The Eastern Tennessee Seismic Zone: Reactivation of an Ancient Continent-Continent Suture Zone

NASA Astrophysics Data System (ADS)

Powell, C. A.

2014-12-01

The eastern Tennessee seismic zone (ETSZ) may represent reactivation of an ancient shear zone that accommodated left-lateral, transpressive motion of the Amazon craton during the Grenville orogeny. Several different lines of evidence support this concept including velocity models for the crust, earthquake hypocenter alignments, focal mechanism solutions, potential field anomalies, paleomagnetic pole positions, and isotopic geochemical studies. The ETSZ trends NE-SW for about 300 km and displays remarkable correlation with the prominent New York - Alabama (NY-AL) aeromagnetic lineament. Vp and Vs models for the crust derived from a local ETSZ earthquake tomography study reveal the presence of a narrow, NE-SW trending, steeply dipping zone of low velocities that extends to a depth of at least 24 km and is associated with the vertical projection of the NY-AL aeromagnetic lineament. The low velocity zone is interpreted as a major basement fault. The recent Mw 4.2 Perry County eastern Kentucky earthquake occurred north of the ETSZ but has a focal depth and mechanism that are similar to those for ETSZ earthquakes. We investigate the possibility that the proposed ancient shear zone extends into eastern Kentucky using Bouguer and aeromagnetic maps. The southern end of the ETSZ is characterized by hypocenters that align along planes dipping at roughly 45 degrees and focal mechanisms that contain large normal faulting components. The NY-AL aeromagnetic lineament also changes trend in the southern end of the ETSZ and the exact location of the lineament is ambiguous. We suggest that the southern portion of the ETSZ involves reactivation of reverse faults (now as normal faults) that mark the ancient transition between a collisional to a more transpressive boundary between Amazonia and Laurentia during the formation of the super continent Rodinia.

Stability, diffusion and interactions of nonlinear excitations in a many body system

NASA Astrophysics Data System (ADS)

Coste, Christophe; Jean, Michel Saint; Dessup, Tommy

2017-04-01

When repelling particles are confined in a quasi-one-dimensional trap by a transverse potential, a configurational phase transition happens. All particles are aligned along the trap axis at large confinement, but below a critical transverse confinement they adopt a staggered row configuration (zigzag phase). This zigzag transition is a subcritical pitchfork bifurcation in extended systems and in systems with cyclic boundary conditions in the longitudinal direction. Among many evidences, phase coexistence is exhibited by localized nonlinear patterns made of a zigzag phase embedded in otherwise aligned particles. We give the normal form at the bifurcation and we show that these patterns can be described as solitary wave envelopes that we call bubbles. They are stable in a large temperature range and can diffuse as quasi-particles, with a diffusion coefficient that may be deduced from the normal form. The potential energy of a bubble is found to be lower than that of the homogeneous bifurcated phase, which explains their stability. We observe also metastable states, that are pairs of solitary wave envelopes which spontaneously evolve toward a stable single bubble. We evidence a strong effect of the discreteness of the underlying particles system and introduce the concept of topological frustration of a bubble pair. A configuration is frustrated when the particles between the two bubbles are not organized in a modulated staggered row. For a nonfrustrated (NF) bubble pair configuration, the bubbles interaction is attractive so that the bubbles come closer and eventually merge as a single bubble. In contrast, the bubbles interaction is found to be repulsive for a frustrated (F) configuration. We describe a model of interacting solitary wave that provides all qualitative characteristics of the interaction force: it is attractive for NF-systems, repulsive for F-systems, and decreases exponentially with the bubbles distance.

A correlative microscopy approach relates microtubule behaviour, local organ geometry, and cell growth at the Arabidopsis shoot apical meristem

PubMed Central

Burian, Agata; Uyttewaal, Magalie

2013-01-01

Cortical microtubules (CMTs) are often aligned in a particular direction in individual cells or even in groups of cells and play a central role in the definition of growth anisotropy. How the CMTs themselves are aligned is not well known, but two hypotheses have been proposed. According to the first hypothesis, CMTs align perpendicular to the maximal growth direction, and, according to the second, CMTs align parallel to the maximal stress direction. Since both hypotheses were formulated on the basis of mainly qualitative assessments, the link between CMT organization, organ geometry, and cell growth is revisited using a quantitative approach. For this purpose, CMT orientation, local curvature, and growth parameters for each cell were measured in the growing shoot apical meristem (SAM) of Arabidopsis thaliana. Using this approach, it has been shown that stable CMTs tend to be perpendicular to the direction of maximal growth in cells at the SAM periphery, but parallel in the cells at the boundary domain. When examining the local curvature of the SAM surface, no strict correlation between curvature and CMT arrangement was found, which implies that SAM geometry, and presumed geometry-derived stress distribution, is not sufficient to prescribe the CMT orientation. However, a better match between stress and CMTs was found when mechanical stress derived from differential growth was also considered. PMID:24153420

A correlative microscopy approach relates microtubule behaviour, local organ geometry, and cell growth at the Arabidopsis shoot apical meristem.

PubMed

Burian, Agata; Ludynia, Michal; Uyttewaal, Magalie; Traas, Jan; Boudaoud, Arezki; Hamant, Olivier; Kwiatkowska, Dorota

2013-12-01

Cortical microtubules (CMTs) are often aligned in a particular direction in individual cells or even in groups of cells and play a central role in the definition of growth anisotropy. How the CMTs themselves are aligned is not well known, but two hypotheses have been proposed. According to the first hypothesis, CMTs align perpendicular to the maximal growth direction, and, according to the second, CMTs align parallel to the maximal stress direction. Since both hypotheses were formulated on the basis of mainly qualitative assessments, the link between CMT organization, organ geometry, and cell growth is revisited using a quantitative approach. For this purpose, CMT orientation, local curvature, and growth parameters for each cell were measured in the growing shoot apical meristem (SAM) of Arabidopsis thaliana. Using this approach, it has been shown that stable CMTs tend to be perpendicular to the direction of maximal growth in cells at the SAM periphery, but parallel in the cells at the boundary domain. When examining the local curvature of the SAM surface, no strict correlation between curvature and CMT arrangement was found, which implies that SAM geometry, and presumed geometry-derived stress distribution, is not sufficient to prescribe the CMT orientation. However, a better match between stress and CMTs was found when mechanical stress derived from differential growth was also considered.

Global Regularity for the Fractional Euler Alignment System

NASA Astrophysics Data System (ADS)

Do, Tam; Kiselev, Alexander; Ryzhik, Lenya; Tan, Changhui

2018-04-01

We study a pressureless Euler system with a non-linear density-dependent alignment term, originating in the Cucker-Smale swarming models. The alignment term is dissipative in the sense that it tends to equilibrate the velocities. Its density dependence is natural: the alignment rate increases in the areas of high density due to species discomfort. The diffusive term has the order of a fractional Laplacian {(-partial _{xx})^{α/2}, α \\in (0, 1)}. The corresponding Burgers equation with a linear dissipation of this type develops shocks in a finite time. We show that the alignment nonlinearity enhances the dissipation, and the solutions are globally regular for all {α \\in (0, 1)}. To the best of our knowledge, this is the first example of such regularization due to the non-local nonlinear modulation of dissipation.

Identifying Natural Alignments Between Ambulatory Surgery Centers and Local Health Systems: Building Broader Communities of Surgical Care.

PubMed

Funk, Russell J; Owen-Smith, Jason; Landon, Bruce E; Birkmeyer, John D; Hollingsworth, John M

2017-02-01

To develop and compare methods for identifying natural alignments between ambulatory surgery centers (ASCs) and hospitals that anchor local health systems. Using all-payer data from Florida's State Ambulatory Surgery and Inpatient Databases (2005-2009), we developed 3 methods for identifying alignments between ASCS and hospitals. The first, a geographic proximity approach, used spatial data to assign an ASC to its nearest hospital neighbor. The second, a predominant affiliation approach, assigned an ASC to the hospital with which it shared a plurality of surgeons. The third, a network community approach, linked an ASC with a larger group of hospitals held together by naturally occurring physician networks. We compared each method in terms of its ability to capture meaningful and stable affiliations and its administrative simplicity. Although the proximity approach was simplest to implement and produced the most durable alignments, ASC surgeon's loyalty to the assigned hospital was low with this method. The predominant affiliation and network community approaches performed better and nearly equivalently on these metrics, capturing more meaningful affiliations between ASCs and hospitals. However, the latter's alignments were least durable, and it was complex to administer. We describe 3 methods for identifying natural alignments between ASCs and hospitals, each with strengths and weaknesses. These methods will help health system managers identify ASCs with which to partner. Moreover, health services researchers and policy analysts can use them to study broader communities of surgical care.

Engineered plant biomass particles coated with bioactive agents

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

Dooley, James H; Lanning, David N

Plant biomass particles coated with a bioactive agent such as a fertilizer or pesticide, characterized by a length dimension (L) aligned substantially parallel to a grain direction and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. In particular, the L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers, the W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers, and the L.times.Wmore » dimensions define a pair of substantially parallel top and bottom surfaces.« less

Longitudinal Stream Profile Morphology and Patterns of Knickpoint Propagation in the Bighorn Range

NASA Astrophysics Data System (ADS)

Safran, E. B.; Anderson, R. S.; Riihimaki, C. A.; Armstrong, J.

2005-12-01

The northern U. S. Rocky Mountains and the adjacent sedimentary basins are in a transient state of response to regional, Late Cenozoic exhumation. Assembling the history of landscape change there requires interpreting the morphology and genesis of transient landforms such as knickpoints in longitudinal stream profiles. We used concavity and normalized channel steepness indices to quantify the longitudinal profile morphology of >75 streams draining the east side of the Bighorn Range and the adjacent Powder River Basin. Our analyses show that individual units in the range-margin sedimentary cover rock exert a strong influence on longitudinal profile morphology. In the Tongue River and Crazy Woman Creek drainages, more than 50% of the streams examined had knickpoints localized within a resistant, siliceous dolomite. Knickpoints on most streams with drainage areas greater than ~100 km2 at the range front have migrated headward into the gneissic and plutonic core of the range. In the Clear Creek drainage, where the lateral extent of sedimentary cover rock is more restricted than in the adjacent drainages, knickpoints do not align with any particular unit. River profiles in the Powder River Basin beyond 10-20 km from the range front exhibit concavities of ~0.3-0.6 and normalized channel steepness indices of 40-60 (using 0.45 as a reference concavity). All profiles analyzed that extend into the mountain range exhibit at least one reach with exceptionally high (>2) concavity and relatively high (100-600) normalized channel steepness index, highlighting zones of transient adjustment to local base-level drop in the basin. Headwater reaches of range-draining streams exhibit variable but moderate values of concavity (0.15-0.9) and normalized channel steepness index (20-100). The varied morphology of these reaches reflects their passage across a relict surface of low relief but also the effects of glaciation and/or the signature of the narrow summit spine that caps the range.

Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment

PubMed Central

Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L.; Yao, Xuebiao

2015-01-01

The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C–MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression. PMID:26240331

Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment.

PubMed

Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L; Yao, Xuebiao

2015-08-18

The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C-MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression.

Cell Alignment Required in Differentiation of Myxococcus xanthus

NASA Astrophysics Data System (ADS)

Kim, Seung K.; Kaiser, Dale

1990-08-01

During fruiting body morphogenesis of Myxococcus xanthus, cell movement is required for transmission of C-factor, a short range intercellular signaling protein necessary for sporulation and developmental gene expression. Nonmotile cells fail to sporulate and to express C-factor-dependent genes, but both defects were rescued by a simple manipulation of cell position that oriented the cells in aligned, parallel groups. A similar pattern of aligned cells normally results from coordinated recruitment of wild-type cells into multicellular aggregates, which later form mature fruiting bodies. It is proposed that directed cell movement establishes critical contacts between adjacent cells, which are required for efficient intercellular C-factor transmission.

An Analysis of State and Local Alignment of Teacher Evaluation in Maryland

ERIC Educational Resources Information Center

Peterson, Serene N.

2014-01-01

This study explored the components of Maryland's newly-implemented teacher evaluation framework and compared state requirements with evaluations to three local school systems' evaluation procedures. The study sought to investigate the relationship between three evaluation protocols in comparison to the state requirements. Three local school…

Bayesian comparison of protein structures using partial Procrustes distance.

PubMed

Ejlali, Nasim; Faghihi, Mohammad Reza; Sadeghi, Mehdi

2017-09-26

An important topic in bioinformatics is the protein structure alignment. Some statistical methods have been proposed for this problem, but most of them align two protein structures based on the global geometric information without considering the effect of neighbourhood in the structures. In this paper, we provide a Bayesian model to align protein structures, by considering the effect of both local and global geometric information of protein structures. Local geometric information is incorporated to the model through the partial Procrustes distance of small substructures. These substructures are composed of β-carbon atoms from the side chains. Parameters are estimated using a Markov chain Monte Carlo (MCMC) approach. We evaluate the performance of our model through some simulation studies. Furthermore, we apply our model to a real dataset and assess the accuracy and convergence rate. Results show that our model is much more efficient than previous approaches.

The place of the Local Group in the cosmic web

NASA Astrophysics Data System (ADS)

Forero-Romero, Jaime E.; González, Roberto

2016-10-01

We use the Bolshoi Simulation to find the most probable location of the Local Group (LG) in the cosmic web. Our LG simulacra are pairs of halos with isolation and kinematic properties consistent with observations. The cosmic web is defined using a tidal tensor approach. We find that the LG's preferred location is regions with a dark matter overdensity close to the cosmic average. This makes filaments and sheets the preferred environment. We also find a strong alignment between the LG and the cosmic web. The orbital angular momentum is preferentially perpendicular to the smallest tidal eigenvector, while the vector connecting the two halos is strongly aligned along the the smallest tidal eigenvector and perpendicular to the largest tidal eigenvector; the pair lies and moves along filaments and sheets. We do not find any evidence for an alignment between the spin of each halo in the pair and the cosmic web.

Initial Alignment for SINS Based on Pseudo-Earth Frame in Polar Regions.

PubMed

Gao, Yanbin; Liu, Meng; Li, Guangchun; Guang, Xingxing

2017-06-16

An accurate initial alignment must be required for inertial navigation system (INS). The performance of initial alignment directly affects the following navigation accuracy. However, the rapid convergence of meridians and the small horizontalcomponent of rotation of Earth make the traditional alignment methods ineffective in polar regions. In this paper, from the perspective of global inertial navigation, a novel alignment algorithm based on pseudo-Earth frame and backward process is proposed to implement the initial alignment in polar regions. Considering that an accurate coarse alignment of azimuth is difficult to obtain in polar regions, the dynamic error modeling with large azimuth misalignment angle is designed. At the end of alignment phase, the strapdown attitude matrix relative to local geographic frame is obtained without influence of position errors and cumbersome computation. As a result, it would be more convenient to access the following polar navigation system. Then, it is also expected to unify the polar alignment algorithm as much as possible, thereby further unifying the form of external reference information. Finally, semi-physical static simulation and in-motion tests with large azimuth misalignment angle assisted by unscented Kalman filter (UKF) validate the effectiveness of the proposed method.

Modeling of Field-Aligned Guided Echoes in the Plasmasphere

NASA Technical Reports Server (NTRS)

Fung, Shing F.; Green, James L.

2004-01-01

The conditions under which high frequency (f>>f(sub uh)) long-range extraordinary-mode discrete field-aligned echoes observed by the Radio Plasma Imager (RPI) on board the Imager for Magnetopause-to-Aurora Global Exploration (IMAGE) satellite in the plasmasphere are investigated by ray tracing modeling. Field-aligned discrete echoes are most commonly observed by RPI in the plasmasphere although they are also observed over the polar cap region. The plasmasphere field-aligned echoes appearing as multiple echo traces at different virtual ranges are attributed to signals reflected successively between conjugate hemispheres that propagate along or nearly along closed geomagnetic field lines. The ray tracing simulations show that field-aligned ducts with as little as 1% density perturbations (depletions) and less than 10 wavelengths wide can guide nearly field-aligned propagating high frequency X mode waves. Effective guidance of wave at a given frequency and wave normal angle (Psi) depends on the cross-field density scale of the duct, such that ducts with stronger density depletions need to be wider in order to maintain the same gradient of refractive index across the magnetic field. While signal guidance by field aligned density gradient without ducting is possible only over the polar region, conjugate field-aligned echoes that have traversed through the equatorial region are most likely guided by ducting.

Automatic frequency and phase alignment of in vivo J-difference-edited MR spectra by frequency domain correlation.

PubMed

Wiegers, Evita C; Philips, Bart W J; Heerschap, Arend; van der Graaf, Marinette

2017-12-01

J-difference editing is often used to select resonances of compounds with coupled spins in 1 H-MR spectra. Accurate phase and frequency alignment prior to subtracting J-difference-edited MR spectra is important to avoid artefactual contributions to the edited resonance. In-vivo J-difference-edited MR spectra were aligned by maximizing the normalized scalar product between two spectra (i.e., the correlation over a spectral region). The performance of our correlation method was compared with alignment by spectral registration and by alignment of the highest point in two spectra. The correlation method was tested at different SNR levels and for a broad range of phase and frequency shifts. In-vivo application of the proposed correlation method showed reduced subtraction errors and increased fit reliability in difference spectra as compared with conventional peak alignment. The correlation method and the spectral registration method generally performed equally well. However, better alignment using the correlation method was obtained for spectra with a low SNR (down to ~2) and for relatively large frequency shifts. Our correlation method for simultaneously phase and frequency alignment is able to correct both small and large phase and frequency drifts and also performs well at low SNR levels.

Field-Induced Alignment of Polar Bent-Ccore Smectic A Liquid Crystals

NASA Astrophysics Data System (ADS)

Shen, Yongqiang; Goodhew, Lisa; Shao, Renfan; Maclennan, Joseph; Clark, Noel; Rudquist, Per

2014-03-01

The SmAPF phase is a promising phase modulator mode. To use the SmAPF materials for applications, we need to obtain uniform, large-area alignment of the samples. However, bent-core liquid crystals are notoriously difficult to align with conventional surface treatment methods because most of them have no nematic phase. We have developed a powerful, new method using in-plane applied electric fields that allows us to create a perfect bookshelf alignment of orthogonal bent-core smectics. By using an interdigitated, finger-like electrode arrangement on one of the cell surfaces, we can align the materials by applying in-plane electric fields. This stripe geometry, which produces curved field lines, allows for only one smectic layer orientation, normal both to the cell walls and to the finger electrodes. After alignment, the cell can be operated in the conventional way by connecting the finger electrodes together to make one effective electrode, opposing continuous, common electrode on the opposite side of the cell. This alignment method opens up the use of these materials in perfectly aligned cells for both amplitude and phase-only modulation applications. This work was supported by NSF MRSEC Grant No. DMR-0820579, by NSF Grant No. DMR-1008300, and by Swedish Research Council (VR) Grant No. 621-2009-3621.

Accelerated probabilistic inference of RNA structure evolution

PubMed Central

Holmes, Ian

2005-01-01

Background Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage. The same problem is faced by other RNA alignment-and-folding algorithms based on Sankoff's 1985 algorithm. It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered. Results We demonstrate how flexible classes of constraint can be imposed, greatly reducing the computational costs while maintaining a high quality of structural homology prediction. Any score-attributed context-free grammar (e.g. energy-based scoring schemes, or conditionally normalized Pair SCFGs) is amenable to this treatment. It is now possible to combine independent structural and alignment constraints of unprecedented general flexibility in Pair SCFG alignment algorithms. We outline several applications to the bioinformatics of RNA sequence and structure, including Waterman-Eggert N-best alignments and progressive multiple alignment. We evaluate the performance of the algorithm on test examples from the RFAM database. Conclusion A program, Stemloc, that implements these algorithms for efficient RNA sequence alignment and structure prediction is available under the GNU General Public License. PMID:15790387

The dynamic nature of alignment and variations in normal knees.

PubMed

Deep, K; Eachempati, K K; Apsingi, S

2015-04-01

The restoration of knee alignment is an important goal during total knee arthroplasty (TKA). In the past surgeons aimed to restore neutral limb alignment during surgery. However, previous studies have demonstrated alignment to be dynamic, varying depending on the position of the limb and the degree of weight-bearing, and between patients. We used a validated computer navigation system to measure the femorotibial mechanical angle (FTMA) in 264 knees in 77 male and 55 female healthy volunteers aged 18 to 35 years (mean 26.2). We found the mean supine alignment to be a varus angle of 1.2° (standard deviation (sd) 4), with few patients having neutral alignment. FTMA differs significantly between males and females (with a mean varus of 1.7° (sd 4) and 0.4° (sd 3.9), respectively; p = 0.008). It changes significantly with posture, the knee hyperextending by a mean of 5.6°, and coronal plane alignment becoming more varus by 2.2° (sd 3.6) on standing compared with supine. Knee alignment is different in different individuals and is dynamic in nature, changing with different postures. This may have implications for the assessment of alignment in TKA, which is achieved in non-weight-bearing conditions and which may not represent the situation observed during weight-bearing. ©2015 The British Editorial Society of Bone & Joint Surgery.

The northwest trending north Boquerón Bay-Punta Montalva Fault Zone; A through going active fault system in southwestern Puerto Rico

USGS Publications Warehouse

Roig‐Silva, Coral Marie; Asencio, Eugenio; Joyce, James

2013-01-01

The North Boquerón Bay–Punta Montalva fault zone has been mapped crossing the Lajas Valley in southwest Puerto Rico. Identification of the fault was based upon detailed analysis of geophysical data, satellite images, and field mapping. The fault zone consists of a series of Cretaceous bedrock faults that reactivated and deformed Miocene limestone and Quaternary alluvial fan sediments. The fault zone is seismically active (local magnitude greater than 5.0) with numerous locally felt earthquakes. Focal mechanism solutions suggest strain partitioning with predominantly east–west left-lateral displacements with small normal faults striking mostly toward the northeast. Northeast-trending fractures and normal faults can be found in intermittent streams that cut through the Quaternary alluvial fan deposits along the southern margin of the Lajas Valley, an east–west-trending 30-km-long fault-controlled depression. Areas of preferred erosion within the alluvial fan trend toward the west-northwest parallel to the onland projection of the North Boquerón Bay fault. The North Boquerón Bay fault aligns with the Punta Montalva fault southeast of the Lajas Valley. Both faults show strong southward tilting of Miocene strata. On the western end, the Northern Boquerón Bay fault is covered with flat-lying Holocene sediments, whereas at the southern end the Punta Montalva fault shows left-lateral displacement of stream drainage on the order of a few hundred meters.

Interfraction Displacement of Primary Tumor and Involved Lymph Nodes Relative to Anatomic Landmarks in Image Guided Radiation Therapy of Locally Advanced Lung Cancer

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

Jan, Nuzhat; Balik, Salim; Hugo, Geoffrey D.

Purpose: To analyze primary tumor (PT) and lymph node (LN) position changes relative to each other and relative to anatomic landmarks during conventionally fractionated radiation therapy for patients with locally advanced lung cancer. Methods and Materials: In 12 patients with locally advanced non-small cell lung cancer PT, LN, carina, and 1 thoracic vertebra were manually contoured on weekly 4-dimensional fan-beam CT scans. Systematic and random interfraction displacements of all contoured structures were identified in the 3 cardinal directions, and resulting setup margins were calculated. Time trends and the effect of volume changes on displacements were analyzed. Results: Three-dimensional displacement vectorsmore » and systematic/random interfraction displacements were smaller for carina than for vertebra both for PT and LN. For PT, mean (SD) 3-dimensional displacement vectors with carina-based alignment were 7 (4) mm versus 9 (5) mm with bony anatomy (P<.0001). For LN, smaller displacements were found with carina- (5 [3] mm, P<.0001) and vertebra-based (6 [3] mm, P=.002) alignment compared with using PT for setup (8 [5] mm). Primary tumor and LN displacements relative to bone and carina were independent (P>.05). Displacements between PT and bone (P=.04) and between PT and LN (P=.01) were significantly correlated with PT volume regression. Displacements between LN and carina were correlated with LN volume change (P=.03). Conclusions: Carina-based setup results in a more reproducible PT and LN alignment than bony anatomy setup. Considering the independence of PT and LN displacement and the impact of volume regression on displacements over time, repeated CT imaging even with PT-based alignment is recommended in locally advanced disease.« less

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

PubMed

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both single and multi-domain comparisons. The CAB-align software is freely available to academic users as stand-alone software at http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Publications.html.

Physician-Hospital Alignment in Orthopedic Surgery.

PubMed

Bushnell, Brandon D

2015-09-01

The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. Copyright 2015, SLACK Incorporated.

Development of Sound Localization Strategies in Children with Bilateral Cochlear Implants

PubMed Central

Zheng, Yi; Godar, Shelly P.; Litovsky, Ruth Y.

2015-01-01

Localizing sounds in our environment is one of the fundamental perceptual abilities that enable humans to communicate, and to remain safe. Because the acoustic cues necessary for computing source locations consist of differences between the two ears in signal intensity and arrival time, sound localization is fairly poor when a single ear is available. In adults who become deaf and are fitted with cochlear implants (CIs) sound localization is known to improve when bilateral CIs (BiCIs) are used compared to when a single CI is used. The aim of the present study was to investigate the emergence of spatial hearing sensitivity in children who use BiCIs, with a particular focus on the development of behavioral localization patterns when stimuli are presented in free-field horizontal acoustic space. A new analysis was implemented to quantify patterns observed in children for mapping acoustic space to a spatially relevant perceptual representation. Children with normal hearing were found to distribute their responses in a manner that demonstrated high spatial sensitivity. In contrast, children with BiCIs tended to classify sound source locations to the left and right; with increased bilateral hearing experience, they developed a perceptual map of space that was better aligned with the acoustic space. The results indicate experience-dependent refinement of spatial hearing skills in children with CIs. Localization strategies appear to undergo transitions from sound source categorization strategies to more fine-grained location identification strategies. This may provide evidence for neural plasticity, with implications for training of spatial hearing ability in CI users. PMID:26288142

Development of Sound Localization Strategies in Children with Bilateral Cochlear Implants.

PubMed

Zheng, Yi; Godar, Shelly P; Litovsky, Ruth Y

2015-01-01

Localizing sounds in our environment is one of the fundamental perceptual abilities that enable humans to communicate, and to remain safe. Because the acoustic cues necessary for computing source locations consist of differences between the two ears in signal intensity and arrival time, sound localization is fairly poor when a single ear is available. In adults who become deaf and are fitted with cochlear implants (CIs) sound localization is known to improve when bilateral CIs (BiCIs) are used compared to when a single CI is used. The aim of the present study was to investigate the emergence of spatial hearing sensitivity in children who use BiCIs, with a particular focus on the development of behavioral localization patterns when stimuli are presented in free-field horizontal acoustic space. A new analysis was implemented to quantify patterns observed in children for mapping acoustic space to a spatially relevant perceptual representation. Children with normal hearing were found to distribute their responses in a manner that demonstrated high spatial sensitivity. In contrast, children with BiCIs tended to classify sound source locations to the left and right; with increased bilateral hearing experience, they developed a perceptual map of space that was better aligned with the acoustic space. The results indicate experience-dependent refinement of spatial hearing skills in children with CIs. Localization strategies appear to undergo transitions from sound source categorization strategies to more fine-grained location identification strategies. This may provide evidence for neural plasticity, with implications for training of spatial hearing ability in CI users.

