds the key Glu214 catalytic side-chain in the adjacent catalytic pocket. This proposed bipartite ADP-ribosylating toxin turn-turn (ARTT) motif places the VIP2 and C3 toxin classes into a single ARTT family characterized by analogous target protein recognition via turn 1 aromatic and turn 2 hydrogen-bonding side-chain moieties. Turn 2 centrally anchors the catalytic Glu214 within the ARTT motif, and furthermore distinguishes the C3 toxin class by a conserved turn 2 Gln and the VIP2 binary toxin class by a conserved turn 2 Glu for appropriate target side-chain hydrogen-bonding recognition. Taken together, these structural results provide a molecular basis for understanding the coupled activity and recognition specificity for C3 and for the newly defined ARTT toxin family, which acts in the depolymerization of the actin cytoskeleton. This beta5 to beta6 region of the toxin fold represents an experimentally testable and potentially general recognition motif region for other ADP-ribosylating toxins that have a similar beta-structure framework. Copyright 2001 Academic Press.

ALMA Long Baseline Campaigns: Phase Characteristics of Atmosphere at Long Baselines in the Millimeter and Submillimeter Wavelengths

NASA Astrophysics Data System (ADS)

Matsushita, Satoki; Asaki, Yoshiharu; Fomalont, Edward B.; Morita, Koh-Ichiro; Barkats, Denis; Hills, Richard E.; Kawabe, Ryohei; Maud, Luke T.; Nikolic, Bojan; Tilanus, Remo P. J.; Vlahakis, Catherine; Whyborn, Nicholas D.

2017-03-01

We present millimeter- and submillimeter-wave phase characteristics measured between 2012 and 2014 of Atacama Large Millimeter/submillimeter Array long baseline campaigns. This paper presents the first detailed investigation of the characteristics of phase fluctuation and phase correction methods obtained with baseline lengths up to ˜15 km. The basic phase fluctuation characteristics can be expressed with the spatial structure function (SSF). Most of the SSFs show that the phase fluctuation increases as a function of baseline length, with a power-law slope of ˜0.6. In many cases, we find that the slope becomes shallower (average of ˜0.2-0.3) at baseline lengths longer than ˜1 km, namely showing a turn-over in SSF. These power law slopes do not change with the amount of precipitable water vapor (PWV), but the fitted constants have a weak correlation with PWV, so that the phase fluctuation at a baseline length of 10 km also increases as a function of PWV. The phase correction method using water vapor radiometers (WVRs) works well, especially for the cases where PWV > 1 {mm}, which reduces the degree of phase fluctuations by a factor of two in many cases. However, phase fluctuations still remain after the WVR phase correction, suggesting the existence of other turbulent constituent that cause the phase fluctuation. This is supported by occasional SSFs that do not exhibit any turn-over; these are only seen when the PWV is low (i.e., when the WVR phase correction works less effectively) or after WVR phase correction. This means that the phase fluctuation caused by this turbulent constituent is inherently smaller than that caused by water vapor. Since in these rare cases there is no turn-over in the SSF up to the maximum baseline length of ˜15 km, this turbulent constituent must have scale height of 10 km or more, and thus cannot be water vapor, whose scale height is around 1 km. Based on the characteristics, this large scale height turbulent constituent is likely to be water ice or a dry component. Excess path length fluctuation after the WVR phase correction at a baseline length of 10 km is large (≳ 200 μ {{m}}), which is significant for high frequency (> 450 {GHz} or < 700 μ {{m}}) observations. These results suggest the need for an additional phase correction method to reduce the degree of phase fluctuation, such as fast switching, in addition to the WVR phase correction. We simulated the fast switching phase correction method using observations of single quasars, and the result suggests that it works well, with shorter cycle times linearly improving the coherence.

Beyond The Human Genome: What's Next? (LBNL Summer Lecture Series)

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

Rokhsar, Daniel

2003-06-18

UC Berkeley's Daniel Rokhsar and his colleagues were instrumental in contributing the sequences for three of the human body's chromosomes in the effort to decipher the blueprint of life- the completion of the DNA sequencing of the human genome. Now he is turning to the structure and function of genes in other organisms, some of them no less important to the planet's future than the human map. Hear the latest in this lecture from Lawrence Berkeley National Laboratory.

Beyond The Human Genome: What's Next? (LBNL Summer Lecture Series)

ScienceCinema

Rokhsar, Daniel

2018-04-27

UC Berkeley's Daniel Rokhsar and his colleagues were instrumental in contributing the sequences for three of the human body's chromosomes in the effort to decipher the blueprint of life- the completion of the DNA sequencing of the human genome. Now he is turning to the structure and function of genes in other organisms, some of them no less important to the planet's future than the human map. Hear the latest in this lecture from Lawrence Berkeley National Laboratory.

Peptoid architectures: elaboration, actuation, and application.

PubMed

Yoo, Barney; Kirshenbaum, Kent

2008-12-01

Peptoids are peptidomimetic oligomers composed of N-substituted glycine units. Their convenient synthesis enables strict control over the sequence of highly diverse monomers and is capable of generating extensive compound libraries. Recent studies are beginning to explore the relationship between peptoid sequence, structure and function. We describe new approaches to direct the conformation of the peptoid backbone, leading to secondary structures such as helices, loops, and turns. These advances are enabling the discovery of bioactive peptoids and will establish modules for the design and assembly of protein mimetics.

Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety.

PubMed

De Gannes, Vidya; Eudoxie, Gaius; Hickey, William J

2013-01-01

Fungal community composition in composts of lignocellulosic wastes was assessed via 454-pyrosequencing of ITS1 libraries derived from the three major composting phases. Ascomycota represented most (93%) of the 27,987 fungal sequences. A total of 102 genera, 120 species, and 222 operational taxonomic units (OTUs; >97% similarity) were identified. Thirty genera predominated (ca. 94% of the sequences), and at the species level, sequences matching Chaetomium funicola and Fusarium oxysporum were the most abundant (26 and 12%, respectively). In all composts, fungal diversity in the mature phase exceeded that of the mesophilic phase, but there was no consistent pattern in diversity changes occurring in the thermophilic phase. Fifteen species of human pathogens were identified, eight of which have not been previously identified in composts. This study demonstrated that deep sequencing can elucidate fungal community diversity in composts, and that this information can have important implications for compost use and human health.

Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety

PubMed Central

De Gannes, Vidya; Eudoxie, Gaius; Hickey, William J.

2013-01-01

Fungal community composition in composts of lignocellulosic wastes was assessed via 454-pyrosequencing of ITS1 libraries derived from the three major composting phases. Ascomycota represented most (93%) of the 27,987 fungal sequences. A total of 102 genera, 120 species, and 222 operational taxonomic units (OTUs; >97% similarity) were identified. Thirty genera predominated (ca. 94% of the sequences), and at the species level, sequences matching Chaetomium funicola and Fusarium oxysporum were the most abundant (26 and 12%, respectively). In all composts, fungal diversity in the mature phase exceeded that of the mesophilic phase, but there was no consistent pattern in diversity changes occurring in the thermophilic phase. Fifteen species of human pathogens were identified, eight of which have not been previously identified in composts. This study demonstrated that deep sequencing can elucidate fungal community diversity in composts, and that this information can have important implications for compost use and human health. PMID:23785368

Long-period gratings in photonic crystal fibers operating near the phase-matching turning point for evanescent chemical and biochemical sensing

NASA Astrophysics Data System (ADS)

Kanka, Jiri

2012-06-01

Fiber-optic long-period grating (LPG) operating near the dispersion turning point in its phase matching curve (PMC), referred to as a Turn Around Point (TAP) LPG, is known to be extremely sensitive to external parameters. Moreover, in a TAP LPG the phase matching condition can be almost satisfied over large spectral range, yielding a broadband LPG operation. TAP LPGs have been investigated, namely for use as broadband mode convertors and biosensors. So far TAP LPGs have been realized in specially designed or post-processed conventional fibers, not yet in PCFs, which allow a great degree of freedom in engineering the fiber's dispersion properties through the control of the PCF structural parameters. We have developed the design optimization technique for TAP PCF LPGs employing the finite element method for PCF modal analysis in a combination with the Nelder-Mead simplex method for minimizing the objective function based on target-specific PCF properties. Using this tool we have designed TAP PCF LPGs for specified wavelength ranges and refractive indices of medium in the air holes. Possible TAP PCF-LPG operational regimes - dual-resonance, broadband mode conversion and transmitted intensity-based operation - will be demonstrated numerically. Potential and limitations of TAP PCF-LPGs for evanescent chemical and biochemical sensing will be assessed.

Lower limb joint motion during a cross cutting movement differs in individuals with and without chronic ankle instability.

PubMed

Koshino, Yuta; Yamanaka, Masanori; Ezawa, Yuya; Ishida, Tomoya; Kobayashi, Takumi; Samukawa, Mina; Saito, Hiroshi; Takeda, Naoki

2014-11-01

To compare the kinematics of lower limb joints between individuals with and without chronic ankle instability (CAI) during cross-turn and -cutting movements. Cross-sectional study. Motion analysis laboratory. Twelve subjects with CAI and twelve healthy controls. Hip flexion, adduction, and internal rotation, knee flexion, and ankle dorsiflexion and inversion angles were calculated in the 200 ms before initial ground contact and from initial ground contact to toe-off (stance phase) in a cross-turn movement during gait and a cross-cutting movement from a forward jump, and compared across the two groups. In the cross-cutting movement, the CAI group exhibited greater hip and knee flexion than the control group during the stance phase, and more hip abduction during the period before initial contact and the stance phase. In the cross-turn movement the joint kinematics were similar in the two groups. CAI subjects exhibited an altered pattern of the proximal joint kinematics during a cross-cutting movement. It is important for clinicians to assess the function of the hip and knee as well as the ankle, and to incorporate coordination training for the entire lower limb into rehabilitation after lateral ankle sprains. Copyright © 2013 Elsevier Ltd. All rights reserved.

The effects of core-reflected waves on finite fault inversions with teleseismic body wave data

NASA Astrophysics Data System (ADS)

Qian, Yunyi; Ni, Sidao; Wei, Shengji; Almeida, Rafael; Zhang, Han

2017-11-01

Teleseismic body waves are essential for imaging rupture processes of large earthquakes. Earthquake source parameters are usually characterized by waveform analyses such as finite fault inversions using only turning (direct) P and SH waves without considering the reflected phases from the core-mantle boundary (CMB). However, core-reflected waves such as ScS usually have amplitudes comparable to direct S waves due to the total reflection from the CMB and might interfere with the S waves used for inversion, especially at large epicentral distances for long duration earthquakes. In order to understand how core-reflected waves affect teleseismic body wave inversion results, we develop a procedure named Multitel3 to compute Green's functions that contain turning waves (direct P, pP, sP, direct S, sS and reverberations in the crust) and core-reflected waves (PcP, pPcP, sPcP, ScS, sScS and associated reflected phases from the CMB). This ray-based method can efficiently generate synthetic seismograms for turning and core-reflected waves independently, with the flexibility to take into account the 3-D Earth structure effect on the timing between these phases. The performance of this approach is assessed through a series of numerical inversion tests on synthetic waveforms of the 2008 Mw7.9 Wenchuan earthquake and the 2015 Mw7.8 Nepal earthquake. We also compare this improved method with the turning-wave only inversions and explore the stability of the new procedure when there are uncertainties in a priori information (such as fault geometry and epicentre location) or arrival time of core-reflected phases. Finally, a finite fault inversion of the 2005 Mw8.7 Nias-Simeulue earthquake is carried out using the improved Green's functions. Using enhanced Green's functions yields better inversion results as expected. While the finite source inversion with conventional P and SH waves is able to recover large-scale characteristics of the earthquake source, by adding PcP and ScS phases, the inverted slip model and moment rate function better match previous results incorporating field observations, geodetic and seismic data.

Whole Genome Complete Resequencing of Bacillus subtilis Natto by Combining Long Reads with High-Quality Short Reads

PubMed Central

Kamada, Mayumi; Hase, Sumitaka; Sato, Kengo; Toyoda, Atsushi; Fujiyama, Asao; Sakakibara, Yasubumi

2014-01-01

De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and it has a function in the production of the traditional Japanese fermented food “natto.” The B. subtilis natto BEST195 genome was previously sequenced with short reads, but it included some incomplete regions. We resequenced the BEST195 genome using a PacBio RS sequencer, and we successfully obtained a complete genome sequence from one scaffold without any gaps, and we also applied Illumina MiSeq short reads to enhance quality. Compared with the previous BEST195 draft genome and Marburg 168 genome, we found that incomplete regions in the previous genome sequence were attributed to GC-bias and repetitive sequences, and we also identified some novel genes that are found only in the new genome. PMID:25329997

Enhanced sequencing coverage with digital droplet multiple displacement amplification

PubMed Central

Sidore, Angus M.; Lan, Freeman; Lim, Shaun W.; Abate, Adam R.

2016-01-01

Sequencing small quantities of DNA is important for applications ranging from the assembly of uncultivable microbial genomes to the identification of cancer-associated mutations. To obtain sufficient quantities of DNA for sequencing, the small amount of starting material must be amplified significantly. However, existing methods often yield errors or non-uniform coverage, reducing sequencing data quality. Here, we describe digital droplet multiple displacement amplification, a method that enables massive amplification of low-input material while maintaining sequence accuracy and uniformity. The low-input material is compartmentalized as single molecules in millions of picoliter droplets. Because the molecules are isolated in compartments, they amplify to saturation without competing for resources; this yields uniform representation of all sequences in the final product and, in turn, enhances the quality of the sequence data. We demonstrate the ability to uniformly amplify the genomes of single Escherichia coli cells, comprising just 4.7 fg of starting DNA, and obtain sequencing coverage distributions that rival that of unamplified material. Digital droplet multiple displacement amplification provides a simple and effective method for amplifying minute amounts of DNA for accurate and uniform sequencing. PMID:26704978

SSAW: A new sequence similarity analysis method based on the stationary discrete wavelet transform.

PubMed

Lin, Jie; Wei, Jing; Adjeroh, Donald; Jiang, Bing-Hua; Jiang, Yue

2018-05-02

Alignment-free sequence similarity analysis methods often lead to significant savings in computational time over alignment-based counterparts. A new alignment-free sequence similarity analysis method, called SSAW is proposed. SSAW stands for Sequence Similarity Analysis using the Stationary Discrete Wavelet Transform (SDWT). It extracts k-mers from a sequence, then maps each k-mer to a complex number field. Then, the series of complex numbers formed are transformed into feature vectors using the stationary discrete wavelet transform. After these steps, the original sequence is turned into a feature vector with numeric values, which can then be used for clustering and/or classification. Using two different types of applications, namely, clustering and classification, we compared SSAW against the the-state-of-the-art alignment free sequence analysis methods. SSAW demonstrates competitive or superior performance in terms of standard indicators, such as accuracy, F-score, precision, and recall. The running time was significantly better in most cases. These make SSAW a suitable method for sequence analysis, especially, given the rapidly increasing volumes of sequence data required by most modern applications.

Seismic analysis of clinoform depositional sequences and shelf-margin trajectories in Lower Cretaceous (Albian) strata, Alaska North Slope

USGS Publications Warehouse

Houseknecht, D.W.; Bird, K.J.; Schenk, C.J.

2009-01-01

Lower Cretaceous strata beneath the Alaska North Slope include clinoform depositional sequences that filled the western Colville foreland basin and overstepped the Beaufort rift shoulder. Analysis of Albian clinoform sequences with two-dimensional (2D) seismic data resulted in the recognition of seismic facies inferred to represent lowstand, transgressive and highstand systems tracts. These are stacked to produce shelf-margin trajectories that appear in low-resolution seismic data to alternate between aggradational and progradational. Higher-resolution seismic data reveal shelf-margin trajectories that are more complex, particularly in net-aggradational areas, where three patterns commonly are observed: (1) a negative (downward) step across the sequence boundary followed by mostly aggradation in the lowstand systems tract (LST), (2) a positive (upward) step across the sequence boundary followed by mostly progradation in the LST and (3) an upward backstep across a mass-failure d??collement. These different shelf-margin trajectories are interpreted as (1) fall of relative sea level below the shelf edge, (2) fall of relative sea level to above the shelf edge and (3) mass-failure removal of shelf-margin sediment. Lowstand shelf margins mapped using these criteria are oriented north-south in the foreland basin, indicating longitudinal filling from west to east. The shelf margins turn westward in the north, where the clinoform depositional system overstepped the rift shoulder, and turn eastward in the south, suggesting progradation of depositional systems from the ancestral Brooks Range into the foredeep. Lowstand shelf-margin orientations are consistently perpendicular to clinoform-foreset-dip directions. Although the Albian clinoform sequences of the Alaska North Slope are generally similar in stratal geometry to clinoform sequences elsewhere, they are significantly thicker. Clinoform-sequence thickness ranges from 600-1000 m in the north to 1700-2000 m in the south, reflecting increased accommodation from the rift shoulder into the foredeep. The unusually thick clinoform sequences suggest significant subsidence followed by rapid sediment influx. No claim to original US government works. Journal Compilation ?? Blackwell Publishing Ltd, European Association of Geoscientists & Engineers and International Association of Sedimentologists.

Extended Main-sequence Turn-offs in Intermediate-age Star Clusters: Stellar Rotation Diminishes, but Does Not Eliminate, Age Spreads

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

Goudfrooij, Paul; Correnti, Matteo; Girardi, Léo, E-mail: goudfroo@stsci.edu

Extended main-sequence turn-off (eMSTO) regions are a common feature in color–magnitude diagrams of young- and intermediate-age star clusters in the Magellanic Clouds. The nature of eMSTOs remains debated in the literature. The currently most popular scenarios are extended star formation activity and ranges of stellar rotation rates. Here we study details of differences in main-sequence turn-off (MSTO) morphology expected from spreads in age versus spreads in rotation rates, using Monte Carlo simulations with the Geneva syclist isochrone models that include the effects of stellar rotation. We confirm a recent finding of Niederhofer et al. that a distribution of stellar rotationmore » velocities yields an MSTO extent that is proportional to the cluster age, as observed. However, we find that stellar rotation yields MSTO crosscut widths that are generally smaller than observed ones at a given age. We compare the simulations with high-quality Hubble Space Telescope data of NGC 1987 and NGC 2249, which are the two only relatively massive star clusters with an age of ∼1 Gyr for which such data is available. We find that the distribution of stars across the eMSTOs of these clusters cannot be explained solely by a distribution of stellar rotation velocities, unless the orientations of rapidly rotating stars are heavily biased toward an equator-on configuration. Under the assumption of random viewing angles, stellar rotation can account for ∼60% and ∼40% of the observed FWHM widths of the eMSTOs of NGC 1987 and NGC 2249, respectively. In contrast, a combination of distributions of stellar rotation velocities and stellar ages fits the observed eMSTO morphologies very well.« less

Multiple stellar populations in Magellanic Cloud clusters - III. The first evidence of an extended main sequence turn-off in a young cluster: NGC 1856

NASA Astrophysics Data System (ADS)

Milone, A. P.; Bedin, L. R.; Piotto, G.; Marino, A. F.; Cassisi, S.; Bellini, A.; Jerjen, H.; Pietrinferni, A.; Aparicio, A.; Rich, R. M.

2015-07-01

Recent studies have shown that the extended main-sequence turn-off (eMSTO) is a common feature of intermediate-age star clusters in the Magellanic Clouds (MCs). The most simple explanation is that these stellar systems harbour multiple generations of stars with an age difference of a few hundred million years. However, while an eMSTO has been detected in a large number of clusters with ages between ˜1-2 Gyr, several studies of young clusters in both MCs and in nearby galaxies do not find any evidence for a prolonged star formation history, i. e. for multiple stellar generations. These results have suggested alternative interpretation of the eMSTOs observed in intermediate-age star clusters. The eMSTO could be due to stellar rotation mimicking an age spread or to interacting binaries. In these scenarios, intermediate-age MC clusters would be simple stellar populations, in close analogy with younger clusters. Here, we provide the first evidence for an eMSTO in a young stellar cluster. We exploit multiband Hubble Space Telescope photometry to study the ˜300-Myr old star cluster NGC 1856 in the Large Magellanic Cloud and detected a broadened MSTO that is consistent with a prolonged star formation which had a duration of about 150 Myr. Below the turn-off, the main sequence (MS) of NGC 1856 is split into a red and blue component, hosting 33 ± 5 and 67 ± 5 per cent of the total number of MS stars, respectively. We discuss these findings in the context of multiple-stellar-generation, stellar-rotation, and interacting-binary hypotheses.

Performance drifts in two-finger cyclical force production tasks performed by one and two actors.

PubMed

Hasanbarani, Fariba; Reschechtko, Sasha; Latash, Mark L

2018-03-01

We explored changes in the cyclical two-finger force performance task caused by turning visual feedback off performed either by the index and middle fingers of the dominant hand or by two index fingers of two persons. Based on an earlier study, we expected drifts in finger force amplitude and midpoint without a drift in relative phase. The subjects performed two rhythmical tasks at 1 Hz while paced by an auditory metronome. One of the tasks required cyclical changes in total force magnitude without changes in the sharing of the force between the two fingers. The other task required cyclical changes in the force sharing without changing total force magnitude. Subjects were provided with visual feedback, which showed total force magnitude and force sharing via cursor motion along the vertical and horizontal axes, respectively. Further, visual feedback was turned off, first on the variable that was not required to change and then on both variables. Turning visual feedback off led to a mean force drift toward lower magnitudes while force amplitude increased. There was a consistent drift in the relative phase in the one-hand task with the index finger leading the middle finger. No consistent relative phase drift was seen in the two-person tasks. The shape of the force cycle changed without visual feedback reflected in the lower similarity to a perfect cosine shape and in the higher time spent at lower force magnitudes. The data confirm findings of earlier studies regarding force amplitude and midpoint changes, but falsify predictions of an earlier proposed model with respect to the relative phase changes. We discuss factors that could contribute to the observed relative phase drift in the one-hand tasks including the leader-follower pattern generalized for two-effector tasks performed by one person.

A minimal peptide scaffold for beta-turn display: optimizing a strand position in disulfide-cyclized beta-hairpins.

PubMed

Cochran, A G; Tong, R T; Starovasnik, M A; Park, E J; McDowell, R S; Theaker, J E; Skelton, N J

2001-01-31

Phage display of peptide libraries has become a powerful tool for the evolution of novel ligands that bind virtually any protein target. However, the rules governing conformational preferences in natural peptides are poorly understood, and consequently, structure-activity relationships in these molecules can be difficult to define. In an effort to simplify this process, we have investigated the structural stability of 10-residue, disulfide-constrained beta-hairpins and assessed their suitability as scaffolds for beta-turn display. Using disulfide formation as a probe, relative free energies of folding were measured for 19 peptides that differ at a one strand position. A tryptophan substitution promotes folding to a remarkable degree. NMR analysis confirms that the measured energies correlate well with the degree of beta-hairpin structure in the disulfide-cyclized peptides. Reexamination of a subset of the strand substitutions in peptides with different turn sequences reveals linear free energy relationships, indicating that turns and strand-strand interactions make independent, additive contributions to hairpin stability. Significantly, the tryptophan strand substitution is highly stabilizing with all turns tested, and peptides that display model turns or the less stable C'-C' ' turn of CD4 on this tryptophan "stem" are highly structured beta-hairpins in water. Thus, we have developed a small, structured beta-turn scaffold, containing only natural L-amino acids, that may be used to display peptide libraries of limited conformational diversity on phage.

The commercial evolution of the Titan program

NASA Astrophysics Data System (ADS)

Isakowitz, Steven

1988-07-01

The present status evaluation of proprietary efforts to turn the once exclusively government-requirements-oriented Titan launch vehicle into a successful commercial competitor is divided into three phases. The first phase notes recent changes in U.S. space transportation policy and the Titan configurations evaluated for commercial feasibility. The second phase is a development history for the current vehicle's marketing organization and the right-to-use agreement for a launch site. Phase three projects the prospective marketing climate for a commercial Titan vehicle and its planned improvements.

Overcoming S-Phase Checkpoint-Mediated Resistance: Sequence-Dependent Synergy of Gemcitabine and SN-38 In Human Carcinoma Cell Lines*

PubMed Central

Gálvez-Peralta, Marina; Dai, Nga T.; Loegering, David A.; Flatten, Karen; Safgren, Stephanie; Wagner, Jill; Ames, Matthew M.; Karnitz, Larry M.; Kaufmann, Scott H.

2008-01-01

Although agents that inhibit DNA synthesis are widely used in the treatment of cancer, the optimal method for combining such agents and the mechanism of their synergy is poorly understood. The present study examined the effects of combining gemcitabine and SN-38 (the active metabolite of irinotecan), two S phase-selective agents that individually have broad antitumor activity, in human cancer cells in vitro. Colony forming assays revealed that simultaneous treatment of Ovcar-5 ovarian cancer cells or BxPC-3 pancreatic cancer cells with gemcitabine and SN-38 resulted in antagonistic effects. In contrast, sequential treatment with the two agents in either order resulted in synergistic antiproliferative effects, although the mechanism of synergy varied with the sequence. In particular, SN-38 arrested cells in S phase, enhanced the accumulation of gemcitabine metabolites and diminished checkpoint kinase 1, thereby sensitizing cells in the SN-38 → gemcitabine sequence. Gemcitabine treatment followed by removal allowed prolonged progression through S phase, contributing to synergy of the gemcitabine → SN-38 sequence. Collectively, these results suggest that S phase selective agents might exhibit more cytotoxicity when administered sequentially rather than simultaneously. PMID:18509065

Self-organizing approach for meta-genomes.

PubMed

Zhu, Jianfeng; Zheng, Wei-Mou

2014-12-01

We extend the self-organizing approach for annotation of a bacterial genome to analyze the raw sequencing data of the human gut metagenome without sequence assembling. The original approach divides the genomic sequence of a bacterium into non-overlapping segments of equal length and assigns to each segment one of seven 'phases', among which one is for the noncoding regions, three for the direct coding regions to indicate the three possible codon positions of the segment starting site, and three for the reverse coding regions. The noncoding phase and the six coding phases are described by two frequency tables of the 64 triplet types or 'codon usages'. A set of codon usages can be used to update the phase assignment and vice versa. An iteration after an initialization leads to a convergent phase assignment to give an annotation of the genome. In the extension of the approach to a metagenome, we consider a mixture model of a number of categories described by different codon usages. The Illumina Genome Analyzer sequencing data of the total DNA from faecal samples are then examined to understand the diversity of the human gut microbiome. Copyright © 2014 Elsevier Ltd. All rights reserved.

Enhanced processive cellulases

DOEpatents

Adney, William S.; Beckham, Gregg T.; Jarvis, Eric; Himmel, Michael E.; Decker, Stephen R.; Linger, Jeffrey G.; Podkaminer, Kara; Baker, John O.; Taylor, II, Larry; Xu, Qi; Singh, Arjun

2017-06-20

Nucleic acid sequences encoding chimeric polypeptides that exhibit enhanced cellulase activities are disclosed herein. These nucleic acids may be expressed in hosts such as fungi, which in turn may be cultured to produce chimeric polypeptides. Also disclosed are chimeric polypeptides and their use in the degradation of cellulosic materials.

Normative Expectations for Medical Talk.

ERIC Educational Resources Information Center

Youssef, Valerie; Silverman, David

1992-01-01

Inappropriate communicative strategies and their effects are assessed using information collected in Trinidad and Tobago (T&T) from counselor-patient interaction in pre- and posttest AIDS counseling. Inappropriateness was assessed by the disruption in conversational turn-taking sequences shown by overlap and shifts in communication format.…

Sequencing of Vocational Development Stages: Further Studies

ERIC Educational Resources Information Center

Hershenson, David B.; Lavery, Gerard J.

1978-01-01

Reports two studies supporting the prediction derived from Hershenson's life-stage vocational development model that average scores on Self-differentiation (worker self-concept and motivation) would exceed those on Competence (work habits, skills, and interpersonal relations), which in turn would exceed those on Independence (appropriateness and…

Backbone hydration determines the folding signature of amino acid residues.