A mean-field theory for self-propelled particles interacting by velocity alignment mechanisms

NASA Astrophysics Data System (ADS)

Peruani, F.; Deutsch, A.; Bär, M.

2008-04-01

A mean-field approach (MFA) is proposed for the analysis of orientational order in a two-dimensional system of stochastic self-propelled particles interacting by local velocity alignment mechanism. The treatment is applied to the cases of ferromagnetic (F) and liquid-crystal (LC) alignment. In both cases, MFA yields a second order phase transition for a critical noise strength and a scaling exponent of 1/2 for the respective order parameters. We find that the critical noise amplitude ηc at which orientational order emerges in the LC case is smaller than in the F-alignment case, i.e. ηLC C<ηF C. A comparison with simulations of individual-based models with F- resp. LC-alignment shows that the predictions about the critical behavior and the qualitative relation between the respective critical noise amplitudes are correct.

Hole localization, water dissociation mechanisms, and band alignment at aqueous-titania interfaces

NASA Astrophysics Data System (ADS)

Lyons, John L.

Photocatalytic water splitting is a promising method for generating clean energy, but materials that can efficiently act as photocatalysts are scarce. This is in part due to the fact that exposure to water can strongly alter semiconductor surfaces and therefore photocatalyst performance. Many materials are not stable in aqueous environments; in other cases, local changes in structure may occur, affecting energy-level alignment. Even in the simplest case, dynamic fluctuations modify the organization of interface water. Accounting for such effects requires knowledge of the dominant local structural motifs and also accurate semiconductor band-edge positions, making quantitative prediction of energy-level alignments computationally challenging. Here we employ a combined theoretical approach to study the structure, energy alignment, and hole localization at aqueous-titania interfaces. We calculate the explicit aqueous-semiconductor interface using ab initio molecular dynamics, which provides the fluctuating atomic structure, the extent of water dissociation, and the resulting electrostatic potential. For both anatase and rutile TiO2 we observe spontaneous water dissociation and re-association events that occur via distinct mechanisms. We also find a higher-density water layer occurring on anatase. In both cases, we find that the second monolayer of water plays a crucial role in controlling the extent of water dissociation. Using hybrid functional calculations, we then investigate the propensity for dissociated waters to stabilize photo-excited carriers, and compare the results of rutile and anatase aqueous interfaces. Finally, we use the GW approach from many-body perturbation theory to obtain the position of semiconductor band edges relative to the occupied 1b1 level and thus the redox levels of water, and examine how local structural modifications affect these offsets. This work was performed in collaboration with N. Kharche, M. Z. Ertem, J. T. Muckerman, and M. S. Hybertsen. It made use of resources at the Center for Functional Nanomaterials, which is a U.S. DOE Office of Science Facility, at Brookhaven National Lab.

Differences in pediatric vertical ground reaction force between planovalgus and neutrally aligned feet.

PubMed

Pauk, Jolanta; Szymul, Joanna

2014-01-01

Ground reaction forces (GRF) reflect the force history of human body contact with the ground. The purpose of this study was to explore human gait abnormalities due to planovalgus by comparing vertical GRF data between individuals with planovalgus and those with neutrally aligned feet. Second we estimated associations between various measurements and vertical GRF parameters in a pediatric population. Boys and girls between the ages of 4 and 18 years (72 planovalgus feet and 74 neutrally aligned feet) took part in this study. Ground reaction forces were recorded by two Kistler platforms and normalized to body weight. Comparison of vertical GRF between planovalgus and neutrally aligned feet suggests that the first and the second peaks of vertical force (Fz1, Fz2) are most affected by planovalgus. The results also indicate that neutrally aligned feet display a different ground reaction force pattern than planovalgus, and that differences between boys and girls may be observed. The shape of the vertical GRF curve can help in clinical interpretation of abnormal gait.

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.

PubMed

Fostier, Jan; Proost, Sebastian; Dhoedt, Bart; Saeys, Yvan; Demeester, Piet; Van de Peer, Yves; Vandepoele, Klaas

2011-03-15

Many comparative genomics studies rely on the correct identification of homologous genomic regions using accurate alignment tools. In such case, the alphabet of the input sequences consists of complete genes, rather than nucleotides or amino acids. As optimal multiple sequence alignment is computationally impractical, a progressive alignment strategy is often employed. However, such an approach is susceptible to the propagation of alignment errors in early pairwise alignment steps, especially when dealing with strongly diverged genomic regions. In this article, we present a novel accurate and efficient greedy, graph-based algorithm for the alignment of multiple homologous genomic segments, represented as ordered gene lists. Based on provable properties of the graph structure, several heuristics are developed to resolve local alignment conflicts that occur due to gene duplication and/or rearrangement events on the different genomic segments. The performance of the algorithm is assessed by comparing the alignment results of homologous genomic segments in Arabidopsis thaliana to those obtained by using both a progressive alignment method and an earlier graph-based implementation. Especially for datasets that contain strongly diverged segments, the proposed method achieves a substantially higher alignment accuracy, and proves to be sufficiently fast for large datasets including a few dozens of eukaryotic genomes. http://bioinformatics.psb.ugent.be/software. The algorithm is implemented as a part of the i-ADHoRe 3.0 package.

Prostate lesion detection and localization based on locality alignment discriminant analysis

NASA Astrophysics Data System (ADS)

Lin, Mingquan; Chen, Weifu; Zhao, Mingbo; Gibson, Eli; Bastian-Jordan, Matthew; Cool, Derek W.; Kassam, Zahra; Chow, Tommy W. S.; Ward, Aaron; Chiu, Bernard

2017-03-01

Prostatic adenocarcinoma is one of the most commonly occurring cancers among men in the world, and it also the most curable cancer when it is detected early. Multiparametric MRI (mpMRI) combines anatomic and functional prostate imaging techniques, which have been shown to produce high sensitivity and specificity in cancer localization, which is important in planning biopsies and focal therapies. However, in previous investigations, lesion localization was achieved mainly by manual segmentation, which is time-consuming and prone to observer variability. Here, we developed an algorithm based on locality alignment discriminant analysis (LADA) technique, which can be considered as a version of linear discriminant analysis (LDA) localized to patches in the feature space. Sensitivity, specificity and accuracy generated by the proposed algorithm in five prostates by LADA were 52.2%, 89.1% and 85.1% respectively, compared to 31.3%, 85.3% and 80.9% generated by LDA. The delineation accuracy attainable by this tool has a potential in increasing the cancer detection rate in biopsies and in minimizing collateral damage of surrounding tissues in focal therapies.

Study of the May 2016 Seismic Swarm at Guadalajara, Jalisco, Mexico.

NASA Astrophysics Data System (ADS)

Nuñez-Cornu, F. J.; Reginfo, W.; Escalona-Alcazar, F. D. J.; Gutierrez Pena, Q. J.; Trejo-Gomez, E.; Suarez-Plascencia, C.; Nunez, D.

2017-12-01

The Metropolitan Zone of Guadalajara (MZG) is the second city of Mexico. This is a region with a high seismic hazard because there are historical reports of both large earthquakes and local seismic swarms. For this reason, it is important to evaluate and identify seismogenic structures that exist in the area. In order to assess the seismic hazard that this structures can represent both the population of the MZG and the facilities of the Geothermal Plant at Cerritos Colorados in La Primavera. In December of 2015 and in May of 2016 two seismic swarms occurred that affected the MZG. The May 2016 swarm was recorded by all stations of the Jalisco Telemetric Seismic and Accelerometric Network (RESAJ), preliminary locations estimated by the Antelope automatic system show an alignment of the earthquakes with an N-S trend west of the ZMG. The earthquakes were relocated, for which the phases were read and the Hypo71 program and a regional velocities model was used. The results allow us to observe two N-S alignments to the west of the MZG, the westernmost of which crosses La Caldera de la Primavera. The focal mechanisms of the earthquakes were calculated using the MecFor program with the Hypo71 outputs as input data. Most of the obtained mechanisms are mechanisms of normal fault with direction parallel to the alignments, suggesting the existence of two active faults that define a graben (graben of Zapopan). The lengths of these faults are 16 and 28 km indicating that they could generate earthquakes with magnitude 6.2 and 6.5, these earthquakes could cause great destruction in the MZG.

A fast alignment method for breast MRI follow-up studies using automated breast segmentation and current-prior registration

NASA Astrophysics Data System (ADS)

Wang, Lei; Strehlow, Jan; Rühaak, Jan; Weiler, Florian; Diez, Yago; Gubern-Merida, Albert; Diekmann, Susanne; Laue, Hendrik; Hahn, Horst K.

2015-03-01

In breast cancer screening for high-risk women, follow-up magnetic resonance images (MRI) are acquired with a time interval ranging from several months up to a few years. Prior MRI studies may provide additional clinical value when examining the current one and thus have the potential to increase sensitivity and specificity of screening. To build a spatial correlation between suspicious findings in both current and prior studies, a reliable alignment method between follow-up studies is desirable. However, long time interval, different scanners and imaging protocols, and varying breast compression can result in a large deformation, which challenges the registration process. In this work, we present a fast and robust spatial alignment framework, which combines automated breast segmentation and current-prior registration techniques in a multi-level fashion. First, fully automatic breast segmentation is applied to extract the breast masks that are used to obtain an initial affine transform. Then, a non-rigid registration algorithm using normalized gradient fields as similarity measure together with curvature regularization is applied. A total of 29 subjects and 58 breast MR images were collected for performance assessment. To evaluate the global registration accuracy, the volume overlap and boundary surface distance metrics are calculated, resulting in an average Dice Similarity Coefficient (DSC) of 0.96 and root mean square distance (RMSD) of 1.64 mm. In addition, to measure local registration accuracy, for each subject a radiologist annotated 10 pairs of markers in the current and prior studies representing corresponding anatomical locations. The average distance error of marker pairs dropped from 67.37 mm to 10.86 mm after applying registration.

Design of New Muzzle for 80mm Diamter Single-Stage Gas Gun

NASA Astrophysics Data System (ADS)

Russell, R. T.; Starks, K. S.; Grote, D. L., II; Vandersall, K. S.; Zhou, M.; Thadhani, N. N.

1999-06-01

In this paper, we describe the design of a new muzzle for the Georgia Institute of Technology's 80mm diameter single-stage gas gun. The muzzle is designed to accommodate both normal and inclined impact experiments. Modular target-holding assemblies are mounted on a hardened tool steel annular plate 3 inches in thickness and 15 inches in diameter. This plate is threaded on to the gun barrel and locked into place by an anti-backlash assembly to prevent loss of alignment. The target mount for normal impact experiments consists of two 4.5 inch diameter semi-cylindrical ring sections with surfaces lapped perpendicular to the major bore axis. The inclined target mount includes a pair of concentric cylinder sections with an inner diameter of 8 inches. Tilt adjustment is achieved around two mutually perpendicular and intersecting axis of rotation, as in a gimbals assembly. Coarse alignment allows for angles between -10 and +30 degrees. Fine alignment is achieved using 3/8 inch machine screws with 40 threads per inch. This mechanism yields a precision of 0.025 inches per revolution, the same precision found in a micrometer. The linear distance between the adjustment mechanisms and the axes of rotation geometrically enhances fine alignment. Velocity measurement assemblies using shear pins, time of arrival pins, and laser/photo-diode circuits are designed as bolt-on modules.

Influence of packing density and surface roughness of vertically-aligned carbon nanotubes on adhesive properties of gecko-inspired mimetics.

PubMed

Chen, Bingan; Zhong, Guofang; Oppenheimer, Pola Goldberg; Zhang, Can; Tornatzky, Hans; Esconjauregui, Santiago; Hofmann, Stephan; Robertson, John

2015-02-18

We have systematically studied the macroscopic adhesive properties of vertically aligned nanotube arrays with various packing density and roughness. Using a tensile setup in shear and normal adhesion, we find that there exists a maximum packing density for nanotube arrays to have adhesive properties. Too highly packed tubes do not offer intertube space for tube bending and side-wall contact to surfaces, thus exhibiting no adhesive properties. Likewise, we also show that the surface roughness of the arrays strongly influences the adhesion properties and the reusability of the tubes. Increasing the surface roughness of the array strengthens the adhesion in the normal direction, but weakens it in the shear direction. Altogether, these results allow progress toward mimicking the gecko's vertical mobility.

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

PubMed

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

2011-04-01

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

Career Pathways: Aligning Public Resources to Support Individual and Regional Economic Advancement in the Knowledge Economy

ERIC Educational Resources Information Center

Jenkins, Davis

2006-01-01

This paper describes career pathways, a framework or approach by which regions can better align publicly supported systems and programs to build a knowledge-economy workforce customized to the needs of local labor markets. A career pathway is a series of connected education and training programs and support services that enable individuals to…

Robust face alignment under occlusion via regional predictive power estimation.

PubMed

Heng Yang; Xuming He; Xuhui Jia; Patras, Ioannis

2015-08-01

Face alignment has been well studied in recent years, however, when a face alignment model is applied on facial images with heavy partial occlusion, the performance deteriorates significantly. In this paper, instead of training an occlusion-aware model with visibility annotation, we address this issue via a model adaptation scheme that uses the result of a local regression forest (RF) voting method. In the proposed scheme, the consistency of the votes of the local RF in each of several oversegmented regions is used to determine the reliability of predicting the location of the facial landmarks. The latter is what we call regional predictive power (RPP). Subsequently, we adapt a holistic voting method (cascaded pose regression based on random ferns) by putting weights on the votes of each fern according to the RPP of the regions used in the fern tests. The proposed method shows superior performance over existing face alignment models in the most challenging data sets (COFW and 300-W). Moreover, it can also estimate with high accuracy (72.4% overlap ratio) which image areas belong to the face or nonface objects, on the heavily occluded images of the COFW data set, without explicit occlusion modeling.

Tweaked residual convolutional network for face alignment

NASA Astrophysics Data System (ADS)

Du, Wenchao; Li, Ke; Zhao, Qijun; Zhang, Yi; Chen, Hu

2017-08-01

We propose a novel Tweaked Residual Convolutional Network approach for face alignment with two-level convolutional networks architecture. Specifically, the first-level Tweaked Convolutional Network (TCN) module predicts the landmark quickly but accurately enough as a preliminary, by taking low-resolution version of the detected face holistically as the input. The following Residual Convolutional Networks (RCN) module progressively refines the landmark by taking as input the local patch extracted around the predicted landmark, particularly, which allows the Convolutional Neural Network (CNN) to extract local shape-indexed features to fine tune landmark position. Extensive evaluations show that the proposed Tweaked Residual Convolutional Network approach outperforms existing methods.

Feature-based Alignment of Volumetric Multi-modal Images

PubMed Central

Toews, Matthew; Zöllei, Lilla; Wells, William M.

2014-01-01

This paper proposes a method for aligning image volumes acquired from different imaging modalities (e.g. MR, CT) based on 3D scale-invariant image features. A novel method for encoding invariant feature geometry and appearance is developed, based on the assumption of locally linear intensity relationships, providing a solution to poor repeatability of feature detection in different image modalities. The encoding method is incorporated into a probabilistic feature-based model for multi-modal image alignment. The model parameters are estimated via a group-wise alignment algorithm, that iteratively alternates between estimating a feature-based model from feature data, then realigning feature data to the model, converging to a stable alignment solution with few pre-processing or pre-alignment requirements. The resulting model can be used to align multi-modal image data with the benefits of invariant feature correspondence: globally optimal solutions, high efficiency and low memory usage. The method is tested on the difficult RIRE data set of CT, T1, T2, PD and MP-RAGE brain images of subjects exhibiting significant inter-subject variability due to pathology. PMID:24683955

Exact calculation of distributions on integers, with application to sequence alignment.

PubMed

Newberg, Lee A; Lawrence, Charles E

2009-01-01

Computational biology is replete with high-dimensional discrete prediction and inference problems. Dynamic programming recursions can be applied to several of the most important of these, including sequence alignment, RNA secondary-structure prediction, phylogenetic inference, and motif finding. In these problems, attention is frequently focused on some scalar quantity of interest, a score, such as an alignment score or the free energy of an RNA secondary structure. In many cases, score is naturally defined on integers, such as a count of the number of pairing differences between two sequence alignments, or else an integer score has been adopted for computational reasons, such as in the test of significance of motif scores. The probability distribution of the score under an appropriate probabilistic model is of interest, such as in tests of significance of motif scores, or in calculation of Bayesian confidence limits around an alignment. Here we present three algorithms for calculating the exact distribution of a score of this type; then, in the context of pairwise local sequence alignments, we apply the approach so as to find the alignment score distribution and Bayesian confidence limits.

The Influence Of Component Alignment On The Life Of Total Knee Prostheses

NASA Astrophysics Data System (ADS)

Bugariu, Delia; Bereteu, Liviu

2012-12-01

An arthritic knee affects the patient's life by causing pain and limiting movement. If the cartilage and the bone surfaces are severely affected, the natural joint is replaced with an artificial joint. The procedure is called total knee arthroplasty (TKA). Lately, the numbers of implanted total knee prostheses grow steadily. An important factor in TKA is the perfect alignment of the total knee prosthesis (TKP) components. Component misalignment can lead to the prosthesis loss by producing wear particles. The paper proposes a study on mechanical behaviors of a TKP based on numerical analysis, using ANSYS software. The numerical analysis is based on both the normal and the changed angle of the components alignment.

Genome alignment with graph data structures: a comparison

PubMed Central

2014-01-01

Background Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference. Graphs have proven to be a powerful tool for coping with the complexity of genome-scale sequence alignments. The potential of graphs to intuitively represent all aspects of genome alignments led to the development of graph-based approaches for genome alignment. These approaches construct a graph from a set of local alignments, and derive a genome alignment through identification and removal of graph substructures that indicate errors in the alignment. Results We compare the structures of commonly used graphs in terms of their abilities to represent alignment information. We describe how the graphs can be transformed into each other, and identify and classify graph substructures common to one or more graphs. Based on previous approaches, we compile a list of modifications that remove these substructures. Conclusion We show that crucial pieces of alignment information, associated with inversions and duplications, are not visible in the structure of all graphs. If we neglect vertex or edge labels, the graphs differ in their information content. Still, many ideas are shared among all graph-based approaches. Based on these findings, we outline a conceptual framework for graph-based genome alignment that can assist in the development of future genome alignment tools. PMID:24712884

Versatile alignment layer method for new types of liquid crystal photonic devices

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

Finnemeyer, V.; Bryant, D.; Lu, L.

2015-07-21

Liquid crystal photonic devices are becoming increasingly popular. These devices often present a challenge when it comes to creating a robust alignment layer in pre-assembled cells. In this paper, we describe a method of infusing a dye into a microcavity to produce an effective photo-definable alignment layer. However, previous research on such alignment layers has shown that they have limited stability, particularly against subsequent light exposure. As such, we further describe a method of utilizing a pre-polymer, infused into the microcavity along with the liquid crystal, to provide photostability. We demonstrate that the polymer layer, formed under ultraviolet irradiation ofmore » liquid crystal cells, has been effectively localized to a thin region near the substrate surface and provides a significant improvement in the photostability of the liquid crystal alignment. This versatile alignment layer method, capable of being utilized in devices from the described microcavities to displays, offers significant promise for new photonics applications.« less

Unsupervised image matching based on manifold alignment.

PubMed

Pei, Yuru; Huang, Fengchun; Shi, Fuhao; Zha, Hongbin

2012-08-01

This paper challenges the issue of automatic matching between two image sets with similar intrinsic structures and different appearances, especially when there is no prior correspondence. An unsupervised manifold alignment framework is proposed to establish correspondence between data sets by a mapping function in the mutual embedding space. We introduce a local similarity metric based on parameterized distance curves to represent the connection of one point with the rest of the manifold. A small set of valid feature pairs can be found without manual interactions by matching the distance curve of one manifold with the curve cluster of the other manifold. To avoid potential confusions in image matching, we propose an extended affine transformation to solve the nonrigid alignment in the embedding space. The comparatively tight alignments and the structure preservation can be obtained simultaneously. The point pairs with the minimum distance after alignment are viewed as the matchings. We apply manifold alignment to image set matching problems. The correspondence between image sets of different poses, illuminations, and identities can be established effectively by our approach.

The effects of window shape and reticle presence on performance in a vertical alignment task

NASA Technical Reports Server (NTRS)

Rosenberg, Erika L.; Haines, Richard F.; Jordan, Kevin

1989-01-01

This study was conducted to evaluate the effect of selected interior work-station orientational cuing upon the ability to align a target image with local vertical in the frontal plane. Angular error from gravitational vertical in an alignment task was measured for 20 observers viewing through two window shapes (square, round), two initial orientations of a computer-generated space shuttle image, and the presence or absence of a stabilized optical alignment reticle. In terms of overall accuracy, it was found that observer error was significantly smaller for the square window and reticle-present conditions than for the round window and reticle-absent conditions. Response bias data reflected an overall tendency to undershoot and greater variability of response in the round window/no reticle condition. These results suggest that environmental cuing information, such as that provided by square window frames and alignment reticles, may aid in subjective orientation and increase accuracy of response in a Space Station proximity operations alignment task.

Ecology of dark matter haloes - II. Effects of interactions on the alignment of halo pairs

NASA Astrophysics Data System (ADS)

L'Huillier, Benjamin; Park, Changbom; Kim, Juhan

2017-04-01

We use the Horizon Run 4 cosmological N-body simulation to study the effects of distant and close interactions on the alignments of the shapes, spins and orbits of targets haloes with their neighbours, and their dependence on the local density environment and neighbour separation. Interacting targets have a significantly lower spin and higher sphericity and oblateness than all targets. Interacting pairs initially have antiparallel spins, but the spins develop parallel alignment as time goes on. Neighbours tend to evolve in the plane of rotation of the target, and in the direction of the major axis of prolate haloes. Moreover, interactions are preferentially radial, while pairs with non-radial orbits are preferentially prograde. The alignment signals are stronger at high mass and for close separations, and independent of the large-scale density. Positive alignment signals are found at redshifts up to 4, and increase with decreasing redshifts. Moreover, the orbits tend to become prograde at low redshift, while no alignment is found at high redshift (z = 4).

12-GHz thin-film transistors on transferrable silicon nanomembranes for high-performance flexible electronics.

PubMed

Sun, Lei; Qin, Guoxuan; Seo, Jung-Hun; Celler, George K; Zhou, Weidong; Ma, Zhenqiang

2010-11-22

Multigigahertz flexible electronics are attractive and have broad applications. A gate-after-source/drain fabrication process using preselectively doped single-crystal silicon nanomembranes (SiNM) is an effective approach to realizing high device speed. However, further downscaling this approach has become difficult in lithography alignment. In this full paper, a local alignment scheme in combination with more accurate SiNM transfer measures for minimizing alignment errors is reported. By realizing 1 μm channel alignment for the SiNMs on a soft plastic substrate, thin-film transistors with a record speed of 12 GHz maximum oscillation frequency are demonstrated. These results indicate the great potential of properly processed SiNMs for high-performance flexible electronics.

Prostate Bed Motion During Intensity-Modulated Radiotherapy Treatment

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

Klayton, Tracy; Price, Robert; Buyyounouski, Mark K.

Purpose: Conformal radiation therapy in the postprostatectomy setting requires accurate setup and localization of the prostatic fossa. In this series, we report prostate bed localization and motion characteristics, using data collected from implanted radiofrequency transponders. Methods and Materials: The Calypso four-dimensional localization system uses three implanted radiofrequency transponders for daily target localization and real-time tracking throughout a course of radiation therapy. We reviewed the localization and tracking reports for 20 patients who received ultrasonography-guided placement of Calypso transponders within the prostate bed prior to a course of intensity-modulated radiation therapy at Fox Chase Cancer Center. Results: At localization, prostate bedmore » displacement relative to bony anatomy exceeded 5 mm in 9% of fractions in the anterior-posterior (A-P) direction and 21% of fractions in the superior-inferior (S-I) direction. The three-dimensional vector length from skin marks to Calypso alignment exceeded 1 cm in 24% of all 652 fractions with available setup data. During treatment, the target exceeded the 5-mm tracking limit for at least 30 sec in 11% of all fractions, generally in the A-P or S-I direction. In the A-P direction, target motion was twice as likely to move posteriorly, toward the rectum, than anteriorly. Fifteen percent of all treatments were interrupted for repositioning, and 70% of patients were repositioned at least once during their treatment course. Conclusion: Set-up errors and motion of the prostatic fossa during radiotherapy are nontrivial, leading to potential undertreatment of target and excess normal tissue toxicity if not taken into account during treatment planning. Localization and real-time tracking of the prostate bed via implanted Calypso transponders can be used to improve the accuracy of plan delivery.« less

A dual-satellite study of the spatial properties of FTEs. [flux transfer events

NASA Technical Reports Server (NTRS)

Saunders, M. A.; Russell, C. T.; Sckopke, N.

1984-01-01

Reconnection at the earth's dayside magnetopause may manifest itself primarily as a localized and transient process called a flux-transfer event (FTE). The spatial properties of FTEs are investigated directly by examining data from the ISEE satellite pair when the satellites were separated by more than 1000 km in the vicinity of the magnetopause. Examples of magnetosheath and boundary layer FTEs, each having a dimension normal to the magnetopause of order an earth radius, R(E), are shown, and this scale-size result is substantiated statistically for magnetosheath FTEs. When combined with other information, a 1-R(E) normal dimension implies that the voltage associated with the FTE process at one magnetopause location is at least 10 kV. These findings strengthen the view that the magnetic field comprising an FTE is twisted, this twisting appearing to be continuous in sense across the magnetopause and corresponding to a core field-aligned current of magnitude a few hundred kA. Changes in plasma flow speed and direction are found to be associated with FTEs. The transverse field and flow perturbations accompanying the three magnetosheath FTEs studied here satisfy approximately the Walen relation, the relation which describes a propagating Alfven wave.

Influences of the Darrieus-Landau instability on premixed turbulent flames

NASA Astrophysics Data System (ADS)

Patyal, Advitya; Matalon, Moshe

2017-11-01

The propagation of turbulent flames in three-dimensional turbulent flows is studied within the context of the hydrodynamic theory. The flame is treated as a surface of density discontinuity with the flow modified by gas expansion resulting from heat released during combustion. The flame is tracked using a level-set method with a propagation speed that depends on the local flame stretch, modulated by a Markstein length. Impact of the Darrieus-Landau instability on the topology of the flame surface is studied. It is shown that similar to passive interfaces, flames under the influence of the hydrodynamic instability resort to cylindrical structures with increasing turbulence intensity, even in 3D. The mechanism of modification of vortical structures in the burned gas is identified in terms of the alignments between the vorticity vector, flame surface normal and eigenvectors of the strain rate tensor. The results indicate that the strain rate tensor is intricately coupled with the normal to the flame surface and creates anisotropy in the orientation of vortical structures, which begins to weaken as the turbulent intensity increases. Furthermore, vorticity budgets are used to highlight the relative importance of baroclinic torque due to Darrieus-Landau instability.

Global faculty development: lessons learned from the Foundation for Advancement of International Medical Education and Research (FAIMER) initiatives.

PubMed

Burdick, William P

2014-08-01

Foundation for Advancement of International Medical Education and Research (FAIMER) faculty development programs have operated since 2001 and are designed to overcome many of the challenges inherent in global health collaborations, including alignment with local needs, avoiding persistent dependency, and development of trust. FAIMER fellowship programs, developed for midcareer faculty members in all health professions from around the world, share goals of strengthening knowledge and skills in education leadership, education methods, and project management and evaluation. Building community is another explicit goal that allows participants to support and learn from each other.The author recommends several practices for successful international collaborations based on 13 years of experience with FAIMER fellowships. These include using authentic education projects to maintain alignment with local needs and apply newly acquired knowledge and skills, teaching leadership across cultures with careful communication and adaptation of concepts to local environments, cultivating a strong field of health professions education to promote diffusion of ideas and advocate for policy change, intentionally promoting field development and leadership to reduce dependency, giving generously of time and resources, learning from others as much as teaching others, and recognizing that effective partnerships revolve around personal relationships to build trust. These strategies have enabled the FAIMER fellowship programs to stay aligned with local needs, reduce dependency, and maintain trust.

G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

PubMed Central

2016-01-01

Abstract Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G‐LoSA. G‐LoSA aligns protein local structures in a sequence order independent way and provides a GA‐score, a chemical feature‐based and size‐independent structure similarity score. Our benchmark validation shows the robust performance of G‐LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure‐centric comparative biology studies. In particular, G‐LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G‐LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer‐aided drug design. We hope that G‐LoSA can be a useful computational method for exploring interesting biological problems through large‐scale comparison of protein local structures and facilitating drug discovery research and development. G‐LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. PMID:26813336

G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design.

PubMed

Lee, Hui Sun; Im, Wonpil

2016-04-01

Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. © 2016 The Protein Society.

Topographic stress perturbations in southern Davis Mountains, west Texas 1. Polarity reversal of principal stresses

USGS Publications Warehouse

Savage, W.Z.; Morin, R.H.

2002-01-01

We have applied a previously developed analytical stress model to interpret subsurface stress conditions inferred from acoustic televiewer logs obtained in two municipal water wells located in a valley in the southern Davis Mountains near Alpine, Texas. The appearance of stress-induced breakouts with orientations that shift by 90?? at two different depths in one of the wells is explained by results from exact solutions for the effects of valleys on gravity and tectonically induced subsurface stresses. The theoretical results demonstrate that above a reference depth termed the hinge point, a location that is dependent on Poisson's ratio, valley shape, and magnitude of the maximum horizontal tectonic stress normal to the long axis of the valley, horizontal stresses parallel to the valley axis are greater than those normal to it. At depths below this hinge point the situation reverses and horizontal stresses normal to the valley axis are greater than those parallel to it. Application of the theoretical model at Alpine is accommodated by the fact that nearby earthquake focal mechanisms establish an extensional stress regime with the regional maximum horizontal principal stress aligned perpendicular to the valley axis. We conclude that the localized stress field associated with a valley setting can be highly variable and that breakouts need to be examined in this context when estimating the orientations and magnitudes of regional principal stresses.

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

Fairchild, R.G.; Bond, V.P.

The characteristics of dose distribution, beam alignment, and radiobiological advantages accorded to high LET radiation were reviewed and compared for various particle beam radiotherapeutic modalities (neutron, Auger electrons, p, ..pi../sup -/, He, C, Ne, and Ar ions). Merit factors were evaluated on the basis of effective dose to tumor relative to normal tissue, linear energy transfer (LET), and dose localization, at depths of 1, 4, and 10 cm. In general, it was found that neutron capture therapy using an epithermal neutron beam provided the best merit factors available for depths up to 8 cm. The position of fast neutron therapymore » on the Merit Factor Tables was consistently lower than that of other particle modalities, and above only /sup 60/Co. The largest body of clinical data exists for fast neutron therapy; results are considered by some to be encouraging. It then follows that if benefits with fast neutron therapy are real, additional gains are within reach with other modalities.« less

Information-theoretical noninvasive damage detection in bridge structures

NASA Astrophysics Data System (ADS)

Sudu Ambegedara, Amila; Sun, Jie; Janoyan, Kerop; Bollt, Erik

2016-11-01

Damage detection of mechanical structures such as bridges is an important research problem in civil engineering. Using spatially distributed sensor time series data collected from a recent experiment on a local bridge in Upper State New York, we study noninvasive damage detection using information-theoretical methods. Several findings are in order. First, the time series data, which represent accelerations measured at the sensors, more closely follow Laplace distribution than normal distribution, allowing us to develop parameter estimators for various information-theoretic measures such as entropy and mutual information. Second, as damage is introduced by the removal of bolts of the first diaphragm connection, the interaction between spatially nearby sensors as measured by mutual information becomes weaker, suggesting that the bridge is "loosened." Finally, using a proposed optimal mutual information interaction procedure to prune away indirect interactions, we found that the primary direction of interaction or influence aligns with the traffic direction on the bridge even after damaging the bridge.

Enhanced Andreev reflection in gapped graphene

NASA Astrophysics Data System (ADS)

Majidi, Leyla; Zareyan, Malek

2012-08-01

We theoretically demonstrate unusual features of superconducting proximity effect in gapped graphene that presents a pseudospin symmetry-broken ferromagnet with a net pseudomagnetization. We find that the presence of a band gap makes the Andreev conductance of graphene superconductor/pseudoferromagnet (S/PF) junction to behave similar to that of a graphene ferromagnet-superconductor junction. The energy gap ΔN can enhance the pseudospin inverted Andreev conductance of S/PF junction to reach a limiting maximum value for ΔN≫μ, which depending on the bias voltage can be larger than the value for the corresponding junction with no energy gap. We further demonstrate a damped-oscillatory behavior for the local density of states of the PF region of S/PF junction and a long-range crossed Andreev reflection process in PF/S/PF structure with antiparallel alignment of pseudomagnetizations of PFs, which confirm that, in this respect, the gapped normal graphene behaves like a ferromagnetic graphene.

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

Li, Fei; Zhang, Shujun; Yang, Tiannan

The discovery of ultrahigh piezoelectricity in relaxor-ferroelectric solid solution single crystals is a breakthrough in ferroelectric materials. A key signature of relaxor-ferroelectric solid solutions is the existence of polar nanoregions, a nanoscale inhomogeneity, that coexist with normal ferroelectric domains. Despite two decades of extensive studies, the contribution of polar nanoregions to the underlying piezoelectric properties of relaxor ferroelectrics has yet to be established. Here we quantitatively characterize the contribution of polar nanoregions to the dielectric/piezoelectric responses of relaxor-ferroelectric crystals using a combination of cryogenic experiments and phase-field simulations. The contribution of polar nanoregions to the room-temperature dielectric and piezoelectric propertiesmore » is in the range of 50–80%. A mesoscale mechanism is proposed to reveal the origin of the high piezoelectricity in relaxor ferroelectrics, where the polar nanoregions aligned in a ferroelectric matrix can facilitate polarization rotation. This mechanism emphasizes the critical role of local structure on the macroscopic properties of ferroelectric materials.« less

Dual Endotemponade for Extensive Long-standing Cyclodialysis Using Sulcus-fixated Cionni Ring and PCIOL.

PubMed

Gupta, Shikha; Sagar, Pradeep; Gogia, Varun; Khokhar, Sudarshan; Dada, Tanuj

2016-03-01

A young patient presented with visual acuity of hand movements only, unrecordable intraocular pressure, and total cataract after trauma 12 months ago. She reported failure to improve with conservative therapy as well as a direct cycloplexy elsewhere. After cleft localization on preoperative gonioscopy, ultrasound biomicroscopy (UBM), and intraoperative gonioscopy, a partial-thickness scleral flap was fashioned at the site of maximum cleft height. Following phacoaspiration, a multipiece intraocular lens was implanted in the sulcus; its haptics aligned to the axis with maximum height of cyclodialysis. A Cionni ring placed in sulcus was sutured to sclera under the flap to provide additional tamponading effect. Postoperative UBM and gonioscopy confirmed cleft closure. Normalization of intraocular pressure was found on repeated follow-ups till 1 year (12 to 14 mm Hg). UBM showed increase in sulcus diameter, and "double indentation sign" on the ciliary body.

Self-organized sorting limits behavioral variability in swarms

PubMed Central

Copenhagen, Katherine; Quint, David A.; Gopinathan, Ajay

2016-01-01

Swarming is a phenomenon where collective motion arises from simple local interactions between typically identical individuals. Here, we investigate the effects of variability in behavior among the agents in finite swarms with both alignment and cohesive interactions. We show that swarming is abolished above a critical fraction of non-aligners who do not participate in alignment. In certain regimes, however, swarms above the critical threshold can dynamically reorganize and sort out excess non-aligners to maintain the average fraction close to the critical value. This persists even in swarms with a distribution of alignment interactions, suggesting a simple, robust and efficient mechanism that allows heterogeneously mixed populations to naturally regulate their composition and remain in a collective swarming state or even differentiate among behavioral phenotypes. We show that, for evolving swarms, this self-organized sorting behavior can couple to the evolutionary dynamics leading to new evolutionarily stable equilibrium populations set by the physical swarm parameters. PMID:27550316

Magnetic Alignment in Carps: Evidence from the Czech Christmas Fish Market

PubMed Central

Hart, Vlastimil; Kušta, Tomáš; Němec, Pavel; Bláhová, Veronika; Ježek, Miloš; Nováková, Petra; Begall, Sabine; Červený, Jaroslav; Hanzal, Vladimír; Malkemper, Erich Pascal; Štípek, Kamil; Vole, Christiane; Burda, Hynek

2012-01-01

While magnetoreception in birds has been studied intensively, the literature on magnetoreception in bony fish, and particularly in non-migratory fish, is quite scarce. We examined alignment of common carps (Cyprinus carpio) at traditional Christmas sale in the Czech Republic. The sample comprised measurements of the directional bearings in 14,537 individual fish, distributed among 80 large circular plastic tubs, at 25 localities in the Czech Republic, during 817 sampling sessions, on seven subsequent days in December 2011. We found that carps displayed a statistically highly significant spontaneous preference to align their bodies along the North-South axis. In the absence of any other common orientation cues which could explain this directional preference, we attribute the alignment of the fish to the geomagnetic field lines. It is apparent that the display of magnetic alignment is a simple experimental paradigm of great heuristic potential. PMID:23227241

Self-organized sorting limits behavioral variability in swarms

NASA Astrophysics Data System (ADS)

Copenhagen, Katherine; Quint, David A.; Gopinathan, Ajay

2016-08-01

Swarming is a phenomenon where collective motion arises from simple local interactions between typically identical individuals. Here, we investigate the effects of variability in behavior among the agents in finite swarms with both alignment and cohesive interactions. We show that swarming is abolished above a critical fraction of non-aligners who do not participate in alignment. In certain regimes, however, swarms above the critical threshold can dynamically reorganize and sort out excess non-aligners to maintain the average fraction close to the critical value. This persists even in swarms with a distribution of alignment interactions, suggesting a simple, robust and efficient mechanism that allows heterogeneously mixed populations to naturally regulate their composition and remain in a collective swarming state or even differentiate among behavioral phenotypes. We show that, for evolving swarms, this self-organized sorting behavior can couple to the evolutionary dynamics leading to new evolutionarily stable equilibrium populations set by the physical swarm parameters.

Multi-subject Manifold Alignment of Functional Network Structures via Joint Diagonalization.

PubMed

Nenning, Karl-Heinz; Kollndorfer, Kathrin; Schöpf, Veronika; Prayer, Daniela; Langs, Georg

2015-01-01

Functional magnetic resonance imaging group studies rely on the ability to establish correspondence across individuals. This enables location specific comparison of functional brain characteristics. Registration is often based on morphology and does not take variability of functional localization into account. This can lead to a loss of specificity, or confounds when studying diseases. In this paper we propose multi-subject functional registration by manifold alignment via coupled joint diagonalization. The functional network structure of each subject is encoded in a diffusion map, where functional relationships are decoupled from spatial position. Two-step manifold alignment estimates initial correspondences between functionally equivalent regions. Then, coupled joint diagonalization establishes common eigenbases across all individuals, and refines the functional correspondences. We evaluate our approach on fMRI data acquired during a language paradigm. Experiments demonstrate the benefits in matching accuracy achieved by coupled joint diagonalization compared to previously proposed functional alignment approaches, or alignment based on structural correspondences.

Influence of compressibility on the Lagrangian statistics of vorticity-strain-rate interactions.

PubMed

Danish, Mohammad; Sinha, Sawan Suman; Srinivasan, Balaji

2016-07-01

The objective of this study is to investigate the influence of compressibility on Lagrangian statistics of vorticity and strain-rate interactions. The Lagrangian statistics are extracted from "almost" time-continuous data sets of direct numerical simulations of compressible decaying isotropic turbulence by employing a cubic spline-based Lagrangian particle tracker. We study the influence of compressibility on Lagrangian statistics of alignment in terms of compressibility parameters-turbulent Mach number, normalized dilatation-rate, and flow topology. In comparison to incompressible turbulence, we observe that the presence of compressibility in a flow field weakens the alignment tendency of vorticity toward the largest strain-rate eigenvector. Based on the Lagrangian statistics of alignment conditioned on dilatation and topology, we find that the weakened tendency of alignment observed in compressible turbulence is because of a special group of fluid particles that have an initially negligible dilatation-rate and are associated with stable-focus-stretching topology.

Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

PubMed Central

Shih, Arthur Chun-Chieh; Lee, DT; Peng, Chin-Lin; Wu, Yu-Wei

2007-01-01

Background When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the alignments of many sequences. Results A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important, structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation. Conclusion With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL . PMID:17319966

Laboratory simulation of field-aligned currents

NASA Technical Reports Server (NTRS)

Wessel, Frank J.; Rostoker, Norman

1993-01-01

A summary of progress during the period Apr. 1992 to Mar. 1993 is provided. Objectives of the research are (1) to simulate, via laboratory experiments, the three terms of the field-aligned current equation; (2) to simulate auroral-arc formation processes by configuring the boundary conditions of the experimental chamber and plasma parameters to produce highly localized return currents at the end of a field-aligned current system; and (3) to extrapolate these results, using theoretical and computational techniques, to the problem of magnetospheric-ionospheric coupling and to compare them with published literature signatures of auroral-arc phenomena.

Overcoming Sequence Misalignments with Weighted Structural Superposition

PubMed Central

Khazanov, Nickolay A.; Damm-Ganamet, Kelly L.; Quang, Daniel X.; Carlson, Heather A.

2012-01-01

An appropriate structural superposition identifies similarities and differences between homologous proteins that are not evident from sequence alignments alone. We have coupled our Gaussian-weighted RMSD (wRMSD) tool with a sequence aligner and seed extension (SE) algorithm to create a robust technique for overlaying structures and aligning sequences of homologous proteins (HwRMSD). HwRMSD overcomes errors in the initial sequence alignment that would normally propagate into a standard RMSD overlay. SE can generate a corrected sequence alignment from the improved structural superposition obtained by wRMSD. HwRMSD’s robust performance and its superiority over standard RMSD are demonstrated over a range of homologous proteins. Its better overlay results in corrected sequence alignments with good agreement to HOMSTRAD. Finally, HwRMSD is compared to established structural alignment methods: FATCAT, SSM, CE, and Dalilite. Most methods are comparable at placing residue pairs within 2 Å, but HwRMSD places many more residue pairs within 1 Å, providing a clear advantage. Such high accuracy is essential in drug design, where small distances can have a large impact on computational predictions. This level of accuracy is also needed to correct sequence alignments in an automated fashion, especially for omics-scale analysis. HwRMSD can align homologs with low sequence identity and large conformational differences, cases where both sequence-based and structural-based methods may fail. The HwRMSD pipeline overcomes the dependency of structural overlays on initial sequence pairing and removes the need to determine the best sequence-alignment method, substitution matrix, and gap parameters for each unique pair of homologs. PMID:22733542

Inner Core Anisotropy: Can Seismic Observations be Reconciled with Ab Initio Calculations of Elasticity?

NASA Astrophysics Data System (ADS)

Song, X.; Jordan, T. H.

2016-12-01

Body-wave and normal-mode observations have revealed an inner-core structure that is radially layered, axially anisotropic, and hemispherically asymmetric. Previous theoretical studies have examined the consistency of these features with the elasticity of iron crystals thought to dominate inner-core composition, but a fully consistent model has been elusive. Here we compare the seismic observation with effective-medium models derived from ab initio calculations of the elasticity tensors for hcp-Fe and bcc-Fe. Our estimates are based on Jordan's (GJI, 2015) effective medium theory, which is derived from a self-consistent, second-order Born approximation. The theory provides closed-form expressions for the effective elastic parameters of 3D anisotropic, heterogeneous media in which the local anisotropy is a constant hexagonal stiffness tensor C stochastically oriented about a constant symmetry axis \\hat{s} and the statistics of the small-scale heterogeneities are transversely isotropic in the plane perpendicular to \\hat{s}. The stochastic model is then described by a dimensionless "aspect ratio of the heterogeneity", 0 ≤ η < ∞, and a dimensionless "orientation ratio of the anisotropy", 0 ≤ ξ < ∞. The latter determines the degree to which the axis of C is aligned with \\hat{s}. We compute the loci of models with \\hat{s} oriented along the Earth's rotational axis ( \\hat{s} = north) by varying ξ and η for various ab initio estimates of C. We show that a lot of widely used estimates of C are inconsistent with most published normal-mode models of inner-core anisotropy. In particular, if the P-wave fast axis aligns with the rotational axis, which is required to satisfy the body-wave observations, then these hcp-Fe models predict that the fast polarization of the S waves is in the plane perpendicular to \\hat{s}, which disagrees with most normal-mode models. We have attempted to resolve this discrepancy by examining alternative hcp-Fe models, including radially anisotropic distributions of stochastic anisotropy and heterogeneity (i.e., where \\hat{s} = \\hat{r}), as well as bcc-Fe models. Our calculations constrain the form of C needed to satisfy the seismological inferences.

Stress aligned cracks in the upper crust of the Val d'Agri region as revealed by shear wave splitting

NASA Astrophysics Data System (ADS)

Pastori, M.; Piccinini, D.; Margheriti, L.; Improta, L.; Valoroso, L.; Chiaraluce, L.; Chiarabba, C.

2009-10-01

Shear wave splitting is measured at 19 seismic stations of a temporary network deployed in the Val d'Agri area to record low-magnitude seismic activity. The splitting results suggest the presence of an anisotropic layer between the surface and 15 km depth (i.e. above the hypocentres). The dominant fast polarization direction strikes NW-SE parallel to the Apennines orogen and is approximately parallel to the maximum horizontal stress in the region, as well as to major normal faults bordering the Val d'Agri basin. The size of the normalized delay times in the study region is about 0.01 s km-1, suggesting 4.5 percent shear wave velocity anisotropy (SWVA). On the south-western flank of the basin, where most of the seismicity occurs, we found larger values of normalized delay times, between 0.017 and 0.02 s km-1. These high values suggest a 10 percent of SWVA. These parameters agree with an interpretation of seismic anisotropy in terms of the Extensive-Dilatancy Anisotropy (EDA) model that considers the rock volume pervaded by fluid-saturated microcracks aligned by the active stress field. Anisotropic parameters are consistent with borehole image logs from deep exploration wells in the Val d'Agri oil field that detect pervasive fluid saturated microcracks striking NW-SE parallel to the maximum horizontal stress in the carbonatic reservoir. However, we cannot rule out the contribution of aligned macroscopic fractures because the main Quaternary normal faults are parallel to the maximum horizontal stress. The strong anisotropy and the seismicity concentration testify for active deformation along the SW flank of the basin.

Robust through-the-wall radar image classification using a target-model alignment procedure.

PubMed

Smith, Graeme E; Mobasseri, Bijan G

2012-02-01

A through-the-wall radar image (TWRI) bears little resemblance to the equivalent optical image, making it difficult to interpret. To maximize the intelligence that may be obtained, it is desirable to automate the classification of targets in the image to support human operators. This paper presents a technique for classifying stationary targets based on the high-range resolution profile (HRRP) extracted from 3-D TWRIs. The dependence of the image on the target location is discussed using a system point spread function (PSF) approach. It is shown that the position dependence will cause a classifier to fail, unless the image to be classified is aligned to a classifier-training location. A target image alignment technique based on deconvolution of the image with the system PSF is proposed. Comparison of the aligned target images with measured images shows the alignment process introducing normalized mean squared error (NMSE) ≤ 9%. The HRRP extracted from aligned target images are classified using a naive Bayesian classifier supported by principal component analysis. The classifier is tested using a real TWRI of canonical targets behind a concrete wall and shown to obtain correct classification rates ≥ 97%. © 2011 IEEE

The effect of image alignment on capillary blood flow measurement of the neuroretinal rim using the Heidelberg retina flowmeter

PubMed Central

Sehi, M; Flanagan, J G

2004-01-01

Aim: To examine the influence of image alignment on the repeatability of blood flow measurements of the optic nerve. Methods: 10 normal subjects were examined. Heidelberg retina tomograph imaging was performed to establish best location and focus for the temporal neuroretinal rim. Two high quality Heidelberg retina flowmeter (HRF) images were acquired for three methods of alignment: central, nasal, and temporal. A 10×10 pixel measurement window was selected and exactly reproduced on all images. The interquartile pixel values were used to calculate capillary flow. ANOVA, intraclass correlation coefficients (ICC) and the coefficient of repeatability (CoR) were used for analysis. Results: There was no difference between methods (p = 0.47) or between visits (p = 0.51). The ICCs were 0.83 for the central, 0.34 for the nasal, and 0.42 for the temporal alignment. The CoR was 31.5 for central (mean effect 235.1), 234.6 for nasal, and 256.7 for temporal alignment. Conclusion: Central alignment was the most repeatable method for the measurement of neuroretinal rim capillary blood flow using the HRF. PMID:14736775

A novel dose-based positioning method for CT image-guided proton therapy

PubMed Central

Cheung, Joey P.; Park, Peter C.; Court, Laurence E.; Ronald Zhu, X.; Kudchadker, Rajat J.; Frank, Steven J.; Dong, Lei

2013-01-01

Purpose: Proton dose distributions can potentially be altered by anatomical changes in the beam path despite perfect target alignment using traditional image guidance methods. In this simulation study, the authors explored the use of dosimetric factors instead of only anatomy to set up patients for proton therapy using in-room volumetric computed tomographic (CT) images. Methods: To simulate patient anatomy in a free-breathing treatment condition, weekly time-averaged four-dimensional CT data near the end of treatment for 15 lung cancer patients were used in this study for a dose-based isocenter shift method to correct dosimetric deviations without replanning. The isocenter shift was obtained using the traditional anatomy-based image guidance method as the starting position. Subsequent isocenter shifts were established based on dosimetric criteria using a fast dose approximation method. For each isocenter shift, doses were calculated every 2 mm up to ±8 mm in each direction. The optimal dose alignment was obtained by imposing a target coverage constraint that at least 99% of the target would receive at least 95% of the prescribed dose and by minimizing the mean dose to the ipsilateral lung. Results: The authors found that 7 of 15 plans did not meet the target coverage constraint when using only the anatomy-based alignment. After the authors applied dose-based alignment, all met the target coverage constraint. For all but one case in which the target dose was met using both anatomy-based and dose-based alignment, the latter method was able to improve normal tissue sparing. Conclusions: The authors demonstrated that a dose-based adjustment to the isocenter can improve target coverage and/or reduce dose to nearby normal tissue. PMID:23635262

Towards a strategic alignment of public health and primary care practices at local levels - the case of severe and enduring mental illness.

PubMed

Banarsee, Ricky; Kelly, Cornelius; El-Osta, Austen; Thomas, Paul; Brophy, Chris

2018-03-01

The rapidly increasing number of people who have long-term conditions requires a system of coordinated support for self-care throughout the NHS. A system to support self-care needs to be aligned to systems that support shared-care and community development, making it easier for the multidisciplinary teams who provide care to also help patients and populations to help themselves. Public health practitioners need to work closely with clinicians to achieve this. The best place to coordinate this partnership is a community-based coordinating hub, or local health community - a geographic area of about 50,000 population where different contributions to self-care can be aligned. A shared vision for both health and disease management is needed to ensure consistent messaging by all. A three tier system of shared care can help to combine vertical and horizontal integration. This paper uses severe and enduring mental illness as an exemplar to anticipate the design of such a system.

Analysis of Lagrangian stretching in turbulent channel flow using a database task-parallel particle tracking approach

NASA Astrophysics Data System (ADS)

Meneveau, Charles; Johnson, Perry; Hamilton, Stephen; Burns, Randal

2016-11-01

An intrinsic property of turbulent flows is the exponential deformation of fluid elements along Lagrangian paths. The production of enstrophy by vorticity stretching follows from a similar mechanism in the Lagrangian view, though the alignment statistics differ and viscosity prevents unbounded growth. In this paper, the stretching properties of fluid elements and vorticity along Lagrangian paths are studied in a channel flow at Reτ = 1000 and compared with prior, known results from isotropic turbulence. To track Lagrangian paths in a public database containing Direct Numerical Simulation (DNS) results, the task-parallel approach previously employed in the isotropic database is extended to the case of flow in a bounded domain. It is shown that above 100 viscous units from the wall, stretching statistics are equal to their isotropic values, in support of the local isotropy hypothesis. Normalized by dissipation rate, the stretching in the buffer layer and below is less efficient due to less favorable alignment statistics. The Cramér function characterizing cumulative Lagrangian stretching statistics shows that overall the channel flow has about half of the stretching per unit dissipation compared with isotropic turbulence. Supported by a National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1232825, and by National Science Foundation Grants CBET-1507469, ACI-1261715, OCI-1244820 and by JHU IDIES.

Pediatric occipitocervical fusion: long-term radiographic changes in curvature, growth, and alignment.