PubMed

Bignucolo, Olivier; Leung, Hoi Tik Alvin; Grzesiek, Stephan; Bernèche, Simon

2015-04-08

The relation between the sequence of a protein and its three-dimensional structure remains largely unknown. A lasting dream is to elucidate the side-chain-dependent driving forces that govern the folding process. Different structural data suggest that aromatic amino acids play a particular role in the stabilization of protein structures. To better understand the underlying mechanism, we studied peptides of the sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through comparison of molecular dynamics (MD) trajectories and NMR residual dipolar coupling (RDC) measurements. The RDC data for aromatic substitutions provide evidence for a kink in the peptide backbone. Analysis of the MD simulations shows that the formation of internal hydrogen bonds underlying a helical turn is key to reproduce the experimental RDC values. The simulations further reveal that the driving force leading to such helical-turn conformations arises from the lack of hydration of the peptide chain on either side of the bulky aromatic side chain, which can potentially act as a nucleation point initiating the folding process.

Universal relations for differentially rotating relativistic stars at the threshold to collapse

NASA Astrophysics Data System (ADS)

Bozzola, Gabriele; Stergioulas, Nikolaos; Bauswein, Andreas

2018-03-01

A binary neutron star merger produces a rapidly and differentially rotating compact remnant whose lifespan heavily affects the electromagnetic and gravitational emissions. Its stability depends on both the equation of state (EOS) and the rotation law and it is usually investigated through numerical simulations. Nevertheless, by means of a sufficient criterion for secular instability, equilibrium sequences can be used as a computational inexpensive way to estimate the onset of dynamical instability, which, in general, is close to the secular one. This method works well for uniform rotation and relies on the location of turning points: stellar models that are stationary points in a sequence of equilibrium solutions with constant rest mass or angular momentum. Here, we investigate differentially rotating models (using a large number of EOSs and different rotation laws) and find that several universal relations between properly scaled gravitational mass, rest mass and angular momentum of the turning-point models that are valid for uniform rotation are insensitive to the degree of differential rotation, to high accuracy.

Incorporating beta-turns and a turn mimetic out of context in loop 1 of the WW domain affords cooperatively folded beta-sheets.

PubMed

Kaul, R; Angeles, A R; Jäger, M; Powers, E T; Kelly, J W

2001-06-06

To probe the conformational requirements of loop 1 in the Pin1 WW domain, the residues at the i + 2 and i + 3 positions of a beta-turn within this loop were replaced by dPro-Gly and Asn-Gly, which are known to prefer the conformations required at the i + 1 and i + 2 positions of type II' and type I' beta-turns. Conformational specificity or lack thereof was further examined by incorporating into the i + 2 and i + 3 positions a non-alpha-amino acid-based beta-turn mimetic (4-(2'-aminoethyl)-6-dibenzofuran propionic acid residue, 1), which was designed to replace the i + 1 and i + 2 positions of beta-turns. All these Pin WW variants are monomeric and folded as discerned by analytical ultracentrifugation, NMR, and CD. They exhibit cooperative two-state transitions and display thermodynamic stability within 0.5 kcal/mol of the wild-type WW domain, demonstrating that the acquisition of native structure and stability does not require a specific sequence and, by extension, conformation within loop 1. However, it could be that these loop 1 mutations alter the kinetics of antiparallel beta-sheet folding, which will be addressed by subsequent kinetic studies.

Mars Exploration Rover Entry, Descent, and Landing: A Thermal Perspective

NASA Technical Reports Server (NTRS)

Tsuyuki, Glenn T.; Sunada, Eric T.; Novak, Keith S.; Kinsella, Gary M.; Phillip, Charles J.

2005-01-01

Perhaps the most challenging mission phase for the Mars Exploration Rovers was the Entry, Descent, and Landing (EDL). During this phase, the entry vehicle attached to its cruise stage was transformed into a stowed tetrahedral Lander that was surrounded by inflated airbags through a series of complex events. There was only one opportunity to successfully execute an automated command sequence without any possible ground intervention. The success of EDL was reliant upon the system thermal design: 1) to thermally condition EDL hardware from cruise storage temperatures to operating temperature ranges; 2) to maintain the Rover electronics within operating temperature ranges without the benefit of the cruise single phase cooling loop, which had been evacuated in preparation for EDL; and 3) to maintain the cruise stage propulsion components for the critical turn to entry attitude. Since the EDL architecture was inherited from Mars Pathfinder (MPF), the initial EDL thermal design would be inherited from MPF. However, hardware and implementation differences from MPF ultimately changed the MPF inheritance approach for the EDL thermal design. With the lack of full inheritance, the verification and validation of the EDL thermal design took on increased significance. This paper will summarize the verification and validation approach for the EDL thermal design along with applicable system level thermal testing results as well as appropriate thermal analyses. In addition, the lessons learned during the system-level testing will be discussed. Finally, the in-flight EDL experiences of both MER-A and -B missions (Spirit and Opportunity, respectively) will be presented, demonstrated how lessons learned from Spirit were applied to Opportunity.

Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences

PubMed Central

2016-01-01

X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H–1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions. PMID:28029251

Sequencing Adventure Activities: A New Perspective.

ERIC Educational Resources Information Center

Bisson, Christian

Sequencing in adventure education involves putting activities in an order appropriate to the needs of the group. Contrary to the common assumption that each adventure sequence is unique, a review of literature concerning five sequencing models reveals a certain universality. These models present sequences that move through four phases: group…

Flexible theta sequence compression mediated via phase precessing interneurons

PubMed Central

Chadwick, Angus; van Rossum, Mark CW; Nolan, Matthew F

2016-01-01

Encoding of behavioral episodes as spike sequences during hippocampal theta oscillations provides a neural substrate for computations on events extended across time and space. However, the mechanisms underlying the numerous and diverse experimentally observed properties of theta sequences remain poorly understood. Here we account for theta sequences using a novel model constrained by the septo-hippocampal circuitry. We show that when spontaneously active interneurons integrate spatial signals and theta frequency pacemaker inputs, they generate phase precessing action potentials that can coordinate theta sequences in place cell populations. We reveal novel constraints on sequence generation, predict cellular properties and neural dynamics that characterize sequence compression, identify circuit organization principles for high capacity sequential representation, and show that theta sequences can be used as substrates for association of conditioned stimuli with recent and upcoming events. Our results suggest mechanisms for flexible sequence compression that are suited to associative learning across an animal’s lifespan. DOI: http://dx.doi.org/10.7554/eLife.20349.001 PMID:27929374

Comparative analysis of the prion protein gene sequences in African lion.

PubMed

Wu, Chang-De; Pang, Wan-Yong; Zhao, De-Ming

2006-10-01

The prion protein gene of African lion (Panthera Leo) was first cloned and polymorphisms screened. The results suggest that the prion protein gene of eight African lions is highly homogenous. The amino acid sequences of the prion protein (PrP) of all samples tested were identical. Four single nucleotide polymorphisms (C42T, C81A, C420T, T600C) in the prion protein gene (Prnp) of African lion were found, but no amino acid substitutions. Sequence analysis showed that the higher homology is observed to felis catus AF003087 (96.7%) and to sheep number M31313.1 (96.2%) Genbank accessed. With respect to all the mammalian prion protein sequences compared, the African lion prion protein sequence has three amino acid substitutions. The homology might in turn affect the potential intermolecular interactions critical for cross species transmission of prion disease.

Measurement and Comparison of Taekwondo and Yongmudo Turning Kick Impact Force for Two Target Heights

PubMed Central

O’Sullivan, David; Chung, Chulsoo; Lee, Kikwang; Kim, Euihwan; Kang, Sungchul; Kim, Taewhan; Shin, Insik

2009-01-01

The primary purpose of this research was to compare the impact characteristics of Taekwondo (TKD) and Yongmudo (YMD) player’s turning kick according to the target height. 5 highly skilled YMD and 5 TKD players participated in this study. To measure the impact force, two accelerometers were fixed to a PVC pipe in a sandbag. Each participant performed 10 turning kicks trunk and face height in random order. Only the trial with the most accurate (most central impact) measurement was used in the statistical analysis (p < 0.05).There was a significant difference for impact force according to the target height approximately 6400 ± 898 N, 6393 ± 1382 N for the mid section and 5419 ± 659 N, 5475 ± 1293 N for the high section of TKD and YMD groups, but not between groups. The swing phase for the TKD group was significantly shorter than the YMD group’s. The TKD groups’ recovery phase of the trunk height turning kick was significantly shorter. There was a difference in the players’ center of mass (COM) movement as the TKD players’ moved significantly more forward, suggesting that the TKD players tended to slide towards the target during the execution of the kick. In conclusion, as the turning kick was performed quicker by the TKD players with a similar impact force and more forward motion, it is evaluated to be a better technique of turning kicking. Key Points This impact force measuring device had a significantly smaller standard deviation then that of impact force measuring devices. There was a significant difference between the impact forces according to the height approximately 6400 ± 898N, 6393 ± 1382N for the mid section and 5419 ± 659N, 5475 ± 1293N for the high section of TKD and YMD groups. The turning kick was performed quicker by the TKD players with a similar impact force and more forward motion. PMID:24474880

Sequential processing of quantitative phase images for the study of cell behaviour in real-time digital holographic microscopy.

PubMed

Zikmund, T; Kvasnica, L; Týč, M; Křížová, A; Colláková, J; Chmelík, R

2014-11-01

Transmitted light holographic microscopy is particularly used for quantitative phase imaging of transparent microscopic objects such as living cells. The study of the cell is based on extraction of the dynamic data on cell behaviour from the time-lapse sequence of the phase images. However, the phase images are affected by the phase aberrations that make the analysis particularly difficult. This is because the phase deformation is prone to change during long-term experiments. Here, we present a novel algorithm for sequential processing of living cells phase images in a time-lapse sequence. The algorithm compensates for the deformation of a phase image using weighted least-squares surface fitting. Moreover, it identifies and segments the individual cells in the phase image. All these procedures are performed automatically and applied immediately after obtaining every single phase image. This property of the algorithm is important for real-time cell quantitative phase imaging and instantaneous control of the course of the experiment by playback of the recorded sequence up to actual time. Such operator's intervention is a forerunner of process automation derived from image analysis. The efficiency of the propounded algorithm is demonstrated on images of rat fibrosarcoma cells using an off-axis holographic microscope. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

Kinetics and Muscle Activity Patterns during Unweighting and Reloading Transition Phases in Running

PubMed Central

Sainton, Patrick; Nicol, Caroline; Cabri, Jan; Barthèlemy-Montfort, Joëlle; Chavet, Pascale

2016-01-01

Amongst reduced gravity simulators, the lower body positive pressure (LBPP) treadmill is emerging as an innovative tool for both rehabilitation and fundamental research purposes as it allows running while experiencing reduced vertical ground reaction forces. The appropriate use of such a treadmill requires an improved understanding of the associated neuromechanical changes. This study concentrates on the runner’s adjustments to LBPP-induced unweighting and reloading during running. Nine healthy males performed two running series of nine minutes at natural speed. Each series comprised three sequences of three minutes at: 100% bodyweight (BW), 60 or 80% BW, and 100% BW. The progressive unweighting and reloading transitions lasted 10 to 15 s. The LBPP-induced unweighting level, vertical ground reaction force and center of mass accelerations were analyzed together with surface electromyographic activity from 6 major lower limb muscles. The analyses of stride-to-stride adjustments during each transition established highly linear relationships between the LBPP-induced progressive changes of BW and most mechanical parameters. However, the impact peak force and the loading rate systematically presented an initial 10% increase with unweighting which could result from a passive mechanism of leg retraction. Another major insight lies in the distinct neural adjustments found amongst the recorded lower-limb muscles during the pre- and post-contact phases. The preactivation phase was characterized by an overall EMG stability, the braking phase by decreased quadriceps and soleus muscle activities, and the push-off phase by decreased activities of the shank muscles. These neural changes were mirrored during reloading. These neural adjustments can be attributed in part to the lack of visual cues on the foot touchdown. These findings highlight both the rapidity and the complexity of the neuromechanical changes associated with LBPP-induced unweighting and reloading during running. This in turn emphasizes the need for further investigation of the evolution over time of these neuromechanical changes. PMID:27992539

PULSATION PERIOD VARIATIONS IN THE RRc LYRAE STAR KIC 5520878

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

Hippke, Michael; Learned, John G.; Zee, A.

Learned et al. proposed that a sufficiently advanced extra-terrestrial civilization may tickle Cepheid and RR Lyrae variable stars with a neutrino beam at the right time, thus causing them to trigger early and jogging the otherwise very regular phase of their expansion and contraction. This would turn these stars into beacons to transmit information throughout the galaxy and beyond. The idea is to search for signs of phase modulation (in the regime of short pulse duration) and patterns, which could be indicative of intentional, omnidirectional signaling. We have performed such a search among variable stars using photometric data from themore » Kepler space telescope. In the RRc Lyrae star KIC 5520878, we have found two such regimes of long and short pulse durations. The sequence of period lengths, expressed as time series data, is strongly autocorrelated, with correlation coefficients of prime numbers being significantly higher (p = 99.8%). Our analysis of this candidate star shows that the prime number oddity originates from two simultaneous pulsation periods and is likely of natural origin. Simple physical models elucidate the frequency content and asymmetries of the KIC 5520878 light curve. Despite this SETI null result, we encourage testing of other archival and future time-series photometry for signs of modulated stars. This can be done as a by-product to the standard analysis, and can even be partly automated.« less

The 100 brigthest Blue Straggler Stars.

NASA Astrophysics Data System (ADS)

Morales Durán, C.; Llorente de Andrés, F.; Ahumada, J. A.

2015-05-01

Blue straggler stars (BSS) are characterized by their appearance in the CMD of globular and open clusters, in the Main Sequence extension, above the turn-off and blueward of this. In accordance with the Standard Theory of stellar evolution, BSS should be out of the Main Sequence and over the Giant Branch if they really belong to the cluster and are formed at the same time than the rest of cluster stars. There are several theories that try to explain the existence of BSS but at present prevails the idea that they can be the product of mass transfer in binaries (McCrea, 1964), and the luminosity of the receiver star is incremented in such a way that now it is over the Main Sequence turn-off point of its cluster. Also it is believed that they are the result of stellar fussion of two or several stars, specially in dense systems as the globular cluster nucleus. This work is focalised in all the BSS brihgter the V = 10 mag. that we have been able to identify in open clusters. It is a sample unprecedented by its number and as well it is a sample with plentiful observational information, it is why we hope to be able to assure their membership to the parent cluster and obtain reliable information about their possible origin.

Four-dimensional guidance algorithms for aircraft in an air traffic control environment

NASA Technical Reports Server (NTRS)

Pecsvaradi, T.

1975-01-01

Theoretical development and computer implementation of three guidance algorithms are presented. From a small set of input parameters the algorithms generate the ground track, altitude profile, and speed profile required to implement an experimental 4-D guidance system. Given a sequence of waypoints that define a nominal flight path, the first algorithm generates a realistic, flyable ground track consisting of a sequence of straight line segments and circular arcs. Each circular turn is constrained by the minimum turning radius of the aircraft. The ground track and the specified waypoint altitudes are used as inputs to the second algorithm which generates the altitude profile. The altitude profile consists of piecewise constant flight path angle segments, each segment lying within specified upper and lower bounds. The third algorithm generates a feasible speed profile subject to constraints on the rate of change in speed, permissible speed ranges, and effects of wind. Flight path parameters are then combined into a chronological sequence to form the 4-D guidance vectors. These vectors can be used to drive the autopilot/autothrottle of the aircraft so that a 4-D flight path could be tracked completely automatically; or these vectors may be used to drive the flight director and other cockpit displays, thereby enabling the pilot to track a 4-D flight path manually.

Origin of anti-tumor activity of the cysteine-containing GO peptides and further optimization of their cytotoxic properties

NASA Astrophysics Data System (ADS)

Tyuryaeva, Irina I.; Lyublinskaya, Olga G.; Podkorytov, Ivan S.; Skrynnikov, Nikolai R.

2017-01-01

Antitumor GO peptides have been designed as dimerization inhibitors of prominent oncoprotein mucin 1. In this study we demonstrate that activity of GO peptides is independent of the level of cellular expression of mucin 1. Furthermore, these peptides prove to be broadly cytotoxic, causing cell death also in normal cells such as dermal fibroblasts and endometrial mesenchymal stem cells. To explore molecular mechanism of their cytotoxicity, we have designed and tested a number of new peptide sequences containing the key CxC or CxxC motifs. Of note, these sequences bear no similarity to mucin 1 except that they also contain a pair of proximal cysteines. Several of the new peptides turned out to be significantly more potent than their GO prototypes. The results suggest that cytotoxicity of these peptides stems from their (moderate) activity as disulfide oxidoreductases. It is expected that such peptides, which we have termed DO peptides, are involved in disulfide-dithiol exchange reaction, resulting in formation of adventitious disulfide bridges in cell proteins. In turn, this leads to a partial loss of protein function and rapid onset of apoptosis. We anticipate that coupling DO sequences with tumor-homing transduction domains can create a potentially valuable new class of tumoricidal peptides.

Origin of anti-tumor activity of the cysteine-containing GO peptides and further optimization of their cytotoxic properties

PubMed Central

Tyuryaeva, Irina I.; Lyublinskaya, Olga G.; Podkorytov, Ivan S.; Skrynnikov, Nikolai R.

2017-01-01

Antitumor GO peptides have been designed as dimerization inhibitors of prominent oncoprotein mucin 1. In this study we demonstrate that activity of GO peptides is independent of the level of cellular expression of mucin 1. Furthermore, these peptides prove to be broadly cytotoxic, causing cell death also in normal cells such as dermal fibroblasts and endometrial mesenchymal stem cells. To explore molecular mechanism of their cytotoxicity, we have designed and tested a number of new peptide sequences containing the key CxC or CxxC motifs. Of note, these sequences bear no similarity to mucin 1 except that they also contain a pair of proximal cysteines. Several of the new peptides turned out to be significantly more potent than their GO prototypes. The results suggest that cytotoxicity of these peptides stems from their (moderate) activity as disulfide oxidoreductases. It is expected that such peptides, which we have termed DO peptides, are involved in disulfide-dithiol exchange reaction, resulting in formation of adventitious disulfide bridges in cell proteins. In turn, this leads to a partial loss of protein function and rapid onset of apoptosis. We anticipate that coupling DO sequences with tumor-homing transduction domains can create a potentially valuable new class of tumoricidal peptides. PMID:28091523

Complete mitochondrial genome of Porzana fusca and Porzana pusilla and phylogenetic relationship of 16 Rallidae species.

PubMed

Chen, Peng; Han, Yuqing; Zhu, Chaoying; Gao, Bin; Ruan, Luzhang

2017-12-01

The complete mitochondrial genome sequences of Porzana fusca and Porzana pusilla were determined. The two avian species share a high degree of homology in terms of mitochondrial genome organization and gene arrangement. Their corresponding mitochondrial genomes are 16,935 and 16,978 bp and consist of 37 genes and a control region. Their PCGs were both 11,365 bp long and have similar structure. Their tRNA gene sequences could be folded into canonical cloverleaf secondary structure, except for tRNA Ser (AGY) , which lost its "DHU" arm. Based on the concatenated nucleotide sequences of the complete mitochondrial DNA genes of 16 Rallidae species, reconstruction of phylogenetic trees and analysis of the molecular clock of P. fusca and P. pusilla indicated that these species from a sister group, which in turn are sister group to Rallina eurizonoides. The genus Gallirallus is a sister group to genus Lewinia, and these groups in turn are sister groups to genus Porphyrio. Moreover, molecular clock analyses suggested that the basal divergence of Rallidae could be traced back to 40.47 (41.46‒39.45) million years ago (Mya), and the divergence of Porzana occurred approximately 5.80 (15.16‒0.79) Mya.

Protocol optimization of sacroiliac joint MR Imaging at 3 Tesla: Impact of coil design and motion resistant sequences on image quality.

PubMed

Gondim Teixeira, P A; Bravetti, M; Hossu, G; Lecocq, S; Petit, D; Loeuille, D; Blum, A

2017-12-01

To evaluate the impact of coil design and motion-resistant sequences on the quality of sacroiliac magnetic resonance imaging (MRI) examination in patients with spondyloarthropathy. One hundred and twenty-one patients with suspected sacroiliitis and referred for MRI of the sacroiliac joints were retrospectively evaluated with MRI at 3-Tesla. There were 78 women and 43 men with a mean age of 36.7±11.5 (SD) years (range: 15.8-78.4 years). Conventional and motion-resistant fat-saturated fast-spin echo T2-weighted sequences were performed with two different coils. Image quality was subjectively evaluated by two independent readers (R1 and R2) using a four-point scale. Confidence in the identification of bone marrow edema pattern (BMEP) was also evaluated subjectively using a three-point scale. Phased array body coil yielded improved image quality compared to surface coil (14.1 to 30.4% for R1 and 14.6 to 25.7% for R2; P<0.0001). The impact of the sequence type on quality was also statistically significant (P=0.0046). BMEP was identified in 40 patients and best inter-reader agreement was obtained using the combination of phased-array body coil with motion-resistant T2-weighted sequence (kappa 0.990). The smallest number of indeterminate BMEP zones was seen on MRI set acquired with the phased-array body coil and motion-resistant T2-weighted sequence. Phased array body coil and motion-resistant T2-weighted sequences perform better than surface coil and conventional T2-weighted sequences for the evaluation of sacroiliac joints, increasing confidence in the identification of BMEP. Copyright © 2017 Editions françaises de radiologie. Published by Elsevier Masson SAS. All rights reserved.

Behavior of sheets from Ti-alloys by rolling and heat treatment

NASA Astrophysics Data System (ADS)

Isaenkova, M.; Perlovich, Yu.; Fesenko, V.; Gritskevich, M.; Stolbov, S.; Zaripova, M.

2017-10-01

Sheets from single- and two-phase Ti-alloys (VT1-0, Ti-22Nb-9%Zr and VT-16) were rolled at the room temperature up to various deformation degrees and annealed at temperatures 500-900 °C. The regularities of texture formation in both phases were established. In the technically pure Ti (VT1-0) with the single α-Ti phase the final stable texture component is (0001)±30-40°ND-TD<101 ¯0>. In the two-phase alloy the reorientation of basal axes of α-Ti occurs by the same trajectories as in the single phase alloy. However, in the case of two-phase alloy texture development in α-Ti stops at the intermediate stage, when this texture consists of components with rolling planes (0001)±15-20°ND-RD and (0001)±30-40°ND-TD. The stability of the first components can be provided both by the mutually balanced operation of pyramidal and basal slip systems, activity of which remains at the high deformation degree of two-phase alloy, and by the dynamic α↔β phase transformations, taking place in the distorted structures of α- and β-phases in the course of its cold rolling. At recrystallization of technically pure Ti the basal component disappears in its texture. At the same time, prismatic axes turn by angles 20÷30° depending on the heating rate of the rolled sheet and annealing temperature. At recrystallization of the two-phase Ti-alloy prismatic axes of its α-grains doesn't turn relative to their positions in the rolling texture, as it occurs in the single-phase alloy. This fact indicates to some alternative mode of arising new recrystallized grains in two-phase alloys.

Real-time tracking of respiratory-induced tumor motion by dose-rate regulation

NASA Astrophysics Data System (ADS)

Han-Oh, Yeonju Sarah

We have developed a novel real-time tumor-tracking technology, called Dose-Rate-Regulated Tracking (DRRT), to compensate for tumor motion caused by breathing. Unlike other previously proposed tumor-tracking methods, this new method uses a preprogrammed dynamic multileaf collimator (MLC) sequence in combination with real-time dose-rate control. This new scheme circumvents the technical challenge in MLC-based tumor tracking, that is to control the MLC motion in real time, based on real-time detected tumor motion. The preprogrammed MLC sequence describes the movement of the tumor, as a function of breathing phase, amplitude, or tidal volume. The irregularity of tumor motion during treatment is handled by real-time regulation of the dose rate, which effectively speeds up or slows down the delivery of radiation as needed. This method is based on the fact that all of the parameters in dynamic radiation delivery, including MLC motion, are enslaved to the cumulative dose, which, in turn, can be accelerated or decelerated by varying the dose rate. Because commercially available MLC systems do not allow the MLC delivery sequence to be modified in real time based on the patient's breathing signal, previously proposed tumor-tracking techniques using a MLC cannot be readily implemented in the clinic today. By using a preprogrammed MLC sequence to handle the required motion, the task for real-time control is greatly simplified. We have developed and tested the pre- programmed MLC sequence and the dose-rate regulation algorithm using lung-cancer patients breathing signals. It has been shown that DRRT can track the tumor with an accuracy of less than 2 mm for a latency of the DRRT system of less than 0.35 s. We also have evaluated the usefulness of guided breathing for DRRT. Since DRRT by its very nature can compensate for breathing-period changes, guided breathing was shown to be unnecessary for real-time tracking when using DRRT. Finally, DRRT uses the existing dose-rate control system that is provided for current linear accelerators. Therefore, DRRT can be achieved with minimal modification of existing technology, and this can shorten substantially the time necessary to establish DRRT in clinical practice.

Automated array assembly, phase 2

NASA Technical Reports Server (NTRS)

Daiello, R. V.

1980-01-01

A manufacturing sequence which is capable of mass producing silicon solar cells is described. The sequence was arrived at after the evaluation of many processes and three related manufacturing sequences which are discussed.

Recent taxonomy changes and their impact on biocontrol agents

USDA-ARS?s Scientific Manuscript database

The revolution in DNA sequencing technology has led to and improved understanding of genetics and taxonomy of biocontrol agents. Our lab recently reported the genomes of some important Bacillus bacterial biocontrol agents, which in turn resulted in a change of taxonomy for these commercially importa...

Investigation of isolated substorms: Generation conditions and characteristics of different phases

NASA Astrophysics Data System (ADS)

Vorobjev, V. G.; Yagodkina, O. I.; Zverev, V. L.

2016-11-01

Characteristics of isolated substorms selected by variations in the 1-min values of the AL index are analyzed. The substorms were divided into several types with respect to the behavior of the Bz component of the interplanetary magnetic field (IMF) during the expansion phase. The probability of observations of substorms associated with the northward turn of the Bz component of IMF was 19%, while the substorms taking place at Bz < 0 were observed in 53% of cases. A substantial number of events in which no substorm magnetic activity was observed in the auroral zone after a long (>30 min) period of the southward IMF and a following sharp turn of the Bz component of IMF before the north was detected. The data suggest that a northward IMF turn is neither a necessary nor sufficient condition for generating substorms. It has been shown for substorms of the both types that the average duration of the southward IMF to moment T 0 and the average intensity of the magnetic perturbation in the maximum are approximately the same and amount to 80 min and-650 nT, respectively. However, for substorms at Bz < 0, their mean duration, including the expansive and recovery phases, is on average 30 min longer than that at a northward turn of IMF. Correlations between the loading-unloading processes in the magnetosphere in the periods of magnetospheric substorms were investigated with different functions that determine the efficiency of the energy transfer from the solar wind to the magnetosphere. It has been shown that the highest correlation coefficient ( r = 0.84) is observed when the function suggested by Newell et al. (2007) is used. It has been detected that a simple function VB S yields a high correlation coefficient ( r = 0.75).

Computer Program for Vibration Prediction of Fighter Aircraft Equipments

DTIC Science & Technology

1977-11-01

scribing a useful variety of flight vibration phases . Notice that identical variations can be reflected into the high frequency rolloff curve (equation 13...flight attitudes ranging from straight and level states to a variety of significant flight maneuvers and phases . Pro- gram outputs, digital and...R (f) adjusted value of R(f) due to c (g 2/Hz) SBT (f) special function for the buffet turn flight phase PBT (f) pressure spectral density speqtrum

The effects of the use of piezoelectric motors in a 1.5-Tesla high-field magnetic resonance imaging system (MRI).