PubMed

Martinez-Del-Campo, Eduardo; Turner, Jay D; Soriano-Baron, Hector; Newcomb, Anna G U S; Kalb, Samuel; Theodore, Nicholas

2016-11-01

OBJECTIVE The authors assessed the rate of vertebral growth, curvature, and alignment for multilevel constructs in the cervical spine after occipitocervical fixation (OCF) in pediatric patients and compared these results with those in published reports of growth in normal children. METHODS The authors assessed cervical spine radiographs and CT images of 18 patients who underwent occipitocervical arthrodesis. Measurements were made using postoperative and follow-up images available for 16 patients to determine cervical alignment (cervical spine alignment [CSA], C1-7 sagittal vertical axis [SVA], and C2-7 SVA) and curvature (cervical spine curvature [CSC] and C2-7 lordosis angle). Seventeen patients had postoperative and follow-up images available with which to measure vertebral body height (VBH), vertebral body width (VBW), and vertical growth percentage (VG%-that is, percentage change from postoperative to follow-up). Results for cervical spine growth were compared with normal parameters of 456 patients previously reported on in 2 studies. RESULTS Ten patients were girls and 8 were boys; their mean age was 6.7 ± 3.2 years. Constructs spanned occiput (Oc)-C2 (n = 2), Oc-C3 (n = 7), and Oc-C4 (n = 9). The mean duration of follow-up was 44.4 months (range 24-101 months). Comparison of postoperative to follow-up measures showed that the mean CSA increased by 1.8 ± 2.9 mm (p < 0.01); the mean C2-7 SVA and C1-7 SVA increased by 2.3 mm and 2.7 mm, respectively (p = 0.3); the mean CSC changed by -8.7° (p < 0.01) and the mean C2-7 lordosis angle changed by 2.6° (p = 0.5); and the cumulative mean VG% of the instrumented levels (C2-4) provided 51.5% of the total cervical growth (C2-7). The annual vertical growth rate was 4.4 mm/year. The VBW growth from C2-4 ranged from 13.9% to 16.6% (p < 0.001). The VBW of C-2 in instrumented patients appeared to be of a smaller diameter than that of normal patients, especially among those aged 5 to < 10 years and 10-15 years, with an increased diameter at the immediately inferior vertebral bodies compensating for the decreased width. No cervical deformation, malalignment, or detrimental clinical status was evident in any patient. CONCLUSIONS The craniovertebral junction and the upper cervical spine continue to present normal growth, curvature, and alignment parameters in children with OCF constructs spanning a distance as long as Oc-C4.

Dorsal surgical stabilisation using tension bands for treatment of traumatic atlanto-occipital instability in a cat.

PubMed

Vedrine, B; Maurin, M P

2017-12-01

An atlanto-occipital instability secondary to a dog bite was diagnosed in a 4-year-old Persian cat. Dorsal stabilisation of the instability was made with two OrthoFiber prostheses (Securos), which were used as tension bands between the nuchal crests of the occipital bone and the spinous process of the axis. Total recovery was achieved 4 days after surgery. Normal alignment of the atlanto-occipital joint was observed on survey radiographs taken 6 weeks post-surgery. Although the right loop had failed, the alignment was still normal and no neurological after-effects could be identified. Dorsal divergent tension bands between the nuchal crests of the occipital bone and the spinous process of the axis can be used to stabilise traumatic atlanto-occipital instability. © 2017 Australian Veterinary Association.

Automatic alignment of pre- and post-interventional liver CT images for assessment of radiofrequency ablation

NASA Astrophysics Data System (ADS)

Rieder, Christian; Wirtz, Stefan; Strehlow, Jan; Zidowitz, Stephan; Bruners, Philipp; Isfort, Peter; Mahnken, Andreas H.; Peitgen, Heinz-Otto

2012-02-01

Image-guided radiofrequency ablation (RFA) is becoming a standard procedure for minimally invasive tumor treatment in clinical practice. To verify the treatment success of the therapy, reliable post-interventional assessment of the ablation zone (coagulation) is essential. Typically, pre- and post-interventional CT images have to be aligned to compare the shape, size, and position of tumor and coagulation zone. In this work, we present an automatic workflow for masking liver tissue, enabling a rigid registration algorithm to perform at least as accurate as experienced medical experts. To minimize the effect of global liver deformations, the registration is computed in a local region of interest around the pre-interventional lesion and post-interventional coagulation necrosis. A registration mask excluding lesions and neighboring organs is calculated to prevent the registration algorithm from matching both lesion shapes instead of the surrounding liver anatomy. As an initial registration step, the centers of gravity from both lesions are aligned automatically. The subsequent rigid registration method is based on the Local Cross Correlation (LCC) similarity measure and Newton-type optimization. To assess the accuracy of our method, 41 RFA cases are registered and compared with the manually aligned cases from four medical experts. Furthermore, the registration results are compared with ground truth transformations based on averaged anatomical landmark pairs. In the evaluation, we show that our method allows to automatic alignment of the data sets with equal accuracy as medical experts, but requiring significancy less time consumption and variability.

VIP Barcoding: composition vector-based software for rapid species identification based on DNA barcoding.

PubMed

Fan, Long; Hui, Jerome H L; Yu, Zu Guo; Chu, Ka Hou

2014-07-01

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/. © 2014 John Wiley & Sons Ltd.

High Latitude Precipitating Energy Flux and Joule Heating During Geomagnetic Storms Determined from AMPERE Field-aligned Currents

NASA Astrophysics Data System (ADS)

Robinson, R. M.; Zanetti, L. J.; Anderson, B. J.; Korth, H.; Samara, M.; Michell, R.; Grubbs, G. A., II; Hampton, D. L.; Dropulic, A.

2016-12-01

A high latitude conductivity model based on field-aligned currents measured by the Active Magnetosphere and Planetary Electrodynamics Response Experiment (AMPERE) provides the means for complete specification of electric fields and currents at high latitudes. Based on coordinated measurements made by AMPERE and the Poker Flat Incoherent Scatter Radar, the model determines the most likely value of the ionospheric conductance from the direction, magnitude, and magnetic local time of the field-aligned current. A conductance model driven by field-aligned currents ensures spatial and temporal consistency between the calculated electrodynamic parameters. To validate the results, the Pedersen and Hall conductances were used to calculate the energy flux associated with the energetic particle precipitation. When integrated over the entire hemisphere, the total energy flux compares well with the Hemispheric Power Index derived from the OVATION-PRIME model. The conductances were also combined with the field-aligned currents to calculate the self-consistent electric field, which was then used to compute horizontal currents and Joule heating. The magnetic perturbations derived from the currents replicate most of the variations observed in ground-based magnetograms. The model was used to study high latitude particle precipitation, currents, and Joule heating for 24 magnetic storms. In most cases, the total energy input from precipitating particles and Joule heating exhibits a sharply-peaked maximum at the times of local minima in Dst, suggesting a close coupling between the ring current and the high latitude currents driven by the Region 2 field-aligned currents. The rapid increase and decrease of the high latitude energy deposition suggests an explosive transfer of energy from the magnetosphere to the ionosphere just prior to storm recovery.

Ensemble Manifold Rank Preserving for Acceleration-Based Human Activity Recognition.

PubMed

Tao, Dapeng; Jin, Lianwen; Yuan, Yuan; Xue, Yang

2016-06-01

With the rapid development of mobile devices and pervasive computing technologies, acceleration-based human activity recognition, a difficult yet essential problem in mobile apps, has received intensive attention recently. Different acceleration signals for representing different activities or even a same activity have different attributes, which causes troubles in normalizing the signals. We thus cannot directly compare these signals with each other, because they are embedded in a nonmetric space. Therefore, we present a nonmetric scheme that retains discriminative and robust frequency domain information by developing a novel ensemble manifold rank preserving (EMRP) algorithm. EMRP simultaneously considers three aspects: 1) it encodes the local geometry using the ranking order information of intraclass samples distributed on local patches; 2) it keeps the discriminative information by maximizing the margin between samples of different classes; and 3) it finds the optimal linear combination of the alignment matrices to approximate the intrinsic manifold lied in the data. Experiments are conducted on the South China University of Technology naturalistic 3-D acceleration-based activity dataset and the naturalistic mobile-devices based human activity dataset to demonstrate the robustness and effectiveness of the new nonmetric scheme for acceleration-based human activity recognition.

Ultra short laser pulse modification of wave guides

NASA Astrophysics Data System (ADS)

Rosenfeld, Arkadi; Ashkenasi, David

2003-11-01

The high peak powers of ultra short (ps and sub-ps) pulsed lasers available at relatively low single pulse energies potentially allow for a precise localization of photon energy, either on the surface or inside (transparent) materials. Three dimensional micro structuring of bulk transparent media without any sign of mechanical cracking has shown the potential of ultra short laser processing. In this study, the micro structuring of bulk transparent media was used to modify fused silica and especially the cladding-core interface in normal fused silica wave guides. The idea behind this technique is to enforce a local mismatch for total reflection at the interface at minimal mechanic stress to overcome the barrier for enhanced optical out-coupling. The laser-induced modifications were studied in dependence of pulse width, focal alignment, single pulse energy and pulse overlap. Micro traces with a thickness between 3 and 8 μm were generated with a spacing of 10 μm in the subsurface region using sub-ps and ps laser pulses at a wavelength of 800 nm. The optical leakage enforced by a micro spiral pattern is significant and can be utilized for medical applications or potentially also for telecommunications and fiber laser technology.

Ultrashort laser pulse processing of wave guides for medical applications

NASA Astrophysics Data System (ADS)

Ashkenasi, David; Rosenfeld, Arkadi; Spaniol, Stefan B.; Terenji, Albert

2003-06-01

The availability of ultra short (ps and sub-ps) pulsed lasers has stimulated a growing interest in exploiting the enhanced flexibility of femtosecond and/or picosecond laser technology for micro-machining. The high peak powers available at relatively low single pulse energies potentially allow for a precise localization of photon energy, either on the surface or inside (transparent) materials. Three dimensional micro structuring of bulk transparent media without any sign of mechanical cracking has been demonstrated. In this study, the potential of ultra short laser processing was used to modify the cladding-core interface in normal fused silica wave guides. The idea behind this technique is to enforce a local mismatch for total reflection at the interface at minimal mechanic stress. The laser-induced modifications were studied in dependence of pulse width, focal alignment, single pulse energy and pulse overlap. Micro traces with a thickness between 3 and 8 μm were generated with a spacing of 10 μm in the sub-surface region using sub-ps and ps laser pulses at a wavelength of 800 nm. The optical leakage enforced by a micro spiral pattern is significant and can be utilized for medical applications or potentially also for telecommunications and fiber laser technology.

Total knee arthroplasty with computer-assisted navigation more closely replicates normal knee biomechanics than conventional surgery.

PubMed

McClelland, Jodie A; Webster, Kate E; Ramteke, Alankar A; Feller, Julian A

2017-06-01

Computer-assisted navigation in total knee arthroplasty (TKA) reduces variability and may improve accuracy in the postoperative static alignment. The effect of navigation on alignment and biomechanics during more dynamic movements has not been investigated. This study compared knee biomechanics during level walking of 121 participants: 39 with conventional TKA, 42 with computer-assisted navigation TKA and 40 unimpaired control participants. Standing lower-limb alignment was significantly closer to ideal in participants with navigation TKA. During gait, when differences in walking speed were accounted for, participants with conventional TKA had less knee flexion during stance and swing than controls (P<0.01), but there were no differences between participants with navigation TKA and controls for the same variables. Both groups of participants with TKA had lower knee adduction moments than controls (P<0.01). In summary, there were fewer differences in the biomechanics of computer-assisted navigation TKA patients compared to controls than for patients with conventional TKA. Computer-assisted navigation TKA may restore biomechanics during walking that are closer to normal than conventional TKA. Copyright © 2017 Elsevier B.V. All rights reserved.

Equatorial Ionospheric Disturbance Field-Aligned Plasma Drifts Observed by C/NOFS

NASA Astrophysics Data System (ADS)

Zhang, Ruilong; Liu, Libo; Balan, N.; Le, Huijun; Chen, Yiding; Zhao, Biqiang

2018-05-01

Using C/NOFS satellite observations, this paper studies the disturbance field-aligned plasma drifts in the equatorial topside ionosphere during eight geomagnetic storms in 2011-2015. During all six storms occurred in the solstices, the disturbance field-aligned plasma drift is from winter to summer hemisphere especially in the morning-midnight local time sector and the disturbance is stronger in June solstice. The two storms occurred at equinoxes have very little effect on the field-aligned plasma drift. Using the plasma temperature data from DMSP satellites and Global Positioning System-total electron content, it is suggested that the plasma density gradient seems likely to cause the disturbance winter-to-summer plasma drift while the role of plasma temperature gradient is opposite to the observed plasma drift.

Spontaneous flow in polar active fluids: the effect of a phenomenological self propulsion-like term.

PubMed

Bonelli, Francesco; Gonnella, Giuseppe; Tiribocchi, Adriano; Marenduzzo, Davide

2016-01-01

We present hybrid lattice Boltzmann simulations of extensile and contractile active fluids where we incorporate phenomenologically the tendency of active particles such as cell and bacteria, to move, or swim, along the local orientation. Quite surprisingly, we show that the interplay between alignment and activity can lead to completely different results, according to geometry (periodic boundary conditions or confinement between flat walls) and nature of the activity (extensile or contractile). An interesting generic outcome is that the alignment interaction can transform stationary active patterns into continuously moving ones: the dynamics of these evolving patterns can be oscillatory or chaotic according to the strength of the alignment term. Our results suggest that flow-polarisation alignment can have important consequences on the collective dynamics of active fluids and active gel.

Patient Safety Incident Reporting: Current Trends and Gaps Within the Canadian Health System.

PubMed

Boucaud, Sarah; Dorschner, Danielle

2016-01-01

Patient safety incidents are a national-level phenomenon, requiring a pan-Canadian approach to ensure that incidents are reported and lessons are learned and broadly disseminated. This work explores the variation in current provincial and local approaches to reporting through a literature review. Trends are consolidated and recommendations are offered to foster better alignment of existing systems. These include adopting a common terminology, defining the patient role in reporting, increasing system users' perception of safety and further investigating the areas of home and community care in ensuring standard approaches at the local level. These steps can promote alignment, reducing barriers to a future pan-Canadian reporting and learning system.

Robust video copy detection approach based on local tangent space alignment

NASA Astrophysics Data System (ADS)

Nie, Xiushan; Qiao, Qianping

2012-04-01

We propose a robust content-based video copy detection approach based on local tangent space alignment (LTSA), which is an efficient dimensionality reduction algorithm. The idea is motivated by the fact that the content of video becomes richer and the dimension of content becomes higher. It does not give natural tools for video analysis and understanding because of the high dimensionality. The proposed approach reduces the dimensionality of video content using LTSA, and then generates video fingerprints in low dimensional space for video copy detection. Furthermore, a dynamic sliding window is applied to fingerprint matching. Experimental results show that the video copy detection approach has good robustness and discrimination.

SU-E-T-366: Clinical Implementation of MR-Guided Vaginal Cylinder Brachytherapy

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

Owrangi, A; Jolly, S; Balter, J

2014-06-01

Purpose: To evaluate the accuracy of MR-based vaginal brachytherapy source localization using an in-house MR-visible marker versus the alignment of an applicator model to MR images. Methods: Three consecutive patients undergoing vaginal HDR brachytherapy with a plastic cylinder were scanned with both CT and MRI (including T1- and T2- weighted images). An MR-visible source localization marker, consisting of a sealed thin catheter filled with either water (for T2 contrast) or Gd-doped water (for T1 contrast), was assembled shortly before scanning. Clinically, the applicator channel was digitized on CT with an x-ray marker. To evaluate the efficacy of MR-based applicator reconstruction,more » each MR image volume was aligned locally to the CT images based on the region containing the cylinder. Applicator digitization was performed on the MR images using (1) the MR visible marker and (2) alignment of an applicator surface model from Varian's Brachytherapy Planning software to the MRI images. Resulting source positions were compared with the original CT digitization. Results: Although the source path was visualized by the MR marker, the applicator tip proved difficult to identify due to challenges in achieving a watertight seal. This resulted in observed displacements of the catheter tip, at times >1cm. Deviations between the central source positions identified via aligning the applicator surface model to MR and using the xray marker on CT ranged from 0.07 – 0.19 cm and 0.07 – 0.20 cm on T1- weighted and T2-weighted images, respectively. Conclusion: Based on the current study, aligning the applicator model to MRI provides a practical, current approach to perform MR-based brachytherapy planning. Further study is needed to produce catheters with reliably and reproducibly identifiable tips. Attempts are being made to improve catheter seals, as well as to increase the viscosity of the contrast material to decrease fluid mobility inside the catheter.« less

G-Anchor: a novel approach for whole-genome comparative mapping utilizing evolutionary conserved DNA sequences.

PubMed

Lenis, Vasileios Panagiotis E; Swain, Martin; Larkin, Denis M

2018-05-01

Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses, ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high-performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available from multiple projects, there is an increasing demand for genome comparative analyses. Here, we introduce G-Anchor, a new, fast, and efficient pipeline that uses a strictly limited but highly effective set of local sequence alignments to anchor (or map) an animal genome to another species' reference genome. G-Anchor makes novel use of a databank of highly conserved DNA sequence elements. We demonstrate how these elements may be aligned to a pair of genomes, creating anchors. These anchors enable the rapid mapping of scaffolds from a de novo assembled genome to chromosome assemblies of a reference species. Our results demonstrate that G-Anchor can successfully anchor a vertebrate genome onto a phylogenetically related reference species genome using a desktop or laptop computer within a few hours and with comparable accuracy to that achieved by a highly accurate whole-genome alignment tool such as LASTZ. G-Anchor thus makes whole-genome comparisons accessible to researchers with limited computational resources. G-Anchor is a ready-to-use tool for anchoring a pair of vertebrate genomes. It may be used with large genomes that contain a significant fraction of evolutionally conserved DNA sequences and that are not highly repetitive, polypoid, or excessively fragmented. G-Anchor is not a substitute for whole-genome aligning software but can be used for fast and accurate initial genome comparisons. G-Anchor is freely available and a ready-to-use tool for the pairwise comparison of two genomes.

Sparse alignment for robust tensor learning.

PubMed

Lai, Zhihui; Wong, Wai Keung; Xu, Yong; Zhao, Cairong; Sun, Mingming

2014-10-01

Multilinear/tensor extensions of manifold learning based algorithms have been widely used in computer vision and pattern recognition. This paper first provides a systematic analysis of the multilinear extensions for the most popular methods by using alignment techniques, thereby obtaining a general tensor alignment framework. From this framework, it is easy to show that the manifold learning based tensor learning methods are intrinsically different from the alignment techniques. Based on the alignment framework, a robust tensor learning method called sparse tensor alignment (STA) is then proposed for unsupervised tensor feature extraction. Different from the existing tensor learning methods, L1- and L2-norms are introduced to enhance the robustness in the alignment step of the STA. The advantage of the proposed technique is that the difficulty in selecting the size of the local neighborhood can be avoided in the manifold learning based tensor feature extraction algorithms. Although STA is an unsupervised learning method, the sparsity encodes the discriminative information in the alignment step and provides the robustness of STA. Extensive experiments on the well-known image databases as well as action and hand gesture databases by encoding object images as tensors demonstrate that the proposed STA algorithm gives the most competitive performance when compared with the tensor-based unsupervised learning methods.

Evaluation of Eight Methods for Aligning Orientation of Two Coordinate Systems.

PubMed

Mecheri, Hakim; Robert-Lachaine, Xavier; Larue, Christian; Plamondon, André

2016-08-01

The aim of this study was to evaluate eight methods for aligning the orientation of two different local coordinate systems. Alignment is very important when combining two different systems of motion analysis. Two of the methods were developed specifically for biomechanical studies, and because there have been at least three decades of algorithm development in robotics, it was decided to include six methods from this field. To compare these methods, an Xsens sensor and two Optotrak clusters were attached to a Plexiglas plate. The first optical marker cluster was fixed on the sensor and 20 trials were recorded. The error of alignment was calculated for each trial, and the mean, the standard deviation, and the maximum values of this error over all trials were reported. One-way repeated measures analysis of variance revealed that the alignment error differed significantly across the eight methods. Post-hoc tests showed that the alignment error from the methods based on angular velocities was significantly lower than for the other methods. The method using angular velocities performed the best, with an average error of 0.17 ± 0.08 deg. We therefore recommend this method, which is easy to perform and provides accurate alignment.

Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

DOE PAGES

Tian, Wenhong; Samatova, Nagiza F.

2013-01-01

A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach based onmore » a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (fly), E. coli K12 and S. typhimurium , E. coli K12 and C. crescenttus , we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily.« less

Quantification of Cardiomyocyte Alignment from Three-Dimensional (3D) Confocal Microscopy of Engineered Tissue.

PubMed

Kowalski, William J; Yuan, Fangping; Nakane, Takeichiro; Masumoto, Hidetoshi; Dwenger, Marc; Ye, Fei; Tinney, Joseph P; Keller, Bradley B

2017-08-01

Biological tissues have complex, three-dimensional (3D) organizations of cells and matrix factors that provide the architecture necessary to meet morphogenic and functional demands. Disordered cell alignment is associated with congenital heart disease, cardiomyopathy, and neurodegenerative diseases and repairing or replacing these tissues using engineered constructs may improve regenerative capacity. However, optimizing cell alignment within engineered tissues requires quantitative 3D data on cell orientations and both efficient and validated processing algorithms. We developed an automated method to measure local 3D orientations based on structure tensor analysis and incorporated an adaptive subregion size to account for multiple scales. Our method calculates the statistical concentration parameter, κ, to quantify alignment, as well as the traditional orientational order parameter. We validated our method using synthetic images and accurately measured principal axis and concentration. We then applied our method to confocal stacks of cleared, whole-mount engineered cardiac tissues generated from human-induced pluripotent stem cells or embryonic chick cardiac cells and quantified cardiomyocyte alignment. We found significant differences in alignment based on cellular composition and tissue geometry. These results from our synthetic images and confocal data demonstrate the efficiency and accuracy of our method to measure alignment in 3D tissues.

Automated and Adaptable Quantification of Cellular Alignment from Microscopic Images for Tissue Engineering Applications

PubMed Central

Xu, Feng; Beyazoglu, Turker; Hefner, Evan; Gurkan, Umut Atakan

2011-01-01

Cellular alignment plays a critical role in functional, physical, and biological characteristics of many tissue types, such as muscle, tendon, nerve, and cornea. Current efforts toward regeneration of these tissues include replicating the cellular microenvironment by developing biomaterials that facilitate cellular alignment. To assess the functional effectiveness of the engineered microenvironments, one essential criterion is quantification of cellular alignment. Therefore, there is a need for rapid, accurate, and adaptable methodologies to quantify cellular alignment for tissue engineering applications. To address this need, we developed an automated method, binarization-based extraction of alignment score (BEAS), to determine cell orientation distribution in a wide variety of microscopic images. This method combines a sequenced application of median and band-pass filters, locally adaptive thresholding approaches and image processing techniques. Cellular alignment score is obtained by applying a robust scoring algorithm to the orientation distribution. We validated the BEAS method by comparing the results with the existing approaches reported in literature (i.e., manual, radial fast Fourier transform-radial sum, and gradient based approaches). Validation results indicated that the BEAS method resulted in statistically comparable alignment scores with the manual method (coefficient of determination R2=0.92). Therefore, the BEAS method introduced in this study could enable accurate, convenient, and adaptable evaluation of engineered tissue constructs and biomaterials in terms of cellular alignment and organization. PMID:21370940

Frontiers of controlling energy levels at interfaces

NASA Astrophysics Data System (ADS)

Koch, Norbert

The alignment of electron energy levels at interfaces between semiconductors, dielectrics, and electrodes determines the function and efficiency of all electronic and optoelectronic devices. Reliable guidelines for predicting the level alignment for a given material combination and methods to adjust the intrinsic energy landscape are needed to enable efficient engineering approaches. These are sufficiently understood for established electronic materials, e.g., Si, but for the increasing number of emerging materials, e.g., organic and 2D semiconductors, perovskites, this is work in progress. The intrinsic level alignment and the underlying mechanisms at interfaces between organic and inorganic semiconductors are discussed first. Next, methods to alter the level alignment are introduced, which all base on proper charge density rearrangement at a heterojunction. As interface modification agents we use molecular electron acceptors and donors, as well as molecular photochromic switches that add a dynamic aspect and allow device multifunctionality. For 2D semiconductors surface transfer doping with molecular acceptors/donors transpires as viable method to locally tune the Fermi-level position in the energy gap. The fundamental electronic properties of a prototypical 1D interface between intrinsic and p-doped 2D semiconductor regions are derived from local (scanning probe) and area-averaged (photoemission) spectroscopy experiments. Future research opportunities for attaining unsurpassed interface control through charge density management are discussed.

Understanding the role of the cytoskeleton in wood formation in angiosperm trees: hybrid aspen (Populus tremula x P. tremuloides) as the model species.

PubMed

Chaffey, Nigel; Barlow, Peter; Sundberg, Björn

2002-03-01

The involvement of microfilaments and microtubules in the development of the radial and axial components of secondary xylem (wood) in hybrid aspen (Populus tremula L. x P. tremuloides Michx.) was studied by indirect immunofluorescent localization techniques. In addition to cambial cells, the differentiated cell types considered were early- and late-wood vessel elements, axial parenchyma, normal-wood fibers and gelatinous fibers, and contact and isolation ray cells. Microfilaments were rare in ray cambial cells, but were abundant and axially arranged in their derivatives once cell elongation had begun, and persisted in that orientation in mature ray cells. Microfilaments were axially arranged in fusiform cambial cells and persisted in that orientation in all xylem derivatives of those cells. Microtubules were randomly oriented in ray and fusiform cells of the cambial zone. Dense arrays of parallel-aligned microtubules were oriented near axially in the developing gelatinous fibers, but at a wide range of angles in normal-wood fibers. Ellipses of microfilaments were associated with pit development in fiber cells and isolation ray cells. Rings of co-localized microtubules and microfilaments were associated with developing inter-vessel bordered pits and vessel-contact ray cell contact pits, and, in the case of bordered pits, these rings decreased in diameter as the over-arching pit border increased in size. Although only microtubules were seen at the periphery of the perforation plate of vessel elements, a prominent meshwork of microfilaments overlaid the perforation plate itself. A consensus view of the roles of the cytoskeleton during wood formation in angiosperm trees is presented.

Misaligned Image Integration With Local Linear Model.

PubMed

Baba, Tatsuya; Matsuoka, Ryo; Shirai, Keiichiro; Okuda, Masahiro

2016-05-01

We present a new image integration technique for a flash and long-exposure image pair to capture a dark scene without incurring blurring or noisy artifacts. Most existing methods require well-aligned images for the integration, which is often a burdensome restriction in practical use. We address this issue by locally transferring the colors of the flash images using a small fraction of the corresponding pixels in the long-exposure images. We formulate the image integration as a convex optimization problem with the local linear model. The proposed method makes it possible to integrate the color of the long-exposure image with the detail of the flash image without causing any harmful effects to its contrast, where we do not need perfect alignment between the images by virtue of our new integration principle. We show that our method successfully outperforms the state of the art in the image integration and reference-based color transfer for challenging misaligned data sets.

Orientation of cosmic web filaments with respect to the underlying velocity field

NASA Astrophysics Data System (ADS)

Tempel, E.; Libeskind, N. I.; Hoffman, Y.; Liivamägi, L. J.; Tamm, A.