PubMed

Wendt, O; Oellinger, J; Lüth, T C; Felix, R; Boenick, U

2000-01-01

This paper presents the results of an experimental investigation with two different rotatory piezomotors in a closed 1.5 Tesla high-field MRI. The focus of the investigation was on testing the functionality of these motors within the MRI and to determining the image interference they caused. To obtain a differentiated estimate of the interference the motors were tested in both the passive (turned off, i.e. without current flow) and active (turned on, i.e. with current flow) state during MRI scanning. Three different types of sequences were used for the test: Spin-Echo (SE), Gradient-Echo (GE) and Echo-Planar Imaging (EPI). A plastic container filled with a gadolinium-manganese solution was used for representation of the artefacts. The motors investigated were placed parallel to the container at predetermined distances during the experiment. The results show that the motors investigated suffered no functional limitations in the magnetic field of the MRI but, depending on the type of motor, the measurement distance and the state of the motor, the motors had different effects on the sequence images. A motor in the off-state placed immediately next to the object to be measured mainly causes artefacts because of its material properties. If, on the other hand, the piezomotor is in the on-state images with strong noise result when the motor is immediately next to the object being measured. The images regain their normal quality when the motor is approximately at a distance of 1 m from the object being investigated. Driving the motor inside the MRI, therefore, is only to be recommended during the pauses in scanning: this delivers artefact-free images if minimal, motor-specific distances are kept to. With regard to the three different types of sequences it was determined that the SE sequence was the least sensitive and the EPI sequence the most sensitive to disturbance. The GE sequence showed only minimal differences to the SE sequence with regard to signal-to-noise ratios. Since it requires considerably shorter scan-times it can be considered to be the most effective type of sequence under these conditions.

Episodic sequence memory is supported by a theta-gamma phase code.

PubMed

Heusser, Andrew C; Poeppel, David; Ezzyat, Youssef; Davachi, Lila

2016-10-01

The meaning we derive from our experiences is not a simple static extraction of the elements but is largely based on the order in which those elements occur. Models propose that sequence encoding is supported by interactions between high- and low-frequency oscillations, such that elements within an experience are represented by neural cell assemblies firing at higher frequencies (gamma) and sequential order is encoded by the specific timing of firing with respect to a lower frequency oscillation (theta). During episodic sequence memory formation in humans, we provide evidence that items in different sequence positions exhibit greater gamma power along distinct phases of a theta oscillation. Furthermore, this segregation is related to successful temporal order memory. Our results provide compelling evidence that memory for order, a core component of an episodic memory, capitalizes on the ubiquitous physiological mechanism of theta-gamma phase-amplitude coupling.

An Attempt at Blocking of Position Learning by Training with Reward-Memory Associations

ERIC Educational Resources Information Center

Burns, Richard A.; Johnson, Kendra S.

2006-01-01

Rats were runway trained with sequences of rewards that changed in 3 phases. In Phase 1 (24 days), the sequences were NP', SNP', and P'SNP' (n = 3), or NS', PNS', and S'PNS', where P and P' refer to 4 and 8 plain Noyes pellets, and S and S' are 4 and 8 sucrose pellets. N was a 30-s confinement in the goal without reward. In Phase 2 (14 days) the…

Long Read Alignment with Parallel MapReduce Cloud Platform

PubMed Central

Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

2015-01-01

Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms. PMID:26839887

Long Read Alignment with Parallel MapReduce Cloud Platform.

PubMed

Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

2015-01-01

Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms.

Sequence control of phase separation and dewetting in PS/PVME blend thin films by changing molecular weight of PS.

PubMed

Xia, Tian; Qin, Yaping; Huang, Yajiang; Huang, Ting; Xu, Jianhui; Li, Youbing

2016-11-28

The morphology evolution mechanism of polystyrene (PS)/poly (vinyl methyl ether) (PVME) blend thin films with different PS molecular weights (M w ) was studied. It was found that the morphology evolution was closely related to the molecular weight asymmetry between PS and PVME. In the film where M w (PS) ≈ M w (PVME), dewetting happened at the interface between the bottom layer and substrate after SD phase separation. While in the film where M w (PS) > M w (PVME), dewetting happened at the interface between the middle PS/PVME blend layer and bottom PVME layer near the substrate prior to phase separation. The different sequences of phase separation and dewetting and different interface for dewetting occurrence were studied by regarding the competitive effects of viscoelasticity contrast between polymer components and preferential wetting between PVME and the substrate. The viscoelastic nature of the PS component played a crucial role in the sequence of phase separation and dewetting.

The Global Statistical Response of the Outer Radiation Belt During Geomagnetic Storms

NASA Astrophysics Data System (ADS)

Murphy, K. R.; Watt, C. E. J.; Mann, I. R.; Jonathan Rae, I.; Sibeck, D. G.; Boyd, A. J.; Forsyth, C. F.; Turner, D. L.; Claudepierre, S. G.; Baker, D. N.; Spence, H. E.; Reeves, G. D.; Blake, J. B.; Fennell, J.

2018-05-01

Using the total radiation belt electron content calculated from Van Allen Probe phase space density, the time-dependent and global response of the outer radiation belt during storms is statistically studied. Using phase space density reduces the impacts of adiabatic changes in the main phase, allowing a separation of adiabatic and nonadiabatic effects and revealing a clear modality and repeatable sequence of events in storm time radiation belt electron dynamics. This sequence exhibits an important first adiabatic invariant (μ)-dependent behavior in the seed (150 MeV/G), relativistic (1,000 MeV/G), and ultrarelativistic (4,000 MeV/G) populations. The outer radiation belt statistically shows an initial phase dominated by loss followed by a second phase of rapid acceleration, while the seed population shows little loss and immediate enhancement. The time sequence of the transition to the acceleration is also strongly μ dependent and occurs at low μ first, appearing to be repeatable from storm to storm.

On the Precipitation in an Ag-Containing Mg-Gd-Zr Alloy

NASA Astrophysics Data System (ADS)

Zhang, Yu; Zhu, Yuman; Rong, Wei; Wu, Yujuan; Peng, Liming; Nie, Jian-Feng; Birbilis, Nick

2018-02-01

The evolution of precipitates in a high-strength Mg-2.4Gd-0.4Ag-0.1Zr (at. pct) alloy was investigated using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM). The precipitation of Mg-2.4Gd-0.4Ag-0.1Zr includes β- and γ-type precipitates, the latter involving a hitherto unreported precipitation sequence that is the focus of the present study. The β-type precipitation sequence is described as follows: supersaturated solid solution (S.S.S.S.) → ordered solute clusters → zigzag GP zones → β' → βF' → β 1 → β. Compared with the precipitation sequence of the Mg-Gd system, the proposed β-type precipitation sequence includes ordered solute clusters, zigzag GP zones, and βF' , but excludes β″. The strain field around the coarsened β' phase is supposed to stimulate the formation of the β^'F phase. Furthermore, the βF' phase provides preferential nucleation site for the β 1 phase. The γ-type precipitation sequence is proposed as follows: S.S.S.S. → basal GP zones → γ''' → γ″ → γ. The crystal structures, morphologies, and orientations of the basal GP zone, γ''', γ″, γ phases were comprehensively examined and established herein. The results are described in the context of other, but similar, alloy systems. A holistic description of the precipitate evolution in Ag-containing Mg-Gd alloys is discussed and rationalized.

Hairpin stabilized fluorescent silver nanoclusters for quantitative detection of NAD+ and monitoring NAD+/NADH based enzymatic reactions.

PubMed

Jain, Priyamvada; Chakma, Babina; Patra, Sanjukta; Goswami, Pranab

2017-03-01

A set of 90 mer long ssDNA candidates, with different degrees of cytosine (C-levels) (% and clusters) was analyzed for their function as suitable Ag-nanocluster (AgNC) nucleation scaffolds. The sequence (P4) with highest C-level (42.2%) emerged as the only candidate supporting the nucleation process as evident from its intense fluorescence peak at λ 660 nm . Shorter DNA subsets derived from P4 with only stable hairpin structures could support the AgNC formation. The secondary hairpin structures were confirmed by PAGE, and CD studies. The number of base pairs in the stem region also contributes to the stability of the hairpins. A shorter 29 mer sequence (Sub 3) (ΔG = -1.3 kcal/mol) with 3-bp in the stem of a 7-mer loop conferred highly stable AgNC. NAD + strongly quenched the fluorescence of Sub 3-AgNC in a concentration dependent manner. Time resolved photoluminescence studies revealed the quenching involves a combined static and dynamic interaction where the binding constant and number of binding sites for NAD + were 0.201 L mol -1 and 3.6, respectively. A dynamic NAD + detection range of 50-500 μM with a limit of detection of 22.3 μM was discerned. The NAD + mediated quenching of AgNC was not interfered by NADH, NADP + , monovalent and divalent ions, or serum samples. The method was also used to follow alcohol dehydrogenase and lactate dehydrogenase catalyzed physiological reactions in a turn-on and turn-off assay, respectively. The proposed method with ssDNA-AgNC could therefore be extended to monitor other NAD + /NADH based enzyme catalyzed reactions in a turn-on/turn-off approach. Copyright © 2016 Elsevier B.V. All rights reserved.

Two-dimensional sup 1 H nuclear magnetic resonance study of AaH IT, an anti-insect toxin from the scorpion Androctonus australis Hector. Sequential resonance assignments and folding of the polypeptide chain

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

Darbon, H.; Weber, C.; Braun, W.

1991-02-19

Sequence-specific nuclear magnetic resonance assignments for the polypeptide backbone and for most of the amino acid side-chain protons, as well as the general folding of AaH IT, are described. AaH IT is a neurotoxin purified from the venom of the scorpion Androctonus australis Hector and is specifically active on the insect nervous system. The secondary structure and the hydrogen-bonding patterns in the regular secondary structure elements are deduced from nuclear Overhauser effects and the sequence locations of the slowly exchanging amide protons. The backbone folding is determined by distance geometry calculations with the DISMAN program. The regular secondary structure includesmore » two and a half turns of {alpha}-helix running from residues 21 to 30 and a three-stranded antiparallel {beta}-sheet including peptides 3-5, 34-38, and 41-46. Two tight turns are present, one connecting the end of the {alpha}-helix to an external strand of the {beta}-sheet, i.e., turn 31-34, and another connecting this same strand to the central one, i.e., turn 38-41. The differences in the specificity of these related proteins, which are able to discriminate between mammalian and insect voltage-dependent sodium channels of excitable tissues, are most probably brought about by the position of the C-terminal peptide with regard to a hydrophobic surface common to all scorpion toxins examined thus far. Thus, the interaction of a given scorpion toxin with its receptor might well be governed by the presence of this solvent-exposed hydrophobic surface, whereas adjacent areas modulate the specificity of the interaction.« less

Determination of the stacking fault density in highly defective single GaAs nanowires by means of coherent diffraction imaging

NASA Astrophysics Data System (ADS)

Davtyan, Arman; Biermanns, Andreas; Loffeld, Otmar; Pietsch, Ullrich

2016-06-01

Coherent x-ray diffraction imaging is used to measure diffraction patterns from individual highly defective nanowires, showing a complex speckle pattern instead of well-defined Bragg peaks. The approach is tested for nanowires of 500 nm diameter and 500 nm height predominately composed by zinc-blende (ZB) and twinned zinc-blende (TZB) phase domains. Phase retrieval is used to reconstruct the measured 2-dimensional intensity patterns recorded from single nanowires with 3.48 nm and 0.98 nm spatial resolution. Whereas the speckle amplitudes and distribution are perfectly reconstructed, no unique solution could be obtained for the phase structure. The number of phase switches is found to be proportional to the number of measured speckles and follows a narrow number distribution. Using data with 0.98 nm spatial resolution the mean number of phase switches is in reasonable agreement with estimates taken from TEM. However, since the resolved phase domain still is 3-4 times larger than a single GaAs bilayer we explain the non-ambiguous phase reconstruction by the fact that depending on starting phase and sequence of subroutines used during the phase retrieval the retrieved phase domain host a different sequence of randomly stacked bilayers. Modelling possible arrangements of bilayer sequences within a phase domain demonstrate that the complex speckle patterns measured can indeed be explained by the random arrangement of the ZB and TZB phase domains.

Gate sequence for continuous variable one-way quantum computation

PubMed Central

Su, Xiaolong; Hao, Shuhong; Deng, Xiaowei; Ma, Lingyu; Wang, Meihong; Jia, Xiaojun; Xie, Changde; Peng, Kunchi

2013-01-01

Measurement-based one-way quantum computation using cluster states as resources provides an efficient model to perform computation and information processing of quantum codes. Arbitrary Gaussian quantum computation can be implemented sufficiently by long single-mode and two-mode gate sequences. However, continuous variable gate sequences have not been realized so far due to an absence of cluster states larger than four submodes. Here we present the first continuous variable gate sequence consisting of a single-mode squeezing gate and a two-mode controlled-phase gate based on a six-mode cluster state. The quantum property of this gate sequence is confirmed by the fidelities and the quantum entanglement of two output modes, which depend on both the squeezing and controlled-phase gates. The experiment demonstrates the feasibility of implementing Gaussian quantum computation by means of accessible gate sequences.

Nucleotide sequence analysis reveals linked N-acetyl hydrolase, thioesterase, transport, and regulatory genes encoded by the bialaphos biosynthetic gene cluster of Streptomyces hygroscopicus.

PubMed Central

Raibaud, A; Zalacain, M; Holt, T G; Tizard, R; Thompson, C J

1991-01-01

Nucleotide sequence analysis of a 5,000-bp region of the bialaphos antibiotic production (bap) gene cluster defined five open reading frames (ORFs) which predicted structural genes in the order bah, ORF1, ORF2, and ORF3 followed by the regulatory gene, brpA (H. Anzai, T. Murakami, S. Imai, A. Satoh, K. Nagaoka, and C.J. Thompson, J. Bacteriol. 169:3482-3488, 1987). The four structural genes were translationally coupled and apparently cotranscribed from an undefined promoter(s) under the positive control of the brpA gene product. S1 mapping experiments indicated that brpA was transcribed by two promoters (brpAp1 and brpAp2) which initiate transcription 150 and 157 bp upstream of brp A within an intergenic region and at least one promoter further upstream within the bap gene cluster (brpAp3). All three transcripts were present at low levels during exponential growth and increased just before the stationary phase. The levels of the brpAp3 band continued to increase at the onset of stationary phase, whereas brpAp1-and brpAp2-protected fragments showed no further change. BrpA contained a possible helix-turn-helix motif at its C terminus which was similar to the C-terminal regulatory motif found in the receiver component of a family of two-component transcriptional activator proteins. This motif was not associated with the N-terminal domain conserved in other members of the family. The structural gene cluster sequenced began with bah, encoding a bialaphos acetylhydrolase which removes the N-acetyl group from bialaphos as one of the final steps in the biosynthetic pathway. The observation that Bah was similar to a rat and to a bacterial (Acinetobacter calcoaceticus) lipase probably reflects the fact that the ester bonds of triglycerides and the amide bond linking acetate to phosphinothricin are similar and hydrolysis is catalyzed by structurally related enzymes. This was followed by two regions encoding ORF1 and ORF2 which were similar to each other (48% nucleotide identity, 31% amino acid identity), as well as to GrsT, a protein encoded by a gene located adjacent to gramicidin S synthetase in Bacillus brevis, and to vertebrate (mallard duck and rat) thioesterases. The amino acid sequence and hydrophobicity profile of ORF3 indicated that it was related to a family of membrane transport proteins. It was strikingly similar to the citrate uptake protein encoded by the transposon Tn3411. Images PMID:2066341

Transcriptome analysis of the desert locust central nervous system: production and annotation of a Schistocerca gregaria EST database.

PubMed

Badisco, Liesbeth; Huybrechts, Jurgen; Simonet, Gert; Verlinden, Heleen; Marchal, Elisabeth; Huybrechts, Roger; Schoofs, Liliane; De Loof, Arnold; Vanden Broeck, Jozef

2011-03-21

The desert locust (Schistocerca gregaria) displays a fascinating type of phenotypic plasticity, designated as 'phase polyphenism'. Depending on environmental conditions, one genome can be translated into two highly divergent phenotypes, termed the solitarious and gregarious (swarming) phase. Although many of the underlying molecular events remain elusive, the central nervous system (CNS) is expected to play a crucial role in the phase transition process. Locusts have also proven to be interesting model organisms in a physiological and neurobiological research context. However, molecular studies in locusts are hampered by the fact that genome/transcriptome sequence information available for this branch of insects is still limited. We have generated 34,672 raw expressed sequence tags (EST) from the CNS of desert locusts in both phases. These ESTs were assembled in 12,709 unique transcript sequences and nearly 4,000 sequences were functionally annotated. Moreover, the obtained S. gregaria EST information is highly complementary to the existing orthopteran transcriptomic data. Since many novel transcripts encode neuronal signaling and signal transduction components, this paper includes an overview of these sequences. Furthermore, several transcripts being differentially represented in solitarious and gregarious locusts were retrieved from this EST database. The findings highlight the involvement of the CNS in the phase transition process and indicate that this novel annotated database may also add to the emerging knowledge of concomitant neuronal signaling and neuroplasticity events. In summary, we met the need for novel sequence data from desert locust CNS. To our knowledge, we hereby also present the first insect EST database that is derived from the complete CNS. The obtained S. gregaria EST data constitute an important new source of information that will be instrumental in further unraveling the molecular principles of phase polyphenism, in further establishing locusts as valuable research model organisms and in molecular evolutionary and comparative entomology.

De novo assembly and phasing of a Korean human genome.

PubMed

Seo, Jeong-Sun; Rhie, Arang; Kim, Junsoo; Lee, Sangjin; Sohn, Min-Hwan; Kim, Chang-Uk; Hastie, Alex; Cao, Han; Yun, Ji-Young; Kim, Jihye; Kuk, Junho; Park, Gun Hwa; Kim, Juhyeok; Ryu, Hanna; Kim, Jongbum; Roh, Mira; Baek, Jeonghun; Hunkapiller, Michael W; Korlach, Jonas; Shin, Jong-Yeon; Kim, Changhoon

2016-10-13

Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.

Theory of coherent quantum phase slips in Josephson junction chains with periodic spatial modulations

NASA Astrophysics Data System (ADS)

Svetogorov, Aleksandr E.; Taguchi, Masahiko; Tokura, Yasuhiro; Basko, Denis M.; Hekking, Frank W. J.

2018-03-01

We study coherent quantum phase slips which lift the ground state degeneracy in a Josephson junction ring, pierced by a magnetic flux of the magnitude equal to half of a flux quantum. The quantum phase-slip amplitude is sensitive to the normal mode structure of superconducting phase oscillations in the ring (Mooij-Schön modes). These, in turn, are affected by spatial inhomogeneities in the ring. We analyze the case of weak periodic modulations of the system parameters and calculate the corresponding modification of the quantum phase-slip amplitude.

Risk Factors for Falls in Older Adults With Mild Cognitive Impairment and Mild Alzheimer Disease.

PubMed

Ansai, Juliana Hotta; de Andrade, Larissa Pires; Masse, Fernando Arturo Arriagada; Gonçalves, Jessica; de Medeiros Takahashi, Anielle Cristhine; Vale, Francisco Assis Carvalho; Rebelatto, José Rubens

2017-03-03

Understanding fall risk factors in people with mild cognitive impairment (MCI) and Alzheimer disease (AD) can help to establish specific plans for prevention of falls. The purpose of this study was to identify fall risk factors in older adults with MCI and mild AD. A prospective study was conducted with community-dwelling older adults (40 MCI; 38 mild AD). The assessments consisted of sociodemographic and health variables, caloric expenditure, functional status, functional mobility (10-m walk test, dual-task test, and transition Timed Up and Go phases), cognitive domains, and depressive symptoms. Falls were recorded for 6 months by a falls calendar and monthly telephone calls. Falls were reported in 52.6% and 51.4% of people with MCI and mild AD, respectively. Among people with MCI, lower functional status, higher time spent on walk and dual task tests, and higher depressive symptom scores were associated with falls. Higher time spent on the dual-task test was independently associated with falls. Among people with mild AD, falls were associated with lower time spent on the walk test and turn-to-sit phase, and a higher visuospatial domain score. Lower time spent on the turn-to-sit phase was identified as an independent predictor of falls. Careful attention should be given to dual-task and turn-to-sit activities when detecting risk of falls among older people with MCI and mild AD.

Reticular lamina and basilar membrane vibrations in the basal turn of gerbil and mouse cochleae

NASA Astrophysics Data System (ADS)

Ren, Tianying; He, Wenxuan

2018-05-01

Low-coherence interferometry in living cochleae has provided valuable information for understanding cochlear micromechanics. A recent measurement of the reticular lamina and basilar membrane vibrations in mouse cochleae, however, is inconsistent with data collected from guinea pig cochleae. To determine whether a species difference accounts for the observed difference, a custom-built heterodyne low-coherence interferometer was used to measure reticular lamina and basilar membrane vibrations at the basal turn of sensitive gerbil and mouse cochleae. For the gerbil and mouse, both the reticular lamina and basilar membrane vibrations show sharp tuning and nonlinear compressive growth near the best frequency. The magnitude of the reticular lamina vibration is significantly greater than that of the basilar membrane vibration not only near the best frequency, but also at low frequencies. The phase of the reticular lamina vibration leads the basilar membrane phase by up to 180-degrees at low frequencies, and this phase lead decreases with frequency, approaching zero near the best frequency. The best frequency of the reticular lamina and basilar membrane vibrations at the cochlear basal turn in mice is significantly higher than that in gerbils. Besides this difference, cochlear micromechanical responses in the gerbil are similar to those in the mouse. Thus, the current results indicate that gerbil and mouse cochleae detect and process sounds likely through a similar micromechanical mechanism.

Negotiating towards a Next Turn: Phonetic Resources for "Doing the Same"

ERIC Educational Resources Information Center

Sikveland, Rein Ove

2012-01-01

This paper investigates hearers' use of response tokens (back-channels), in maintaining and differentiating their actions. Initial observations suggest that hearers produce a sequence of phonetically similar responses to disengage from the current topic, and dissimilar responses to engage with the current topic. This is studied systematically by…

Conversation Analysis--A Discourse Approach to Teaching Oral English Skills

ERIC Educational Resources Information Center

Wu, Yan

2013-01-01

This paper explores a pedagocial approach to teaching oral English---Conversation Analysis. First, features of spoken language is described in comparison to written language. Second, Conversation Analysis theory is elaborated in terms of adjacency pairs, turn-taking, repairs, sequences, openings and closings, and feedback. Third, under the…

48 CFR 3.303 - Reporting suspected antitrust violations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... turn in sequence as low bidder, or so that certain competitors bid low only on some sizes of contracts and high on other sizes; (5) Division of the market, so that certain competitors bid low only for..., Attention: Assistant Attorney General, Antitrust Division, and shall include— (1) A brief statement...

Phase incremented echo train acquisition applied to magnetic resonance pore imaging

NASA Astrophysics Data System (ADS)

Hertel, S. A.; Galvosas, P.

2017-02-01

Efficient phase cycling schemes remain a challenge for NMR techniques if the pulse sequences involve a large number of rf-pulses. Especially complex is the Carr Purcell Meiboom Gill (CPMG) pulse sequence where the number of rf-pulses can range from hundreds to several thousands. Our recent implementation of Magnetic Resonance Pore Imaging (MRPI) is based on a CPMG rf-pulse sequence in order to refocus the effect of internal gradients inherent in porous media. While the spin dynamics for spin- 1 / 2 systems in CPMG like experiments are well understood it is still not straight forward to separate the desired pathway from the spectrum of unwanted coherence pathways. In this contribution we apply Phase Incremented Echo Train Acquisition (PIETA) to MRPI. We show how PIETA offers a convenient way to implement a working phase cycling scheme and how it allows one to gain deeper insights into the amplitudes of undesired pathways.

Compression of computer generated phase-shifting hologram sequence using AVC and HEVC

NASA Astrophysics Data System (ADS)

Xing, Yafei; Pesquet-Popescu, Béatrice; Dufaux, Frederic

2013-09-01

With the capability of achieving twice the compression ratio of Advanced Video Coding (AVC) with similar reconstruction quality, High Efficiency Video Coding (HEVC) is expected to become the newleading technique of video coding. In order to reduce the storage and transmission burden of digital holograms, in this paper we propose to use HEVC for compressing the phase-shifting digital hologram sequences (PSDHS). By simulating phase-shifting digital holography (PSDH) interferometry, interference patterns between illuminated three dimensional( 3D) virtual objects and the stepwise phase changed reference wave are generated as digital holograms. The hologram sequences are obtained by the movement of the virtual objects and compressed by AVC and HEVC. The experimental results show that AVC and HEVC are efficient to compress PSDHS, with HEVC giving better performance. Good compression rate and reconstruction quality can be obtained with bitrate above 15000kbps.

Performance Analysis of Direct-Sequence Code-Division Multiple-Access Communications with Asymmetric Quadrature Phase-Shift-Keying Modulation

NASA Technical Reports Server (NTRS)

Wang, C.-W.; Stark, W.

2005-01-01

This article considers a quaternary direct-sequence code-division multiple-access (DS-CDMA) communication system with asymmetric quadrature phase-shift-keying (AQPSK) modulation for unequal error protection (UEP) capability. Both time synchronous and asynchronous cases are investigated. An expression for the probability distribution of the multiple-access interference is derived. The exact bit-error performance and the approximate performance using a Gaussian approximation and random signature sequences are evaluated by extending the techniques used for uniform quadrature phase-shift-keying (QPSK) and binary phase-shift-keying (BPSK) DS-CDMA systems. Finally, a general system model with unequal user power and the near-far problem is considered and analyzed. The results show that, for a system with UEP capability, the less protected data bits are more sensitive to the near-far effect that occurs in a multiple-access environment than are the more protected bits.

Microbial dynamics in upflow anaerobic sludge blanket (UASB) bioreactor granules in response to short-term changes in substrate feed

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

Kovacik, William P.; Scholten, Johannes C.; Culley, David E.

2010-08-01

The complexity and diversity of the microbial communities in biogranules from an upflow anaerobic sludge blanket (UASB) bioreactor were determined in response to short-term changes in substrate feeds. The reactor was fed simulated brewery wastewater (SBWW) (70% ethanol, 15% acetate, 15% propionate) for 1.5 months (phase 1), acetate / sulfate for 2 months (phase 2), acetate-alone for 3 months (phase 3), and then a return to SBWW for 2 months (phase 4). Performance of the reactor remained relatively stable throughout the experiment as shown by COD removal and gas production. 16S rDNA, methanogen-associated mcrA and sulfate reducer-associated dsrAB genes weremore » PCR amplified, then cloned and sequenced. Sequence analysis of 16S clone libraries showed a relatively simple community composed mainly of the methanogenic Archaea (Methanobacterium and Methanosaeta), members of the Green Non-Sulfur (Chloroflexi) group of Bacteria, followed by fewer numbers of Syntrophobacter, Spirochaeta, Acidobacteria and Cytophaga-related Bacterial sequences. Methanogen-related mcrA clone libraries were dominated throughout by Methanobacter and Methanospirillum related sequences. Although not numerous enough to be detected in our 16S rDNA libraries, sulfate reducers were detected in dsrAB clone libraries, with sequences related to Desulfovibrio and Desulfomonile. Community diversity levels (Shannon-Weiner index) generally decreased for all libraries in response to a change from SBWW to acetate-alone feed. But there was a large transitory increase noted in 16S diversity at the two-month sampling on acetate-alone, entirely related to an increase in Bacterial diversity. Upon return to SBWW conditions in phase 4, all diversity measures returned to near phase 1 levels.« less

Chemical fractionation in the solar nebula

NASA Technical Reports Server (NTRS)

Grossman, L.

1977-01-01

The sequence of condensation of minerals from a cooling gas of solar composition has been calculated from thermodynamic data over the pressure range 0.001-0.00001 atm, assuming that complete chemical equilibrium is maintained. The results suggest that the Ca-Al-rich inclusions Allende and other carbonaceous chondrites are aggregates of the highest temperature condensates. Complete condensation of these elements is followed, 100 deg later, by the onset of the crystallization of nickel-iron, forsterite and enstatite. Transport of Ca-Al-rich refractory condensates from one part of the nebula to another before the condensation of these lower-temperature phases may have been responsible for the refractory element fractionations between the different classes of chondrites and possibly for the inferred refractory element enrichment of the Moon. The temperature gap between the condensation temperatures of nickel-iron and forsterite increases with increasing total pressure. Because pressure and temperature probably increased with decreasing heliocentric distance in the solar nebula, Mercury may have accreted from a condensate assemblage having a higher metal/silicate ratio than Venus or Earth which may, in turn, have formed from less oxidized material than Mars.

Early events in the folding of an amphipathic peptide: A multinanosecond molecular dynamics study

NASA Technical Reports Server (NTRS)

Chipot, C.; Maigret, B.; Pohorille, A.

1999-01-01

Folding of the capped LQQLLQQLLQL peptide is investigated at the water-hexane interface by molecular dynamics simulations for 161.5 ns. Initially placed in the aqueous phase as a beta-strand, the peptide rapidly adsorbs to the interface, where it adopts an amphipathic conformation. The marginal presence of nonamphipathic structures throughout the complete trajectory indicates that the corresponding conformations are strongly disfavored at the interface. It is further suggestive that folding in an interfacial environment proceeds through a pathway of successive amphipathic intermediates. The energetic and entropic penalties involved in the conformational changes along this pathway markedly increase the folding time scales of LQQLLQQLLQL, explaining why the alpha-helix, the hypothesized lowest free energy structure for a sequence with a hydrophobic periodicity of 3.6, has not been reached yet. The formation of a type I beta-turn at the end of the simulation confirms the importance of such motifs as initiation sites allowing the peptide to coalesce towards a secondary structure. Proteins 1999;36:383-399. Copyright 1999 Wiley-Liss, Inc.

A versatile computer-controlled pulsed nuclear quadrupole resonance spectrometer

NASA Astrophysics Data System (ADS)

Fisher, Gregory; MacNamara, Ernesto; Santini, Robert E.; Raftery, Daniel

1999-12-01

A new, pulsed nuclear quadrupole resonance (NQR) spectrometer capable of performing a variety of pulsed and swept experiments is described. The spectrometer features phase locked, superheterodyne detection using a commercial spectrum analyzer and a fully automatic, computer-controlled tuning and matching network. The tuning and matching network employs stepper motors which turn high power air gap capacitors in a "moving grid" optimization strategy to minimize the reflected power from a directional coupler. In the duplexer circuit, digitally controlled relays are used to switch different lengths of coax cable appropriate for the different radio frequencies. A home-built pulse programmer card controls the timing of radio frequency pulses sent to the probe, while data acquisition and control software is written in Microsoft Quick Basic. Spin-echo acquisition experiments are typically used to acquire the data, although a variety of pulse sequences can be employed. Scan times range from one to several hours depending upon the step resolution and the spectral range required for each experiment. Pure NQR spectra of NaNO2 and 3-aminopyridine are discussed.

The UDP-glycosyltransferase (UGT) superfamily expressed in humans, insects and plants: Animal-plant arms-race and co-evolution.

PubMed

Bock, Karl Walter

2016-01-01

UDP-glycosyltransferases (UGTs) are major phase II enzymes of a detoxification system evolved in all kingdoms of life. Lipophilic endobiotics such as hormones and xenobiotics including phytoalexins and drugs are conjugated by vertebrates mainly with glucuronic acid, by invertebrates and plants mainly with glucose. Plant-herbivore arms-race has been the major driving force for evolution of large UGT and other enzyme superfamilies. The UGT superfamily is defined by a common protein structure and signature sequence of 44 amino acids responsible for binding the UDP moiety of the sugar donor. Plants developed toxic phytoalexins stored as glucosides. Upon herbivore attack these conjugates are converted to highly reactive compounds. In turn, animals developed large families of UGTs in their intestine and liver to detoxify these phytoalexins. Interestingly, phytoalexins, exemplified by quercetin glucuronides and glucosinolate-derived isocyanates, are known insect attractant pigments in plants, and antioxidants, anti-inflammatory and chemopreventive compounds of humans. It is to be anticipated that phytochemicals may provide a rich source in beneficial drugs. Copyright © 2015. Published by Elsevier Inc.

Unaddressed participants’ gaze in multi-person interaction: optimizing recipiency

PubMed Central

Holler, Judith; Kendrick, Kobin H.

2015-01-01

One of the most intriguing aspects of human communication is its turn-taking system. It requires the ability to process on-going turns at talk while planning the next, and to launch this next turn without considerable overlap or delay. Recent research has investigated the eye movements of observers of dialogs to gain insight into how we process turns at talk. More specifically, this research has focused on the extent to which we are able to anticipate the end of current and the beginning of next turns. At the same time, there has been a call for shifting experimental paradigms exploring social-cognitive processes away from passive observation toward on-line processing. Here, we present research that responds to this call by situating state-of-the-art technology for tracking interlocutors’ eye movements within spontaneous, face-to-face conversation. Each conversation involved three native speakers of English. The analysis focused on question–response sequences involving just two of those participants, thus rendering the third momentarily unaddressed. Temporal analyses of the unaddressed participants’ gaze shifts from current to next speaker revealed that unaddressed participants are able to anticipate next turns, and moreover, that they often shift their gaze toward the next speaker before the current turn ends. However, an analysis of the complex structure of turns at talk revealed that the planning of these gaze shifts virtually coincides with the points at which the turns first become recognizable as possibly complete. We argue that the timing of these eye movements is governed by an organizational principle whereby unaddressed participants shift their gaze at a point that appears interactionally most optimal: It provides unaddressed participants with access to much of the visual, bodily behavior that accompanies both the current speaker’s and the next speaker’s turn, and it allows them to display recipiency with regard to both speakers’ turns. PMID:25709592

ω-Turn: a novel β-turn mimic in globular proteins stabilized by main-chain to side-chain C−H···O interaction.

PubMed

Dhar, Jesmita; Chakrabarti, Pinak; Saini, Harpreet; Raghava, Gajendra Pal Singh; Kishore, Raghuvansh

2015-02-01

Mimicry of structural motifs is a common feature in proteins. The 10-membered hydrogen-bonded ring involving the main-chain C − O in a β-turn can be formed using a side-chain carbonyl group leading to Asx-turn. We show that the N − H component of hydrogen bond can be replaced by a C(γ) -H group in the side chain, culminating in a nonconventional C − H···O interaction. Because of its shape this β-turn mimic is designated as ω-turn, which is found to occur ∼ three times per 100 residues. Three residues (i to i + 2) constitute the turn with the C − H···O interaction occurring between the terminal residues, constraining the torsion angles ϕi + 1, ψi + 1, ϕi + 2 and χ'1(i + 2) (using the interacting C(γ) atom). Based on these angles there are two types of ω-turns, each of which can be further divided into two groups. C(β) -branched side-chains, and Met and Gln have high propensities to occur at i + 2; for the last two residues the carbonyl oxygen may participate in an additional interaction involving the S and amino group, respectively. With Cys occupying the i + 1 position, such turns are found in the metal-binding sites. N-linked glycosylation occurs at the consensus pattern Asn-Xaa-Ser/Thr; with Thr at i + 2, the sequence can adopt the secondary structure of a ω-turn, which may be the recognition site for protein modification. Location between two β-strands is the most common occurrence in protein tertiary structure, and being generally exposed ω-turn may constitute the antigenic determinant site. It is a stable scaffold and may be used in protein engineering and peptide design. © 2014 Wiley Periodicals, Inc.

Shotgun metagenomic data streams: surfing without fear

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

Berendzen, Joel R

2010-12-06

Timely information about bio-threat prevalence, consequence, propagation, attribution, and mitigation is needed to support decision-making, both routinely and in a crisis. One DNA sequencer can stream 25 Gbp of information per day, but sampling strategies and analysis techniques are needed to turn raw sequencing power into actionable knowledge. Shotgun metagenomics can enable biosurveillance at the level of a single city, hospital, or airplane. Metagenomics characterizes viruses and bacteria from complex environments such as soil, air filters, or sewage. Unlike targeted-primer-based sequencing, shotgun methods are not blind to sequences that are truly novel, and they can measure absolute prevalence. Shotgun metagenomicmore » sampling can be non-invasive, efficient, and inexpensive while being informative. We have developed analysis techniques for shotgun metagenomic sequencing that rely upon phylogenetic signature patterns. They work by indexing local sequence patterns in a manner similar to web search engines. Our methods are laptop-fast and favorable scaling properties ensure they will be sustainable as sequencing methods grow. We show examples of application to soil metagenomic samples.« less

Phase transition sequence in ferroelectric Aurivillius compounds investigated by single crystal X-ray diffraction

NASA Astrophysics Data System (ADS)

Boullay, P.; Tellier, J.; Mercurio, D.; Manier, M.; Zuñiga, F. J.; Perez-Mato, J. M.

2012-09-01

The investigation of the phase transition sequence in SrBi2Ta2O9 (SBT) and SrBi2Nb2O9 (SBN) is reported using single-crystal X-ray diffraction. By monitoring specific reflections as a function of temperature, sensitive either to the superstructure formation or to polar displacements, it was possible to check the existence or not of an intermediate phase. This latter was confirmed in SBT, but within experimental accuracy could not be detected in SBN.

DNA unzipping phase diagram calculated via replica theory.

PubMed

Roland, C Brian; Hatch, Kristi Adamson; Prentiss, Mara; Shakhnovich, Eugene I

2009-05-01

We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). Toward this end, we study a statistical-mechanics model for the fluctuating structure of a long molecule of dsDNA, and compute the equilibrium phase diagram for the experiment in which the molecule is unzipped under applied force. We consider a perfect-matching dsDNA model, in which the loops are volume-excluding chains with arbitrary loop exponent c . We include stacking interactions, hydrogen bonds, and main-chain entropy. We include sequence heterogeneity at the level of random sequences; in particular, there is no correlation in the base-pairing (bp) energy from one sequence position to the next. We present heuristic arguments to demonstrate that the low-temperature macrostate does not exhibit degenerate ergodicity breaking. We use this claim to understand the results of our replica-theoretic calculation of the equilibrium properties of the system. As a function of temperature, we obtain the minimal force at which the molecule separates completely. This critical-force curve is a line in the temperature-force phase diagram that marks the regions where the molecule exists primarily as a double helix versus the region where the molecule exists as two separate strands. We compare our random-sequence model to magnetic tweezer experiments performed on the 48 502 bp genome of bacteriophage lambda . We find good agreement with the experimental data, which is restricted to temperatures between 24 and 50 degrees C . At higher temperatures, the critical-force curve of our random-sequence model is very different for that of the homogeneous-sequence version of our model. For both sequence models, the critical force falls to zero at the melting temperature T_{c} like |T-T_{c}|;{alpha} . For the homogeneous-sequence model, alpha=1/2 almost exactly, while for the random-sequence model, alpha approximately 0.9 . Importantly, the shape of the critical-force curve is connected, via our theory, to the manner in which the helix fraction falls to zero at T_{c} . The helix fraction is the property that is used to classify the melting transition as a type of phase transition. In our calculation, the shape of the critical-force curve holds strong evidence that the zero-force melting transition of long natural dsDNA should be classified as a higher-order (continuous) phase transition. Specifically, the order is 3rd or greater.

Error catastrophe and phase transition in the empirical fitness landscape of HIV

NASA Astrophysics Data System (ADS)

Hart, Gregory R.; Ferguson, Andrew L.

2015-03-01

We have translated clinical sequence databases of the p6 HIV protein into an empirical fitness landscape quantifying viral replicative capacity as a function of the amino acid sequence. We show that the viral population resides close to a phase transition in sequence space corresponding to an "error catastrophe" beyond which there is lethal accumulation of mutations. Our model predicts that the phase transition may be induced by drug therapies that elevate the mutation rate, or by forcing mutations at particular amino acids. Applying immune pressure to any combination of killer T-cell targets cannot induce the transition, providing a rationale for why the viral protein can exist close to the error catastrophe without sustaining fatal fitness penalties due to adaptive immunity.

Random Blume-Emery-Griffiths model on the Bethe lattice

NASA Astrophysics Data System (ADS)

Albayrak, Erhan

2015-12-01

The random phase transitions of the Blume-Emery-Griffiths (BEG) model for the spin-1 system are investigated on the Bethe lattice and the phase diagrams of the model are obtained. The biquadratic exchange interaction (K) is turned on, i.e. the BEG model, with probability p either attractively (K > 0) or repulsively (K < 0) and turned off, which leads to the BC model, with the probability (1 - p) throughout the Bethe lattice. By taking the bilinear exchange interaction parameter J as a scaling parameter, the effects of the competitions between the reduced crystal fields (D / J), reduced biquadratic exchange interaction parameter (K / J) and the reduced temperature (kT / J) for given values of the probability when the coordination number is q=4, i.e. on a square lattice, are studied in detail.

Smart design of a long-period fiber grating refractive index sensor based on dual-peak resonance near the phase-matching turning point.

PubMed

Ling, Qiang; Gu, Zhengtian; Gao, Kan

2018-04-01

This paper presents a smart design way for the long-period fiber grating (LPFG) refractive index sensor, which is based on high sensitivity of LPFG near phase-matching turning point (PMTP) to the surrounding refractive index (SRI). On the basis of the coupled mode theory of LPFG, cladding etching and film coating have opposite effects on the shift of the dual peaks. Therefore, an LPFG can be controlled by the cladding etching and film coating successively, until it operates near PMTP. Experimentally, an LPFG operating near PMTP was fabricated, and the glycerol solution concentration monitoring test was performed. The results show that the sensitivity of this LPFG to the SRI is as high as 5602 nm/refractive index unit.

Shoulder Muscle Activation of Novice and Resistance Trained Women during Variations of Dumbbell Press Exercises

PubMed Central

Luczak, Joshua; Bosak, Andy; Riemann, Bryan L.

2013-01-01

Previous research has compared the effects of trunk inclination angle on muscle activation using barbells and Smith machines in men. Whether similar effects occur with the use of dumbbells or in women remains unknown. The purpose was to compare upper extremity surface electromyographical (EMG) activity between dumbbell bench, incline, and shoulder presses. Dominate arm EMG data were recorded for collegiate-aged female resistance trained individuals (n = 12) and novice female resistance trained exercisers (n = 12) from which average EMG amplitude for each repetition phase (concentric, eccentric) was computed. No significant differences were found between experienced and novice resistance trained individuals. For the upper trapezius and anterior deltoid muscles, shoulder press activation was significantly greater than incline press which in turn was significantly greater than bench press across both phases. The bench and incline presses promoted significantly greater pectoralis major sternal activation compared to the shoulder press (both phases). While pectoralis major clavicular activation during the incline press eccentric phase was significantly greater than both the bench and shoulder presses, activation during the bench press concentric phase promoted significantly greater activation than the incline press which in turn was significantly greater than the shoulder press. These results provide evidence for selecting exercises in resistance and rehabilitation programs. PMID:26464884

Abdicating power for control: a precision timing strategy to modulate function of flight power muscles.

PubMed

Sponberg, S; Daniel, T L

2012-10-07

Muscles driving rhythmic locomotion typically show strong dependence of power on the timing or phase of activation. This is particularly true in insects' main flight muscles, canonical examples of muscles thought to have a dedicated power function. However, in the moth (Manduca sexta), these muscles normally activate at a phase where the instantaneous slope of the power-phase curve is steep and well below maximum power. We provide four lines of evidence demonstrating that, contrary to the current paradigm, the moth's nervous system establishes significant control authority in these muscles through precise timing modulation: (i) left-right pairs of flight muscles normally fire precisely, within 0.5-0.6 ms of each other; (ii) during a yawing optomotor response, left-right muscle timing differences shift throughout a wider 8 ms timing window, enabling at least a 50 per cent left-right power differential; (iii) timing differences correlate with turning torque; and (iv) the downstroke power muscles alone causally account for 47 per cent of turning torque. To establish (iv), we altered muscle activation during intact behaviour by stimulating individual muscle potentials to impose left-right timing differences. Because many organisms also have muscles operating with high power-phase gains (Δ(power)/Δ(phase)), this motor control strategy may be ubiquitous in locomotor systems.

Abdicating power for control: a precision timing strategy to modulate function of flight power muscles

PubMed Central

Sponberg, S.; Daniel, T. L.

2012-01-01

Muscles driving rhythmic locomotion typically show strong dependence of power on the timing or phase of activation. This is particularly true in insects' main flight muscles, canonical examples of muscles thought to have a dedicated power function. However, in the moth (Manduca sexta), these muscles normally activate at a phase where the instantaneous slope of the power–phase curve is steep and well below maximum power. We provide four lines of evidence demonstrating that, contrary to the current paradigm, the moth's nervous system establishes significant control authority in these muscles through precise timing modulation: (i) left–right pairs of flight muscles normally fire precisely, within 0.5–0.6 ms of each other; (ii) during a yawing optomotor response, left—right muscle timing differences shift throughout a wider 8 ms timing window, enabling at least a 50 per cent left–right power differential; (iii) timing differences correlate with turning torque; and (iv) the downstroke power muscles alone causally account for 47 per cent of turning torque. To establish (iv), we altered muscle activation during intact behaviour by stimulating individual muscle potentials to impose left—right timing differences. Because many organisms also have muscles operating with high power–phase gains (Δpower/Δphase), this motor control strategy may be ubiquitous in locomotor systems. PMID:22833272

Inertial Oscillation of a Vertical Rotating Draft with Application to a Supercell Storm: Video Supplement to NASA-TP-3230

NASA Technical Reports Server (NTRS)

Costen, Robert C.; Stock, Larry V.

1992-01-01

In this video (8 min., color, sound, VHS), animation depicts the inertial oscillation of a new mathematical model ('vertical rotating draft') for spinning up a single supercell storm. The oscillation consists of a long quiescent phase when the draft is large in diameter and rotates anticyclonically and a short intense phase when the draft is small and cyclonic. During the intense phase, the rotating draft resembles a supercell. The physical basis for the oscillation is depicted by tracking air parcels in the draft as they move along inertial circles (projected on a horizontal plane), where the horizontal pressure gradient is zero and the Coriolis force balances the centrifugal force. A side view of the oscillation shows that contraction and expansion are linked, respectively, to buoyantly driven compressible downdraft and updraft. An aerial view tracks the draft as it moves above the surface of the Earth and turns to the right during the intense phase. Radar echoes from a supercell storm are superimposed for comparison. The data appear to support only the intense phase. A critical experiment would measure the predominantly downward flow that theoretically occurs before the right turn in a supercell track and causes contraction and spin-up.

Phase imaging in brain using SWIFT

NASA Astrophysics Data System (ADS)

Lehto, Lauri Juhani; Garwood, Michael; Gröhn, Olli; Corum, Curtis Andrew

2015-03-01

The majority of MRI phase imaging is based on gradient recalled echo (GRE) sequences. This work studies phase contrast behavior due to small off-resonance frequency offsets in brain using SWIFT, a FID-based sequence with nearly zero acquisition delay. 1D simulations and a phantom study were conducted to describe the behavior of phase accumulation in SWIFT. Imaging experiments of known brain phase contrast properties were conducted in a perfused rat brain comparing GRE and SWIFT. Additionally, a human brain sample was imaged. It is demonstrated how SWIFT phase is orientation dependent and correlates well with GRE, linking SWIFT phase to similar off-resonance sources as GRE. The acquisition time is shown to be analogous to TE for phase accumulation time. Using experiments with and without a magnetization transfer preparation, the likely effect of myelin water pool contribution is seen as a phase increase for all acquisition times. Due to the phase accumulation during acquisition, SWIFT phase contrast can be sensitized to small frequency differences between white and gray matter using low acquisition bandwidths.

Partial amino acid sequence of the branched chain amino acid aminotransferase (TmB) of E. coli JA199 pDU11

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

Feild, M.J.; Armstrong, F.B.

1987-05-01

E. coli JA199 pDU11 harbors a multicopy plasmid containing the ilv GEDAY gene cluster of S. typhimurium. TmB, gene product of ilv E, was purified, crystallized, and subjected to Edman degradation using a gas phase sequencer. The intact protein yielded an amino terminal 31 residue sequence. Both carboxymethylated apoenzyme and (/sup 3/H)-NaBH-reduced holoenzyme were then subjected to digestion by trypsin. The digests were fractionated using reversed phase HPLC, and the peptides isolated were sequenced. The borohydride-treated holoenzyme was used to isolate the cofactor-binding peptide. The peptide is 27 residues long and a comparison with known sequences of other aminotransferases revealedmore » limited homology. Peptides accounting for 211 of 288 predicted residues have been sequenced, including 9 residues of the carboxyl terminus. Comparison of peptides with the inferred amino acid sequence of the E. coli K-12 enzyme has helped determine the sequence of the amino terminal 59 residues; only two differences between the sequences are noted in this region.« less

Quantification of wing and body kinematics in connection to torque generation during damselfly yaw turn

NASA Astrophysics Data System (ADS)

Zeyghami, Samane; Bode-Oke, Ayodeji T.; Dong, HaiBo

2017-01-01

This study provides accurate measurements of the wing and body kinematics of three different species of damselflies in free yaw turn flights. The yaw turn is characterized by a short acceleration phase which is immediately followed by an elongated deceleration phase. Most of the heading change takes place during the latter stage of the flight. Our observations showed that yaw turns are executed via drastic rather than subtle changes in the kinematics of all four wings. The motion of the inner and outer wings were found to be strongly linked through their orientation as well as their velocities with the inner wings moving faster than the outer wings. By controlling the pitch angle and wing velocity, a damselfly adjusts the angle of attack. The wing angle of attack exerted the strongest influence on the yaw torque, followed by the flapping and deviation velocities of the wings. Moreover, no evidence of active generation of counter torque was found in the flight data implying that deceleration and stopping of the maneuver is dominated by passive damping. The systematic analysis carried out on the free flight data advances our understanding of the mechanisms by which these insects achieve their observed maneuverability. In addition, the inspiration drawn from this study can be employed in the design of low frequency flapping wing micro air vehicles (MAV's).

Kinematic, kinetic and EMG analysis of four front crawl flip turn techniques.

PubMed

Pereira, Suzana Matheus; Ruschel, Caroline; Hubert, Marcel; Machado, Leandro; Roesler, Helio; Fernandes, Ricardo Jorge; Vilas-Boas, João Paulo

2015-01-01

This study aimed to analyse the kinematic, kinetic and electromyographic characteristics of four front crawl flip turn technique variants. The variants distinguished from each other by differences in body position (i.e., dorsal, lateral, ventral) during rolling, wall support, pushing and gliding phases. Seventeen highly trained swimmers (17.9 ± 3.2 years old) participated in interventional sessions and performed three trials of each variant, being monitored with a 3-D video system, a force platform and an electromyography (EMG) system. Studied variables: rolling time and distance, wall support time, push-off time, peak force and horizontal impulse at wall support and push-off, centre of mass horizontal velocity at the end of the push-off, gliding time, centre of mass depth, distance, average and final velocity during gliding, total turn time and electrical activity of Gastrocnemius Medialis, Tibialis Anterior, Biceps Femoris and Vastus Lateralis muscles. Depending on the variant, total turn time ranged from 2.37 ± 0.32 to 2.43 ± 0.33 s, push-off force from 1.86 ± 0.33 to 1.92 ± 0.26 BW and centre of mass velocity during gliding from 1.78 ± 0.21 to 1.94 ± 0.22 m · s(-1). The variants were not distinguishable in terms of kinematical, kinetic and EMG parameters during the rolling, wall support, pushing and gliding phases.

Novel methods to optimize genotypic imputation for low-coverage, next-generation sequence data in crop plants

USDA-ARS?s Scientific Manuscript database

Next-generation sequencing technology such as genotyping-by-sequencing (GBS) made low-cost, but often low-coverage, whole-genome sequencing widely available. Extensive inbreeding in crop plants provides an untapped, high quality source of phased haplotypes for imputing missing genotypes. We introduc...

Identification and analysis of multigene families by comparison of exon fingerprints.

PubMed

Brown, N P; Whittaker, A J; Newell, W R; Rawlings, C J; Beck, S

1995-06-02

Gene families are often recognised by sequence homology using similarity searching to find relationships, however, genomic sequence data provides gene architectural information not used by conventional search methods. In particular, intron positions and phases are expected to be relatively conserved features, because mis-splicing and reading frame shifts should be selected against. A fast search technique capable of detecting possible weak sequence homologies apparent at the intron/exon level of gene organization is presented for comparing spliceosomal genes and gene fragments. FINEX compares strings of exons delimited by intron/exon boundary positions and intron phases (exon fingerprint) using a global dynamic programming algorithm with a combined intron phase identity and exon size dissimilarity score. Exon fingerprints are typically two orders of magnitude smaller than their nucleic acid sequence counterparts giving rise to fast search times: a ranked search against a library of 6755 fingerprints for a typical three exon fingerprint completes in under 30 seconds on an ordinary workstation, while a worst case largest fingerprint of 52 exons completes in just over one minute. The short "sequence" length of exon fingerprints in comparisons is compensated for by the large exon alphabet compounded of intron phase types and a wide range of exon sizes, the latter contributing the most information to alignments. FINEX performs better in some searches than conventional methods, finding matches with similar exon organization, but low sequence homology. A search using a human serum albumin finds all members of the multigene family in the FINEX database at the top of the search ranking, despite very low amino acid percentage identities between family members. The method should complement conventional sequence searching and alignment techniques, offering a means of identifying otherwise hard to detect homologies where genomic data are available.

Resolving coiled shapes reveals new reorientation behaviors in C. elegans

PubMed Central

Broekmans, Onno D; Rodgers, Jarlath B; Ryu, William S; Stephens, Greg J

2016-01-01

We exploit the reduced space of C. elegans postures to develop a novel tracking algorithm which captures both simple shapes and also self-occluding coils, an important, yet unexplored, component of 2D worm behavior. We apply our algorithm to show that visually complex, coiled sequences are a superposition of two simpler patterns: the body wave dynamics and a head-curvature pulse. We demonstrate the precise Ω-turn dynamics of an escape response and uncover a surprising new dichotomy in spontaneous, large-amplitude coils; deep reorientations occur not only through classical Ω-shaped postures but also through larger postural excitations which we label here as δ-turns. We find that omega and delta turns occur independently, suggesting a distinct triggering mechanism, and are the serpentine analog of a random left-right step. Finally, we show that omega and delta turns occur with approximately equal rates and adapt to food-free conditions on a similar timescale, a simple strategy to avoid navigational bias. DOI: http://dx.doi.org/10.7554/eLife.17227.001 PMID:27644113

Phase attraction in sensorimotor synchronization with auditory sequences: effects of single and periodic distractors on synchronization accuracy.

PubMed

Repp, Bruno H

2003-04-01

Four experiments showed that both single and periodic distractor tones affected the timing of finger taps produced in synchrony with an isochronous auditory target sequence. Single distractors had only small effects, but periodic distractors occurring at various fixed or changing phase relationships exerted strong phase attraction. The attraction was asymmetric, being stronger when distractors preceded target tones than when they lagged behind. A large pitch difference between target and distractor tones (20 vs. 3 semitones) did not reduce phase attraction substantially, although in the case of continuously changing phase relationships it did prevent complete capture of the taps by the distractors. The results support the hypothesis that phase attraction is an automatic process that is sensitive primarily to event onsets.

Construction Strategy for an Internal Amplification Control for Real-Time Diagnostic Assays Using Nucleic Acid Sequence-Based Amplification: Development and Clinical Application

PubMed Central

Rodríguez-Lázaro, David; D'Agostino, Martin; Pla, Maria; Cook, Nigel

2004-01-01

An important analytical control in molecular amplification-based methods is an internal amplification control (IAC), which should be included in each reaction mixture. An IAC is a nontarget nucleic acid sequence which is coamplified simultaneously with the target sequence. With negative results for the target nucleic acid, the absence of an IAC signal indicates that amplification has failed. A general strategy for the construction of an IAC for inclusion in molecular beacon-based real-time nucleic acid sequence-based amplification (NASBA) assays is presented. Construction proceeds in two phases. In the first phase, a double-stranded DNA molecule that contains nontarget sequences flanked by target sequences complementary to the NASBA primers is produced. At the 5′ end of this DNA molecule is a T7 RNA polymerase binding sequence. In the second phase of construction, RNA transcripts are produced from the DNA by T7 RNA polymerase. This RNA is the IAC; it is amplified by the target NASBA primers and is detected by a molecular beacon probe complementary to the internal nontarget sequences. As a practical example, an IAC for use in an assay for the detection of Mycobacterium avium subsp. paratuberculosis is described, its incorporation and optimization within the assay are detailed, and its application to spiked and natural clinical samples is shown to illustrate the correct interpretation of the diagnostic results. PMID:15583319

Sensitivity to structure in action sequences: An infant event-related potential study.