2014-01-01

The large-scale structure of the Universe is characterized by a web-like structure made of voids, sheets, filaments and knots. The structure of this so-called cosmic web is dictated by the local velocity shear tensor. In particular, the local direction of a filament should be strongly aligned with hat{e}_3, the eigenvector associated with the smallest eigenvalue of the tensor. That conjecture is tested here on the basis of a cosmological simulation. The cosmic web delineated by the halo distribution is probed by a marked point process with interactions (the Bisous model), detecting filaments directly from the halo distribution (P-web). The detected P-web filaments are found to be strongly aligned with the local hat{e}_3: the alignment is within 30° for ˜80 per cent of the elements. This indicates that large-scale filaments defined purely from the distribution of haloes carry more than just morphological information, although the Bisous model does not make any prior assumption on the underlying shear tensor. The P-web filaments are also compared to the structure revealed from the velocity shear tensor itself (V-web). In the densest regions, the P- and V-web filaments overlap well (90 per cent), whereas in lower density regions, the P-web filaments preferentially mark sheets in the V-web.

Theory of electrical conductivity and dielectric permittivity of highly aligned graphene-based nanocomposites.

PubMed

Xia, Xiaodong; Hao, Jia; Wang, Yang; Zhong, Zheng; Weng, George J

2017-05-24

Highly aligned graphene-based nanocomposites are of great interest due to their excellent electrical properties along the aligned direction. Graphene fillers in these composites are not necessarily perfectly aligned, but their orientations are highly confined to a certain angle, [Formula: see text] with 90° giving rise to the randomly oriented state and 0° to the perfectly aligned one. Recent experiments have shown that electrical conductivity and dielectric permittivity of highly aligned graphene-polymer nanocomposites are strongly dependent on this distribution angle, but at present no theory seems to exist to address this issue. In this work we present a new effective-medium theory that is derived from the underlying physical process including the effects of graphene orientation, filler loading, aspect ratio, percolation threshold, interfacial tunneling, and Maxwell-Wagner-Sillars polarization, to determine these two properties. The theory is formulated in the context of preferred orientational average. We highlight this new theory with an application to rGO/epoxy nanocomposites, and demonstrate that the calculated in-plane and out-of-plane conductivity and permittivity are in agreement with the experimental data as the range of graphene orientations changes from the randomly oriented to the highly aligned state. We also show that the percolation thresholds of highly aligned graphene nanocomposites are in general different along the planar and the normal directions, but they converge into a single one when the statistical distribution of graphene fillers is spherically symmetric.

Is the aligning prism measured with the Mallett unit correlated with fusional vergence reserves?

PubMed

Conway, Miriam L; Thomas, Jennifer; Subramanian, Ahalya

2012-01-01

The Mallett Unit is a clinical test designed to detect the fixation disparity that is most likely to occur in the presence of a decompensated heterophoria. It measures the associated phoria, which is the "aligning prism" needed to nullify the subjective disparity. The technique has gained widespread acceptance within professions such as optometry, for investigating suspected cases of decompensating heterophoria; it is, however, rarely used by orthoptists and ophthalmologists. The aim of this study was to investigate whether fusional vergence reserves, measured routinely by both orthoptists and ophthalmologists to detect heterophoria decompensation, were correlated with aligning prism (associated phoria) in a normal clinical population. Aligning prism (using the Mallett Unit) and fusional vergence reserves (using a prism bar) were measured in 500 participants (mean 41.63 years; standard deviation 11.86 years) at 40 cm and 6 m. At 40 cm a strong correlation (p<0.001) between base in aligning prism (Exo FD) and positive fusional reserves was found. Of the participants with zero aligning prism 30% had reduced fusional reserves. At 6 m a weak correlation between base out aligning prism (Eso FD) and negative fusional reserves was found to break (p = 0.01) and to recovery (p = 0.048). Of the participants with zero aligning prism 12% reported reduced fusional reserves. For near vision testing, the strong inverse correlation between base in aligning prism (Exo FD) and fusional vergence reserves supports the notion that both measures are indicators of decompensation of heterophoria. For distance vision testing and for those patients reporting zero aligning prism further research is required to determine why the relationship appears to be weak/non-existent?

Is the Aligning Prism Measured with the Mallett Unit Correlated with Fusional Vergence Reserves?

PubMed Central

Conway, Miriam L.; Thomas, Jennifer; Subramanian, Ahalya

2012-01-01

Background The Mallett Unit is a clinical test designed to detect the fixation disparity that is most likely to occur in the presence of a decompensated heterophoria. It measures the associated phoria, which is the “aligning prism” needed to nullify the subjective disparity. The technique has gained widespread acceptance within professions such as optometry, for investigating suspected cases of decompensating heterophoria; it is, however, rarely used by orthoptists and ophthalmologists. The aim of this study was to investigate whether fusional vergence reserves, measured routinely by both orthoptists and ophthalmologists to detect heterophoria decompensation, were correlated with aligning prism (associated phoria) in a normal clinical population. Methodology/Principal Findings Aligning prism (using the Mallett Unit) and fusional vergence reserves (using a prism bar) were measured in 500 participants (mean 41.63 years; standard deviation 11.86 years) at 40 cm and 6 m. At 40 cm a strong correlation (p<0.001) between base in aligning prism (Exo FD) and positive fusional reserves was found. Of the participants with zero aligning prism 30% had reduced fusional reserves. At 6 m a weak correlation between base out aligning prism (Eso FD) and negative fusional reserves was found to break (p = 0.01) and to recovery (p = 0.048). Of the participants with zero aligning prism 12% reported reduced fusional reserves. Conclusions/Significance For near vision testing, the strong inverse correlation between base in aligning prism (Exo FD) and fusional vergence reserves supports the notion that both measures are indicators of decompensation of heterophoria. For distance vision testing and for those patients reporting zero aligning prism further research is required to determine why the relationship appears to be weak/non-existent? PMID:22905174

Stable azodye photo-alignment layer for liquid crystal devices achieved by "turning off" dye photosensitivity

NASA Astrophysics Data System (ADS)

McGinty, C.; Finnemeyer, V.; Reich, R.; Clark, H.; Berry, S.; Bos, P.

2017-11-01

We have previously proposed a low cost, versatile process for stabilizing azodye photo-alignment layers for liquid crystal devices by utilizing a surface localized reactive mesogen (RM) layer. The RM is applied by dissolving the monomer in a liquid crystal material prior to filling the cell. In this paper, we show the significant effect of azodye layer thickness on the long term stability of these alignment layers when exposed to polarized light. We demonstrate, surprisingly, that thin azodye layers (˜3 nm) provide improved stability over thicker (˜40 nm) layers. Using this process, we show cells which have been stable to exposure with polarized light through one month. Additionally, we demonstrate the use of a photo-alignment layer to align the liquid crystals that afterwards can be rendered insensitive to polarized light. This was accomplished by using the process described above with the additional step of eliminating the photosensitivity of the azodye layer through photo-bleaching; the result is an RM alignment layer that will be stable when exposed to polarized light in the dye absorption band.

Track Geometry Development : UMTA Urban Rail Supporting Technology Program

DOT National Transportation Integrated Search

1974-04-01

Measurement of transit system track geometry parameters, under normal operating conditions, is essential for planning and conducting an effective maintenance program. The pertinent parameters are profile, gage, alignment, and cross level. Present met...

Characteristic Exponent of Normal and Oblique Rolls in Homeotropically Aligned Nematic Liquid Crystal

NASA Astrophysics Data System (ADS)

Saraswati, V.; Nugroho, F.

2018-04-01

Soft-mode turbulence (SMT) is one of an experimental example of spatiotemporal chaos, observed in electroconvection system of homeotropically aligned nematic liquid crystal (NLC), due to a non-linear interaction between Nambu-Goldstone mode denoted by the C(r)- director and the convective mode q(r). There are two types of stripe patterns in the SMT, namely normal rolls (NR) and oblique rolls (OR) which separated by a point of applied frequency, called the Lifshitz frequency (f L ). We report a study of the phase transition from normal to oblique rolls by observing the patterns with an applied frequency below and beyond of fL . The temporal fluctuations of the pattern images had been analyzed using autocorrelation function. It fits with Kohlrausch Williams Watts (KWW) function, showing there is a dynamical glass-forming liquid in the transition of NR-OR regime. Also, we found a new type of defect in the NR regime which never been reported before, a dynamic defect which takes the shape of a ring first to a spot in the end.

Free-surface liquid jet impingement on rib patterned superhydrophobic surfaces

NASA Astrophysics Data System (ADS)

Maynes, D.; Johnson, M.; Webb, B. W.

2011-05-01

We report experimental results characterizing the dynamics of a liquid jet impinging normally on hydrophilic, hydrophobic, and superhydrophobic surfaces spanning the Weber number (based on the jet velocity and diameter) range from 100 to 1900. The superhydrophobic surfaces are fabricated with both hydrophobically coated silicon and polydimethylsiloxane that exhibit alternating microribs and cavities. For all surfaces a transition from a thin radially moving liquid sheet occurs. This takes the form of the classical hydraulic jump for the hydrophilic surfaces but is markedly different for the hydrophobic and superhydrophobic surfaces, where the transition is significantly influenced by surface tension and a break-up into droplets is observed at high Weber number. For the superhydrophobic surfaces, the transition exhibits an elliptical shape with the major axis being aligned parallel to the ribs, concomitant with the frictional resistance being smaller in the parallel direction than in the transverse direction. However, the total projected area of the ellipse exhibits a nearly linear dependence on the jet Weber number, and was nominally invariant with varying hydrophobicity and relative size of the ribs and cavities. For the hydrophobic and superhydrophobic scenarios, the local Weber number based on the local radial velocity and local depth of the radially moving liquid sheet is observed to be of order unity at the transition location. The results also reveal that for increasing relative size of the cavities, the ratio of the ellipse axis (major-to-minor) increases.

Impact of materials engineering on edge placement error (Conference Presentation)

NASA Astrophysics Data System (ADS)

Freed, Regina; Mitra, Uday; Zhang, Ying

2017-04-01

Transistor scaling has transitioned from wavelength scaling to multi-patterning techniques, due to the resolution limits of immersion of immersion lithography. Deposition and etch have enabled scaling in the by means of SADP and SAQP. Spacer based patterning enables extremely small linewidths, sufficient for several future generations of transistors. However, aligning layers in Z-direction, as well as aligning cut and via patterning layers, is becoming a road-block due to global and local feature variation and fidelity. This presentation will highlight the impact of deposition and etch on this feature alignment (EPE) and illustrate potential paths toward lowering EPE using material engineering.

Algorithms for Automatic Alignment of Arrays

NASA Technical Reports Server (NTRS)

Chatterjee, Siddhartha; Gilbert, John R.; Oliker, Leonid; Schreiber, Robert; Sheffler, Thomas J.

1996-01-01

Aggregate data objects (such as arrays) are distributed across the processor memories when compiling a data-parallel language for a distributed-memory machine. The mapping determines the amount of communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: an alignment that maps all the objects to an abstract template, followed by a distribution that maps the template to the processors. This paper describes algorithms for solving the various facets of the alignment problem: axis and stride alignment, static and mobile offset alignment, and replication labeling. We show that optimal axis and stride alignment is NP-complete for general program graphs, and give a heuristic method that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. We also show how local graph contractions can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. We show how to model the static offset alignment problem using linear programming, and we show that loop-dependent mobile offset alignment is sometimes necessary for optimum performance. We describe an algorithm with for determining mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself or can be used to improve performance. We describe an algorithm based on network flow that replicates objects so as to minimize the total amount of broadcast communication in replication.

Modeling of field-aligned guided echoes in the plasmasphere

NASA Astrophysics Data System (ADS)

Fung, Shing F.; Green, James L.

2005-01-01

Ray tracing modeling is used to investigate the plasma conditions under which high-frequency (f ≫ fuh) extraordinary mode waves can be guided along geomagnetic field lines. These guided signals have often been observed as long-range discrete echoes in the plasmasphere by the Radio Plasma Imager (RPI) onboard the Imager for Magnetopause-to-Aurora Global Exploration satellite. Field-aligned discrete echoes are most commonly observed by RPI in the plasmasphere, although they are also observed over the polar cap region. The plasmasphere field-aligned echoes appearing as multiple echo traces at different virtual ranges are attributed to signals reflected successively between conjugate hemispheres that propagate along or nearly along closed geomagnetic field lines. The ray tracing simulations show that field-aligned ducts with as little as 1% density perturbations (depletions) and <10 wavelengths wide can guide nearly field-aligned propagating high-frequency X mode waves. Effective guidance of a wave at a given frequency and wave normal angle (Ψ) depends on the cross-field density scale of the duct, such that ducts with stronger density depletions need to be wider in order to maintain the same gradient of refractive index across the magnetic field. While signal guidance by field aligned density gradient without ducting is possible only over the polar region, conjugate field-aligned echoes that have traversed through the equatorial region are most likely guided by ducting.

3-D Localization Method for a Magnetically Actuated Soft Capsule Endoscope and Its Applications

PubMed Central

Yim, Sehyuk; Sitti, Metin

2014-01-01

In this paper, we present a 3-D localization method for a magnetically actuated soft capsule endoscope (MASCE). The proposed localization scheme consists of three steps. First, MASCE is oriented to be coaxially aligned with an external permanent magnet (EPM). Second, MASCE is axially contracted by the enhanced magnetic attraction of the approaching EPM. Third, MASCE recovers its initial shape by the retracting EPM as the magnetic attraction weakens. The combination of the estimated direction in the coaxial alignment step and the estimated distance in the shape deformation (recovery) step provides the position of MASCE in 3-D. It is experimentally shown that the proposed localization method could provide 2.0–3.7 mm of distance error in 3-D. This study also introduces two new applications of the proposed localization method. First, based on the trace of contact points between the MASCE and the surface of the stomach, the 3-D geometrical model of a synthetic stomach was reconstructed. Next, the relative tissue compliance at each local contact point in the stomach was characterized by measuring the local tissue deformation at each point due to the preloading force. Finally, the characterized relative tissue compliance parameter was mapped onto the geometrical model of the stomach toward future use in disease diagnosis. PMID:25383064

Culturally grounded indicators of resilience in social-ecological systems

Treesearch

Eleanor Sterling; Tamara Ticktin; Tē Kipa Kepa Morgan; Georgina Cullman; Diana Alvira; Pelika Andrade; Nadia Bergamini; Erin Betley; Kate Burrows; Sophie Caillon; Joachim Claudet; Rachel Dacks; Pablo Eyzaguirre; Chris Filardi; Nadav Gazit; Christian Giardina; Stacy Jupiter; Kealohanuiopuna Kinney; Joe McCarter; Manuel Mejia; Kanoe Morishige; Jennifer Newell; Lihla Noori; John Parks; Pua‘ala Pascua; Ashwin Ravikumar; Jamie Tanguay; Amanda Sigouin; Tina Stege; Mark Stege; Alaka Wali

2017-01-01

Measuring progress toward sustainability goals is a multifaceted task. International, regional, and national organizations and agencies seek to promote resilience and capacity for adaptation at local levels. However, their measurement systems may be poorly aligned with local contexts, cultures, and needs. Understanding how to build effective, culturally grounded...

Collective Motion in Behaviorally Heterogeneous Systems

NASA Astrophysics Data System (ADS)

Copenhagen, Katherine

Collective motion is a widespread phenomenon in nature where individuals actively propel themselves, gather together and move as a group. Some examples of collective motion are bird flocks, fish schools, bacteria swarms, cell clusters, and crowds of people. Many models seek to understand the effects of activity in collective systems including things such as environmental disorder, density, and interaction details primarily at infinite size limits and with uniform populations. In this dissertation I investigate the effects of finite sizes and behavioral heterogeneity as it exists in nature. Behavioral heterogeneity can originate from several different sources. Mixed populations of individuals can have inherently different behaviors such as mutant bacteria, injured fish, or agents that prefer individualistic behavior over coordinated motion. Alternatively, agents may modify their own behavior based on some local environmental dependency, such as local substrate, or density. In cases such as mutant cheaters in bacteria or malfunctioning drones in swarms, mixed populations of behaviorally heterogeneous agents can be modelled as arising in the form of aligning and non-aligning agents. When this kind of heterogeneity is introduced, there is a critical carrying capacity of non-aligners above which the system is unable to form a cohesive ordered group. However, if the cohesion of the group is relaxed to allow for fracture, the system will actively sort out non-aligning agents the system will exist at a critical non-aligner fraction. A similar heterogeneity could result in a mixture of high and low noise individuals. In this case there is also a critical carry capacity beyond which the system is unable to reach an ordered state, however the nature of this transition depends on the model details. Agents which are part of an ordered collective may vary their behavior as the group changes environments such as a flock of birds flying into a cloud. Using a unique model of a flock where the group behaves as a rigid disk reveals interesting behaviors as the system crosses a boundary between interfaces. The collective rotates and reorients or becomes stuck on the boundary as it crosses. I also investigate the effects of variable behavior depending on local density, and find that a frustration driven transient rotational phase arises in clusters where agents with low local density move faster than those with high local density as in cell clusters. All together I have shown that behavioral heterogeneity in collective motion can lead to unique phases and behaviors that are not seen in their homogeneous counterparts.

Assessing the local mechanical environment in medial opening wedge high tibial osteotomy using finite element analysis.

PubMed

Pauchard, Yves; Ivanov, Todor G; McErlain, David D; Milner, Jaques S; Giffin, J Robert; Birmingham, Trevor B; Holdsworth, David W

2015-03-01

High-tibial osteotomy (HTO) is a surgical technique aimed at shifting load away from one tibiofemoral compartment, in order the reduce pain and progression of osteoarthritis (OA). Various implants have been designed to stabilize the osteotomy and previous studies have been focused on determining primary stability (a global measure) that these designs provide. It has been shown that the local mechanical environment, characterized by bone strains and segment micromotion, is important in understanding healing and these data are not currently available. Finite element (FE) modeling was utilized to assess the local mechanical environment provided by three different fixation plate designs: short plate with spacer, long plate with spacer and long plate without spacer. Image-based FE models of the knee were constructed from healthy individuals (N = 5) with normal knee alignment. An HTO gap was virtually added without changing the knee alignment and HTO implants were inserted. Subsequently, the local mechanical environment, defined by bone compressive strain and wedge micromotion, was assessed. Furthermore, implant stresses were calculated. Values were computed under vertical compression in zero-degree knee extension with loads set at 1 and 2 times the subject-specific body weight (1 BW, 2 BW). All studied HTO implant designs provide an environment for successful healing at 1 BW and 2 BW loading. Implant von Mises stresses (99th percentile) were below 60 MPa in all experiments, below the material yield strength and significantly lower in long spacer plates. Volume fraction of high compressive strain ( > 3000 microstrain) was below 5% in all experiments and no significant difference between implants was detected. Maximum vertical micromotion between bone segments was below 200 μm in all experiments and significantly larger in the implant without a tooth. Differences between plate designs generally became apparent only at 2 BW loading. Results suggest that with compressive loading of 2 BW, long spacer plates experience the lowest implant stresses, and spacer plates (long or short) result in smaller wedge micromotion, potentially beneficial for healing. Values are sensitive to subject bone geometry, highlighting the need for subject-specific modeling. This study demonstrates the benefits of using image-based FE modeling and bone theory to fine-tune HTO implant design.

On the alignment of cellulose microfibrils by cortical microtubules: a review and a model.

PubMed

Baskin, T I

2001-01-01

The hypothesis that microtubules align microfibrils, termed the alignment hypothesis, states that there is a causal link between the orientation of cortical microtubules and the orientation of nascent microfibrils. I have assessed the generality of this hypothesis by reviewing what is known about the relation between microtubules and microfibrils in a wide group of examples: in algae of the family Characeae, Closterium acerosum, Oocystis solitaria, and certain genera of green coenocytes and in land plant tip-growing cells, xylem, diffusely growing cells, and protoplasts. The salient features about microfibril alignment to emerge are as follows. Cellulose microfibrils can be aligned by cortical microtubules, thus supporting the alignment hypothesis. Alignment of microfibrils can occur independently of microtubules, showing that an alternative to the alignment hypothesis must exist. Microfibril organization is often random, suggesting that self-assembly is insufficient. Microfibril organization differs on different faces of the same cell, suggesting that microfibrils are aligned locally, not with respect to the entire cell. Nascent microfibrils appear to associate tightly with the plasma membrane. To account for these observations, I present a model that posits alignment to be mediated through binding the nascent microfibril. The model, termed templated incorporation, postulates that the nascent microfibril is incorporated into the cell wall by binding to a scaffold that is oriented; further, the scaffold is built and oriented around either already incorporated microfibrils or plasma membrane proteins, or both. The role of cortical microtubules is to bind and orient components of the scaffold at the plasma membrane. In this way, spatial information to align the microfibrils may come from either the cell wall or the cell interior, and microfibril alignment with and without microtubules are subsets of a single mechanism.

Alignment-free detection of horizontal gene transfer between closely related bacterial genomes.

PubMed

Domazet-Lošo, Mirjana; Haubold, Bernhard

2011-09-01

Bacterial epidemics are often caused by strains that have acquired their increased virulence through horizontal gene transfer. Due to this association with disease, the detection of horizontal gene transfer continues to receive attention from microbiologists and bioinformaticians alike. Most software for detecting transfer events is based on alignments of sets of genes or of entire genomes. But despite great advances in the design of algorithms and computer programs, genome alignment remains computationally challenging. We have therefore developed an alignment-free algorithm for rapidly detecting horizontal gene transfer between closely related bacterial genomes. Our implementation of this algorithm is called alfy for "ALignment Free local homologY" and is freely available from http://guanine.evolbio.mpg.de/alfy/. In this comment we demonstrate the application of alfy to the genomes of Staphylococcus aureus. We also argue that-contrary to popular belief and in spite of increasing computer speed-algorithmic optimization is becoming more, not less, important if genome data continues to accumulate at the present rate.

Alignment of the Stanford Linear Collider Arcs: Concepts and results

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

Pitthan, R.; Bell, B.; Friedsam, H.

1987-02-01

The alignment of the Arcs for the Stanford Linear Collider at SLAC has posed problems in accelerator survey and alignment not encountered before. These problems come less from the tight tolerances of 0.1 mm, although reaching such a tight statistically defined accuracy in a controlled manner is difficult enough, but from the absence of a common reference plane for the Arcs. Traditional circular accelerators, including HERA and LEP, have been designed in one plane referenced to local gravity. For the SLC Arcs no such single plane exists. Methods and concepts developed to solve these and other problems, connected with themore » unique design of SLC, range from the first use of satellites for accelerator alignment, use of electronic laser theodolites for placement of components, computer control of the manual adjustment process, complete automation of the data flow incorporating the most advanced concepts of geodesy, strict separation of survey and alignment, to linear principal component analysis for the final statistical smoothing of the mechanical components.« less

Finite geometry effects of field-aligned currents

NASA Technical Reports Server (NTRS)

Fung, Shing F.; Hoffman, R. A.

1992-01-01

Results are presented of model calculations of the magnetic field produced by finite current regions that would be measured by a spaceborne magnetometer. Conditions were examined under which the infinite current sheet approximation can be applied to the calculation of the field-aligned current (FAC) density, using satellite magnetometer data. The accuracy of the three methods used for calculating the current sheet normal direction with respect to the spacecraft trajectory was assessed. It is shown that the model can be used to obtain the position and the orientation of the spacecraft trajectory through the FAC region.

Experimental findings on the underwater measurements uncertainty of speed of sound and the alignment system

NASA Astrophysics Data System (ADS)

Santos, T. Q.; Alvarenga, A. V.; Oliveira, D. P.; Mayworm, R. C.; Souza, R. M.; Costa-Félix, R. P. B.

2016-07-01

Speed of sound is an important quantity to characterize reference materials for ultrasonic applications, for instance. The alignment between the transducer and the test body is an key activity in order to perform reliable and consistent measurement. The aim of this work is to evaluate the influence of the alignment system to the expanded uncertainty of such measurement. A stainless steel cylinder was previously calibrated on an out of water system typically used for calibration of non-destructive blocks. Afterwards, the cylinder was calibrated underwater with two distinct alignment system: fixed and mobile. The values were statistically compared to the out-of-water measurement, considered the golden standard for such application. For both alignment systems, the normalized error was less than 0.8, leading to conclude that the both measurement system (under and out-of-water) do not diverge significantly. The gold standard uncertainty was 2.7 m-s-1, whilst the fixed underwater system resulted in 13 m-s-1, and the mobile alignment system achieved 6.6 m-s-1. After the validation of the underwater system for speed of sound measurement, it will be applied to certify Encapsulated Tissue Mimicking Material as a reference material for biotechnology application.

Directional plasticity rapidly improves 3D vestibulo-ocular reflex alignment in monkeys using a multichannel vestibular prosthesis.

PubMed

Dai, Chenkai; Fridman, Gene Y; Chiang, Bryce; Rahman, Mehdi A; Ahn, Joong Ho; Davidovics, Natan S; Della Santina, Charles C

2013-12-01

Bilateral loss of vestibular sensation can be disabling. We have shown that a multichannel vestibular prosthesis (MVP) can partly restore vestibular sensation as evidenced by improvements in the 3-dimensional angular vestibulo-ocular reflex (3D VOR). However, a key challenge is to minimize misalignment between the axes of eye and head rotation, which is apparently caused by current spread beyond each electrode's targeted nerve branch. We recently reported that rodents wearing a MVP markedly improve 3D VOR alignment during the first week after MVP activation, probably through the same central nervous system adaptive mechanisms that mediate cross-axis adaptation over time in normal individuals wearing prisms that cause visual scene movement about an axis different than the axis of head rotation. We hypothesized that rhesus monkeys would exhibit similar improvements with continuous prosthetic stimulation over time. We created bilateral vestibular deficiency in four rhesus monkeys via intratympanic injection of gentamicin. A MVP was mounted to the cranium, and eye movements in response to whole-body passive rotation in darkness were measured repeatedly over 1 week of continuous head motion-modulated prosthetic electrical stimulation. 3D VOR responses to whole-body rotations about each semicircular canal axis were measured on days 1, 3, and 7 of chronic stimulation. Horizontal VOR gain during 1 Hz, 50 °/s peak whole-body rotations before the prosthesis was turned on was <0.1, which is profoundly below normal (0.94 ± 0.12). On stimulation day 1, VOR gain was 0.4-0.8, but the axis of observed eye movements aligned poorly with head rotation (misalignment range ∼30-40 °). Substantial improvement of axis misalignment was observed after 7 days of continuous motion-modulated prosthetic stimulation under normal diurnal lighting. Similar improvements were noted for all animals, all three axes of rotation tested, for all sinusoidal frequencies tested (0.05-5 Hz), and for high-acceleration transient rotations. VOR asymmetry changes did not reach statistical significance, although they did trend toward slight improvement over time. Prior studies had already shown that directional plasticity reduces misalignment when a subject with normal labyrinths views abnormal visual scene movement. Our results show that the converse is also true: individuals receiving misoriented vestibular sensation under normal viewing conditions rapidly adapt to restore a well-aligned 3D VOR. Considering the similarity of VOR physiology across primate species, similar effects are likely to occur in humans using a MVP to treat bilateral vestibular deficiency.

Temporary divergence paralysis in viral meningitis.