PubMed

Monroy, Claire D; Gerson, Sarah A; Domínguez-Martínez, Estefanía; Kaduk, Katharina; Hunnius, Sabine; Reid, Vincent

2017-05-06

Infants are sensitive to structure and patterns within continuous streams of sensory input. This sensitivity relies on statistical learning, the ability to detect predictable regularities in spatial and temporal sequences. Recent evidence has shown that infants can detect statistical regularities in action sequences they observe, but little is known about the neural process that give rise to this ability. In the current experiment, we combined electroencephalography (EEG) with eye-tracking to identify electrophysiological markers that indicate whether 8-11-month-old infants detect violations to learned regularities in action sequences, and to relate these markers to behavioral measures of anticipation during learning. In a learning phase, infants observed an actor performing a sequence featuring two deterministic pairs embedded within an otherwise random sequence. Thus, the first action of each pair was predictive of what would occur next. One of the pairs caused an action-effect, whereas the second did not. In a subsequent test phase, infants observed another sequence that included deviant pairs, violating the previously observed action pairs. Event-related potential (ERP) responses were analyzed and compared between the deviant and the original action pairs. Findings reveal that infants demonstrated a greater Negative central (Nc) ERP response to the deviant actions for the pair that caused the action-effect, which was consistent with their visual anticipations during the learning phase. Findings are discussed in terms of the neural and behavioral processes underlying perception and learning of structured action sequences. Copyright © 2017 Elsevier Ltd. All rights reserved.

Solvent-induced conformational flexibility of a bicyclic proline analogue: Octahydroindole-2-carboxylic acid.

PubMed

Torras, Juan; Warren, Javier G; Revilla-López, Guillem; Jiménez, Ana I; Cativiela, Carlos; Alemán, Carlos

2014-03-01

The conformational preferences of the N-acetyl-N'-methylamide derivatives of the four octahydroindole-2-carboxylic acid (Oic) stereoisomers have been investigated in the gas-phase and in aqueous solution using quantum mechanical calculations. In addition to the conformational effects provoked by the stereochemical diversity of Oic, which presents three chiral centers, results provide evidence of interesting and rather unusual features. The conformational preferences of the Oic stereoisomers in solution are only well described by applying a complete and systematic search process, results achieved by simple re-optimization of the gas-phase minima being very imprecise. This is because the conformational rigidity detected in the gas-phase, which is imposed by the chemical restrictions of the fused bicyclic skeleton, disappears in aqueous solution, the four stereoisomers behaving as flexible molecules in this environment. Thus, in general, the γ-turn is the only minimum energy conformation in the gas-phase while in aqueous solution the helical, polyproline-II and γ-turn motifs are energetically favored. Molecular dynamics simulations indicate that the conformational flexibility predicted by quantum mechanical calculations for the four Oic stereoisomers in solution is satisfactorily reproduced by classical force-fields. Copyright © 2014 Wiley Periodicals, Inc.

Investigation of the Iterative Phase Retrieval Algorithm for Interferometric Applications

NASA Astrophysics Data System (ADS)

Gombkötő, Balázs; Kornis, János

2010-04-01

Sequentially recorded intensity patterns reflected from a coherently illuminated diffuse object can be used to reconstruct the complex amplitude of the scattered beam. Several iterative phase retrieval algorithms are known in the literature to obtain the initially unknown phase from these longitudinally displaced intensity patterns. When two sequences are recorded in two different states of a centimeter sized object in optical setups that are similar to digital holographic interferometry-but omitting the reference wave-, displacement, deformation, or shape measurement is theoretically possible. To do this, the retrieved phase pattern should contain information not only about the intensities and locations of the point sources of the object surface, but their relative phase as well. Not only experiments require strict mechanical precision to record useful data, but even in simulations several parameters influence the capabilities of iterative phase retrieval, such as object to camera distance range, uniform or varying camera step sequence, speckle field characteristics, and sampling. Experiments were done to demonstrate this principle with an as large as 5×5 cm sized deformable object as well. Good initial results were obtained in an imaging setup, where the intensity pattern sequences were recorded near the image plane.

Whole-Genome Sequence of Coxiella burnetii Nine Mile RSA439 (Phase II, Clone 4), a Laboratory Workhorse Strain

PubMed Central

Beare, Paul A.; Moses, Abraham S.; Martens, Craig A.; Heinzen, Robert A.

2017-01-01

ABSTRACT Here, we report the whole-genome sequence of Coxiella burnetii Nine Mile RSA439 (phase II, clone 4), a laboratory strain used extensively to investigate the biology of this intracellular bacterial pathogen. The genome consists of a 1.97-Mb chromosome and a 37.32-kb plasmid. PMID:28596399

Whole-Genome Sequence of Coxiella burnetii Nine Mile RSA439 (Phase II, Clone 4), a Laboratory Workhorse Strain.

PubMed

Millar, Jess A; Beare, Paul A; Moses, Abraham S; Martens, Craig A; Heinzen, Robert A; Raghavan, Rahul

2017-06-08

Here, we report the whole-genome sequence of Coxiella burnetii Nine Mile RSA439 (phase II, clone 4), a laboratory strain used extensively to investigate the biology of this intracellular bacterial pathogen. The genome consists of a 1.97-Mb chromosome and a 37.32-kb plasmid. Copyright © 2017 Millar et al.

A Sequenced Instructional Program in Physical Education for the Handicapped, Phase III. Producing and Disseminating Demonstration Packages. Final Report.

ERIC Educational Resources Information Center

Carr, Dorothy B.; Avance, Lyonel D.

Presented is a sequenced instructional program in physical education which constitutes the third of a three-phase, 4-year project, funded by Title III, for handicapped children, preschool through high school levels, in the Los Angeles Unified School District. Described are the project setting and the following accomplishments: a curriculum guide…

Nominal Profile Refinements Report: Target in 120 Nautical Mile Circular Orbit

NASA Technical Reports Server (NTRS)

1974-01-01

The compability of the nominal rendezvous sequence with low target orbits is addressed. It was found that for targets in low earth orbits certain modifications of the nominal sequence are required to achieve a feasible anytime liftoff capability, notably the use of elliptical phasing orbits and the allowance of up to two days for rendezvous under certain phasing conditions.

GapFiller: a de novo assembly approach to fill the gap within paired reads

PubMed Central

2012-01-01

Background Next Generation Sequencing technologies are able to provide high genome coverages at a relatively low cost. However, due to limited reads' length (from 30 bp up to 200 bp), specific bioinformatics problems have become even more difficult to solve. De novo assembly with short reads, for example, is more complicated at least for two reasons: first, the overall amount of "noisy" data to cope with increased and, second, as the reads' length decreases the number of unsolvable repeats grows. Our work's aim is to go at the root of the problem by providing a pre-processing tool capable to produce (in-silico) longer and highly accurate sequences from a collection of Next Generation Sequencing reads. Results In this paper a seed-and-extend local assembler is presented. The kernel algorithm is a loop that, starting from a read used as seed, keeps extending it using heuristics whose main goal is to produce a collection of error-free and longer sequences. In particular, GapFiller carefully detects reliable overlaps and operates clustering similar reads in order to reconstruct the missing part between the two ends of the same insert. Our tool's output has been validated on 24 experiments using both simulated and real paired reads datasets. The output sequences are declared correct when the seed-mate is found. In the experiments performed, GapFiller was able to extend high percentages of the processed seeds and find their mates, with a false positives rate that turned out to be nearly negligible. Conclusions GapFiller, starting from a sufficiently high short reads coverage, is able to produce high coverages of accurate longer sequences (from 300 bp up to 3500 bp). The procedure to perform safe extensions, together with the mate-found check, turned out to be a powerful criterion to guarantee contigs' correctness. GapFiller has further potential, as it could be applied in a number of different scenarios, including the post-processing validation of insertions/deletions detection pipelines, pre-processing routines on datasets for de novo assembly pipelines, or in any hierarchical approach designed to assemble, analyse or validate pools of sequences. PMID:23095524

Efficient algorithms for polyploid haplotype phasing.

PubMed

He, Dan; Saha, Subrata; Finkers, Richard; Parida, Laxmi

2018-05-09

Inference of haplotypes, or the sequence of alleles along the same chromosomes, is a fundamental problem in genetics and is a key component for many analyses including admixture mapping, identifying regions of identity by descent and imputation. Haplotype phasing based on sequencing reads has attracted lots of attentions. Diploid haplotype phasing where the two haplotypes are complimentary have been studied extensively. In this work, we focused on Polyploid haplotype phasing where we aim to phase more than two haplotypes at the same time from sequencing data. The problem is much more complicated as the search space becomes much larger and the haplotypes do not need to be complimentary any more. We proposed two algorithms, (1) Poly-Harsh, a Gibbs Sampling based algorithm which alternatively samples haplotypes and the read assignments to minimize the mismatches between the reads and the phased haplotypes, (2) An efficient algorithm to concatenate haplotype blocks into contiguous haplotypes. Our experiments showed that our method is able to improve the quality of the phased haplotypes over the state-of-the-art methods. To our knowledge, our algorithm for haplotype blocks concatenation is the first algorithm that leverages the shared information across multiple individuals to construct contiguous haplotypes. Our experiments showed that it is both efficient and effective.

Iteration and superposition encryption scheme for image sequences based on multi-dimensional keys

NASA Astrophysics Data System (ADS)

Han, Chao; Shen, Yuzhen; Ma, Wenlin

2017-12-01

An iteration and superposition encryption scheme for image sequences based on multi-dimensional keys is proposed for high security, big capacity and low noise information transmission. Multiple images to be encrypted are transformed into phase-only images with the iterative algorithm and then are encrypted by different random phase, respectively. The encrypted phase-only images are performed by inverse Fourier transform, respectively, thus new object functions are generated. The new functions are located in different blocks and padded zero for a sparse distribution, then they propagate to a specific region at different distances by angular spectrum diffraction, respectively and are superposed in order to form a single image. The single image is multiplied with a random phase in the frequency domain and then the phase part of the frequency spectrums is truncated and the amplitude information is reserved. The random phase, propagation distances, truncated phase information in frequency domain are employed as multiple dimensional keys. The iteration processing and sparse distribution greatly reduce the crosstalk among the multiple encryption images. The superposition of image sequences greatly improves the capacity of encrypted information. Several numerical experiments based on a designed optical system demonstrate that the proposed scheme can enhance encrypted information capacity and make image transmission at a highly desired security level.

Dynamical Galam model

NASA Astrophysics Data System (ADS)

Cheon, Taksu; Galam, Serge

2018-06-01

We introduce a model of temporal evolution of political opinions which amounts to a dynamical extension of Galam model in which the proportions of inflexibles are treated as dynamical variables. We find that the critical value of inflexibles in the original Galam model now turns into a fixed point of the system whose stability controls the phase trajectory of the political opinions. The appearance of two phases is found, in which majority-preserving and regime-changing limit cycles are respectively dominant, and the phase transition between them is observed.

Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing.

PubMed

Nong, Rachel Yuan; Wu, Di; Yan, Junhong; Hammond, Maria; Gu, Gucci Jijuan; Kamali-Moghaddam, Masood; Landegren, Ulf; Darmanis, Spyros

2013-06-01

Solid-phase proximity ligation assays share properties with the classical sandwich immunoassays for protein detection. The proteins captured via antibodies on solid supports are, however, detected not by single antibodies with detectable functions, but by pairs of antibodies with attached DNA strands. Upon recognition by these sets of three antibodies, pairs of DNA strands brought in proximity are joined by ligation. The ligated reporter DNA strands are then detected via methods such as real-time PCR or next-generation sequencing (NGS). We describe how to construct assays that can offer improved detection specificity by virtue of recognition by three antibodies, as well as enhanced sensitivity owing to reduced background and amplified detection. Finally, we also illustrate how the assays can be applied for parallel detection of proteins, taking advantage of the oligonucleotide ligation step to avoid background problems that might arise with multiplexing. The protocol for the singleplex solid-phase proximity ligation assay takes ~5 h. The multiplex version of the assay takes 7-8 h depending on whether quantitative PCR (qPCR) or sequencing is used as the readout. The time for the sequencing-based protocol includes the library preparation but not the actual sequencing, as times may vary based on the choice of sequencing platform.

A shared representation of order between encoding and recognition in visual short-term memory.

PubMed

Kalm, Kristjan; Norris, Dennis

2017-07-15

Many complex tasks require people to bind individual events into a sequence that can be held in short term memory (STM). For this purpose information about the order of the individual events in the sequence needs to be maintained in an active and accessible form in STM over a period of few seconds. Here we investigated how the temporal order information is shared between the presentation and response phases of an STM task. We trained a classification algorithm on the fMRI activity patterns from the presentation phase of the STM task to predict the order of the items during the subsequent recognition phase. While voxels in a number of brain regions represented positional information during either presentation and recognition phases, only voxels in the lateral prefrontal cortex (PFC) and the anterior temporal lobe (ATL) represented position consistently across task phases. A shared positional code in the ATL might reflect verbal recoding of visual sequences to facilitate the maintenance of order information over several seconds. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Phase-Specific Vocalizations of Male Mice at the Initial Encounter during the Courtship Sequence

PubMed Central

Matsumoto, Yui K.; Okanoya, Kazuo

2016-01-01

Mice produce ultrasonic vocalizations featuring a variety of syllables. Vocalizations are observed during social interactions. In particular, males produce numerous syllables during courtship. Previous studies have shown that vocalizations change according to sexual behavior, suggesting that males vary their vocalizations depending on the phase of the courtship sequence. To examine this process, we recorded large sets of mouse vocalizations during male–female interactions and acoustically categorized these sounds into 12 vocal types. We found that males emitted predominantly short syllables during the first minute of interaction, more long syllables in the later phases, and mainly harmonic sounds during mounting. These context- and time-dependent changes in vocalization indicate that vocal communication during courtship in mice consists of at least three stages and imply that each vocalization type has a specific role in a phase of the courtship sequence. Our findings suggest that recording for a sufficiently long time and taking the phase of courtship into consideration could provide more insights into the role of vocalization in mouse courtship behavior in future study. PMID:26841117

Two-phase framework for near-optimal multi-target Lambert rendezvous

NASA Astrophysics Data System (ADS)

Bang, Jun; Ahn, Jaemyung

2018-03-01

This paper proposes a two-phase framework to obtain a near-optimal solution of multi-target Lambert rendezvous problem. The objective of the problem is to determine the minimum-cost rendezvous sequence and trajectories to visit a given set of targets within a maximum mission duration. The first phase solves a series of single-target rendezvous problems for all departure-arrival object pairs to generate the elementary solutions, which provides candidate rendezvous trajectories. The second phase formulates a variant of traveling salesman problem (TSP) using the elementary solutions prepared in the first phase and determines the final rendezvous sequence and trajectories of the multi-target rendezvous problem. The validity of the proposed optimization framework is demonstrated through an asteroid exploration case study.

Development of Quantitative Adverse Outcome Pathways Using Health-Protective Assumptions to Fill Data Gaps

EPA Science Inventory

In an adverse outcome pathway (AOP), the target site dose participates in a molecular initiating event (MIE), which in turn triggers a sequence of key events leading to an adverse outcome (AO). Quantitative AOPs (QAOP) are needed if AOP characterization is to address risk as well...

Badging a Conference

ERIC Educational Resources Information Center

Fontichiaro, Kristin; Ginsberg, Sharona; Lungu, Victoria; Masura, Shauna; Roslund, Samantha

2013-01-01

This article describes digital badging, which turns the traditional cloth badges into digital data with badges earned and stored online. It notes how digital badging systems help people issue and achieve learning challenges in a sequence such as this: (1) A badge issuer creates a challenge using an online badging tool such as P2PU.org,…

How Good Is Good Enough?

ERIC Educational Resources Information Center

Wiggins, Grant

2014-01-01

Education has a long-standing practice of turning worthwhile learning goals into lists of bits. One might even say that this practice is the original sin in curriculum design: take a complex whole, divide it into small pieces, string those together in a rigid sequence of instruction and testing, and call completion of this sequence…

The Dissatisfaction Theory of American Democracy: A Guide for Politics in Local School Districts.

ERIC Educational Resources Information Center

Lutz, Frank W.; Iannaccone, Laurence

Raymond Callahan's superintendent vulnerability thesis suggests that school superintendent behavior is subject to the political winds of local school boards, in turn dominated by the economic values of American businessmen. This thesis inspired a body of research termed "dissatisfaction theory," which describes the sequence of events…

Hierarchically Organized Behavior and Its Neural Foundations: A Reinforcement Learning Perspective

ERIC Educational Resources Information Center

Botvinick, Matthew M.; Niv, Yael; Barto, Andrew C.

2009-01-01

Research on human and animal behavior has long emphasized its hierarchical structure--the divisibility of ongoing behavior into discrete tasks, which are comprised of subtask sequences, which in turn are built of simple actions. The hierarchical structure of behavior has also been of enduring interest within neuroscience, where it has been widely…

Action or Reaction, Learning or Display: Interactional Development and Usage-Based Data

ERIC Educational Resources Information Center

Huth, Thorsten

2013-01-01

This paper investigates how instances of language use can serve as analytic anchors for insight into interactional development over time. I present a usage-based, longitudinal study of multi-turn sequences underlying telephone openings in order to specify if and to whom "language learning" may be relevantly ascribed. Two successive…

Low noise charge ramp electrometer

DOEpatents

Morgan, John P.; Piper, Thomas C.

1992-01-01

An electrometer capable of measuring small currents without the use of a feedback resistor which tends to contribute a large noise factor to the measured data. The electrometer eliminates the feedback resistor through the use of a feedback capacitor located across the electrometer amplifier. The signal from the electrometer amplifier is transferred to a electrometer buffer amplifier which serves to transfer the signal to several receptors. If the electrometer amplifier is approaching saturation, the buffer amplifier signals a reset discriminator which energizes a coil whose magnetic field closes a magnetic relay switch which in turn resets or zeros the feedback capacitor. In turn, a reset complete discriminator restarts the measurement process when the electrometer amplifier approaches its initial condition. The buffer amplifier also transmits the voltage signal from the electrometer amplifier to a voltage-to-frequency converter. The signals from the voltage-to-frequency converter are counted over a fixed period of time and the information is relayed to a data processor. The timing and sequencing of the small current measuring system is under the control of a sequence control logic unit.

A Thiazole Coumarin (TC) Turn-On Fluorescence Probe for AT-Base Pair Detection and Multipurpose Applications in Different Biological Systems

NASA Astrophysics Data System (ADS)

Narayanaswamy, Nagarjun; Kumar, Manoj; Das, Sadhan; Sharma, Rahul; Samanta, Pralok K.; Pati, Swapan K.; Dhar, Suman K.; Kundu, Tapas K.; Govindaraju, T.

2014-09-01

Sequence-specific recognition of DNA by small turn-on fluorescence probes is a promising tool for bioimaging, bioanalytical and biomedical applications. Here, the authors report a novel cell-permeable and red fluorescent hemicyanine-based thiazole coumarin (TC) probe for DNA recognition, nuclear staining and cell cycle analysis. TC exhibited strong fluorescence enhancement in the presence of DNA containing AT-base pairs, but did not fluoresce with GC sequences, single-stranded DNA, RNA and proteins. The fluorescence staining of HeLa S3 and HEK 293 cells by TC followed by DNase and RNase digestion studies depicted the selective staining of DNA in the nucleus over the cytoplasmic region. Fluorescence-activated cell sorting (FACS) analysis by flow cytometry demonstrated the potential application of TC in cell cycle analysis in HEK 293 cells. Metaphase chromosome and malaria parasite DNA imaging studies further confirmed the in vivo diagnostic and therapeutic applications of probe TC. Probe TC may find multiple applications in fluorescence spectroscopy, diagnostics, bioimaging and molecular and cell biology.

Low noise charge ramp electrometer

DOEpatents

Morgan, J.P.; Piper, T.C.

1992-10-06

An electrometer capable of measuring small currents without the use of a feedback resistor which tends to contribute a large noise factor to the measured data. The electrometer eliminates the feedback resistor through the use of a feedback capacitor located across the electrometer amplifier. The signal from the electrometer amplifier is transferred to a electrometer buffer amplifier which serves to transfer the signal to several receptors. If the electrometer amplifier is approaching saturation, the buffer amplifier signals a reset discriminator which energizes a coil whose magnetic field closes a magnetic relay switch which in turn resets or zeros the feedback capacitor. In turn, a reset complete discriminator restarts the measurement process when the electrometer amplifier approaches its initial condition. The buffer amplifier also transmits the voltage signal from the electrometer amplifier to a voltage-to-frequency converter. The signals from the voltage-to-frequency converter are counted over a fixed period of time and the information is relayed to a data processor. The timing and sequencing of the small current measuring system is under the control of a sequence control logic unit. 2 figs.

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

Fogh, R.H.; Mabbutt, B.C.; Kem, W.R.

Sequence-specific assignments are reported for the 500-MHz H nuclear magnetic resonance (NMR) spectrum of the 48-residue polypeptide neurotoxin I from the sea anemone Stichodactyla helianthus (Sh I). Spin systems were first identified by using two-dimensional relayed or multiple quantum filtered correlation spectroscopy, double quantum spectroscopy, and spin lock experiments. Specific resonance assignments were then obtained from nuclear Overhauser enhancement (NOE) connectivities between protons from residues adjacent in the amino acid sequence. Of a total of 265 potentially observable resonances, 248 (i.e., 94%) were assigned, arising from 39 completely and 9 partially assigned amino acid spin systems. The secondary structure ofmore » Sh I was defined on the basis of the pattern of sequential NOE connectivities. NOEs between protons on separate strands of the polypeptide backbone, and backbone amide exchange rates. Sh I contains a four-stranded antiparallel {beta}-sheet encompassing residues 1-5, 16-24, 30-33, and 40-46, with a {beta}-bulge at residues 17 and 18 and a reverse turn, probably a type II {beta}-turn, involving residues 27-30. No evidence of {alpha}-helical structure was found.« less

A Thiazole Coumarin (TC) Turn-On Fluorescence Probe for AT-Base Pair Detection and Multipurpose Applications in Different Biological Systems

PubMed Central

Narayanaswamy, Nagarjun; Kumar, Manoj; Das, Sadhan; Sharma, Rahul; Samanta, Pralok K.; Pati, Swapan K.; Dhar, Suman K.; Kundu, Tapas K.; Govindaraju, T.

2014-01-01

Sequence-specific recognition of DNA by small turn-on fluorescence probes is a promising tool for bioimaging, bioanalytical and biomedical applications. Here, the authors report a novel cell-permeable and red fluorescent hemicyanine-based thiazole coumarin (TC) probe for DNA recognition, nuclear staining and cell cycle analysis. TC exhibited strong fluorescence enhancement in the presence of DNA containing AT-base pairs, but did not fluoresce with GC sequences, single-stranded DNA, RNA and proteins. The fluorescence staining of HeLa S3 and HEK 293 cells by TC followed by DNase and RNase digestion studies depicted the selective staining of DNA in the nucleus over the cytoplasmic region. Fluorescence-activated cell sorting (FACS) analysis by flow cytometry demonstrated the potential application of TC in cell cycle analysis in HEK 293 cells. Metaphase chromosome and malaria parasite DNA imaging studies further confirmed the in vivo diagnostic and therapeutic applications of probe TC. Probe TC may find multiple applications in fluorescence spectroscopy, diagnostics, bioimaging and molecular and cell biology. PMID:25252596

Characterization of beta-turn and Asx-turns mimicry in a model peptide: stabilization via C--H . . . O interaction.

PubMed

Thakur, A K; Kishore, R

2006-04-15

The chemical synthesis and single-crystal X-ray diffraction analysis of a model peptide, Boc-Thr-Thr-NH2 (1) comprised of proteinogenic residues bearing an amphiphilic Cbeta -stereogenic center, has been described. Interestingly, the analysis of its molecular structure revealed the existence of a distinct conformation that mimics a typical beta-turn and Asx-turns, i.e., the two Thr residues occupy the left- and right-corner positions. The main-chain torsion angles of the N- and C-terminal residues i.e., semiextended: phi = -68.9 degrees , psi = 128.6 degrees ; semifolded: phi = -138.1 degrees , psi = 2.5 degrees conformations, respectively, in conjunction with a gauche- disposition of the obligatory C-terminus Thr CgammaH3 group, characterize the occurrence of the newly described beta-turn- and Asx-turns-like topology. The preferred molecular structure is suggested to be stabilized by an effective nonconventional main-chain to side-chain Ci=O . . . H--Cgamma(i+2)-type intraturn hydrogen bond. Noteworthy, the observed topology of the resulting 10-membered hydrogen-bonded ring is essentially similar to the one perceived for a classical beta-turn and the Asx-turns, stabilized by a conventional intraturn hydrogen bond. Considering the signs as well as magnitudes of the backbone torsion angles and the orientation of the central peptide bond, the overall mimicked topology resembles the type II beta-turn or type II Asx-turns. An analysis of Xaa-Thr sequences in high-resolution X-ray elucidated protein structures revealed the novel topology prevalence in functional proteins (unpublished). In view of indubitable structural as well as functional importance of nonconventional interactions in bioorganic and biomacromolecules, we intend to highlight the participation of Thr CgammaH in the creation of a short-range C=O . . . H--Cgamma -type interaction in peptides and proteins. Copyright 2006 Wiley Periodicals, Inc.

Incoherent averaging of phase singularities in speckle-shearing interferometry.

PubMed

Mantel, Klaus; Nercissian, Vanusch; Lindlein, Norbert

2014-08-01

Interferometric speckle techniques are plagued by the omnipresence of phase singularities, impairing the phase unwrapping process. To reduce the number of phase singularities by physical means, an incoherent averaging of multiple speckle fields may be applied. It turns out, however, that the results may strongly deviate from the expected √N behavior. Using speckle-shearing interferometry as an example, we investigate the mechanism behind the reduction of phase singularities, both by calculations and by computer simulations. Key to an understanding of the reduction mechanism during incoherent averaging is the representation of the physical averaging process in terms of certain vector fields associated with each speckle field.

Methods, systems and apparatus for adjusting duty cycle of pulse width modulated (PWM) waveforms

DOEpatents

Gallegos-Lopez, Gabriel; Kinoshita, Michael H; Ransom, Ray M; Perisic, Milun

2013-05-21

Embodiments of the present invention relate to methods, systems and apparatus for controlling operation of a multi-phase machine in a vector controlled motor drive system when the multi-phase machine operates in an overmodulation region. The disclosed embodiments provide a mechanism for adjusting a duty cycle of PWM waveforms so that the correct phase voltage command signals are applied at the angle transitions. This can reduce variations/errors in the phase voltage command signals applied to the multi-phase machine so that phase current may be properly regulated thus reducing current/torque oscillation, which can in turn improve machine efficiency and performance, as well as utilization of the DC voltage source.

Selenium-containing organic nanoparticles as silent precursors for ultra-sensitive thiol-responsive transmembrane anion transport.

PubMed

Lang, Chao; Zhang, Xin; Dong, Zeyuan; Luo, Quan; Qiao, Shanpeng; Huang, Zupeng; Fan, Xiaotong; Xu, Jiayun; Liu, Junqiu

2016-02-07

An anion transporter with a selenoxide group was able to form nanoparticles in water, whose activity was fully turned off due to the aggregation effect. The formed nanoparticles have a uniform size and can be readily dispersed in water at high concentrations. Turn-on of the nanoparticles by reducing molecules is proposed to be a combined process, including the reduction of selenoxide to selenide, disassembly of the nanoparticles and location of the transporter to the lipid membrane. Accordingly, a special acceleration phase can be observed in the turn-on kinetic curves. Since turn-on of the nanoparticles is quantitatively related to the amount of reductant, the nanoparticles can be activated in a step-by-step manner. Due to the sensibility of this system to thiols, cysteine can be detected at low nanomolar concentrations. This ultra-sensitive thiol-responsive transmembrane anion transport system is quite promising in biological applications.

Programmable Iterative Optical Image And Data Processing

NASA Technical Reports Server (NTRS)

Jackson, Deborah J.

1995-01-01

Proposed method of iterative optical image and data processing overcomes limitations imposed by loss of optical power after repeated passes through many optical elements - especially, beam splitters. Involves selective, timed combination of optical wavefront phase conjugation and amplification to regenerate images in real time to compensate for losses in optical iteration loops; timing such that amplification turned on to regenerate desired image, then turned off so as not to regenerate other, undesired images or spurious light propagating through loops from unwanted reflections.

Phase separation in the six-vertex model with a variety of boundary conditions

NASA Astrophysics Data System (ADS)

Lyberg, I.; Korepin, V.; Ribeiro, G. A. P.; Viti, J.

2018-05-01

We present numerical results for the six-vertex model with a variety of boundary conditions. Adapting an algorithm for domain wall boundary conditions, proposed in the work of Allison and Reshetikhin [Ann. Inst. Fourier 55(6), 1847-1869 (2005)], we examine some modifications of these boundary conditions. To be precise, we discuss partial domain wall boundary conditions, reflecting ends, and half turn boundary conditions (domain wall boundary conditions with half turn symmetry). Dedicated to the memory of Ludwig Faddeev

Injection envelope matching in storage rings

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

Minty, M.G.; Spence, W.L.

1995-05-01

The shape and size of the transverse phase space injected into a storage ring can be deduced from turn-by-turn measurements of the transient behavior of the beam envelope in the ring. Envelope oscillations at 2 x the {beta}-tron frequency indicate the presence of a {beta}-mismatch, while envelope oscillations at the {beta}-tron frequency are the signature of a dispersion function mismatch. Experiments in injection optimization using synchrotron radiation imaging of the beam and a fast-gated camera at the SLC damping rings are reported.

Injection envelope matching in storage rings

NASA Astrophysics Data System (ADS)

Minty, M. G.; Spence, W. L.

1995-05-01

The shape and size of the transverse phase space injected into a storage ring can be deduced from turn-by-turn measurements of the transient behavior of the beam envelope in the ring. Envelope oscillations at 2 x the beta-tron frequency indicate the presence of a beta-mismatch, while envelope oscillations at the beta-tron frequency are the signature of a dispersion function mismatch. Experiments in injection optimization using synchrotron radiation imaging of the beam and a fast-gated camera at the SLC damping rings are reported.

Genesis of a flexible turning center

NASA Astrophysics Data System (ADS)

Sanclemente, Paul; French, Robert D.

GE - Aircraft Engines has designed, built, and is operating a flexible turning center for jet engine hardware. Although the plant is in the forefront of manufacturing technology development, it was intended from the start to be a production facility. So while there was much to learn from being involved in all phases of the project, meeting production schedules was, and is, key to its success. This paper reviews the early history of the project and ends with a view of its recent production status.

Leg coordination during turning on an extremely narrow substrate in a bug, Mesocerus marginatus (Heteroptera, Coreidae).

PubMed

Frantsevich, Leonid I; Cruse, Holk

2005-10-01

The turning movement of a bug, Mesocerus marginatus, is observed when it walks upside-down below a horizontal beam and, at the end of the beam, performs a sharp turn by 180 degrees . The turn at the end of the beam is accomplished in three to five steps, without strong temporal coordination among legs. During the stance, leg endpoints (tarsi) run through rounded trajectories, rotating to the same side in all legs. During certain phases of the turn, a leg is strongly depressed and the tarsus crosses the midline. Swing movements rotate to the same side as do leg endpoints in stance, in strong contrast to the typical swing movements found in turns or straight walk on a flat surface. Terminal location is found after the search through a trajectory that first moves away from the body and then loops back to find substrate. When a leg during stance has crossed the midline, in the following swing movement the leg may move even stronger on the contralateral side, i.e. is stronger depressed, in contrast to swing movements in normal walking, where the leg is elevated. These results suggest that the animals apply a different control strategy compared to walking and turning on a flat surface.

Fluorescence turn-on detection of target sequence DNA based on silicon nanodot-mediated quenching.

PubMed

Zhang, Yanan; Ning, Xinping; Mao, Guobin; Ji, Xinghu; He, Zhike

2018-05-01

We have developed a new enzyme-free method for target sequence DNA detection based on the dynamic quenching of fluorescent silicon nanodots (SiNDs) toward Cy5-tagged DNA probe. Fascinatingly, the water-soluble SiNDs can quench the fluorescence of cyanine (Cy5) in Cy5-tagged DNA probe in homogeneous solution, and the fluorescence of Cy5-tagged DNA probe can be restored in the presence of target sequence DNA (the synthetic target miRNA-27a). Based on this phenomenon, a SiND-featured fluorescent sensor has been constructed for "turn-on" detection of the synthetic target miRNA-27a for the first time. This newly developed approach possesses the merits of low cost, simple design, and convenient operation since no enzymatic reaction, toxic reagents, or separation procedures are involved. The established method achieves a detection limit of 0.16 nM, and the relative standard deviation of this method is 9% (1 nM, n = 5). The linear range is 0.5-20 nM, and the recoveries in spiked human fluids are in the range of 90-122%. This protocol provides a new tactic in the development of the nonenzymic miRNA biosensors and opens a promising avenue for early diagnosis of miRNA-associated disease. Graphical abstract The SiND-based fluorescent sensor for detection of S-miR-27a.

SeqMule: automated pipeline for analysis of human exome/genome sequencing data.

PubMed

Guo, Yunfei; Ding, Xiaolei; Shen, Yufeng; Lyon, Gholson J; Wang, Kai

2015-09-18

Next-generation sequencing (NGS) technology has greatly helped us identify disease-contributory variants for Mendelian diseases. However, users are often faced with issues such as software compatibility, complicated configuration, and no access to high-performance computing facility. Discrepancies exist among aligners and variant callers. We developed a computational pipeline, SeqMule, to perform automated variant calling from NGS data on human genomes and exomes. SeqMule integrates computational-cluster-free parallelization capability built on top of the variant callers, and facilitates normalization/intersection of variant calls to generate consensus set with high confidence. SeqMule integrates 5 alignment tools, 5 variant calling algorithms and accepts various combinations all by one-line command, therefore allowing highly flexible yet fully automated variant calling. In a modern machine (2 Intel Xeon X5650 CPUs, 48 GB memory), when fast turn-around is needed, SeqMule generates annotated VCF files in a day from a 30X whole-genome sequencing data set; when more accurate calling is needed, SeqMule generates consensus call set that improves over single callers, as measured by both Mendelian error rate and consistency. SeqMule supports Sun Grid Engine for parallel processing, offers turn-key solution for deployment on Amazon Web Services, allows quality check, Mendelian error check, consistency evaluation, HTML-based reports. SeqMule is available at http://seqmule.openbioinformatics.org.

Lower extremity control during turns initiated with and without hip external rotation.

PubMed

Zaferiou, Antonia M; Flashner, Henryk; Wilcox, Rand R; McNitt-Gray, Jill L

2017-02-08

The pirouette turn is often initiated in neutral and externally rotated hip positions by dancers. This provides an opportunity to investigate how dancers satisfy the same mechanical objectives at the whole-body level when using different leg kinematics. The purpose of this study was to compare lower extremity control strategies during the turn initiation phase of pirouettes performed with and without hip external rotation. Skilled dancers (n=5) performed pirouette turns with and without hip external rotation. Joint kinetics during turn initiation were determined for both legs using ground reaction forces (GRFs) and segment kinematics. Hip muscle activations were monitored using electromyography. Using probability-based statistical methods, variables were compared across turn conditions as a group and within-dancer. Despite differences in GRFs and impulse generation between turn conditions, at least 90% of each GRF was aligned with the respective leg plane. A majority of the net joint moments at the ankle, knee, and hip acted about an axis perpendicular to the leg plane. However, differences in shank alignment relative to the leg plane affected the distribution of the knee net joint moment when represented with respect to the shank versus the thigh. During the initiation of both turns, most participants used ankle plantar flexor moments, knee extensor moments, flexor and abductor moments at the push leg׳s hip, and extensor and abductor moments at the turn leg׳s hip. Representation of joint kinetics using multiple reference systems assisted in understanding control priorities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure

PubMed Central

2013-01-01

Background Candida albicans is a ubiquitous opportunistic fungal pathogen that afflicts immunocompromised human hosts. With rare and transient exceptions the yeast is diploid, yet despite its clinical relevance the respective sequences of its two homologous chromosomes have not been completely resolved. Results We construct a phased diploid genome assembly by deep sequencing a standard laboratory wild-type strain and a panel of strains homozygous for particular chromosomes. The assembly has 700-fold coverage on average, allowing extensive revision and expansion of the number of known SNPs and indels. This phased genome significantly enhances the sensitivity and specificity of allele-specific expression measurements by enabling pooling and cross-validation of signal across multiple polymorphic sites. Additionally, the diploid assembly reveals pervasive and unexpected patterns in allelic differences between homologous chromosomes. Firstly, we see striking clustering of indels, concentrated primarily in the repeat sequences in promoters. Secondly, both indels and their repeat-sequence substrate are enriched near replication origins. Finally, we reveal an intimate link between repeat sequences and indels, which argues that repeat length is under selective pressure for most eukaryotes. This connection is described by a concise one-parameter model that explains repeat-sequence abundance in C. albicans as a function of the indel rate, and provides a general framework to interpret repeat abundance in species ranging from bacteria to humans. Conclusions The phased genome assembly and insights into repeat plasticity will be valuable for better understanding allele-specific phenomena and genome evolution. PMID:24025428

Effect of magnetic and electric coupling fields on micro- and nano- structure of carbon films in the CVD diamond process and their electron field emission property

NASA Astrophysics Data System (ADS)

Wang, Yijia; Li, Jiaxin; Hu, Naixiu; Jiang, Yunlu; Wei, Qiuping; Yu, Zhiming; Long, Hangyu; Zhu, Hekang; Xie, Youneng; Ma, Li; Lin, Cheng-Te; Su, Weitao

2018-03-01

In this paper, both electric field and magnetic field were used to assist the hot filament chemical vapor deposition (HFCVD) and we systematically investigated the effects of which on the (1) phase composition, (2) grain size, (3) thickness and (4) preferred orientation of diamond films through SEM, Raman and XRD. The application of magnetic field in electric field, so called ‘the magnetic and electric coupling fields’, enhanced the graphitization and refinement of diamond crystals, slowed down the decrease of film thickness along with the increase of bias current, and suppressed diamond (100) orientation. During the deposition process, the electric field provided additional energy to HFCVD system and generated large number of energetic particles which might annihilate at the substrate and lose kinetic energy, while the Lorentz force, provided by magnetic field, could constrict charged particles (including electrons) to do spiral movement, which prolonged their moving path and life, thus the system energy increased. With the graphitization of diamond films intensified, the preferred orientation of diamond films completely evolved from (110) to (100), until the orientation and diamond phase disappeared, which can be attributed to (I) the distribution and concentration ratio of carbon precursors (C2H2 and CH3) and (II) graphitization sequence of diamond crystal facets. Since the electron field emission property of carbon film is sensitive to the phase composition, thickness and preferred orientation, nano- carbon cones, prepared by the negative bias current of 20 mA and magnetic field strength of 80 Gauss, exhibited the lowest turn-on field of 6.1 V -1 μm-1.

The Role of Integrated Modelling and Assessment for Decision-Making: Lessons from Water Allocation Issues in Australia

NASA Astrophysics Data System (ADS)

Jakeman, A. J.; Guillaume, J. H. A.; El Sawah, S.; Hamilton, S.

2014-12-01

Integrated modelling and assessment (IMA) is best regarded as a process that can support environmental decision-making when issues are strongly contested and uncertainties pervasive. To be most useful, the process must be multi-dimensional and phased. Principally, it must be tailored to the problem context to encompass diverse issues of concern, management settings and stakeholders. This in turn requires the integration of multiple processes and components of natural and human systems and their corresponding spatial and temporal scales. Modellers therefore need to be able to integrate multiple disciplines, methods, models, tools and data, and many sources and types of uncertainty. These dimensions are incorporated into iteration between the various phases of the IMA process, including scoping, problem framing and formulation, assessing options and communicating findings. Two case studies in Australia are employed to share the lessons of how integration can be achieved in these IMA phases using a mix of stakeholder participation processes and modelling tools. One case study aims to improve the relevance of modelling by incorporating stakeholder's views of irrigated viticulture and water management decision making. It used a novel methodology with the acronym ICTAM, consisting of Interviews to elicit mental models, Cognitive maps to represent and analyse individual and group mental models, Time-sequence diagrams to chronologically structure the decision making process, an All-encompassing conceptual model, and computational Models of stakeholder decision making. The second case uses a hydro-economic river network model to examine basin-wide impacts of water allocation cuts and adoption of farm innovations. The knowledge exchange approach used in each case was designed to integrate data and knowledge bearing in mind the contextual dimensions of the problem at hand, and the specific contributions that environmental modelling was thought to be able to make.

Neural Basis of Stimulus-Angle-Dependent Motor Control of Wind-Elicited Walking Behavior in the Cricket Gryllus bimaculatus

PubMed Central

Oe, Momoko; Ogawa, Hiroto

2013-01-01

Crickets exhibit oriented walking behavior in response to air-current stimuli. Because crickets move in the opposite direction from the stimulus source, this behavior is considered to represent ‘escape behavior’ from an approaching predator. However, details of the stimulus-angle-dependent control of locomotion during the immediate phase, and the neural basis underlying the directional motor control of this behavior remain unclear. In this study, we used a spherical-treadmill system to measure locomotory parameters including trajectory, turn angle and velocity during the immediate phase of responses to air-puff stimuli applied from various angles. Both walking direction and turn angle were correlated with stimulus angle, but their relationships followed different rules. A shorter stimulus also induced directionally-controlled walking, but reduced the yaw rotation in stimulus-angle-dependent turning. These results suggest that neural control of the turn angle requires different sensory information than that required for oriented walking. Hemi-severance of the ventral nerve cords containing descending axons from the cephalic to the prothoracic ganglion abolished stimulus-angle-dependent control, indicating that this control required descending signals from the brain. Furthermore, we selectively ablated identified ascending giant interneurons (GIs) in vivo to examine their functional roles in wind-elicited walking. Ablation of GI8-1 diminished control of the turn angle and decreased walking distance in the initial response. Meanwhile, GI9-1b ablation had no discernible effect on stimulus-angle-dependent control or walking distance, but delayed the reaction time. These results suggest that the ascending signals conveyed by GI8-1 are required for turn-angle control and maintenance of walking behavior, and that GI9-1b is responsible for rapid initiation of walking. It is possible that individual types of GIs separately supply the sensory signals required to control wind-elicited walking. PMID:24244644

Crash sequence based risk matrix for motorcycle crashes.

PubMed

Wu, Kun-Feng; Sasidharan, Lekshmi; Thor, Craig P; Chen, Sheng-Yin

2018-04-05

Considerable research has been conducted related to motorcycle and other powered-two-wheeler (PTW) crashes; however, it always has been controversial among practitioners concerning with types of crashes should be first targeted and how to prioritize resources for the implementation of mitigating actions. Therefore, there is a need to identify types of motorcycle crashes that constitute the greatest safety risk to riders - most frequent and most severe crashes. This pilot study seeks exhibit the efficacy of a new approach for prioritizing PTW crash causation sequences as they relate to injury severity to better inform the application of mitigating countermeasures. To accomplish this, the present study constructed a crash sequence-based risk matrix to identify most frequent and most severe motorcycle crashes in an attempt to better connect causes and countermeasures of PTW crashes. Although the frequency of each crash sequence can be computed from crash data, a crash severity model is needed to compare the levels of crash severity among different crash sequences, while controlling for other factors that also have effects on crash severity such drivers' age, use of helmet, etc. The construction of risk matrix based on crash sequences involve two tasks: formulation of crash sequence and the estimation of a mixed-effects (ME) model to adjust the levels of severities for each crash sequence to account for other crash contributing factors that would have an effect on the maximum level of crash severity in a crash. Three data elements from the National Automotive Sampling System - General Estimating System (NASS-GES) data were utilized to form a crash sequence: critical event, crash types, and sequence of events. A mixed-effects model was constructed to model the severity levels for each crash sequence while accounting for the effects of those crash contributing factors on crash severity. A total of 8039 crashes involving 8208 motorcycles occurred during 2011 and 2013 were included in this study, weighted to represent 338,655 motorcyclists involved in traffic crashes in three years (2011-2013)(NHTSA, 2013). The top five most frequent and severe types of crash sequences were identified, accounting for 23 percent of all the motorcycle crashes included in the study, and they are (1) run-off-road crashes on the right, and hitting roadside objects, (2) cross-median crashes, and rollover, (3) left-turn oncoming crashes, and head-on, (4) crossing over (passing through) or turning into opposite direction at intersections, and (5) side-impacted. In addition to crash sequences, several other factors were also identified to have effects on crash severity: use of helmet, presence of horizontal curves, alcohol consumption, road surface condition, roadway functional class, and nighttime condition. Copyright © 2018 Elsevier Ltd. All rights reserved.

Identification of a 'Candidatus Phytoplasma hispanicum'-related strain, associated with yellows-type diseases, in smoke-tree sharpshooter (Homalodisca liturata Ball).

PubMed

Servín-Villegas, Rosalía; Caamal-Chan, Maria Goretty; Chavez-Medina, Alicia; Loera-Muro, Abraham; Barraza, Aarón; Medina-Hernández, Diana; Holguín-Peña, Ramón Jaime

2018-04-11

The 16SrXIII group from phytoplasma bacteria were identified in salivary glands from Homalodisca liturata, which were collected in El Comitán on the Baja California peninsula in Mexico. We were able to positively identify 15 16S rRNA gene sequences with the corresponding signature sequence of 'CandidatusPhytoplasma' (CAAGAYBATKATGTKTAGCYGGDCT) and in silico restriction fragment length polymorphism (RFLP) profiles (F value estimations) coupled with a phylogenetic analysis to confirm their relatedness to 'CandidatusPhytoplasma hispanicum', which in turn belongs to the 16SrXIII group. A restriction analysis was carried out with AluI and EcoRI to confirm that the five sequences belongs to subgroup D. The rest of the sequences did not exhibit any known RFLP profile related to a subgroup reported in the 16SrXIII group.

Properties of the Tent map for decimal fractions with fixed precision

NASA Astrophysics Data System (ADS)

Chetverikov, V. M.

2018-01-01

The one-dimensional discrete Tent map is a well-known example of a map whose fixed points are all unstable on the segment [0,1]. This map leads to the positivity of the Lyapunov exponent for the corresponding recurrent sequence. Therefore in a situation of general position, this sequence must demonstrate the properties of deterministic chaos. However if the first term of the recurrence sequence is taken as a decimal fraction with a fixed number “k” of digits after the decimal point and all calculations are carried out accurately, then the situation turns out to be completely different. In this case, first, the Tent map does not lead to an increase in significant digits in the terms of the sequence, and secondly, demonstrates the existence of a finite number of eventually periodic orbits, which are attractors for all other decimal numbers with the number of significant digits not exceeding “k”.

Manned space flight nuclear system safety. Volume 3: Reactor system preliminary nuclear safety analysis. Part 2A: Accident model document, appendix

NASA Technical Reports Server (NTRS)

1972-01-01

The detailed abort sequence trees for the reference zirconium hydride (ZrH) reactor power module that have been generated for each phase of the reference Space Base program mission are presented. The trees are graphical representations of causal sequences. Each tree begins with the phase identification and the dichotomy between success and failure. The success branch shows the mission phase objective as being achieved. The failure branch is subdivided, as conditions require, into various primary initiating abort conditions.

Mesomorphic phase transitions of 3F7HPhF studied by complementary methods

NASA Astrophysics Data System (ADS)

Deptuch, Aleksandra; Jaworska-Gołąb, Teresa; Marzec, Monika; Pociecha, Damian; Fitas, Jakub; Żurowska, Magdalena; Tykarska, Marzena; Hooper, James

2018-02-01

Physical properties and the phase sequence of (S)-4‧-(1-methylheptyloxycarbonyl)biphenyl-4-yl 4-[7-(2,2,3,3,4,4,4-heptafluorobutoxy) heptyl-1-oxy]-2-fluorobenzoate exhibiting the liquid crystalline paraelectric smectic A*, ferroelectric smectic C* and antiferroelectric smectic CA* phases were studied by complementary methods in the temperature range from -125 to 120 °C. Differential scanning calorimetry measurements together with polarizing optical microscopy provided the phase sequence, including the glass transition and a cold crystallization. X-ray diffraction was used to obtain the unit-cell parameters of the crystal phase, as well as the layer thickness and correlation length in the liquid crystalline smectic phases. The tilt angle was found to reach 45°, as determined from the measurements of the layer thickness and molecular modeling. Relaxation processes in the smectic phases and the fragility parameter were studied using frequency-domain dielectric spectroscopy.

Generation of spiral optical beams using a spatial light modulator

NASA Astrophysics Data System (ADS)

Rodrigo, Peter J.; Alonzo, Carlo A.; Gluckstad, Jesper

2005-08-01

Recently, a new type of beam termed "spiral optical beam" has been introduced [Alonzo, et al., Opt. Express 13, 1749 (2005)]. Spiral beams are created from multiplicative mixtures of helical and conical phase distributions. Helico-conical phase fronts that generate these novel beams are not achieved with a sequence of a corkscrew wave-plate and an axicon (as this sequence gives a sum of helical and conical phase terms). Nevertheless, the availability of phase-only spatial light modulators (SLM) allows one to directly imprint helico-conical phase functions on an incident plane wave and provides an easy way to modify the profile of the encoded phase. Focusing the phase-modified field results in spiral intensity distributions that may find use for optical manipulation of mesoscopic particles. In this paper, we have extended the discussion to translation and rotation (as well as chirality switching) of the spiral beams using SLM control.

Modeling left-turn crash occurrence at signalized intersections by conflicting patterns.

PubMed

Wang, Xuesong; Abdel-Aty, Mohamed

2008-01-01

In order to better understand the underlying crash mechanisms, left-turn crashes occurring at 197 four-legged signalized intersections over 6 years were classified into nine patterns based on vehicle maneuvers and then were assigned to intersection approaches. Crash frequency of each pattern was modeled at the approach level by mainly using Generalized Estimating Equations (GEE) with the Negative Binomial as the link function to account for the correlation among the crash data. GEE with a binomial logit link function was also applied for patterns with fewer crashes. The Cumulative Residuals test shows that, for correlated left-turn crashes, GEE models usually outperformed basic Negative Binomial models. The estimation results show that there are obvious differences in the factors that cause the occurrence of different left-turn collision patterns. For example, for each pattern, the traffic flows to which the colliding vehicles belong are identified to be significant. The width of the crossing distance (represented by the number of through lanes on the opposing approach of the left-turning traffic) is associated with more left-turn traffic colliding with opposing through traffic (Pattern 5), but with less left-turning traffic colliding with near-side crossing through traffic (Pattern 8). The safety effectiveness of the left-turning signal is not consistent for different crash patterns; "protected" phasing is correlated with fewer Pattern 5 crashes, but with more Pattern 8 crashes. The study indicates that in order to develop efficient countermeasures for left-turn crashes and improve safety at signalized intersections, left-turn crashes should be considered in different patterns.

A comparison of subtalar joint motion during anticipated medial cutting turns and level walking using a multi-segment foot model.

PubMed

Jenkyn, T R; Shultz, R; Giffin, J R; Birmingham, T B

2010-02-01

The weight-bearing in-vivo kinematics and kinetics of the talocrural joint, subtalar joint and joints of the foot were quantified using optical motion analysis. Twelve healthy subjects were studied during level walking and anticipated medial turns at self-selected pace. A multi-segment model of the foot using skin-mounted marker triads tracked four foot segments: the hindfoot, midfoot, lateral and medial forefoot. The lower leg and thigh were also tracked. Motion between each of the segments could occur in three degrees of rotational freedom, but only six inter-segmental motions were reported in this study: (1) talocrural dorsi-plantar-flexion, (2) subtalar inversion-eversion, (3) frontal plane hindfoot motion, (4) transverse plane hindfoot motion, (5) forefoot supination-pronation twisting and (6) the height-to-length ratio of the medial longitudinal arch. The motion at the subtalar joint during stance phase of walking (eversion then inversion) was reversed during a turning task (inversion then eversion). The external subtalar joint moment was also changed from a moderate eversion moment during walking to a larger inversion moment during the turn. The kinematics of the talocrural joint and the joints of the foot were similar between these two tasks. During a medial turn, the subtalar joint may act to maintain the motions in the foot and talocrural joint that occur during level walking. This is occurring despite the conspicuously different trajectory of the centre of mass of the body. This may allow the foot complex to maintain its function of energy absorption followed by energy return during stance phase that is best suited to level walking. Copyright 2009 Elsevier B.V. All rights reserved.

Evolution of the Olympus Mons Caldera, Mars

NASA Technical Reports Server (NTRS)

Mouginis-Mark, Peter J.; Robinson, Mark S.; Zuber, Maria T.

1990-01-01

Extensive high-resolution (15 to 20 m/pixel) coverage of Olympus Mons volcano permits the investigation of the sequence of events associated with the evolution of the nested summit caldera. The sequence of the intra-caldera events is well illustrated by image data collected on orbits 473S and 474S of Viking Orbiter 1. These data cover both the oldest and youngest portions of the caldera floor. The chronology inferred from the observations is presented which in turn can be interpreted in terms of the internal structure of the volcano (i.e., magma chamber depth and the existence of dikes).

Guidelines for exclusive.

DOT National Transportation Integrated Search

1985-01-01

The objective of this research was to develop guidelines for the use of exclusive/permissive left-turn signal phasing. This was achieved by collecting data on traffic and roadway conditions for exclusive, exclusive/permissive, and permissive left-tur...

The topological pressure-temperature phase diagram of fluoxetine nitrate: monotropy unexpectedly turning into enantiotropy

NASA Astrophysics Data System (ADS)

Céolin, René; Rietveld, Ivo B.

2017-04-01

The phase behavior of pharmaceuticals is important for regulatory requirements and dosage form development. Racemic fluoxetine nitrate possesses two crystalline forms for which initial measurements indicated that they have a monotropic relationship with form I the only stable form. By constructing the topological pressure-temperature phase diagram, it has been shown that unexpectedly form II has a stable domain in the phase diagram and can be easily obtained by heating and grinding. The pressure necessary to obtain form II is only 11 MPa, which is much lower than most pressure used for tableting in the pharmaceutical industry.

Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p

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

Miller, Matthew T.; Higgin, Joshua J.; Hall, Traci M.Tanaka

2008-06-06

Pumilio/FBF (PUF) family proteins are found in eukaryotic organisms and regulate gene expression post-transcriptionally by binding to sequences in the 3' untranslated region of target transcripts. PUF proteins contain an RNA binding domain that typically comprises eight {alpha}-helical repeats, each of which recognizes one RNA base. Some PUF proteins, including yeast Puf4p, have altered RNA binding specificity and use their eight repeats to bind to RNA sequences with nine or ten bases. Here we report the crystal structures of Puf4p alone and in complex with a 9-nucleotide (nt) target RNA sequence, revealing that Puf4p accommodates an 'extra' nucleotide by modestmore » adaptations allowing one base to be turned away from the RNA binding surface. Using structural information and sequence comparisons, we created a mutant Puf4p protein that preferentially binds to an 8-nt target RNA sequence over a 9-nt sequence and restores binding of each protein repeat to one RNA base.« less

Investigation of timing effects in modified composite quadrupolar echo pulse sequences by mean of average Hamiltonian theory

NASA Astrophysics Data System (ADS)

Mananga, Eugene Stephane

2018-01-01

The utility of the average Hamiltonian theory and its antecedent the Magnus expansion is presented. We assessed the concept of convergence of the Magnus expansion in quadrupolar spectroscopy of spin-1 via the square of the magnitude of the average Hamiltonian. We investigated this approach for two specific modified composite pulse sequences: COM-Im and COM-IVm. It is demonstrated that the size of the square of the magnitude of zero order average Hamiltonian obtained on the appropriated basis is a viable approach to study the convergence of the Magnus expansion. The approach turns to be efficient in studying pulse sequences in general and can be very useful to investigate coherent averaging in the development of high resolution NMR technique in solids. This approach allows comparing theoretically the two modified composite pulse sequences COM-Im and COM-IVm. We also compare theoretically the current modified composite sequences (COM-Im and COM-IVm) to the recently published modified composite pulse sequences (MCOM-I, MCOM-IV, MCOM-I_d, MCOM-IV_d).

Towards decoding the conifer giga-genome.