PubMed

Bakker, Stef L M; Gan, Ivan M

2008-06-01

A 43-year-old woman who reported diplopia and headache was found to have comitant esotropia at distance fixation and normal alignment at reading distance (divergence paralysis). Eye movement, including abduction, was normal as was the rest of the neurologic examination. Brain MRI was normal. Lumbar puncture showed an elevated opening pressure and a cerebrospinal fluid formula consistent with viral meningitis. The patient was treated with intravenous fluids and analgesics and with a temporary prism to alleviate diplopia. Within 3 weeks, she had fully recovered. This is the first report of divergence palsy in viral meningitis.

Understanding the nanoscale local buckling behavior of vertically aligned MWCNT arrays with van der Waals interactions

NASA Astrophysics Data System (ADS)

Li, Yupeng; Kim, Hyung-Ick; Wei, Bingqing; Kang, Junmo; Choi, Jae-Boong; Nam, Jae-Do; Suhr, Jonghwan

2015-08-01

The local buckling behavior of vertically aligned carbon nanotubes (VACNTs) has been investigated and interpreted in the view of a collective nanotube response by taking van der Waals interactions into account. To the best of our knowledge, this is the first report on the case of collective VACNT behavior regarding van der Waals force among nanotubes as a lateral support effect during the buckling process. The local buckling propagation and development of VACNTs were experimentally observed and theoretically analyzed by employing finite element modeling with lateral support from van der Waals interactions among nanotubes. Both experimental and theoretical analyses show that VACNTs buckled in the bottom region with many short waves and almost identical wavelengths, indicating a high mode buckling. Furthermore, the propagation and development mechanism of buckling waves follow the wave damping effect.The local buckling behavior of vertically aligned carbon nanotubes (VACNTs) has been investigated and interpreted in the view of a collective nanotube response by taking van der Waals interactions into account. To the best of our knowledge, this is the first report on the case of collective VACNT behavior regarding van der Waals force among nanotubes as a lateral support effect during the buckling process. The local buckling propagation and development of VACNTs were experimentally observed and theoretically analyzed by employing finite element modeling with lateral support from van der Waals interactions among nanotubes. Both experimental and theoretical analyses show that VACNTs buckled in the bottom region with many short waves and almost identical wavelengths, indicating a high mode buckling. Furthermore, the propagation and development mechanism of buckling waves follow the wave damping effect. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03581c

Surface Spectroscopic Signatures of Mechanical Deformation in HDPE.

PubMed

Averett, Shawn C; Stanley, Steven K; Hanson, Joshua J; Smith, Stacey J; Patterson, James E

2018-01-01

High-density polyethylene (HDPE) has been extensively studied, both as a model for semi-crystalline polymers and because of its own industrial utility. During cold drawing, crystalline regions of HDPE are known to break up and align with the direction of tensile load. Structural changes due to deformation should also manifest at the surface of the polymer, but until now, a detailed molecular understanding of how the surface responds to mechanical deformation has been lacking. This work establishes a precedent for using vibrational sum-frequency generation (VSFG) spectroscopy to investigate changes in the molecular-level structure of the surface of HDPE after cold drawing. X-ray diffraction (XRD) was used to confirm that the observed surface behavior corresponds to the expected bulk response. Before tensile loading, the VSFG spectra indicate that there is significant variability in the surface structure and tilt of the methylene groups away from the surface normal. After deformation, the VSFG spectroscopic signatures are notably different. These changes suggest that hydrocarbon chains at the surface of visibly necked HDPE are aligned with the direction of loading, while the associated methylene groups are oriented with the local C 2 v symmetry axis roughly parallel to the surface normal. Small amounts of unaltered material are also found at the surface of necked HDPE, with the relative amount of unaltered material decreasing as the amount of deformation increases. Aspects of the nonresonant SFG response in the transition zone between necked and undeformed polymer provide additional insight into the deformation process and may provide the first indication of mechanical deformation. Nonlinear surface spectroscopy can thus be used as a noninvasive and nondestructive tool to probe the stress history of a HPDE sample in situations where X-ray techniques are not available or not applicable. Vibrational sum-frequency generation thus has great potential as a platform for material state awareness (MSA) and should be considered as part of a broader suite of tools for such applications.

Cholesterol-Based Grafted Polymer Brushes as Alignment Coating with Temperature-Tuned Anchoring for Nematic Liquid Crystals.

PubMed

Stetsyshyn, Yurij; Raczkowska, Joanna; Budkowski, Andrzej; Awsiuk, Kamil; Kostruba, Andriy; Nastyshyn, Svyatoslav; Harhay, Khrystyna; Lychkovskyy, Edward; Ohar, Halyna; Nastishin, Yuriy

2016-10-11

Novel alignment coating with temperature-tuned anchoring for nematic liquid crystals (NLCs) was successfully fabricated in three step process, involving polymerization of poly(cholesteryl methacrylate) (PChMa) from oligoproxide grafted to the glass surface premodified with 3-aminopropyltriethoxysilane. Molecular composition, thickness, wettability of the PChMa coating and its alignment action for a NLC were examined with time of flight-secondary ion mass spectrometry, ellipsometry, contact angle measurements, polarization optical microscopy and commercially produced PolScope technique allowing for mapping of the optic axis and optical retardance within the microscope field view. We find that the PChMa coating provides a specific monotonous increase (decrease) in the tilt angle of the NLC director with respect to the substrates normal upon heating (cooling) referred to as anchoring tuning.

An unsupervised video foreground co-localization and segmentation process by incorporating motion cues and frame features

NASA Astrophysics Data System (ADS)

Zhang, Chao; Zhang, Qian; Zheng, Chi; Qiu, Guoping

2018-04-01

Video foreground segmentation is one of the key problems in video processing. In this paper, we proposed a novel and fully unsupervised approach for foreground object co-localization and segmentation of unconstrained videos. We firstly compute both the actual edges and motion boundaries of the video frames, and then align them by their HOG feature maps. Then, by filling the occlusions generated by the aligned edges, we obtained more precise masks about the foreground object. Such motion-based masks could be derived as the motion-based likelihood. Moreover, the color-base likelihood is adopted for the segmentation process. Experimental Results show that our approach outperforms most of the State-of-the-art algorithms.

Dynamical formation of spatially localized arrays of aligned nanowires in plastic films with magnetic anisotropy.

PubMed

Fragouli, Despina; Buonsanti, Raffaella; Bertoni, Giovanni; Sangregorio, Claudio; Innocenti, Claudia; Falqui, Andrea; Gatteschi, Dante; Cozzoli, Pantaleo Davide; Athanassiou, Athanassia; Cingolani, Roberto

2010-04-27

We present a simple technique for magnetic-field-induced formation, assembling, and positioning of magnetic nanowires in a polymer film. Starting from a polymer/iron oxide nanoparticle casted solution that is allowed to dry along with the application of a weak magnetic field, nanocomposite films incorporating aligned nanocrystal-built nanowire arrays are obtained. The control of the dimensions of the nanowires and of their localization across the polymer matrix is achieved by varying the duration of the applied magnetic field, in combination with the evaporation dynamics. These multifunctional anisotropic free-standing nanocomposite films, which demonstrate high magnetic anisotropy, can be used in a wide field of technological applications, ranging from sensors to microfluidics and magnetic devices.

Memory-efficient dynamic programming backtrace and pairwise local sequence alignment.

PubMed

Newberg, Lee A

2008-08-15

A backtrace through a dynamic programming algorithm's intermediate results in search of an optimal path, or to sample paths according to an implied probability distribution, or as the second stage of a forward-backward algorithm, is a task of fundamental importance in computational biology. When there is insufficient space to store all intermediate results in high-speed memory (e.g. cache) existing approaches store selected stages of the computation, and recompute missing values from these checkpoints on an as-needed basis. Here we present an optimal checkpointing strategy, and demonstrate its utility with pairwise local sequence alignment of sequences of length 10,000. Sample C++-code for optimal backtrace is available in the Supplementary Materials. Supplementary data is available at Bioinformatics online.

Spontaneous Magnetic Alignment by Yearling Snapping Turtles: Rapid Association of Radio Frequency Dependent Pattern of Magnetic Input with Novel Surroundings

PubMed Central

Landler, Lukas; Painter, Michael S.; Youmans, Paul W.; Hopkins, William A.; Phillips, John B.

2015-01-01

We investigated spontaneous magnetic alignment (SMA) by juvenile snapping turtles using exposure to low-level radio frequency (RF) fields at the Larmor frequency to help characterize the underlying sensory mechanism. Turtles, first introduced to the testing environment without the presence of RF aligned consistently towards magnetic north when subsequent magnetic testing conditions were also free of RF (‘RF off → RF off’), but were disoriented when subsequently exposed to RF (‘RF off → RF on’). In contrast, animals initially introduced to the testing environment with RF present were disoriented when tested without RF (‘RF on → RF off’), but aligned towards magnetic south when tested with RF (‘RF on → RF on’). Sensitivity of the SMA response of yearling turtles to RF is consistent with the involvement of a radical pair mechanism. Furthermore, the effect of RF appears to result from a change in the pattern of magnetic input, rather than elimination of magnetic input altogether, as proposed to explain similar effects in other systems/organisms. The findings show that turtles first exposed to a novel environment form a lasting association between the pattern of magnetic input and their surroundings. However, under natural conditions turtles would never experience a change in the pattern of magnetic input. Therefore, if turtles form a similar association of magnetic cues with the surroundings each time they encounter unfamiliar habitat, as seems likely, the same pattern of magnetic input would be associated with multiple sites/localities. This would be expected from a sensory input that functions as a global reference frame, helping to place multiple locales (i.e., multiple local landmark arrays) into register to form a global map of familiar space. PMID:25978736

Spontaneous magnetic alignment by yearling snapping turtles: rapid association of radio frequency dependent pattern of magnetic input with novel surroundings.

PubMed

Landler, Lukas; Painter, Michael S; Youmans, Paul W; Hopkins, William A; Phillips, John B

2015-01-01

We investigated spontaneous magnetic alignment (SMA) by juvenile snapping turtles using exposure to low-level radio frequency (RF) fields at the Larmor frequency to help characterize the underlying sensory mechanism. Turtles, first introduced to the testing environment without the presence of RF aligned consistently towards magnetic north when subsequent magnetic testing conditions were also free of RF ('RF off → RF off'), but were disoriented when subsequently exposed to RF ('RF off → RF on'). In contrast, animals initially introduced to the testing environment with RF present were disoriented when tested without RF ('RF on → RF off'), but aligned towards magnetic south when tested with RF ('RF on → RF on'). Sensitivity of the SMA response of yearling turtles to RF is consistent with the involvement of a radical pair mechanism. Furthermore, the effect of RF appears to result from a change in the pattern of magnetic input, rather than elimination of magnetic input altogether, as proposed to explain similar effects in other systems/organisms. The findings show that turtles first exposed to a novel environment form a lasting association between the pattern of magnetic input and their surroundings. However, under natural conditions turtles would never experience a change in the pattern of magnetic input. Therefore, if turtles form a similar association of magnetic cues with the surroundings each time they encounter unfamiliar habitat, as seems likely, the same pattern of magnetic input would be associated with multiple sites/localities. This would be expected from a sensory input that functions as a global reference frame, helping to place multiple locales (i.e., multiple local landmark arrays) into register to form a global map of familiar space.

Location of the Common Peroneal Nerve in Valgus Knees-Is the Reported Safe Zone for Well-Aligned Knees Applicable?

PubMed

Yang, Dejin; Shao, Hongyi; Zhou, Yixin; Tang, Hao; Guo, Shengjie

2017-11-01

Lateral soft-tissue release can jeopardize the common peroneal nerve (CPN) in total knee arthroplasty for valgus knees. Previous studies reporting safe zones to protect the CPN were based on well-aligned knees. We conducted this study to compare the localization of the CPN in well-aligned knees and in valgus knees. We conducted a consecutive 3-dimensional radiographic study on magnetic resonance images of 58 well-aligned knees and 39 valgus knees. We measured the distance between the CPN and the tibia, as well as the mediolateral, anteroposterior, and angular location of the CPN. We compared the results between well-aligned knees and valgus knees. We found that there is an increased distance between the CPN and the tibia at the level of the tibial cut, but not at the joint line in valgus knees. It is safer to release the posterolateral capsule at the tibial side than at the level above this. The angular location and the mediolateral or anteroposterior location of the CPN in valgus knees are similar to those of well-aligned knees. The location of the CPN in valgus knees is similar to that in well-aligned knees. The previously reported safe zone in well-aligned knees is applicable in valgus knees to protect the CPN. Copyright © 2017 Elsevier Inc. All rights reserved.

Revisiting the phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered alignment of hypervariable sequences improves species tree inference.

PubMed

Swain, Timothy D

2018-01-01

The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in Text S1. Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA. Copyright © 2017 Elsevier Inc. All rights reserved.

Subcritical transition scenarios via linear and nonlinear localized optimal perturbations in plane Poiseuille flow

NASA Astrophysics Data System (ADS)

Farano, Mirko; Cherubini, Stefania; Robinet, Jean-Christophe; De Palma, Pietro

2016-12-01

Subcritical transition in plane Poiseuille flow is investigated by means of a Lagrange-multiplier direct-adjoint optimization procedure with the aim of finding localized three-dimensional perturbations optimally growing in a given time interval (target time). Space localization of these optimal perturbations (OPs) is achieved by choosing as objective function either a p-norm (with p\\gg 1) of the perturbation energy density in a linear framework; or the classical (1-norm) perturbation energy, including nonlinear effects. This work aims at analyzing the structure of linear and nonlinear localized OPs for Poiseuille flow, and comparing their transition thresholds and scenarios. The nonlinear optimization approach provides three types of solutions: a weakly nonlinear, a hairpin-like and a highly nonlinear optimal perturbation, depending on the value of the initial energy and the target time. The former shows localization only in the wall-normal direction, whereas the latter appears much more localized and breaks the spanwise symmetry found at lower target times. Both solutions show spanwise inclined vortices and large values of the streamwise component of velocity already at the initial time. On the other hand, p-norm optimal perturbations, although being strongly localized in space, keep a shape similar to linear 1-norm optimal perturbations, showing streamwise-aligned vortices characterized by low values of the streamwise velocity component. When used for initializing direct numerical simulations, in most of the cases nonlinear OPs provide the most efficient route to transition in terms of time to transition and initial energy, even when they are less localized in space than the p-norm OP. The p-norm OP follows a transition path similar to the oblique transition scenario, with slightly oscillating streaks which saturate and eventually experience secondary instability. On the other hand, the nonlinear OP rapidly forms large-amplitude bent streaks and skips the phases of streak saturation, providing a contemporary growth of all of the velocity components due to strong nonlinear coupling.

CORAL: aligning conserved core regions across domain families.

PubMed

Fong, Jessica H; Marchler-Bauer, Aron

2009-08-01

Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units. CORAL computes optimal local alignment of two profiles with heuristics to preserve continuity within core regions. We benchmarked its performance on curated domains in CDD, which have pre-defined core regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive curator-optimized alignments as standards of truth. CORAL improves alignment accuracy on core regions over general profile methods, returning a balanced score of 0.57 for over 80% of all domain families in CDD, compared with the highest balanced score of 0.45 from other methods. Further, CORAL provides E-values to aid in detecting homologous protein families and, by respecting block boundaries, produces alignments with improved 'readability' that facilitate manual refinement. CORAL will be included in future versions of the NCBI Cn3D/CDTree software, which can be downloaded at http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml. Supplementary data are available at Bioinformatics online.

Going, Going, Gone: Localizing Abrupt Offsets of Moving Objects

ERIC Educational Resources Information Center

Maus, Gerrit W.; Nijhawan, Romi

2009-01-01

When a moving object abruptly disappears, this profoundly influences its localization by the visual system. In Experiment 1, 2 aligned objects moved across the screen, and 1 of them abruptly disappeared. Observers reported seeing the objects misaligned at the time of the offset, with the continuing object leading. Experiment 2 showed that the…

The anterior borders of the clavicle and the acromion are not always aligned in the intact acromioclavicular joint: a cadaveric study.

PubMed

Barth, Johannes; Boutsiadis, Achilleas; Narbona, Pablo; Lädermann, Alexandre; Arrigoni, Paolo; Adams, Christopher R; Burkhart, Stephen S; Denard, Patrick J

2017-07-01

The aim of this study was to find reliable anatomic landmarks of the normal acromioclavicular joint (ACJ) that could enable the precise evaluation of the horizontal displacement of the clavicle after dislocation. The hypothesis was that the anterior borders of the acromion and the clavicle are always aligned in intact ACJs. In 30 cadaveric specimens, the anterior and posterior borders of the ACJ's articular facets and the most prominent anterior and posterior bony landmarks of the acromion and the clavicle were identified. The anterior and posterior overhang of the acromion and the clavicle was measured in relation to the borders of the articular facets. Therefore, the possible anterior and posterior alignment of the ACJ was evaluated. Anteriorly, only 18 ACJs (60%) were aligned whereas 7 (24%) had major overhang of the acromion and 3 (10%) had major overhang of the clavicle. Similarly, 18 cases (60%) were posteriorly aligned, whereas 6 (20%) had major clavicular overhang and 4 (14%) had major overhang of the acromion. In 78% of these cases, the ACJ was aligned as well anteriorly as posteriorly (P < .001). Finally, the larger the width of the acromion (P = .032) or the clavicle (P = .049), the better the posterior joint alignment. Our hypothesis was not verified. The acromion and clavicle are not perfectly aligned in a significant number of specimens with intact ACJs (40% of cases). The most reliable landmarks remain their articular facets. Copyright © 2017 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

DNA Translator and Aligner: HyperCard utilities to aid phylogenetic analysis of molecules.

PubMed

Eernisse, D J

1992-04-01

DNA Translator and Aligner are molecular phylogenetics HyperCard stacks for Macintosh computers. They manipulate sequence data to provide graphical gene mapping, conversions, translations and manual multiple-sequence alignment editing. DNA Translator is able to convert documented GenBank or EMBL documented sequences into linearized, rescalable gene maps whose gene sequences are extractable by clicking on the corresponding map button or by selection from a scrolling list. Provided gene maps, complete with extractable sequences, consist of nine metazoan, one yeast, and one ciliate mitochondrial DNAs and three green plant chloroplast DNAs. Single or multiple sequences can be manipulated to aid in phylogenetic analysis. Sequences can be translated between nucleic acids and proteins in either direction with flexible support of alternate genetic codes and ambiguous nucleotide symbols. Multiple aligned sequence output from diverse sources can be converted to Nexus, Hennig86 or PHYLIP format for subsequent phylogenetic analysis. Input or output alignments can be examined with Aligner, a convenient accessory stack included in the DNA Translator package. Aligner is an editor for the manual alignment of up to 100 sequences that toggles between display of matched characters and normal unmatched sequences. DNA Translator also generates graphic displays of amino acid coding and codon usage frequency relative to all other, or only synonymous, codons for approximately 70 select organism-organelle combinations. Codon usage data is compatible with spreadsheet or UWGCG formats for incorporation of additional molecules of interest. The complete package is available via anonymous ftp and is free for non-commercial uses.

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

PubMed Central

2011-01-01

Background Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome. Methods We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays. Results Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%. We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the SLC45A3-ELK4 e4-e2 TIC to ERG-negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer cell lines. Conclusions Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues. Prostate and reference samples exhibit a wide range of TIC events, involving more genes than estimated previously using ESTs. Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as MSMB-NCOA4, may play functional roles in cancer. PMID:21261984

Straightening the Eyes Doesn't Rebalance the Brain

PubMed Central

Zhou, Jiawei; Wang, Yonghua; Feng, Lixia; Wang, Jiafeng; Hess, Robert F.

2017-01-01

Surgery to align the two eyes is commonly used in treating strabismus. However, the role of strabismic surgery on patients' binocular visual processing is not yet fully understood. In this study, we asked two questions: (1) Does realigning the eyes by strabismic surgery produce an immediate benefit to patients' sensory eye balance? (2) If not, is there a subsequent period of “alignment adaptation” akin to refractive adaptation where sensory benefits to binocular function accrue? Seventeen patients with strabismus (mean age: 17.06 ± 5.16 years old) participated in our experiment. All participants had normal or corrected to normal visual acuity (LogMAR < 0.10) in the two eyes. We quantitatively measured their sensory eye balance before and after surgery using a binocular phase combination paradigm. For the seven patients whose sensory eye balance was measured before surgery, we found no significant change [t(6) = −0.92; p = 0.39] in the sensory eye balance measured 0.5–1 months after the surgery, indicating that the surgical re-alignment didn't by itself produce any immediate benefit for sensory eye balance. To answer the second question, we measured 16 patients' sensory eye balance at around 5–12 months after their eyes had been surgically re-aligned and compared this with our measurements 0.5–1 months after surgery. We found no significant change [t(15) = −0.89; p = 0.39] in sensory eye balance 5–12 months after the surgery. These results suggest that strabismic surgery while being necessary is not itself sufficient for re-establishing balanced sensory eye dominance. PMID:28955214

Beauty and the beast: Aligning national curriculum standards with state (high school) graduation requirements

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

Linder-Scholer, B.

1994-12-31

An overview of SCI/MATH/MN - Minnesota`s standards-based, systemic approach to the reform and improvement of the K-12 science and mathematics education delivery system - is offered as an illustration of the challenges of aligning state educational practices with the national curriculum standards, and as a model for business involvement in state educational policy issues that will enable fundamental, across-the-system reform. SCI/MATH/MN illustrates the major challenges involved in developing a statewide vision for math and science education reform, articulating frameworks aligned with the national standards, building capacity for system-oriented change at the local level, and involving business in systemic reform.

Distributioin, orientation and scales of the field-aligned currents measured by Swarm

NASA Astrophysics Data System (ADS)

Yang, J.; Dunlop, M. W.

2016-12-01

We have statistically studied the R1, R2 and net field aligned currents using the FAC data of the Swarm satellites. We also have investigated the statistical, dual-spacecraft correlations of field-aligned current signatures between two Swarm spacecraft (A and C). For the first time we have inferred the orientations of the current sheets of FACs directly, using the maximum correlations, obtained from sliding data segments, which show clear trends in magnetic local time (MLT). To compare with this we also check the MVAB method. To explore the scale and variability of the current sheet supposition, we investigate the MLT dependence of the maximum correlations in different time shift or longitude shift bins.

Perceptually aligning apical frequency regions leads to more binaural fusion of speech in a cochlear implant simulation.

PubMed

Staisloff, Hannah E; Lee, Daniel H; Aronoff, Justin M

2016-07-01

For bilateral cochlear implant users, the left and right arrays are typically not physically aligned, resulting in a degradation of binaural fusion, which can be detrimental to binaural abilities. Perceptually aligning the two arrays can be accomplished by disabling electrodes in one ear that do not have a perceptually corresponding electrode in the other side. However, disabling electrodes at the edges of the array will cause compression of the input frequency range into a smaller cochlear extent, which may result in reduced spectral resolution. An alternative approach to overcome this mismatch would be to only align one edge of the array. By aligning either only the apical or basal end of the arrays, fewer electrodes would be disabled, potentially causing less reduction in spectral resolution. The goal of this study was to determine the relative effect of aligning either the basal or apical end of the electrode with regards to binaural fusion. A vocoder was used to simulate cochlear implant listening conditions in normal hearing listeners. Speech signals were vocoded such that the two ears were either predominantly aligned at only the basal or apical end of the simulated arrays. The experiment was then repeated with a spectrally inverted vocoder to determine whether the detrimental effects on fusion were related to the spectral-temporal characteristics of the stimuli or the location in the cochlea where the misalignment occurred. In Experiment 1, aligning the basal portion of the simulated arrays led to significantly less binaural fusion than aligning the apical portions of the simulated array. However, when the input was spectrally inverted, aligning the apical portion of the simulated array led to significantly less binaural fusion than aligning the basal portions of the simulated arrays. These results suggest that, for speech, with its predominantly low frequency spectral-temporal modulations, it is more important to perceptually align the apical portion of the array to better preserve binaural fusion. By partially aligning these arrays, cochlear implant users could potentially increase their ability to fuse speech sounds presented to the two ears while maximizing spectral resolution. Copyright © 2016 Elsevier B.V. All rights reserved.

Differences in male and female spino-pelvic alignment in asymptomatic young adults: a three-dimensional analysis using upright low-dose digital biplanar X-rays.

PubMed

Janssen, Michiel M A; Drevelle, Xavier; Humbert, Ludovic; Skalli, Wafa; Castelein, René M

2009-11-01

A three-dimensional analysis of spino-pelvic alignment in 60 asymptomatic young adult males and females. To analyze the differences in sagittal spino-pelvic alignment in a group of asymptomatic young adult males and females and describe gender specific reference values. Several spinal disorders like idiopathic scoliosis and Scheuermann's disease have a well-known sex-related prevalence ratio. As spino-pelvic alignment plays an important role in spinal biomechanics, it is imperative to analyze possible differences between the male and female spino-pelvic alignment. Furthermore, in spinal fusion surgery, normal sagittal balance should be recreated as closely as possible. An innovative biplanar ultra low-dose radiographic technique was used to obtain three-dimensional reconstructions of the spine (T1-L5), sacrum, and pelvis in a freestanding position of 30 asymptomatic young male and 30 young female adults. Values were calculated for thoracic kyphosis (T4-T12), lumbar lordosis (L1-S1), total and regional lumbopelvic lordosis (PRT12, PRL2, PRL4, and PRL5), sagittal plumb line of T1, T4, and T9 (HAT1, HAT4, and HAT9), T1-L5 sagittal spinal inclination, T9 sagittal offset, and pelvic parameters (pelvic tilt, sacral slope, and pelvic incidence). In addition, vertebral inclination in the sagittal plane of each vertebra was measured. Differences in spino-pelvic alignment between the sexes were analyzed. The female spine was more dorsally inclined (11 degrees vs. 8 degrees ; P = 0.003). High thoracic and thoracolumbar vertebrae were more dorsally inclined in women than in men. Thoracic kyphosis, lumbar lordosis, regional lumbopelvic lordosis, sagittal plumb lines, T9 sagittal offset, and pelvic parameters were not statistically different between the sexes. These results indicate that the female spine is definitely different from the male spine. The spine as whole and individual vertebrae in certain regions of the normal spine is more backwardly inclined in females than in males. Based on our previous research this signifies that these spinal regions are subjected to different biomechanical loading conditions. These vertebral segments are possibly less rotationally stable in females than in males.

A study of an alignment-less lithography method as an educational resource

NASA Astrophysics Data System (ADS)

Kai, Kazuho; Shiota, Koki; Nagaoka, Shiro; Mahmood, Mohamad Rusop Bin Haji; Kawai, Akira

2016-07-01

A simplification of the lithography process was studied. The simplification method of photolithography, named "alignment-less lithography" was proposed by omitting the photomask alignment process in photolithography process using mechanically aligned photomasks and substrate by using a simple jig on which countersinks were formed. Photomasks made of glass and the photomasks made of transparent plastic sheets were prepared for the process. As the result, approximately 5µm in the case of the glass mask, and 20µm in the case of the OHP mask were obtained with repetitive accuracies, respectively. It was confirmed that the alignment-less lithography method was successful. The possibility of the application to an educational program, such as a heuristic for solving problems was suggested using the method with the OHP mask. The nMOS FET fabrication process was successfully demonstrated using this method. The feasibility of this process was confirmed. It is expected that a totally simplified device fabrication process can be achievable when combined with other simplifications, such ass the simplified impurity diffusion processes using PSG and BSG thin film as diffusion source prepared by the Sol-Gel material under normal air environment.

A synoptic study of the nature and effects of field aligned low energy electron precipitation in the auroral regions. Ph.D. Thesis - Catholic Univ. of America

NASA Technical Reports Server (NTRS)

Berko, F. W.

1972-01-01

A synoptic study is presented of field-aligned precipitation events observed during a 16-month period, representing a full 4 pi precession of the satellite orbital plane in magnetic local time. The morphology of this type of precipitation, its nature, and relationships between this phenomenon and other geophysical events are discussed in the context of the 16-month data base.

Mechanoresponsive, omni-directional and local matrix-degrading actin protrusions in human mesenchymal stem cells microencapsulated in a 3D collagen matrix.

PubMed

Ho, Fu Chak; Zhang, Wei; Li, Yuk Yin; Chan, Barbara Pui

2015-01-01

Cells are known to respond to multiple niche signals including extracellular matrix and mechanical loading. In others and our own studies, mechanical loading has been shown to induce the formation of cell alignment in 3D collagen matrix with random meshwork, challenging our traditional understanding on the necessity of having aligned substrates as the prerequisite of alignment formation. This motivates our adventure in deciphering the mechanism of loading-induced cell alignment and hence the discovery of the novel protrusive functional structure at the cell-matrix interface. Here we report the formation of mechanoresponsive, omni-directional and local matrix-degrading actin protrusions in human mesenchymal stem cells (hMSCs) microencapsulated in collagen following a shifted actin assembly/disassembly balance. These actin protrusive structures exhibit morphological and compositional similarity to filopodia and invadopodia but differ from them in stability, abundance, signaling and function. Without ruling out the possibility that these structures may comprise special subsets of filopodia and invadopodia, we propose to name them as mechanopodia so as to reveal their mechano-inductive mechanism. We also suggest that more intensive investigations are needed to delineate the functional significance and physiological relevance of these structures. This work identifies a brand new target for cell-matrix interaction and mechanoregulation studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Weak tectono-magmatic relationships along an obliquely convergent plate boundary: Sumatra, Indonesia

NASA Astrophysics Data System (ADS)

Acocella, Valerio; Bellier, Olivier; Sandri, Laura; Sébrier, Michel; Pramumijoyo, Subagyo

2018-02-01

The tectono-magmatic relationships along obliquely convergent plate boundaries, where strain partitioning promotes strike-slip structures along the volcanic arc, are poorly known. Here it is unclear if and, in case, how the strike-slip structures control volcanic processes, distribution and size. To better define the possible tectono-magmatic relationships along strike-slip arcs, we merge available information on the case study of Sumatra (Indonesia) with field structural data. The Sumatra arc (entire volcanic belt) consists of 48 active volcanoes. Of these, 46% lie within 10 km from the dextral Great Sumatra Fault (GSF), which carries most horizontal displacement on the overriding plate, whereas 27% lie at >20 km from the GSF. Among the volcanoes at <10 km from GSF, 48% show a possible structural relation to the GSF, whereas only 28% show a clear structural relation, lying in pull-aparts or releasing bends; these localized areas of transtension (local extensional zone) do not develop magmatic segments. There is no relation between the GSF along-strike slip rate variations and the volcanic productivity. The preferred N30°-N40°E volcano alignment and elongation are subparallel to the convergence vector or to the GSF. The structural field data, collected in the central and southern GSF, show, in addition to the dextral motions along NW-SE to N-S striking faults, also normal motions (extending WNW-ESE or NE-SW), suggesting local reactivations of the GSF. Overall, the collected data suggest a limited tectonic control on arc volcanism. The tectonic control is mostly expressed by the mean depth of the slab surface below the volcanoes (130±20 km) and, subordinately, local extension along the GSF. The latter, when WNW-ESE oriented (more common), may be associated with the overall tectonic convergence, as suggested by the structural data; conversely, when NE-SW oriented (less common), the extension may result from co- and post-seismic arc normal extension, as supported by the 2004 mega-earthquake measurements. Overall, the strike-slip arc of Sumatra has intermediate features between those of extensional and contractional arcs.

Zipping, entanglement, and the elastic modulus of aligned single-walled carbon nanotube films

PubMed Central

Won, Yoonjin; Gao, Yuan; Panzer, Matthew A.; Xiang, Rong; Maruyama, Shigeo; Kenny, Thomas W.; Cai, Wei; Goodson, Kenneth E.

2013-01-01

Reliably routing heat to and from conversion materials is a daunting challenge for a variety of innovative energy technologies––from thermal solar to automotive waste heat recovery systems––whose efficiencies degrade due to massive thermomechanical stresses at interfaces. This problem may soon be addressed by adhesives based on vertically aligned carbon nanotubes, which promise the revolutionary combination of high through-plane thermal conductivity and vanishing in-plane mechanical stiffness. Here, we report the data for the in-plane modulus of aligned single-walled carbon nanotube films using a microfabricated resonator method. Molecular simulations and electron microscopy identify the nanoscale mechanisms responsible for this property. The zipping and unzipping of adjacent nanotubes and the degree of alignment and entanglement are shown to govern the spatially varying local modulus, thereby providing the route to engineered materials with outstanding combinations of mechanical and thermal properties. PMID:24309375

Photonic Sorting of Aligned, Crystalline Carbon Nanotube Textiles.

PubMed

Bulmer, John S; Gspann, Thurid S; Orozco, Francisco; Sparkes, Martin; Koerner, Hilmar; Di Bernardo, A; Niemiec, Arkadiusz; Robinson, J W A; Koziol, Krzysztof K; Elliott, James A; O'Neill, William

2017-10-11

Floating catalyst chemical vapor deposition uniquely generates aligned carbon nanotube (CNT) textiles with individual CNT lengths magnitudes longer than competing processes, though hindered by impurities and intrinsic/extrinsic defects. We present a photonic-based post-process, particularly suited for these textiles, that selectively removes defective CNTs and other carbons not forming a threshold thermal pathway. In this method, a large diameter laser beam rasters across the surface of a partly aligned CNT textile in air, suspended from its ends. This results in brilliant, localized oxidation, where remaining material is an optically transparent film comprised of few-walled CNTs with profound and unique improvement in microstructure alignment and crystallinity. Raman spectroscopy shows substantial D peak suppression while preserving radial breathing modes. This increases the undoped, specific electrical conductivity at least an order of magnitude to beyond that of single-crystal graphite. Cryogenic conductivity measurements indicate intrinsic transport enhancement, opposed to simply removing nonconductive carbons/residual catalyst.

Self aligned hysteresis free carbon nanotube field-effect transistors

NASA Astrophysics Data System (ADS)

Shlafman, M.; Tabachnik, T.; Shtempluk, O.; Razin, A.; Kochetkov, V.; Yaish, Y. E.

2016-04-01

Hysteresis phenomenon in the transfer characteristics of carbon nanotube field effect transistor (CNT FET) is being considered as the main obstacle for successful realization of electronic devices based on CNTs. In this study, we prepare four kinds of CNTFETs and explore their hysteretic behavior. Two kinds of devices comprise on-surface CNTs (type I) and suspended CNTs (type II) with thin insulating layer underneath and a single global gate which modulates the CNT conductance. The third and fourth types (types III and IV) consist of suspended CNT over a metallic local gate underneath, where for type IV the local gate was patterned self aligned with the source and drain electrodes. The first two types of devices, i.e., type I and II, exhibit substantial hysteresis which increases with scanning range and sweeping time. Under high vacuum conditions and moderate electric fields ( |E |>4 ×106 V /cm ), the hysteresis for on-surface devices cannot be eliminated, as opposed to suspended devices. Interestingly, type IV devices exhibit no hysteresis at all at ambient conditions, and from the different roles which the global and local gates play for the four types of devices, we could learn about the hysteresis mechanism of this system. We believe that these self aligned hysteresis free FETs will enable the realization of different electronic devices and sensors based on CNTs.

Shear-Sensitive Liquid Crystal Coating Method Applied Through Transparent Test Surfaces

NASA Technical Reports Server (NTRS)

Reda, Daniel C.; Wilder, Michael C.

1999-01-01

Research conducted at NASA Ames Research Center has shown that the color-change response of a shear-sensitive liquid crystal coating (SSLCC) to aerodynamic shear depends on both the magnitude of the local shear vector and its direction relative to the observer's in-plane line of sight. In conventional applications, the surface of the SSLCC exposed to aerodynamic shear is illuminated with white light from the normal direction and observed from an oblique above-plane view angle of order 30 deg. In this top-light/top-view mode, shear vectors with components directed away from the observer cause the SSLCC to exhibit color-change responses. At any surface point, the maximum color change (measured from the no-shear red or orange color) always occurs when the local vector is aligned with, and directed away from, the observer. The magnitude of the color change at this vector-observer-aligned orientation scales directly with shear stress magnitude. Conversely, any surface point exposed to a shear vector with a component directed toward the observer exhibits a non-color-change response, always characterized by a rusty-red or brown color, independent of both shear magnitude and direction. These unique, highly directional color-change responses of SSLCCs to aerodynamic shear allow for the full-surface visualization and measurement of continuous shear stress vector distributions. The objective of the present research was to investigate application of the SSLCC method through a transparent test surface. In this new back-light/back-view mode, the exposed surface of the SSLCC would be subjected to aerodynamic shear stress while the contact surface between the SSLCC and the solid, transparent wall would be illuminated and viewed in the same geometrical arrangement as applied in conventional applications. It was unknown at the outset whether or not color-change responses would be observable from the contact surface of the SSLCC, and, if seen, how these color-change responses might relate to those observed in standard practice.

Maintaining Aura's Orbit Requirements While Performing Orbit Maintenance Maneuvers Containing an Orbit Normal Delta-V Component

NASA Technical Reports Server (NTRS)

Johnson, Megan R.; Petersen, Jeremy D.

2014-01-01

The Earth Observing System (EOS) Afternoon Constellation consists of five member missions (GCOM-W1, Aqua, CALIPSO, CloudSat, and Aura), each of which maintain a frozen, sun-synchronous orbit with a 16-day repeating ground track that follows the Worldwide Reference System-2 (WRS-2). Under nominal science operations for Aura, the propulsion system is oriented such that the resultant thrust vector is aligned 13.493 degrees away from the velocity vector along the yaw axis. When performing orbit maintenance maneuvers, the spacecraft performs a yaw slew to align the thrust vector in the appropriate direction. A new Drag Make Up (DMU) maneuver operations scheme has been implemented for Aura alleviating the need for the 13.493 degree yaw slew. The focus of this investigation is to assess the impact that no-slew DMU maneuver operations will have on Aura's Mean Local Time (MLT) which drives the required along track separation between Aura and the constellation members, as well as Aura's frozen orbit properties, eccentricity and argument of perigee. Seven maneuver strategies were analyzed to determine the best operational approach. A mirror pole strategy, with maneuvers alternating at the North and South poles, was implemented operationally to minimize impact to the MLT. Additional analysis determined that the mirror pole strategy could be further modified to include frozen orbit maneuvers and thus maintain both MLT and the frozen orbit properties under noslew operations.

Processes of Compression-Expansion and Subsidence-Uplift detected by the Spatial Inclinometer (IESHI) in the El Hierro Island eruption (October, 2011)

NASA Astrophysics Data System (ADS)

Prates, G.; Berrocoso, M.; Fernández-Ros, A.; García, A.; Ortiz, R.

2012-04-01

El Hierro Island (Canary Islands, Spain) has undergone a submarine eruption a few kilometers to its southeast, detected October 10, on the rift alignment that cuts across the island. However, the seismicity level suddenly increased around July 17 and ground deformation was detected by the only continuously observed GNSS-GPS (Global Navigation Satellite Systems - Global Positioning System) benchmark FRON in the El Golfo area. Based on that information several other GNSS-GPS benchmarks were installed, some of which continuously observed as well. A normal vector analysis was applied to these collected data. The normal vector magnitude variation identified local extension-compression regimes, while the normal vector inclination showed the relative height variation between the three benchmarks that define the plan to which normal vector is analyzed. To accomplish this analysis the data was previously processed to achieve positioning solutions every 30 minutes using the Bernese GPS Software 5.0, further enhanced by a Discrete Kalman Filter, giving an overall millimeter level precision. These solutions were reached using the IGS (International GNSS Service) ultra-rapid orbits and the double-differenced ionosphere-free combination. With this strategy the positioning solutions were attained in near real-time. Later with the IGS rapid orbits the data was reprocessed to provide added confidence to the solutions. Two triangles were then considered, a smaller one located in the El Golfo area within the historically collapsed caldera, and a larger one defined by benchmarks placed in Valverde, El Golfo and La Restinga, the town closest to the eruption's location, covering almost the entire Island's surface above sea level. With these two triangles the pre-eruption and post-eruption deformation suffered by El Hierro's surface will be further analyzed.

Local vibrational modes of the water dimer - Comparison of theory and experiment

NASA Astrophysics Data System (ADS)

Kalescky, R.; Zou, W.; Kraka, E.; Cremer, D.

2012-12-01

Local and normal vibrational modes of the water dimer are calculated at the CCSD(T)/CBS level of theory. The local H-bond stretching frequency is 528 cm-1 compared to a normal mode stretching frequency of just 143 cm-1. The adiabatic connection scheme between local and normal vibrational modes reveals that the lowering is due to mass coupling, a change in the anharmonicity, and coupling with the local HOH bending modes. The local mode stretching force constant is related to the strength of the H-bond whereas the normal mode stretching force constant and frequency lead to an erroneous underestimation of the H-bond strength.

Dielectric properties of vertically aligned multi-walled carbon nanotubes in the terahertz and mid-infrared range

NASA Astrophysics Data System (ADS)

Thomson, Mark D.; Zouaghi, Wissem; Meng, Fanqi; Wiecha, Matthias M.; Rabia, Kaneez; Heinlein, Thorsten; Hussein, Laith; Babu, Deepu; Yadav, Sandeep; Engstler, Jörg; Schneider, Jörg J.; Nicoloso, Norbert; Rychetský, Ivan; Kužel, Petr; Roskos, Hartmut G.

2018-01-01

We investigate the broadband dielectric properties of vertically aligned, multi-wall carbon nanotubes (VACNT), over both the terahertz (THz) and mid-infrared spectral ranges. The nominally undoped, metallic VACNT samples are probed at normal incidence, i.e. the response is predominantly due to polarisation perpendicular to the CNT axis. A detailed comparison of various conductivity models and previously reported results is presented for the non-Drude behaviour we observe in the conventional THz range (up to 2.5 THz). Extension to the mid-infrared range reveals an absorption peak at \

Silicon on insulator self-aligned transistors

DOEpatents

McCarthy, Anthony M.

2003-11-18

A method for fabricating thin-film single-crystal silicon-on-insulator (SOI) self-aligned transistors. Standard processing of silicon substrates is used to fabricate the transistors. Physical spaces, between the source and gate, and the drain and gate, introduced by etching the polysilicon gate material, are used to provide connecting implants (bridges) which allow the transistor to perform normally. After completion of the silicon substrate processing, the silicon wafer is bonded to an insulator (glass) substrate, and the silicon substrate is removed leaving the transistors on the insulator (glass) substrate. Transistors fabricated by this method may be utilized, for example, in flat panel displays, etc.

Is the low-l microwave background cosmic?

PubMed

Schwarz, Dominik J; Starkman, Glenn D; Huterer, Dragan; Copi, Craig J

2004-11-26

The large-angle (low-l) correlations of the cosmic microwave background exhibit several statistically significant anomalies compared to the standard inflationary cosmology. We show that the quadrupole plane and the three octopole planes are far more aligned than previously thought (99.9% C.L.). Three of these planes are orthogonal to the ecliptic at 99.1% C.L., and the normals to these planes are aligned at 99.6% C.L. with the direction of the cosmological dipole and with the equinoxes. The remaining octopole plane is orthogonal to the supergalactic plane at 99.6% C.L.

Effect of stump flexion contracture with and without prosthetic alignment intervention towards postural stability among transtibial prosthesis users

NASA Astrophysics Data System (ADS)

Ghazali, M. F.; Razak, N. A. Abd; Abu Osman, N. A.; Gholizadeh, H.

2017-06-01

Knee flexion contracture on a stump side is a phenomenon in which the stump cannot move in normal range of motion (ROM) or cannot be fully extended. This study has been carried out by using Biodex Stability System (BSS) in order to investigate the effect of stump flexion contracture towards the postural stability among the transtibial prosthesis users with the intervention of alignment accommodation. The BSS provides the reading of anterior-posterior stability index (APSI), medial-lateral stability index (MLSI), and overall stability index (OSI). Higher reading of the index indicates lesser stability. Each of the subjects had been tested in three different sessions that were Visit 1 (before contracture improvement), Visit 2 (after contracture improvement without alignment readjustment), and Visit 3 (after contracture improvement with alignment readjustment). The APSI reading was significantly higher during Visit 2 compared to Visit 1 and Visit 3. The OSI during Visit 2 was also found significantly higher compared to Visit 3. In Visit 2, the degree of contracture was significantly improved with 44.1% less than Visit 1. The stability index in anterior-posterior aspect (APSI) was proven to be lower as the prosthetic alignment was adjusted according to the ROM of knee. This finding explained that the alignment set up based on the adaptation with the stump’s ROM can contribute positively in maintaining postural stability.

Evolution of the shock front and turbulence structures in the shock/turbulence interaction

NASA Technical Reports Server (NTRS)

Kevlahan, N.; Mahesh, K.; Lee, S.

1992-01-01

The interaction of a weak shock front with isotropic turbulence has been investigated using Direct Numerical Simulation (DNS). Two problems were considered: the ability of the field equation (the equation for a propagating surface) to model the shock; and a quantitative study of the evolution of turbulence structure using the database generated by Lee et al. Field equation model predictions for front shape have been compared with DNS results; good agreement is found for shock wave interaction with 2D turbulence and for a single steady vorticity wave. In the interaction of 3D isotropic turbulence with a normal shock, strong alignment of vorticity with the intermediate eigenvector of the rate of strain tensor (S(sup *)(sub ij) = S(sub ij) - (1/3)(delta(sub ij))(S(sub kk))) is seen to develop upstream of the shock and to be further amplified on passage through the shock. Vorticity tends to align at 90 deg to the largest eigenvector, but there is no preferred alignment with the smallest eigenvector. Upstream of the shock, the alignments continue to develop even after the velocity derivative skewness saturates. There is a significant tendency, which increases with time throughout the computational domain, for velocity to align with vorticity. The alignment between velocity and vorticity is strongest in eddy regions and weakest in convergence regions.

Structure-rheology relationship in a sheared lamellar fluid.

PubMed

Jaju, S J; Kumaran, V

2016-03-01

The structure-rheology relationship in the shear alignment of a lamellar fluid is studied using a mesoscale model which provides access to the lamellar configurations and the rheology. Based on the equations and free energy functional, the complete set of dimensionless groups that characterize the system are the Reynolds number (ργL(2)/μ), the Schmidt number (μ/ρD), the Ericksen number (μγ/B), the interface sharpness parameter r, the ratio of the viscosities of the hydrophilic and hydrophobic parts μ(r), and the ratio of the system size and layer spacing (L/λ). Here, ρ and μ are the fluid density and average viscosity, γ is the applied strain rate, D is the coefficient of diffusion, B is the compression modulus, μ(r) is the maximum difference in the viscosity of the hydrophilic and hydrophobic parts divided by the average viscosity, and L is the system size in the cross-stream direction. The lattice Boltzmann method is used to solve the concentration and momentum equations for a two dimensional system of moderate size (L/λ=32) and for a low Reynolds number, and the other parameters are systematically varied to examine the qualitative features of the structure and viscosity evolution in different regimes. At low Schmidt numbers where mass diffusion is faster than momentum diffusion, there is fast local formation of randomly aligned domains with "grain boundaries," which are rotated by the shear flow to align along the extensional axis as time increases. This configuration offers a high resistance to flow, and the layers do not align in the flow direction even after 1000 strain units, resulting in a viscosity higher than that for an aligned lamellar phase. At high Schmidt numbers where momentum diffusion is fast, the shear flow disrupts layers before they are fully formed by diffusion, and alignment takes place by the breakage and reformation of layers by shear, resulting in defects (edge dislocations) embedded in a background of nearly aligned layers. At high Ericksen number where the viscous forces are large compared to the restoring forces due to layer compression and bending, shear tends to homogenize the concentration field, and the viscosity decreases significantly. At very high Ericksen number, shear even disrupts the layering of the lamellar phase. At low Ericksen number, shear results in the formation of well aligned layers with edge dislocations. However, these edge dislocations take a long time to anneal; the relatively small misalignment due to the defects results in a large increase in viscosity due to high layer stiffness and due to shear localization, because the layers between defects get pinned and move as a plug with no shear. An increase in the viscosity contrast between the hydrophilic and hydrophobic parts does not alter the structural characteristics during alignment. However, there is a significant increase in the viscosity, due to pinning of the layers between defects, which results in a plug flow between defects and a localization of the shear to a part of the domain.

Object recognition and localization from 3D point clouds by maximum-likelihood estimation

NASA Astrophysics Data System (ADS)

Dantanarayana, Harshana G.; Huntley, Jonathan M.

2017-08-01

We present an algorithm based on maximum-likelihood analysis for the automated recognition of objects, and estimation of their pose, from 3D point clouds. Surfaces segmented from depth images are used as the features, unlike `interest point'-based algorithms which normally discard such data. Compared to the 6D Hough transform, it has negligible memory requirements, and is computationally efficient compared to iterative closest point algorithms. The same method is applicable to both the initial recognition/pose estimation problem as well as subsequent pose refinement through appropriate choice of the dispersion of the probability density functions. This single unified approach therefore avoids the usual requirement for different algorithms for these two tasks. In addition to the theoretical description, a simple 2 degrees of freedom (d.f.) example is given, followed by a full 6 d.f. analysis of 3D point cloud data from a cluttered scene acquired by a projected fringe-based scanner, which demonstrated an RMS alignment error as low as 0.3 mm.

Molecular dynamics study of response of liquid N,N-dimethylformamide to externally applied electric field using a polarizable force field

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

Gao, Weimin; Niu, Haitao; Lin, Tong

2014-01-28

The behavior of Liquid N,N-dimethylformamide subjected to a wide range of externally applied electric fields (from 0.001 V/nm to 1 V/nm) has been investigated through molecular dynamics simulation. To approach the objective the AMOEBA polarizable force field was extended to include the interaction of the external electric field with atomic partial charges and the contribution to the atomic polarization. The simulation results were evaluated with quantum mechanical calculations. The results from the present force field for the liquid at normal conditions were compared with the experimental and molecular dynamics results with non-polarizable and other polarizable force fields. The uniform externalmore » electric fields of higher than 0.01 V/nm have a significant effect on the structure of the liquid, which exhibits a variation in numerous properties, including molecular polarization, local cluster structure, rotation, alignment, energetics, and bulk thermodynamic and structural properties.« less

The origin of ultrahigh piezoelectricity in relaxor-ferroelectric solid solution crystals

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

Li, Fei; Zhang, Shujun; Yang, Tiannan

The discovery of ultrahigh piezoelectricity in relaxor-ferroelectric solid solution single crystals is a breakthrough in ferroelectric materials. A key signature of relaxor-ferroelectric solid solutions is the existence of polar nanoregions, a nanoscale inhomogeneity, that coexist with normal ferroelectric domains. Despite two decades of extensive studies, the contribution of polar nanoregions to the underlying piezoelectric properties of relaxor ferroelectrics has yet to be established. Here we quantitatively characterize the contribution of polar nanoregions to the dielectric/piezoelectric responses of relaxor-ferroelectric crystals using a combination of cryogenic experiments and phase-field simulations. The contribution of polar nanoregions to the room-temperature dielectric and piezoelectric propertiesmore » is in the range of 50–80%. A mesoscale mechanism is proposed to reveal the origin of the high piezoelectricity in relaxor ferroelectrics, where the polar nanoregions aligned in a ferroelectric matrix can facilitate polarization rotation. This mechanism emphasizes the critical role of local structure on the macroscopic properties of ferroelectric materials.« less

The origin of ultrahigh piezoelectricity in relaxor-ferroelectric solid solution crystals

DOE PAGES

Li, Fei; Zhang, Shujun; Yang, Tiannan; ...

2016-12-19

The discovery of ultrahigh piezoelectricity in relaxor-ferroelectric solid solution single crystals is a breakthrough in ferroelectric materials. A key signature of relaxor-ferroelectric solid solutions is the existence of polar nanoregions, a nanoscale inhomogeneity, that coexist with normal ferroelectric domains. Despite two decades of extensive studies, the contribution of polar nanoregions to the underlying piezoelectric properties of relaxor ferroelectrics has yet to be established. Here we quantitatively characterize the contribution of polar nanoregions to the dielectric/piezoelectric responses of relaxor-ferroelectric crystals using a combination of cryogenic experiments and phase-field simulations. The contribution of polar nanoregions to the room-temperature dielectric and piezoelectric propertiesmore » is in the range of 50–80%. A mesoscale mechanism is proposed to reveal the origin of the high piezoelectricity in relaxor ferroelectrics, where the polar nanoregions aligned in a ferroelectric matrix can facilitate polarization rotation. This mechanism emphasizes the critical role of local structure on the macroscopic properties of ferroelectric materials.« less

Reconstruction with fascia lata allograft of the posterior vertebra elements after resection for aneurysmal bone cyst in a child

PubMed Central

Schuster, Sergio; Biagini, Roberto; Casadei, Roberto; De Paolis, Massimiliano; Bertoni, Franco; Boriani, Stefano; Mercuri, Mario

2007-01-01

We report a case of ABC in a child where, after resection of the posterior spinal column of L1, we did a biological reconstruction using a posterior tension band with a segment of fascia lata allograft in tension between T12 and L2. After the long term follow up, X-ray and MRI controls showed a satisfactory alignment of the spine and no local recurrence. The patient now has no sign of spinal instability or deviation, with no kind of discomfort or pain, and has a normal life. In our experience this biological tension band interferes minimally with the growth of the spine, and has a less number of complications in comparison with other more aggressive methods and so is a good option for restoring the stability in young patients with benign spinal tumors that arises on the posterior column without having any kind of potential deviations. PMID:17426986

Ray-tracing studies and path-integrated gains of ELF unducted whistler mode waves in the earth's magnetosphere

NASA Technical Reports Server (NTRS)

Huang, C. Y.; Goertz, C. K.