PubMed

Mackay, John; Dean, Jeffrey F D; Plomion, Christophe; Peterson, Daniel G; Cánovas, Francisco M; Pavy, Nathalie; Ingvarsson, Pär K; Savolainen, Outi; Guevara, M Ángeles; Fluch, Silvia; Vinceti, Barbara; Abarca, Dolores; Díaz-Sala, Carmen; Cervera, María-Teresa

2012-12-01

Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation sequencers. The purpose of this review is to describe the context for these new initiatives. A knowledge foundation has been acquired in several conifers of commercial and ecological interest through large-scale cDNA analyses, construction of genetic maps and gene mapping studies aiming to link phenotype and genotype. Exploratory sequencing in pines and spruces have pointed out some of the unique properties of these giga-genomes and suggested strategies that may be needed to extract value from their sequencing. The hope is that recent and pending developments in sequencing technology will contribute to rapidly filling the knowledge vacuum surrounding their structure, contents and evolution. Researchers are also making plans to use comparative analyses that will help to turn the data into a valuable resource for enhancing and protecting the world's conifer forests.

Design of multi-phase dynamic chemical networks

NASA Astrophysics Data System (ADS)

Chen, Chenrui; Tan, Junjun; Hsieh, Ming-Chien; Pan, Ting; Goodwin, Jay T.; Mehta, Anil K.; Grover, Martha A.; Lynn, David G.

2017-08-01

Template-directed polymerization reactions enable the accurate storage and processing of nature's biopolymer information. This mutualistic relationship of nucleic acids and proteins, a network known as life's central dogma, is now marvellously complex, and the progressive steps necessary for creating the initial sequence and chain-length-specific polymer templates are lost to time. Here we design and construct dynamic polymerization networks that exploit metastable prion cross-β phases. Mixed-phase environments have been used for constructing synthetic polymers, but these dynamic phases emerge naturally from the growing peptide oligomers and create environments suitable both to nucleate assembly and select for ordered templates. The resulting templates direct the amplification of a phase containing only chain-length-specific peptide-like oligomers. Such multi-phase biopolymer dynamics reveal pathways for the emergence, self-selection and amplification of chain-length- and possibly sequence-specific biopolymers.

An on/off Berry phase switch in circular graphene resonators

NASA Astrophysics Data System (ADS)

Ghahari, Fereshte; Walkup, Daniel; Gutiérrez, Christopher; Rodriguez-Nieva, Joaquin F.; Zhao, Yue; Wyrick, Jonathan; Natterer, Fabian D.; Cullen, William G.; Watanabe, Kenji; Taniguchi, Takashi; Levitov, Leonid S.; Zhitenev, Nikolai B.; Stroscio, Joseph A.

2017-05-01

The phase of a quantum state may not return to its original value after the system’s parameters cycle around a closed path; instead, the wave function may acquire a measurable phase difference called the Berry phase. Berry phases typically have been accessed through interference experiments. Here, we demonstrate an unusual Berry phase-induced spectroscopic feature: a sudden and large increase in the energy of angular-momentum states in circular graphene p-n junction resonators when a relatively small critical magnetic field is reached. This behavior results from turning on a π Berry phase associated with the topological properties of Dirac fermions in graphene. The Berry phase can be switched on and off with small magnetic field changes on the order of 10 millitesla, potentially enabling a variety of optoelectronic graphene device applications.

Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity

NASA Astrophysics Data System (ADS)

Simon, Joseph R.; Carroll, Nick J.; Rubinstein, Michael; Chilkoti, Ashutosh; López, Gabriel P.

2017-06-01

Dynamic protein-rich intracellular structures that contain phase-separated intrinsically disordered proteins (IDPs) composed of sequences of low complexity (SLC) have been shown to serve a variety of important cellular functions, which include signalling, compartmentalization and stabilization. However, our understanding of these structures and our ability to synthesize models of them have been limited. We present design rules for IDPs possessing SLCs that phase separate into diverse assemblies within droplet microenvironments. Using theoretical analyses, we interpret the phase behaviour of archetypal IDP sequences and demonstrate the rational design of a vast library of multicomponent protein-rich structures that ranges from uniform nano-, meso- and microscale puncta (distinct protein droplets) to multilayered orthogonally phase-separated granular structures. The ability to predict and program IDP-rich assemblies in this fashion offers new insights into (1) genetic-to-molecular-to-macroscale relationships that encode hierarchical IDP assemblies, (2) design rules of such assemblies in cell biology and (3) molecular-level engineering of self-assembled recombinant IDP-rich materials.

Rapid Measurement and Correction of Phase Errors from B0 Eddy Currents: Impact on Image Quality for Non-Cartesian Imaging

PubMed Central

Brodsky, Ethan K.; Klaers, Jessica L.; Samsonov, Alexey A.; Kijowski, Richard; Block, Walter F.

2014-01-01

Non-Cartesian imaging sequences and navigational methods can be more sensitive to scanner imperfections that have little impact on conventional clinical sequences, an issue which has repeatedly complicated the commercialization of these techniques by frustrating transitions to multi-center evaluations. One such imperfection is phase errors caused by resonant frequency shifts from eddy currents induced in the cryostat by time-varying gradients, a phenomemon known as B0 eddy currents. These phase errors can have a substantial impact on sequences that use ramp sampling, bipolar gradients, and readouts at varying azimuthal angles. We present a method for measuring and correcting phase errors from B0 eddy currents and examine the results on two different scanner models. This technique yields significant improvements in image quality for high-resolution joint imaging on certain scanners. The results suggest that correction of short time B0 eddy currents in manufacturer provided service routines would simplify adoption of non-Cartesian sampling methods. PMID:22488532

Incorporation of a Bio-Active Reverse-Turn Heterocycle into a Peptide Template Using Solid-Phase Synthesis to Probe Melanocortin Receptor Selectivity and Ligand Conformations by 2D 1H NMR

PubMed Central

Singh, Anamika; Wilczynski, Andrzej; Holder, Jerry R.; Witek, Rachel M.; Dirain, Marvin L.; Xiang, Zhimin; Edison, Arthur S.; Haskell-Luevano, Carrie

2011-01-01

Using a solid-phase synthetic approach, a bioactive reverse turn heterocyclic was incorporated into a cyclic peptide template to probe melanocortin receptor potency and ligand structural conformations. The five melanocortin receptor isoforms (MC1R-MC5R) are G-protein coupled receptors (GPCRs) that are regulated by endogenous agonists and antagonists. This pathway is involved in pigmentation, weight, and energy homeostasis. Herein, we report novel analogues of the chimeric AGRP-melanocortin peptide template integrated with a small molecule moiety to probe the structural and functional consequences of the core His-Phe-Arg-Trp peptide domain using a reverse-turn heterocycle. A series of six compounds are reported that result in inactive to full agonists with nM potency. Biophysical structural analysis [2D 1H NMR and computer-assisted molecular modeling (CAMM)] were performed on selected analogues, resulting in the identification that these peptide-small molecule hybrids possessed increased flexibility and fewer discrete conformational families as compared to the reference peptide and result in a novel template for further structure-function studies. PMID:21306168

Vertical cross-spectral phases in atmospheric flow

NASA Astrophysics Data System (ADS)

Chougule, A.; Mann, J.; Kelly, M.

2014-11-01

The cross-spectral phases between velocity components at two heights are analyzed from observations at the Høvsøre test site under diabatic conditions. These phases represent the degree to which turbulence sensed at one height leads (or lags) in time the turbulence sensed at the other height. The phase angle of the cross-wind component is observed to be significantly greater than the phase for the along-wind component, which in turn is greater than the phase for the vertical component. The cross-wind and along-wind phases increase with stream-wise wavenumber and vertical separation distance, but there is no significant change in the phase angle of vertical velocity. The phase angles for all atmospheric stabilities show similar order in phasing. The phase angles from the Høvsøre observations under neutral condition are compared with a rapid distortion theory model which show similar order in phase shift.

Predicting relative sea level changes at the aftermath of Marinoan (635 Ma) Snowball meltdown

NASA Astrophysics Data System (ADS)

Irie, Y.; Nakada, M.; Okuno, J.; Bao, H.

2016-12-01

Earth system recovery from a Snowball state constitutes one of the best tests of the resilience of life on planet Earth. A distinct and probably brief relative sea level (RSL) drop has been identified in the cap dolostones deposited in a general transgression sequence at the aftermath of Marinoan Snowball meltdown in South China and other late Neoproterozoic blocks. However, the magnitude and duration or the very existence of this RSL drop event can vary at different geographical sites because of spatial and temporal variations in sea level due to glacial isostatic adjustment (GIA) even for tectonically stable areas. An accurate prediction of this drop can in turn help us infer independently the rate of dynamic recovery of the Earth system from a Snowball state, e.g. the timing and duration of the Marinoan 17O depletion (MOSD) event that was also closely linked to the rise and drawdown of atmospheric O2 and CO2, respectively. Here we model the RSL changes by considering all GIA-related relaxation processes. We evaluated the RSL to the sea level at 10 Myr after the complete glacial meltdown and tested slightly different paleogeographic configurations. Our modeling results show that the RSL drop occurs in the syn-deglacial phase (melting phase) for the inland regions and in the post-deglacial phase (time after the complete melting) for continental margins. The RSL drop in the post-deglacial phase is mainly determined by the relaxation processes with a timescale of longer than 20 kyr. The predicted RSL change in South China for lower mantle viscosity of 1022-1023 Pa s and a syn-deglacial time of <100 kyr is consistent with the observationally inferred RSL change regardless of uncertainties on the length of the continental shelf or the paleogeography of South China. A comparison between our model predicted and sedimentary-record inferred RSL change in South China put an independent constraint on the duration of the MOSD event at 70 kyr or shorter.

Activation of the protein tyrosine phosphatase SHP2 via the interleukin-6 signal transducing receptor protein gp130 requires tyrosine kinase Jak1 and limits acute-phase protein expression.

PubMed

Schaper, F; Gendo, C; Eck, M; Schmitz, J; Grimm, C; Anhuf, D; Kerr, I M; Heinrich, P C

1998-11-01

Stimulation of the interleukin-6 (IL-6) signalling pathway occurs via the IL-6 receptor-glycoprotein 130 (IL-6R-gp130) receptor complex and results in the regulation of acute-phase protein genes in liver cells. Ligand binding to the receptor complex leads to tyrosine phosphorylation and activation of Janus kinases (Jak), phosphorylation of the signal transducing subunit gp130, followed by recruitment and phosphorylation of the signal transducer and activator of transcription factors STAT3 and STAT1 and the src homology domain (SH2)-containing protein tyrosine phosphatase (SHP2). The tyrosine phosphorylated STAT factors dissociate from the receptor, dimerize and translocate to the nucleus where they bind to enhancer sequences of IL-6 target genes. Phosphorylated SHP2 is able to bind growth factor receptor bound protein (grb2) and thus might link the Jak/STAT pathway to the ras/raf/mitogen-activated protein kinase pathway. Here we present data on the dose-dependence, kinetics and kinase requirements for SHP2 phosphorylation after the activation of the signal transducer, gp130, of the IL-6-type family receptor complex. When human fibrosarcoma cell lines deficient in Jak1, Jak2 or tyrosine kinase 2 (Tyk2) were stimulated with IL-6-soluble IL-6R complexes it was found that only in Jak1-, but not in Jak 2- or Tyk2-deficient cells, SHP2 activation was greatly impaired. It is concluded that Jak1 is required for the tyrosine phosphorylation of SHP2. This phosphorylation depends on Tyr-759 in the cytoplasmatic domain of gp130, since a Tyr-759-->Phe exchange abrogates SHP2 activation and in turn leads to elevated and prolonged STAT3 and STAT1 activation as well as enhanced acute-phase protein gene induction. Therefore, SHP2 plays an important role in acute-phase gene regulation.

Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases.

PubMed

Meinhardt, Lyndel W; Costa, Gustavo Gilson Lacerda; Thomazella, Daniela P T; Teixeira, Paulo José P L; Carazzolle, Marcelo Falsarella; Schuster, Stephan C; Carlson, John E; Guiltinan, Mark J; Mieczkowski, Piotr; Farmer, Andrew; Ramaraj, Thiruvarangan; Crozier, Jayne; Davis, Robert E; Shao, Jonathan; Melnick, Rachel L; Pereira, Gonçalo A G; Bailey, Bryan A

2014-02-27

The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp. We sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase. Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. These genes are being used to develop a new understanding of how this disease interaction progresses and to identify potential targets to reduce the impact of this devastating disease.

Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases

PubMed Central

2014-01-01

Background The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp. Results We sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase. Conclusions Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. These genes are being used to develop a new understanding of how this disease interaction progresses and to identify potential targets to reduce the impact of this devastating disease. PMID:24571091

Theoretical model for the discrete flexoelectric effect and a description for the sequence of intermediate smectic phases with increasing periodicity.

PubMed

Emelyanenko, A V; Osipov, M A

2003-11-01

A general phenomenological description and a simple molecular model is proposed for the "discrete" flexoelectric effect in tilted smectic liquid crystal phases. This effect defines a polarization in a smectic layer induced by a difference of director orientations in the two smectic layers adjacent to it. It is shown that the "discrete" flexoelectric effect is determined by electrostatic dipole-quadrupole interaction between positionally correlated molecules located in adjacent smectic layers, while the corresponding dipole-dipole interaction is responsible for a coupling between polarization vectors in neighboring layers. It is shown that a simple phenomenological model of a ferrielectric smectic liquid crystal, which has recently been proposed in the literature, can be used to describe the whole sequence of intermediate chiral smectic C* phases with increasing periods, and to determine the nonplanar structure of each phase without additional assumptions. In this sequence the phases with three- and four-layer periodicities have the same structure, as observed in the experiment. The theory predicts also the structure of intermediate phases with longer periods that have not been studied experimentally so far. The structures of intermediate phases with periodicities of up to nine layers are presented together with the phase diagrams, and a relationship between molecular chirality and the three-dimensional structure of intermediate phases is discussed. It is considered also how the coupling between the spontaneous polarization determined by molecular chirality and the induced polarization determined by the discrete flexoelectric effect stabilizes the nonplanar structure of intermediate phases.

Dipolar recoupling in solid state NMR by phase alternating pulse sequences

PubMed Central

Lin, J.; Bayro, M.; Griffin, R. G.; Khaneja, N.

2009-01-01

We describe some new developments in the methodology of making heteronuclear and homonuclear recoupling experiments in solid state NMR insensitive to rf-inhomogeneity by phase alternating the irradiation on the spin system every rotor period. By incorporating delays of half rotor periods in the pulse sequences, these phase alternating experiments can be made γ encoded. The proposed methodology is conceptually different from the standard methods of making recoupling experiments robust by the use of ramps and adiabatic pulses in the recoupling periods. We show how the concept of phase alternation can be incorporated in the design of homonuclear recoupling experiments that are both insensitive to chemical-shift dispersion and rf-inhomogeneity. PMID:19157931

Infant auditory short-term memory for non-linguistic sounds.

PubMed

Ross-Sheehy, Shannon; Newman, Rochelle S

2015-04-01

This research explores auditory short-term memory (STM) capacity for non-linguistic sounds in 10-month-old infants. Infants were presented with auditory streams composed of repeating sequences of either 2 or 4 unique instruments (e.g., flute, piano, cello; 350 or 700 ms in duration) followed by a 500-ms retention interval. These instrument sequences either stayed the same for every repetition (Constant) or changed by 1 instrument per sequence (Varying). Using the head-turn preference procedure, infant listening durations were recorded for each stream type (2- or 4-instrument sequences composed of 350- or 700-ms notes). Preference for the Varying stream was taken as evidence of auditory STM because detection of the novel instrument required memory for all of the instruments in a given sequence. Results demonstrate that infants listened longer to Varying streams for 2-instrument sequences, but not 4-instrument sequences, composed of 350-ms notes (Experiment 1), although this effect did not hold when note durations were increased to 700 ms (Experiment 2). Experiment 3 replicates and extends results from Experiments 1 and 2 and provides support for a duration account of capacity limits in infant auditory STM. Copyright © 2014 Elsevier Inc. All rights reserved.

Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers.

PubMed

Wang, Jun; Bonnesen, Peter V; Rangel, E; Vallejo, E; Sanchez-Castillo, Ariadna; James Cleaves Ii, H; Baddorf, Arthur P; Sumpter, Bobby G; Pan, Minghu; Maksymovych, Petro; Fuentes-Cabrera, Miguel

2016-01-04

Self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N(9)-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two or more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. These characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Further, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.

Evaluating transportation systems management & operations (TSM&O) benefits to alternative intersection treatments.

DOT National Transportation Integrated Search

2015-12-01

This research provides a comprehensive review and assessment of current alternative intersection methods : which successfully eliminate the left-turn phase. With increasing traffic and limited resources, the Florida : Department of Transportati...

A safety mechanism for observational learning.

PubMed

Badets, Arnaud; Boutin, Arnaud; Michelet, Thomas

2018-04-01

This empirical article presents the first evidence of a "safety mechanism" based on an observational-learning paradigm. It is accepted that during observational learning, a person can use different strategies to learn a motor skill, but it is unknown whether the learner is able to circumvent the encoding of an uncompleted observed skill. In this study, participants were tested in a dyadic protocol in which an observer watched a participant practicing two different motor sequences during a learning phase. During this phase, one of the two motor sequences was interrupted by a stop signal that precluded motor learning. The results of the subsequent retention test revealed that both groups learned the two motor sequences, but only the physical practice group showed worse performance for the interrupted sequence. The observers were consequently able to use a safety strategy to learn both sequences equally. Our findings are discussed in light of the implications of the action observation network for sequence learning and the cognitive mechanisms of error-based observation.

Extended phase graphs with anisotropic diffusion

NASA Astrophysics Data System (ADS)

Weigel, M.; Schwenk, S.; Kiselev, V. G.; Scheffler, K.; Hennig, J.

2010-08-01

The extended phase graph (EPG) calculus gives an elegant pictorial description of magnetization response in multi-pulse MR sequences. The use of the EPG calculus enables a high computational efficiency for the quantitation of echo intensities even for complex sequences with multiple refocusing pulses with arbitrary flip angles. In this work, the EPG concept dealing with RF pulses with arbitrary flip angles and phases is extended to account for anisotropic diffusion in the presence of arbitrary varying gradients. The diffusion effect can be expressed by specific diffusion weightings of individual magnetization pathways. This can be represented as an action of a linear operator on the magnetization state. The algorithm allows easy integration of diffusion anisotropy effects. The formalism is validated on known examples from literature and used to calculate the effective diffusion weighting in multi-echo sequences with arbitrary refocusing flip angles.

The sequence, and its evolutionary implications, of a Thermococcus celer protein associated with transcription

NASA Technical Reports Server (NTRS)

Kaine, B. P.; Mehr, I. J.; Woese, C. R.

1994-01-01

Through random search, a gene from Thermococcus celer has been identified and sequenced that appears to encode a transcription-associated protein (110 amino acid residues). The sequence has clear homology to approximately the last half of an open reading frame reported previously for Sulfolobus acidocaldarius [Langer, D. & Zillig, W. (1993) Nucleic Acids Res. 21, 2251]. The protein translations of these two archaeal genes in turn are homologs of a small subunit found in eukaryotic RNA polymerase I (A12.2) and the counterpart of this from RNA polymerase II (B12.6). Homology is also seen with the eukaryotic transcription factor TFIIS, but it involves only the terminal 45 amino acids of the archaeal proteins. Evolutionary implications of these homologies are discussed.

Sequencing the Unknown

NASA Image and Video Library

2017-12-19

Being able to identify microbes in real time aboard the International Space Station, without having to send them back to Earth for identification first, would be revolutionary for the world of microbiology and space exploration, and the Genes in Space-3 team turned that possibility into a reality this year when it completed the first-ever sample-to-sequence process entirely aboard the space station. This advance could aid in the ability to diagnose and treat astronaut ailments in real time, as well as assisting in the identification of DNA-based life on other planets. It could also benefit other experiments aboard the orbiting laboratory. HD Download: https://archive.org/details/jsc2017m001160_Sequencing_the_Unknown _______________________________________ FOLLOW THE SPACE STATION! Twitter: https://twitter.com/Space_Station Facebook: https://www.facebook.com/ISS Instagram: https://instagram.com/iss/

Contryphan-Bt: A pyroglutamic acid containing conopeptide isolated from the venom of Conus betulinus.

PubMed

Han, Penggang; Cao, Ying; Liu, Shangyi; Dai, Xiandong; Yao, Ge; Fan, Chongxu; Wu, Wenjian; Chen, Jisheng

2017-09-01

A new member of the contryphans family was isolated from the venom of Conus betilinus, a vermivorous species distributed in the South China Sea. Its sequence, ZSGCO(D-W)KPWC-NH 2 (Z, pyroglutamic acid), was established by a combination of de novo MS/MS sequencing and venom-duct transcriptome sequencing. The occurrence of D-Trp 6 was confirmed by chemical synthesis and HPLC behavior comparison. Like known contryphans, contryphan-Bt produces the "stiff-tail" syndrome in mice and contains one disulfide bond, a hydroxyproline, a D-tryptophan, and an amidated C-terminus. However, contryphan-Bt differs from previously identified contryphans by a pyroglutamic acid at the N terminus. CD spectrum reveals that contryphan-Bt possess β-turn in solution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Solar Conjunction Ends: Nirgal Vallis

NASA Technical Reports Server (NTRS)

2004-01-01

28 September 2004 For the past several weeks, Mars was on the other side of the Sun relative to Earth. During this period, known as solar conjunction, radio communication with spacecraft orbiting and roving on Mars was limited. As is always done during solar conjunction, on 7 September 2004, the Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) was turned off. On Saturday, 25 September 2004, the MOC team gathered at Malin Space Science Systems to command the instrument to turn back on again. After a successful turn-on, MOC acquired its first narrow angle camera image, shown here, on orbit 24808 (24,808th orbit since the start of the Mapping phase of the MGS mission in March 1999).

The 25 September image shows a portion of Nirgal Vallis, an ancient valley system in the Mare Erythraeum region of Mars. The valley floor is covered by large, ripple-like bedforms created by wind. This early southern winter image is located near 27.4oS, 42.9oW, and covers an area approximately 3 km (1.9 mi) across. Sunlight illuminates the scene from the upper left.

This was the 4th solar conjunction period that MGS and MOC have been through since the spacecraft reached the red planet in September 1997. The four solar conjunction periods, where MOC was turned off, were:

First solar conjunction: 29 April - 1 June 1998 Second solar conjunction: 22 June - 12 July 2000 Third solar conjunction: 1 August - 18 August 2002 Fourth solar conjunction: 7 September - 25 September 2004.

In late October, MGS MOC will mark the start of its fourth Mars year since the beginning of the Mapping Phase of the mission in March 1999. MGS and MOC have already been orbiting Mars for more than 4 Mars years, including the pre-Mapping aerobrake and science phasing orbit insertion periods.

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.

PubMed

Delaneau, Olivier; Marchini, Jonathan

2014-06-13

A major use of the 1000 Genomes Project (1000 GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000 GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants.

Phase formation and texture of thin nickel germanides on Ge(001) and Ge(111)

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

De Schutter, B., E-mail: deschutter.bob@ugent.be; Detavernier, C.; Van Stiphout, K.

2016-04-07

We studied the solid-phase reaction between a thin Ni film and a single crystal Ge(001) or Ge(111) substrate during a ramp anneal. The phase formation sequence was determined using in situ X-ray diffraction and in situ Rutherford backscattering spectrometry (RBS), while the nature and the texture of the phases were studied using X-ray pole figures and transmission electron microscopy. The phase sequence is characterized by the formation of a single transient phase before NiGe forms as the final and stable phase. X-ray pole figures were used to unambiguously identify the transient phase as the ϵ-phase, a non-stoichiometric Ni-rich germanide withmore » a hexagonal crystal structure that can exist for Ge concentrations between 34% and 48% and which forms with a different epitaxial texture on both substrate orientations. The complementary information gained from both RBS and X-ray pole figure measurements revealed a simultaneous growth of both the ϵ-phase and NiGe over a small temperature window on both substrate orientations.« less

Developmental Time Course of the Acquisition of Sequential Egocentric and Allocentric Navigation Strategies

ERIC Educational Resources Information Center

Bullens, Jessie; Igloi, Kinga; Berthoz, Alain; Postma, Albert; Rondi-Reig, Laure

2010-01-01

Navigation in a complex environment can rely on the use of different spatial strategies. We have focused on the employment of "allocentric" (i.e., encoding interrelationships among environmental cues, movements, and the location of the goal) and "sequential egocentric" (i.e., sequences of body turns associated with specific choice points)…

Reactive Sequences in the Evolution of Maryland's Consequential Accountability Regime

ERIC Educational Resources Information Center

Mawhinney, Hanne B.

2013-01-01

An institutional analysis is presented of the policy, political, and legislative events associated with the failure of an attempt in 2006 by the state of Maryland to take control of 11 schools in Baltimore City and turn them over to independent managers or into charter schools under No Child Left Behind. The place of the failed…

Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing

USDA-ARS?s Scientific Manuscript database

Fungal plant pathogens secrete effector molecules to establish disease on their hosts, while plants in turn utilize immune receptors to intercept these effectors. The tomato immune receptor Ve1 governs resistance to race 1 strains of the soil-borne vascular wilt fungi Verticillium dahliae and V. alb...

Using Audience Response Systems during Interactive Lectures to Promote Active Learning and Conceptual Understanding of Stoichiometry

ERIC Educational Resources Information Center

Cotes, Sandra; Cotuá, José

2014-01-01

This article describes a method of instruction using an active learning strategy for teaching stoichiometry through a process of gradual knowledge building. Students identify their misconceptions and progress through a sequence of questions based on the same chemical equation. An infrared device and software registered as the TurningPoint Audience…

Effects of Frequency Separation and Diotic/Dichotic Presentations on the Alternation Frequency Limits in Audition Derived from a Temporal Phase Discrimination Task.

PubMed

Kanaya, Shoko; Fujisaki, Waka; Nishida, Shin'ya; Furukawa, Shigeto; Yokosawa, Kazuhiko

2015-02-01

Temporal phase discrimination is a useful psychophysical task to evaluate how sensory signals, synchronously detected in parallel, are perceptually bound by human observers. In this task two stimulus sequences synchronously alternate between two states (say, A-B-A-B and X-Y-X-Y) in either of two temporal phases (ie A and B are respectively paired with X and Y, or vice versa). The critical alternation frequency beyond which participants cannot discriminate the temporal phase is measured as an index characterizing the temporal property of the underlying binding process. This task has been used to reveal the mechanisms underlying visual and cross-modal bindings. To directly compare these binding mechanisms with those in another modality, this study used the temporal phase discrimination task to reveal the processes underlying auditory bindings. The two sequences were alternations between two pitches. We manipulated the distance between the two sequences by changing intersequence frequency separation, or presentation ears (diotic vs dichotic). Results showed that the alternation frequency limit ranged from 7 to 30 Hz, becoming higher as the intersequence distance decreased, as is the case with vision. However, unlike vision, auditory phase discrimination limits were higher and more variable across participants. © 2015 SAGE Publications.

Pressure Induced Phase Transition and Electronic Properties of 1d ZnO Nanocrystal: AN AB INITIO Study

NASA Astrophysics Data System (ADS)

Srivastava, Anurag; Tyagi, Neha

2012-10-01

We have analyzed the one-dimensional (1D) ZnO nanocrystals in its wurtzite (B4); zinc-blende (B3) and rocksalt (B1) type phases, by means of density functional theory (DFT) calculations. The energetic stability of nanocrystal has been analyzed using Revised Perdew-Burke-Ernzerhof (revPBE) type parameterized GGA potential. The B3 type phase is most stable amongst other phases of nanocrystals. The computation of ground state properties for all the phases of ZnO nanocrystals finds that the bulk modulus are smaller than their bulk counterpart, in turn softening the material at reduced dimensions. The electronic band structure analysis confirms the semiconducting nature of B4 type phase whereas other two are metallic.

VML 3.0 Reactive Sequencing Objects and Matrix Math Operations for Attitude Profiling

NASA Technical Reports Server (NTRS)

Grasso, Christopher A.; Riedel, Joseph E.

2012-01-01

VML (Virtual Machine Language) has been used as the sequencing flight software on over a dozen JPL deep-space missions, most recently flying on GRAIL and JUNO. In conjunction with the NASA SBIR entitled "Reactive Rendezvous and Docking Sequencer", VML version 3.0 has been enhanced to include object-oriented element organization, built-in queuing operations, and sophisticated matrix / vector operations. These improvements allow VML scripts to easily perform much of the work that formerly would have required a great deal of expensive flight software development to realize. Autonomous turning and tracking makes considerable use of new VML features. Profiles generated by flight software are managed using object-oriented VML data constructs executed in discrete time by the VML flight software. VML vector and matrix operations provide the ability to calculate and supply quaternions to the attitude controller flight software which produces torque requests. Using VML-based attitude planning components eliminates flight software development effort, and reduces corresponding costs. In addition, the direct management of the quaternions allows turning and tracking to be tied in with sophisticated high-level VML state machines. These state machines provide autonomous management of spacecraft operations during critical tasks like a hypothetic Mars sample return rendezvous and docking. State machines created for autonomous science observations can also use this sort of attitude planning system, allowing heightened autonomy levels to reduce operations costs. VML state machines cannot be considered merely sequences - they are reactive logic constructs capable of autonomous decision making within a well-defined domain. The state machine approach enabled by VML 3.0 is progressing toward flight capability with a wide array of applicable mission activities.

Coordination analysis of players' distribution in football using cross-correlation and vector coding techniques.

PubMed

Moura, Felipe Arruda; van Emmerik, Richard E A; Santana, Juliana Exel; Martins, Luiz Eduardo Barreto; Barros, Ricardo Machado Leite de; Cunha, Sergio Augusto

2016-12-01

The purpose of this study was to investigate the coordination between teams spread during football matches using cross-correlation and vector coding techniques. Using a video-based tracking system, we obtained the trajectories of 257 players during 10 matches. Team spread was calculated as functions of time. For a general coordination description, we calculated the cross-correlation between the signals. Vector coding was used to identify the coordination patterns between teams during offensive sequences that ended in shots on goal or defensive tackles. Cross-correlation showed that opponent teams have a tendency to present in-phase coordination, with a short time lag. During offensive sequences, vector coding results showed that, although in-phase coordination dominated, other patterns were observed. We verified that during the early stages, offensive sequences ending in shots on goal present greater anti-phase and attacking team phase periods, compared to sequences ending in tackles. Results suggest that the attacking team may seek to present a contrary behaviour of its opponent (or may lead the adversary behaviour) in the beginning of the attacking play, regarding to the distribution strategy, to increase the chances of a shot on goal. The techniques allowed detecting the coordination patterns between teams, providing additional information about football dynamics and players' interaction.

Interplanetary field and plasma during initial phase of geomagnetic storms

NASA Technical Reports Server (NTRS)

Patel, V. L.; Wiskerchen, M. J.

1975-01-01

A study has been conducted of a large number of geomagnetic storms occurring during the period from 1966 to 1970. Questions of data selection are discussed and the large-scale interplanetary magnetic field during the initial phase is examined. Small-scale interplanetary fields during the initial phase are also considered, taking into account important features of small-scale variations in the interplanetary field and plasma for three storms. Details concerning 23 geomagnetic storms and the interplanetary magnetic field are presented in a table. A study of the initial phase of these storms indicates that in most of these events, the solar-ecliptic Z component of the interplanetary magnetic field turns southward when the main phase decrease begins.

Calculation of the absolute free energy of a smectic-A phase

NASA Astrophysics Data System (ADS)

Huang, Chien-Cheng; Ramachandran, Sanoop; Ryckaert, Jean-Paul

2014-12-01

In this paper, we provide a scheme to compute the absolute free energy of a smectic-A phase via the "indirect method." The state of interest is connected through a three-step reversible path to a reference state. This state consists of a low-density layer of rods coupled to two external fields maintaining these rods close to the layer's plane and oriented preferably normal to the layer. The low-density free energy of the reference state can be computed on the basis of the relevant second virial coefficients between two rods coupled to the two external fields. We apply this technique to the Gay-Berne potential for calamitics with a parameter set leading to stable isotropic (I), nematic (N), smectic-A (SmA), and crystal (Cr) phases. We locate the I-SmA phase transition at low pressure and the sequence of phase transitions I-N-SmA along higher-pressure isobars and we establish the location of the I-N-SmA triple point. Close to this triple point, we show that the N-SmA transition is clearly first order. Our results are compared to the coexistence lines of the approximate phase diagram elucidated by de Miguel et al. [J. Chem. Phys. 121, 11183 (2004), 10.1063/1.1810472] established through the direct observation of the sequence of phase transitions occurring along isobars under heating or cooling sequences of runs. Finally, we discuss the potential of our technique in studying similar transitions observed on layered phases under confinement.

Anticipatory phase correction in sensorimotor synchronization.

PubMed

Repp, Bruno H; Moseley, Gordon P

2012-10-01

Studies of phase correction in sensorimotor synchronization often introduce timing perturbations that are unpredictable with regard to direction, magnitude, and position in the stimulus sequence. If participants knew any or all of these parameters in advance, would they be able to anticipate perturbations and thus regain synchrony more quickly? In Experiment 1, we asked musically trained participants to tap in synchrony with short isochronous tone sequences containing a phase shift (PS) of -100, -40, 40, or 100 ms and provided advance information about its direction, position, or both (but not about its magnitude). The first two conditions had little effect, but in the third condition participants shifted their tap in anticipation of the PS, though only by about ±40 ms on average. The phase correction response to the residual PS was also enhanced. In Experiment 2, we provided complete advance information about PSs of various magnitudes either at the time of the immediately preceding tone ("late") or at the time of the tone one position back ("early") while also varying sequence tempo. Anticipatory phase correction was generally conservative and was impeded by fast tempo in the "late" condition. At fast tempi in both conditions, advancing a tap was more difficult than delaying a tap. The results indicate that temporal constraints on anticipatory phase correction resemble those on reactive phase correction. While the latter is usually automatic, this study shows that phase correction can also be controlled consciously for anticipatory purposes. Copyright © 2011 Elsevier B.V. All rights reserved.

Reactions between palladium and gallium arsenide: Bulk versus thin-film studies

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

Lin, J.; Hsieh, K.; Schulz, K.J.

1988-01-01

Reactions between Pd and GaAs have been studied using bulk-diffusion couples of Pd (approx.0.6 mm thick)/GaAs and thin-film Pd (50 and 160 nm)/GaAs samples. The sequence of phase formation at 600 /sup 0/C between bulk Pd and GaAs was established. Initial formation of the solution phase ..mu.. and the ternary phase T does not represent the stable configuration. The stable configuration is GaAs chemically bondepsilonchemically bondlambdachemically bond..gamma..chemically bond..nu..chemically bondPd and is termed the diffusion path between GaAs and Pd. The sequence of phase formation for the bulk-diffusion couples is similar at 500 /sup 0/C. Phase formation for the thin-film Pd/GaAsmore » specimens was studied at 180, 220, 250, 300, 350, 400, 450, 600, and 1000 /sup 0/C for various annealing times. The sequence of phase formation obtained from the thin-film experiments is rationalized readily from the known ternary phase equilibria of Ga--Pd--As and the results from the bulk-diffusion couples of Pd/GaAs. The thin-film results reported in the literature are likewise rationalized. The diffusion path concept provides a useful guide in understanding the phase formation in Pd--GaAs interface or any other M--GaAs interface. This information is important in designing a uniform, stable contact for the metallization of GaAs.« less

Using a plenoptic sensor to reconstruct vortex phase structures.

PubMed

Wu, Chensheng; Ko, Jonathan; Davis, Christopher C

2016-07-15

A branch point problem and its solution commonly involve recognizing and reconstructing a vortex phase structure around a singular point. In laser beam propagation through random media, the destructive phase contributions from various parts of a vortex phase structure will cause a dark area in the center of the beam's intensity profile. This null of intensity can, in turn, prevent the vortex phase structure from being recognized. In this Letter, we show how to use a plenoptic sensor to transform the light field of a vortex beam so that a simple and direct reconstruction algorithm can be applied to reveal the vortex phase structure. As a result, we show that the plenoptic sensor is effective in detecting branch points and can be used to reconstruct phase distortion in a beam in a wide sense.

Effect of patient-centered communication training on discussion and detection of nonadherence in glaucoma.

PubMed

Hahn, Steven R; Friedman, David S; Quigley, Harry A; Kotak, Sameer; Kim, Elizabeth; Onofrey, Meaghan; Eagan, Corey; Mardekian, Jack

2010-07-01

To assess communication about adherence and to determine the impact of communication skills training on physicians' approach to nonadherence. Sociolinguistic analysis of videotaped community ophthalmologists' encounters with patients with glaucoma before and after training. Patients in both phases and physicians in phase I knew communication was being studied but not what the focus of the study was. In phase II, physicians knew the targeted communication behaviors. Twenty-three ophthalmologists and 100 regularly scheduled patients with glaucoma (50 per phase). An educational program with videotaped vignettes of simulated patient encounters using audience response and role play to teach patient-centered communication skills, including a 4-step adherence assessment and the use of open-ended questions in ask-tell-ask sequences. Physician eliciting an acknowledgment of nonadherence during a clinical encounter compared with acknowledgment of nonadherence during a postvisit research interview (primary outcome), and performance of targeted communication and substantive discussion of adherence. After intervention, physicians increased the proportion of open-ended questions (15% vs 6%; P = 0.001) and specifically about medication taking (82% compared with 18% of encounters; P<0.001). Compared with the absence of ask-tell-ask communication, 32% of phase II encounters included a complete ask-tell-ask sequence, 78% included an ask-tell sequence, and 32% a tell-ask sequence (P<0.001). Three of 4 steps for assessment of adherence were more common in phase II, and substantial discussions of adherence occurred in 86% versus 30% of encounters (P<0.001). In phase II, physicians elicited acknowledgment of nonadherence in 78% (7/9) of those who acknowledged nonadherence in the postvisit interview compared with 25% in phase I (3/12; P = 0.03). This study demonstrates that experienced community physicians significantly improved their communication strategies and ability to detect and address nonadherence after a 3-hour educational program. Proprietary or commercial disclosure may be found after the references. Copyright 2010 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Reconstruction of the 2014 eruption sequence of Ontake Volcano from recorded images and interviews

NASA Astrophysics Data System (ADS)

Oikawa, Teruki; Yoshimoto, Mitsuhiro; Nakada, Setsuya; Maeno, Fukashi; Komori, Jiro; Shimano, Taketo; Takeshita, Yoshihiro; Ishizuka, Yoshihiro; Ishimine, Yasuhiro

2016-05-01

A phreatic eruption at Mount Ontake (3067 m) on September 27, 2014, led to 64 casualties, including missing people. In this paper, we clarify the eruption sequence of the 2014 eruption from recorded images (photographs and videos obtained by climbers) and interviews with mountain guides and workers in mountain huts. The onset of eruption was sudden, without any clear precursory surface phenomena (such as ground rumbling or strong smell of sulfide). Our data indicate that the eruption sequence can be divided into three phases. Phase 1: The eruption started with dry pyroclastic density currents (PDCs) caused by ash column collapse. The PDCs flowed down 2.5 km SW and 2 km NW from the craters. In addition, PDCs moved horizontally by approximately 1.5 km toward N and E beyond summit ridges. The temperature of PDCs at the summit area partially exceeded 100 °C, and an analysis of interview results suggested that the temperature of PDCs was mostly in the range of 30-100 °C. At the summit area, there were violent falling ballistic rocks. Phase 2: When the outflow of PDCs stopped, the altitude of the eruption column increased; tephra with muddy rain started to fall; and ambient air temperature decreased. Falling ballistic rocks were almost absent during this phase. Phase 3: Finally, muddy hot water flowed out from the craters. These models reconstructed from observations are consistent with the phreatic eruption models and typical eruption sequences recorded at similar volcanoes.

Texture analysis of common renal masses in multiple MR sequences for prediction of pathology

NASA Astrophysics Data System (ADS)

Hoang, Uyen N.; Malayeri, Ashkan A.; Lay, Nathan S.; Summers, Ronald M.; Yao, Jianhua

2017-03-01

This pilot study performs texture analysis on multiple magnetic resonance (MR) images of common renal masses for differentiation of renal cell carcinoma (RCC). Bounding boxes are drawn around each mass on one axial slice in T1 delayed sequence to use for feature extraction and classification. All sequences (T1 delayed, venous, arterial, pre-contrast phases, T2, and T2 fat saturated sequences) are co-registered and texture features are extracted from each sequence simultaneously. Random forest is used to construct models to classify lesions on 96 normal regions, 87 clear cell RCCs, 8 papillary RCCs, and 21 renal oncocytomas; ground truths are verified through pathology reports. The highest performance is seen in random forest model when data from all sequences are used in conjunction, achieving an overall classification accuracy of 83.7%. When using data from one single sequence, the overall accuracies achieved for T1 delayed, venous, arterial, and pre-contrast phase, T2, and T2 fat saturated were 79.1%, 70.5%, 56.2%, 61.0%, 60.0%, and 44.8%, respectively. This demonstrates promising results of utilizing intensity information from multiple MR sequences for accurate classification of renal masses.

Sequence-dependent rotation axis changes and interaction torque use in overarm throwing.

PubMed

Hansen, Clint; Rezzoug, Nasser; Gorce, Philippe; Venture, Gentiane; Isableu, Brice

2016-01-01

We examined the role of rotation axes during an overarm throwing task. Participants performed such task and were asked to throw a ball at maximal velocity at a target. The purpose of this study was to examine whether the minimum inertia axis would be exploited during the throwing phases, a time when internal-external rotations of the shoulder are particularly important. A motion capture system was used to evaluate the performance and to compute the potential axes of rotation (minimum inertia axis, shoulder-centre of mass axis and the shoulder-elbow axis). More specifically, we investigated whether a velocity-dependent change in rotational axes can be observed in the different throwing phases and whether the control obeys the principle of minimum inertia resistance. Our results showed that the limbs' rotational axis mainly coincides with the minimum inertia axis during the cocking phase and with the shoulder-elbow axis during the acceleration phase. Besides these rotation axes changes, the use of interaction torque is also sequence-dependent. The sequence-dependent rotation axes changes associated with the use of interaction torque during the acceleration phase could be a key factor in the production of hand velocity at ball release.

Anatomy of major coal successions: Facies analysis and sequence architecture of a brown coal-bearing valley fill to lacustrine tract (Upper Valdarno Basin, Northern Apennines, Italy)

NASA Astrophysics Data System (ADS)

Ielpi, Alessandro

2012-07-01

A late Pliocene incised valley fill to lacustrine succession, which contains an interbedded brown coal seam (< 20 m thick), is examined in terms of facies analysis, physical stratigraphy and sequence architecture. The succession (< 50 m thick) constitutes the first depositional event of the Castelnuovo Synthem, which is the oldest unconformity bounded stratigraphic unit of the nonmarine Upper Valdarno Basin, Northern Apennines (Italy). The integration of field surveys and borehole logs identified the following event sequence: first valley filling stages by coarse alluvial fan and channelised streams; the progressive setting of low gradient floodbasins with shallow floodplain lakes; subsequent major waterlogging and extensive peat mire development; and system drowning and establishment of permanent lacustrine conditions. The deposits are grouped in a set of nested valley fills and are arranged as high-frequency depositional sequences. The sequences are bounded by minor erosive truncations and have distinctive upward trends: lowstand system tract thinning; transgressive system tract thickening; highstand system tract thinning and eventual non-deposition; and the smoothing of along-sequence boundary sub-aerial incisions. Such features fit in with the notion of an idealised model where second-order (high-frequency) fluctuations, modulated by first-order (low-frequency) base-level rising, have short-lived standing + falling phases and prolonged transgressions, respectively. Furthermore, the general sequence architecture reveals how a mixed palustrine-siliciclastic system differs substantially from a purely siliciclastic one. In the transgressive phases, terrigenous starvation induces prevailing peat accumulation, generating abnormally thick transgressive system tracts that eventually come to occupy much of the same transgression-generated accommodation space. In the highstand phases, the development of thick highstand system tracts is then prevented by sediment upstream trapping due to retrogressive fluvial aggradations, probably coupled with low-accommodation settings inherited from the transgressive phases.

Intestinal Microbiota of White Shrimp Penaeus vannamei Under Intensive Cultivation Conditions in Ecuador.

PubMed

Gainza, Oreste; Ramírez, Carolina; Ramos, Alfredo Salinas; Romero, Jaime

2018-04-01

The goal of the study was to characterize the intestinal tract bacterial microbiota composition of Penaeus vannamei in intensive commercial ponds in Ecuador, comparing two shrimp-farming phases: nursery and harvest. Bacterial microbiota was examined by sequencing amplicons V2-V3 of the 16S rRNA using Ion Torrent technology. Archaea sequences were detected in both phases. Sequence analyses revealed quantitative and qualitative differences between the nursery phase and the harvest phase in shrimp intestinal microbiota composition. The main differences were observed at the phylum level during the nursery phase, and the prevailing phyla were CKC4 (37.3%), Proteobacteria (29.8%), Actinobacteria (11.6%), and Firmicutes (10.1%). In the harvest phase, the prevailing phyla were Proteobacteria (28.4%), Chloroflexi (19.9%), and Actinobacteria (15.1%). At the genus level, microbiota from the nursery phase showed greater relative abundances of CKC4 uncultured bacterium (37%) and Escherichia-Shigella (18%). On the contrary, in the microbiota of harvested shrimp, the prevailing genera were uncultured Caldilinea (19%) and Alphaproteobacteria with no other assigned rate (10%). The analysis of similarity ANOSIM test (beta diversity) indicated significant differences between the shrimp microbiota for these two farming phases. Similarly, alfa-diversity analysis (Chao1) indicated that the microbiota at harvest was far more diverse than the microbiota during the nursery phase, which showed a homogeneous composition. These results suggest that shrimp microbiota diversify their composition during intensive farming. The present work offers the most detailed description of the microbiota of P. vannamei under commercial production conditions to date.

Basilar membrane vibration is not involved in the reverse propagation of otoacoustic emissions

PubMed Central

He, W.; Ren, T.

2013-01-01

To understand how the inner ear-generated sound, i.e., otoacoustic emission, exits the cochlea, we created a sound source electrically in the second turn and measured basilar membrane vibrations at two longitudinal locations in the first turn in living gerbil cochleae using a laser interferometer. For a given longitudinal location, electrically evoked basilar membrane vibrations showed the same tuning and phase lag as those induced by sounds. For a given frequency, the phase measured at a basal location led that at a more apical location, indicating that either an electrical or an acoustical stimulus evoked a forward travelling wave. Under postmortem conditions, the electrically evoked emissions showed no significant change while the basilar membrane vibration nearly disappeared. The current data indicate that basilar membrane vibration was not involved in the backward propagation of otoacoustic emissions and that sounds exit the cochlea probably through alternative media, such as cochlear fluids. PMID:23695199

Optical properties of dip coated titanium-di-oxide (TiO2) thin films annealed at different temperatures

NASA Astrophysics Data System (ADS)

Biswas, Sayari; Kar, Asit Kumar

2018-02-01

Titanium dioxide (TiO2) thin films were synthesized by hydrothermal assisted sol-gel dip coating method on quartz substrate. The sol was prepared by hydrothermal method at 90 °C. Dip coating method was used to deposit the thin films. Later films were annealed at four different temperatures -600 °C, 800 °C, 1000 °C and 1200 °C. XRD study showed samples annealed at 600 °C are almost amorphous. At 800 °C, film turns into anatase phase and with further increment of annealing temperature they turn into rutile phase. Transmission spectra of thin films show sharp rise in the violet-ultraviolet transition region and a maximum transmittance of ˜60% was observed in the visible region for the sample annealed at the lowest temperature. Band gap of the prepared films varies from 2.9 eV to 3.5 eV.

Two dimensional vibrations of the guinea pig apex organ of Corti measured in vivo using phase sensitive Fourier domain optical coherence tomography

NASA Astrophysics Data System (ADS)

Ramamoorthy, Sripriya; Zhang, Yuan; Petrie, Tracy; Fridberger, Anders; Ren, Tianying; Wang, Ruikang; Jacques, Steven L.; Nuttall, Alfred L.

2015-02-01

In this study, we measure the in vivo apical-turn vibrations of the guinea pig organ of Corti in both axial and radial directions using phase-sensitive Fourier domain optical coherence tomography. The apical turn in guinea pig cochlea has best frequencies around 100 - 500 Hz which are relevant for human speech. Prior measurements of vibrations in the guinea pig apex involved opening the otic capsule, which has been questioned on the basis of the resulting changes to cochlear hydrodynamics. Here this limitation is overcome by measuring the vibrations through bone without opening the otic capsule. Furthermore, we have significantly reduced the surgery needed to access the guinea pig apex in the axial direction by introducing a miniature mirror inside the bulla. The method and preliminary data are discussed in this article.

The Effect of Dilution on Microsegregation in AWS ER NiCrMo-14 Alloy Welding Claddings

NASA Astrophysics Data System (ADS)

Miná, Émerson Mendonça; da Silva, Yuri Cruz; Dille, Jean; Silva, Cleiton Carvalho

2016-12-01

Dilution and microsegregation are phenomena inherent to claddings, which, in turn, directly affect their main properties. This study evaluated microsegregation in the fusion zone with different dilution levels. The overlays were welded by the TIG cold wire feed process. Dilution was calculated from the geometric characteristics of the claddings and from the conservation of mass equation using chemical composition measurements. Microsegregation was calculated using energy dispersive X-ray spectroscopy measurements of the dendrites and the chemical composition of the fusion zone. The dilution of the claddings was increased by reducing the wire feed rate. Fe showed potential to be incorporated into the solid phase ( k > 1), and this increased with the increase of dilution. Mo, in turn, was segregated into the liquid phase ( k < 1) and also increased with the increase of dilution. However, Cr and W showed a slight decrease in their partition coefficients ( k) with the increase of dilution.

AGARD Conference Proceedings on Guidance and Control of Precision Guided Weapons Held in Geilo, Norway from 3-6 May 1988

DTIC Science & Technology

1989-01-11

EFFECT OF BANK-TO-TURN VERSUS SKID-TO-TURN STEERING ON THE MANOEUVRABILITY OF AUTONOMOUS PRECISION GUIDED MUUNITION AGAINST GROUND TARGETS by B.J.Damen...space. Basic Relationships of an Interferometer Gyro The Sagnac effect in the fiber optic gyro causes a phase shift in the sensor col during rotation with... a read-out coupler and an.avalanche photodiode for optical detection. The opto module is rigidly connected with the sensor module via a fiber link

Installation Restoration Program. Phase 2. Confirmation/Quantification. Stage 1. Air Force Plant 38, Porter, New York, RCRA (Resource Conservation and Recovery Act) Sites

DTIC Science & Technology

1988-04-01

sites throughout Alaska, Idaho , Oregon, and Washington, including work at 10 sites on the National Priorities List. Major geohydrologic investigations...Mary’s Hospital, 5300 Military Rd., Lewiston , 278-4000 Hospital Emergetcy Room Niagara Falls Memorial Medical Center, 621 10th N.F. 278-4000 Poison...Hospital ( Lewiston ): Exit AFP 38; head West on Balmer Road; Turn left and head south on State Highway 18; Turn left on State Highway 104 ( Lewiston Rd

Identification of amino acid residues in protein SRP72 required for binding to a kinked 5e motif of the human signal recognition particle RNA.

PubMed

Iakhiaeva, Elena; Iakhiaev, Alexei; Zwieb, Christian

2010-11-13

Human cells depend critically on the signal recognition particle (SRP) for the sorting and delivery of their proteins. The SRP is a ribonucleoprotein complex which binds to signal sequences of secretory polypeptides as they emerge from the ribosome. Among the six proteins of the eukaryotic SRP, the largest protein, SRP72, is essential for protein targeting and possesses a poorly characterized RNA binding domain. We delineated the minimal region of SRP72 capable of forming a stable complex with an SRP RNA fragment. The region encompassed residues 545 to 585 of the full-length human SRP72 and contained a lysine-rich cluster (KKKKKKKKGK) at postions 552 to 561 as well as a conserved Pfam motif with the sequence PDPXRWLPXXER at positions 572 to 583. We demonstrated by site-directed mutagenesis that both regions participated in the formation of a complex with the RNA. In agreement with biochemical data and results from chymotryptic digestion experiments, molecular modeling of SRP72 implied that the invariant W577 was located inside the predicted structure of an RNA binding domain. The 11-nucleotide 5e motif contained within the SRP RNA fragment was shown by comparative electrophoresis on native polyacrylamide gels to conform to an RNA kink-turn. The model of the complex suggested that the conserved A240 of the K-turn, previously identified as being essential for the binding to SRP72, could protrude into a groove of the SRP72 RNA binding domain, similar but not identical to how other K-turn recognizing proteins interact with RNA. The results from the presented experiments provided insights into the molecular details of a functionally important and structurally interesting RNA-protein interaction. A model for how a ligand binding pocket of SRP72 can accommodate a new RNA K-turn in the 5e region of the eukaryotic SRP RNA is proposed.

Identification of amino acid residues in protein SRP72 required for binding to a kinked 5e motif of the human signal recognition particle RNA

PubMed Central

2010-01-01

Background Human cells depend critically on the signal recognition particle (SRP) for the sorting and delivery of their proteins. The SRP is a ribonucleoprotein complex which binds to signal sequences of secretory polypeptides as they emerge from the ribosome. Among the six proteins of the eukaryotic SRP, the largest protein, SRP72, is essential for protein targeting and possesses a poorly characterized RNA binding domain. Results We delineated the minimal region of SRP72 capable of forming a stable complex with an SRP RNA fragment. The region encompassed residues 545 to 585 of the full-length human SRP72 and contained a lysine-rich cluster (KKKKKKKKGK) at postions 552 to 561 as well as a conserved Pfam motif with the sequence PDPXRWLPXXER at positions 572 to 583. We demonstrated by site-directed mutagenesis that both regions participated in the formation of a complex with the RNA. In agreement with biochemical data and results from chymotryptic digestion experiments, molecular modeling of SRP72 implied that the invariant W577 was located inside the predicted structure of an RNA binding domain. The 11-nucleotide 5e motif contained within the SRP RNA fragment was shown by comparative electrophoresis on native polyacrylamide gels to conform to an RNA kink-turn. The model of the complex suggested that the conserved A240 of the K-turn, previously identified as being essential for the binding to SRP72, could protrude into a groove of the SRP72 RNA binding domain, similar but not identical to how other K-turn recognizing proteins interact with RNA. Conclusions The results from the presented experiments provided insights into the molecular details of a functionally important and structurally interesting RNA-protein interaction. A model for how a ligand binding pocket of SRP72 can accommodate a new RNA K-turn in the 5e region of the eukaryotic SRP RNA is proposed. PMID:21073748

Zadoff-Chu sequence-based hitless ranging scheme for OFDMA-PON configured 5G fronthaul uplinks

NASA Astrophysics Data System (ADS)

Reza, Ahmed Galib; Rhee, June-Koo Kevin

2017-05-01

A Zadoff-Chu (ZC) sequence-based low-complexity hitless upstream time synchronization scheme is proposed for an orthogonal frequency division multiple access passive optical network configured cloud radio access network fronthaul. The algorithm is based on gradual loading of the ZC sequences, where the phase discontinuity due to the cyclic prefix is alleviated by a frequency domain phase precoder, eliminating the requirements of guard bands to mitigate intersymbol interference and inter-carrier interference. Simulation results for uncontrolled-wavelength asynchronous transmissions from four concurrent transmitting optical network units are presented to demonstrate the effectiveness of the proposed scheme.

Phase stability limit of c-BN under hydrostatic and non-hydrostatic pressure conditions

NASA Astrophysics Data System (ADS)

Xiao, Jianwei; Du, Jinglian; Wen, Bin; Melnik, Roderick; Kawazoe, Yoshiyuki; Zhang, Xiangyi

2014-04-01

Phase stability limit of cubic boron nitride (c-BN) has been investigated by the crystal structure search technique. It indicated that this limit is ˜1000 GPa at hydrostatic pressure condition. Above this pressure, c-BN turns into a metastable phase with respect to rocksalt type boron nitride (rs-BN). However, rs-BN cannot be retained at 0 GPa owing to its instability at pressure below 250 GPa. For non-hydrostatic pressure conditions, the phase stability limit of c-BN is substantially lower than that under hydrostatic pressure conditions and it is also dramatically different for other pressure mode.