1983-01-01

Gyroresonance and Landau resonance interactions between unducted low-frequency whistler waves and trapped electrons in the earth's plasmasphere have been studied. Ray paths for waves launched near the plasmapause have been traced. In agreement with recent findings by Thorne et al. (1979), waves have been found which return through the equatorial zone with field-aligned wave normal angles. However, when the growth along the ray path is calculated for such waves, assuming an electron distribution function of the form E exp -n sin exp m alpha, it is found that for all the waves considered, the local growth rate becomes negative before plasmapause reflection, limiting the total gain to small values. Most waves reach zero gain before reflection. This is the result of Landau damping at oblique propagation angles, which necessarily occurs before reflection can take place. It is concluded that the concept of cyclic ray paths does not provide an explanation for the generation of unguided plasmaspheric hiss.

SPAR X Technical Report for Experiment 76-22 Directional Solidification of Magnetic Composites

NASA Technical Reports Server (NTRS)

Bethin, J.

1984-01-01

The effects of gravity on Bridgman-Stockbarger directional solidification of off-eutectic Bi/MnBi were studied in reduced gravity aboard the SPAR X flight and compared to normal-gravity investigations and previous eutectic Bi/MnBi SPAR flight experiments. The directional solidification of off-eutectic Bi/MnBi results in either a dendritic structure connected with local cooperative growth or a coupled low volume fraction faceted/non faceted aligned rod eutectic whose Mn macrosegregation, MnBi rod size, interrod spacing, and thermal and magnetic properties are sensitive functions of the solidification processing conditions. Two hypoeutectic and two hypereutectic samples were solidified during 605 sec of furnace travel, with an initial 265 sec low-gravity interval. Comparison Earth-gravity samples were solidified in the same furance assembly under identical processing conditions. Macrosegregation in the low-g samples was consistent with a metastable increase in Mn solubility in the Bi matrix, in partial agreement with previous Bi/MnBi SPAR findings of MnBi volume reduction.

Deficiency in chromosome congression by the inhibition of Plk1 polo box domain-dependent recognition.

PubMed

Watanabe, Nobumoto; Sekine, Tomomi; Takagi, Masatoshi; Iwasaki, Jun-ichi; Imamoto, Naoko; Kawasaki, Hisashi; Osada, Hiroyuki

2009-01-23

Polo-like kinase 1 (Plk1) is one of the key regulators of mitotic cell division. In addition to an N-terminal protein kinase catalytic domain, Plk1 possesses a phosphopeptide binding domain named polo box domain (PBD) at its C terminus. PBD is postulated to be essential for Plk1 localization and substrate targeting. Here, we developed a high-throughput screening system to identify inhibitors of PBD-dependent binding and screened a chemical library. We isolated a benzotropolone-containing natural compound derived from nutgalls (purpurogallin (PPG)) that inhibited PBD-dependent binding in vitro and in vivo. PPG not only delayed the onset of mitosis but also prolonged the progression of mitosis in HeLa cells. Although apparently normal bipolar spindles were formed even in the presence of PPG, the perturbation of chromosome alignment at metaphase plates activated the spindle assembly checkpoint pathway. These results demonstrate the predominant role of PBD-dependent binding on smooth chromosome congression at metaphase.

High-throughput sequence alignment using Graphics Processing Units

PubMed Central

Schatz, Michael C; Trapnell, Cole; Delcher, Arthur L; Varshney, Amitabh

2007-01-01

Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs) in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA) from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU. PMID:18070356

Schooling and Local Environmental Knowledge: Do They Complement or Substitute Each Other?

ERIC Educational Resources Information Center

Reyes-Garcia, Victoria; Kightley, Eric; Ruiz-Mallen, Isabel; Fuentes-Pelaez, Nuria; Demps, Katie; Huanca, Tomas; Martinez-Rodriguez, Maria Ruth

2010-01-01

Schooling and the knowledge acquired at school have been considered both a cause of loss of indigenous knowledge (because it opens pathways to the non-indigenous world and worldviews) and a potential remedy to its demise (if educational curricula is aligned with indigenous realities by giving instruction in local languages and incorporating local…

The Impacts of the WIA One-Stop Center Model on Local Training Services

ERIC Educational Resources Information Center

Cajayon, Felicito

2012-01-01

This study examined the Workforce Investment Act (WIA) One-Stop Center model, which is the local service mechanism for providing employment and training services. It reviewed the processes and service patterns of four program designs that offer an array of services that align with the WIA program's allowable activities. The purpose of the study…

Measurements of mechanical anisotropy in brain tissue and implications for transversely isotropic material models of white matter

PubMed Central

Feng, Yuan; Okamoto, Ruth J.; Namani, Ravi; Genin, Guy M.; Bayly, Philip V.

2013-01-01

White matter in the brain is structurally anisotropic, consisting largely of bundles of aligned, myelin-sheathed axonal fibers. White matter is believed to be mechanically anisotropic as well. Specifically, transverse isotropy is expected locally, with the plane of isotropy normal to the local mean fiber direction. Suitable material models involve strain energy density functions that depend on the I4 and I5 pseudo-invariants of the Cauchy–Green strain tensor to account for the effects of relatively stiff fibers. The pseudo-invariant I4 is the square of the stretch ratio in the fiber direction; I5 contains contributions of shear strain in planes parallel to the fiber axis. Most, if not all, published models of white matter depend on I4 but not on I5. Here, we explore the small strain limits of these models in the context of experimental measurements that probe these dependencies. Models in which strain energy depends on I4 but not I5 can capture differences in Young’s (tensile) moduli, but will not exhibit differences in shear moduli for loading parallel and normal to the mean direction of axons. We show experimentally, using a combination of shear and asymmetric indentation tests, that white matter does exhibit such differences in both tensile and shear moduli. Indentation tests were interpreted through inverse fitting of finite element models in the limit of small strains. Results highlight that: (1) hyperelastic models of transversely isotropic tissues such as white matter should include contributions of both the I4 and I5 strain pseudo-invariants; and (2) behavior in the small strain regime can usefully guide the choice and initial parameterization of more general material models of white matter. PMID:23680651

Mapping of Crustal Anisotropy in the New Madrid Seismic Zone with Shear Wave Splitting

NASA Astrophysics Data System (ADS)

Martin, P.; Arroucau, P.; Vlahovic, G.

2013-12-01

Crustal anisotropy in the New Madrid seismic zone (NMSZ) is investigated by analyzing shear wave splitting measurements from local earthquake data. For the initial data set, the Center for Earthquake Research and Information (CERI) provided over 3000 events, along with 900 seismograms recorded by the Portable Array for Numerical Data Acquisition (PANDA) network. Data reduction led to a final data set of 168 and 43 useable events from the CERI and PANDA data, respectively. From this, 186 pairs of measurements were produced from the CERI data set as well as 49 from the PANDA data set, by means of the automated shear wave splitting measurement program MFAST. Results from this study identified two dominant fast polarization directions, striking NE-SW and WNW-ESE. These are interpreted to be due to stress aligned microcracks in the upper crust. The NE-SW polarization direction is consistent with the maximum horizontal stress orientation of the region and has previously been observed in the NMSZ, while the WNW-ESE polarization direction has not. Path normalized time delays from this study range from 1-33 ms/km for the CERI network data, and 2-31 ms/km for the PANDA data, giving a range of estimated differential shear wave anisotropy between 1% and 8%, with the majority of large path normalized time delays (>20 ms/km) located along the Reelfoot fault segment. The estimated differential shear wave anisotropy values from this study are higher than those previously determined in the region, and are attributed to high crack densities and high pore fluid pressures, which agree with previous results from local earthquake tomography and microseismic swarm analysis in the NMSZ.

Statistics of strain rates and surface density function in a flame-resolved high-fidelity simulation of a turbulent premixed bluff body burner

NASA Astrophysics Data System (ADS)

Sandeep, Anurag; Proch, Fabian; Kempf, Andreas M.; Chakraborty, Nilanjan

2018-06-01

The statistical behavior of the surface density function (SDF, the magnitude of the reaction progress variable gradient) and the strain rates, which govern the evolution of the SDF, have been analyzed using a three-dimensional flame-resolved simulation database of a turbulent lean premixed methane-air flame in a bluff-body configuration. It has been found that the turbulence intensity increases with the distance from the burner, changing the flame curvature distribution and increasing the probability of the negative curvature in the downstream direction. The curvature dependences of dilatation rate ∇ṡu → and displacement speed Sd give rise to variations of these quantities in the axial direction. These variations affect the nature of the alignment between the progress variable gradient and the local principal strain rates, which in turn affects the mean flame normal strain rate, which assumes positive values close to the burner but increasingly becomes negative as the effect of turbulence increases with the axial distance from the burner exit. The axial distance dependences of the curvature and displacement speed also induce a considerable variation in the mean value of the curvature stretch. The axial distance dependences of the dilatation rate and flame normal strain rate govern the behavior of the flame tangential strain rate, and its mean value increases in the downstream direction. The current analysis indicates that the statistical behaviors of different strain rates and displacement speed and their curvature dependences need to be included in the modeling of flame surface density and scalar dissipation rate in order to accurately capture their local behaviors.

Accuracy in breast shape alignment with 3D surface fitting algorithms.

PubMed

Riboldi, Marco; Gierga, David P; Chen, George T Y; Baroni, Guido

2009-04-01

Surface imaging is in use in radiotherapy clinical practice for patient setup optimization and monitoring. Breast alignment is accomplished by searching for a tentative spatial correspondence between the reference and daily surface shape models. In this study, the authors quantify whole breast shape alignment by relying on texture features digitized on 3D surface models. Texture feature localization was validated through repeated measurements in a silicone breast phantom, mounted on a high precision mechanical stage. Clinical investigations on breast shape alignment included 133 fractions in 18 patients treated with accelerated partial breast irradiation. The breast shape was detected with a 3D video based surface imaging system so that breathing was compensated. An in-house algorithm for breast alignment, based on surface fitting constrained by nipple matching (constrained surface fitting), was applied. Results were compared with a commercial software where no constraints are utilized (unconstrained surface fitting). Texture feature localization was validated within 2 mm in each anatomical direction. Clinical data show that unconstrained surface fitting achieves adequate accuracy in most cases, though nipple mismatch is considerably higher than residual surface distances (3.9 mm vs 0.6 mm on average). Outliers beyond 1 cm can be experienced as the result of a degenerate surface fit, where unconstrained surface fitting is not sufficient to establish spatial correspondence. In the constrained surface fitting algorithm, average surface mismatch within 1 mm was obtained when nipple position was forced to match in the [1.5; 5] mm range. In conclusion, optimal results can be obtained by trading off the desired overall surface congruence vs matching of selected landmarks (constraint). Constrained surface fitting is put forward to represent an improvement in setup accuracy for those applications where whole breast positional reproducibility is an issue.

Scale dependence of the alignment between strain rate and rotation in turbulent shear flow

NASA Astrophysics Data System (ADS)

Fiscaletti, D.; Elsinga, G. E.; Attili, A.; Bisetti, F.; Buxton, O. R. H.

2016-10-01

The scale dependence of the statistical alignment tendencies of the eigenvectors of the strain-rate tensor ei, with the vorticity vector ω , is examined in the self-preserving region of a planar turbulent mixing layer. Data from a direct numerical simulation are filtered at various length scales and the probability density functions of the magnitude of the alignment cosines between the two unit vectors | ei.ω ̂| are examined. It is observed that the alignment tendencies are insensitive to the concurrent large-scale velocity fluctuations, but are quantitatively affected by the nature of the concurrent large-scale velocity-gradient fluctuations. It is confirmed that the small-scale (local) vorticity vector is preferentially aligned in parallel with the large-scale (background) extensive strain-rate eigenvector e1, in contrast to the global tendency for ω to be aligned in parallel with the intermediate strain-rate eigenvector [Hamlington et al., Phys. Fluids 20, 111703 (2008), 10.1063/1.3021055]. When only data from regions of the flow that exhibit strong swirling are included, the so-called high-enstrophy worms, the alignment tendencies are exaggerated with respect to the global picture. These findings support the notion that the production of enstrophy, responsible for a net cascade of turbulent kinetic energy from large scales to small scales, is driven by vorticity stretching due to the preferential parallel alignment between ω and nonlocal e1 and that the strongly swirling worms are kinematically significant to this process.

The group migration of Dictyostelium cells is regulated by extracellular chemoattractant degradation.

PubMed

Garcia, Gene L; Rericha, Erin C; Heger, Christopher D; Goldsmith, Paul K; Parent, Carole A

2009-07-01

Starvation of Dictyostelium induces a developmental program in which cells form an aggregate that eventually differentiates into a multicellular structure. The aggregate formation is mediated by directional migration of individual cells that quickly transition to group migration in which cells align in a head-to-tail manner to form streams. Cyclic AMP acts as a chemoattractant and its production, secretion, and degradation are highly regulated. A key protein is the extracellular phosphodiesterase PdsA. In this study we examine the role and localization of PdsA during chemotaxis and streaming. We find that pdsA(-) cells respond chemotactically to a narrower range of chemoattractant concentrations compared with wild-type (WT) cells. Moreover, unlike WT cells, pdsA(-) cells do not form streams at low cell densities and form unusual thick and transient streams at high cell densities. We find that the intracellular pool of PdsA is localized to the endoplasmic reticulum, which may provide a compartment for storage and secretion of PdsA. Because we find that cAMP synthesis is normal in cells lacking PdsA, we conclude that signal degradation regulates the external cAMP gradient field generation and that the group migration behavior of these cells is compromised even though their signaling machinery is intact.

The Group Migration of Dictyostelium Cells Is Regulated by Extracellular Chemoattractant Degradation

PubMed Central

Garcia, Gene L.; Rericha, Erin C.; Heger, Christopher D.; Goldsmith, Paul K.

2009-01-01

Starvation of Dictyostelium induces a developmental program in which cells form an aggregate that eventually differentiates into a multicellular structure. The aggregate formation is mediated by directional migration of individual cells that quickly transition to group migration in which cells align in a head-to-tail manner to form streams. Cyclic AMP acts as a chemoattractant and its production, secretion, and degradation are highly regulated. A key protein is the extracellular phosphodiesterase PdsA. In this study we examine the role and localization of PdsA during chemotaxis and streaming. We find that pdsA− cells respond chemotactically to a narrower range of chemoattractant concentrations compared with wild-type (WT) cells. Moreover, unlike WT cells, pdsA− cells do not form streams at low cell densities and form unusual thick and transient streams at high cell densities. We find that the intracellular pool of PdsA is localized to the endoplasmic reticulum, which may provide a compartment for storage and secretion of PdsA. Because we find that cAMP synthesis is normal in cells lacking PdsA, we conclude that signal degradation regulates the external cAMP gradient field generation and that the group migration behavior of these cells is compromised even though their signaling machinery is intact. PMID:19477920

Mediolateral force distribution at the knee joint shifts across activities and is driven by tibiofemoral alignment.

PubMed

Kutzner, I; Bender, A; Dymke, J; Duda, G; von Roth, P; Bergmann, G

2017-06-01

Tibiofemoral alignment is important to determine the rate of progression of osteoarthritis and implant survival after total knee arthroplasty (TKA). Normally, surgeons aim for neutral tibiofemoral alignment following TKA, but this has been questioned in recent years. The aim of this study was to evaluate whether varus or valgus alignment indeed leads to increased medial or lateral tibiofemoral forces during static and dynamic weight-bearing activities. Tibiofemoral contact forces and moments were measured in nine patients with instrumented knee implants. Medial force ratios were analysed during nine daily activities, including activities with single-limb support (e.g. walking) and double-limb support (e.g. knee bend). Hip-knee-ankle angles in the frontal plane were analysed using full-leg coronal radiographs. The medial force ratio strongly correlated with the tibiofemoral alignment in the static condition of one-legged stance (R² = 0.88) and dynamic single-limb loading (R² = 0.59) with varus malalignment leading to increased medial force ratios of up to 88%. In contrast, the correlation between leg alignment and magnitude of medial compartment force was much less pronounced. A lateral shift of force occurred during activities with double-limb support and higher knee flexion angles. The medial force ratio depends on both the tibiofemoral alignment and the nature of the activity involved. It cannot be generalised to a single value. Higher medial ratios during single-limb loading are associated with varus malalignment in TKA. The current trend towards a 'constitutional varus' after joint replacement, in terms of overall tibiofemoral alignment, should be considered carefully with respect to the increased medial force ratio. Cite this article: Bone Joint J 2017;99-B:779-87. ©2017 The British Editorial Society of Bone & Joint Surgery.

Emergency radiology: straightening of the cervical spine in MDCT after trauma—a sign of injury or normal variant?

PubMed Central

Deak, Zsuszsanna; Krtakovska, Aina; Ruschi, Francesco; Kammer, Nora; Wirth, Stefan; Reiser, Maximilian; Geyer, Lucas

2016-01-01

Objective: To evaluate whether straightening of the cervical spine (C-spine) alignment after trauma can be considered a significant multidetector CT (MDCT) finding. Methods: 160 consecutive patients after C-spine trauma admitted to a Level 1 trauma centre received MDCT according to Canadian Cervical Spine Rule and National Emergency X-Radiography Utilization Study indication rule; subgroups with and without cervical collar immobilization (CCI +/−) were compared with a control group (n = 20) of non-traumatized patients. Two independent readers evaluated retrospectively the alignment, determined the absolute rotational angle of the posterior surface of C2 and C7 (ARA C2–7) and grouped the results for lordosis (<−13°), straight (−13 to +6°) and kyphosis (>+6°). Results: In the two CCI−/CCI+ study groups, the straight or kyphotic alignment significantly (p = 0.001) predominated over lordosis. The number of patients with straight C-spine alignment was higher in the CCI+ group (CCI+ 69% vs CCI− 49%, p = 0.05). A comparison of the CCI+ group vs the CCI− group revealed a slightly smaller number of kyphotic (10% vs 18%, p = 0.34) and lordotic (21% vs 33%, p = 0.33) alignments. Statistically, however, the differences were of no significance. The control group revealed no significant differences. Conclusion: Straightening of the C-spine alone is not a definitive sign of injury but is a biomechanical variation due to CCI and neck positioning during MDCT or active patient control. Advances in knowledge: Straightening of the C-spine alignment in MDCT alone is not a definitive sign of injury. Straightening of the C-spine alignment is related to neck positioning and active patient control. CCI has a straightening effect on the cervical alignment. PMID:26764283

Culture on electrospun polyurethane scaffolds decreases atrial natriuretic peptide expression by cardiomyocytes in vitro.

PubMed

Rockwood, Danielle N; Akins, Robert E; Parrag, Ian C; Woodhouse, Kimberly A; Rabolt, John F

2008-12-01

The function of the mammalian heart depends on the functional alignment of cardiomyocytes, and controlling cell alignment is an important consideration in biomaterial design for cardiac tissue engineering and research. The physical cues that guide functional cell alignment in vitro and the impact of substrate-imposed alignment on cell phenotype, however, are only partially understood. In this report, primary cardiac ventricular cells were grown on electrospun, biodegradable polyurethane (ES-PU) with either aligned or unaligned microfibers. ES-PU scaffolds supported high-density cultures and cell subpopulations remained intact over two weeks in culture. ES-PU cultures contained electrically-coupled cardiomyocytes with connexin-43 localized to points of cell:cell contact. Multi-cellular organization correlated with microfiber orientation and aligned materials yielded highly oriented cardiomyocyte groupings. Atrial natriuretic peptide, a molecular marker that shows decreasing expression during ventricular cell maturation, was significantly lower in cultures grown on ES-PU scaffolds than in those grown on tissue culture polystyrene. Cells grown on aligned ES-PU had significantly lower steady state levels of ANP and constitutively released less ANP over time indicating that scaffold-imposed cell organization resulted in a shift in cell phenotype to a more mature state. We conclude that the physical organization of microfibers in ES-PU scaffolds impacts both multi-cellular architecture and cardiac cell phenotype in vitro.

Web-Beagle: a web server for the alignment of RNA secondary structures.

PubMed

Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

2015-07-01

Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

SU-E-J-214: Comparative Assessment On IGRT On Partial Bladder Cancer Treatment Between CT-On-Rails (CTOR) and KV Cone Beam CT (CBCT)

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

Lin, T; Ma, C

2014-06-01

Purpose: Image-Guided radiation therapy(IGRT) depends on reliable online patient-specific anatomy information to address random and progressive anatomy changes. Large margins have been suggested to bladder cancer treatment due to large daily bladder anatomy variation. KV Cone beam CT(CBCT) has been used in IGRT localization prevalently; however, its lack of soft tissue contrast makes clinicians hesitate to perform daily soft tissue alignment with CBCT for partial bladder cancer treatment. This study compares the localization uncertainties of bladder cancer IGRT using CTon- Rails(CTOR) and CBCT. Methods: Three T2N0M0 bladder cancer patients (total of 66 Gy to partial bladder alone) were localized dailymore » with either CTOR or CBCT for their entire treatment course. A total of 71 sets of CTOR and 22 sets of CBCT images were acquired and registered with original planning CT scans by radiation therapists and approved by radiation oncologists for the daily treatment. CTOR scanning entailed 2mm slice thickness, 0.98mm axial voxel size, 120kVp and 240mAs. CBCT used a half fan pelvis protocol from Varian OBI system with 2mm slice thickness, 0.98axial voxel size, 125kVp, and 680mAs. Daily localization distribution was compared. Accuracy of CTOR and CBCT on partial bladder alignment was also evaluated by comparing bladder PTV coverage. Results: 1cm all around PTV margins were used in every patient except target superior limit margin to 0mm due to bowel constraint. Daily shifts on CTOR averaged to 0.48, 0.24, 0.19 mms(SI,Lat,AP directions); CBCT averaged to 0.43, 0.09, 0.19 mms(SI,Lat,AP directions). The CTOR daily localization showed superior results of V100% of PTV(102% CTOR vs. 89% CBCT) and bowel(Dmax 69.5Gy vs. 78Gy CBCT). CTOR images showed much higher contrast on bladder PTV alignment. Conclusion: CTOR daily localization for IGRT is more dosimetrically beneficial for partial bladder cancer treatment than kV CBCT localization and provided better soft tissue PTV identification.« less

Microstructure and seismic anisotropy of phyllite from Geumseongri Formation and Munjuri Formation in Korea

NASA Astrophysics Data System (ADS)

Han, S.; Jung, H.

2016-12-01

Mica is a mineral group that shows the strongest seismic anisotropy among the minerals comprising continental crust of the Earth. It is also noteworthy that alignment of mica can strongly affect magnitude and symmetry of seismic anisotropy if a seismic wave passes through a rock composed of mica more than 20-40%. Thus, it is highly necessary to analyze mica-rich rocks to investigate the origin of seismic anisotropy observed in continental crust. In this study, muscovite-quartz phyllites from Geumseongri and Munjuri Formation in Korea were analyzed using Electron Backscattered Diffraction (EBSD) to measure lattice preferred orientation (LPO) of minerals. The samples are mainly composed of muscovite, quartz, albite, chlorite, and biotite with minor calcite and rutile. The EBSD analysis showed that the muscovite [001] axis was strongly aligned normal to the foliation while both [100] and [010] axes were dispersed parallel to the foliation. Chlorite and biotite also exhibited similar LPO except for the chlorite [001] axis in the sample 2619, dispersed normal to the lineation. LPOs of quartz were weak in most samples. The albite (010) pole in the sample 2363M and (001) pole in the sample 2364Q were aligned normal to the foliation. Seismic anisotropy was calculated based on the LPO and modal composition of the specimens. The anisotropy of P-wave (Vp) for quartz was in the range of 4.3 - 9.3% and 3.3 - 6.7% for albite. The maximum shear wave anisotropy (AVs) was in the range of 5.3 - 11.2% for quartz and 3.9 - 5.4% for albite. The Vp anisotropy and maximum AVs anisotropy of mica were in the range of 19.3 - 53.4% and 11.6 - 62.9%, respectively, which are much larger than those of other minerals. As a result, The Vp and maximum AVs anisotropy for whole rock were in the range of 11.8 - 44% and 11.6 - 51.8%, respectively. These results show that modal composition and alignment of mica mainly control the magnitude and symmetry of seismic anisotropy.

Log-odds sequence logos

PubMed Central

Yu, Yi-Kuo; Capra, John A.; Stojmirović, Aleksandar; Landsman, David; Altschul, Stephen F.

2015-01-01

Motivation: DNA and protein patterns are usefully represented by sequence logos. However, the methods for logo generation in common use lack a proper statistical basis, and are non-optimal for recognizing functionally relevant alignment columns. Results: We redefine the information at a logo position as a per-observation multiple alignment log-odds score. Such scores are positive or negative, depending on whether a column’s observations are better explained as arising from relatedness or chance. Within this framework, we propose distinct normalized maximum likelihood and Bayesian measures of column information. We illustrate these measures on High Mobility Group B (HMGB) box proteins and a dataset of enzyme alignments. Particularly in the context of protein alignments, our measures improve the discrimination of biologically relevant positions. Availability and implementation: Our new measures are implemented in an open-source Web-based logo generation program, which is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/logoddslogo/index.html. A stand-alone version of the program is also available from this site. Contact: altschul@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25294922

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline.

PubMed

Dowsey, Andrew W; Dunn, Michael J; Yang, Guang-Zhong

2008-04-01

The quest for high-throughput proteomics has revealed a number of challenges in recent years. Whilst substantial improvements in automated protein separation with liquid chromatography and mass spectrometry (LC/MS), aka 'shotgun' proteomics, have been achieved, large-scale open initiatives such as the Human Proteome Organization (HUPO) Brain Proteome Project have shown that maximal proteome coverage is only possible when LC/MS is complemented by 2D gel electrophoresis (2-DE) studies. Moreover, both separation methods require automated alignment and differential analysis to relieve the bioinformatics bottleneck and so make high-throughput protein biomarker discovery a reality. The purpose of this article is to describe a fully automatic image alignment framework for the integration of 2-DE into a high-throughput differential expression proteomics pipeline. The proposed method is based on robust automated image normalization (RAIN) to circumvent the drawbacks of traditional approaches. These use symbolic representation at the very early stages of the analysis, which introduces persistent errors due to inaccuracies in modelling and alignment. In RAIN, a third-order volume-invariant B-spline model is incorporated into a multi-resolution schema to correct for geometric and expression inhomogeneity at multiple scales. The normalized images can then be compared directly in the image domain for quantitative differential analysis. Through evaluation against an existing state-of-the-art method on real and synthetically warped 2D gels, the proposed analysis framework demonstrates substantial improvements in matching accuracy and differential sensitivity. High-throughput analysis is established through an accelerated GPGPU (general purpose computation on graphics cards) implementation. Supplementary material, software and images used in the validation are available at http://www.proteomegrid.org/rain/.

Characterization of cartilage defects detected by MRI in Kellgren-Lawrence grade 0 or 1 knees.

PubMed

Taguchi, Kenji; Chiba, Ko; Okazaki, Narihiro; Kido, Yasuo; Miyamoto, Takashi; Yonekura, Akihiko; Tomita, Masato; Uetani, Masataka; Osaki, Makoto

2017-09-01

Osteoarthritis of the knee is generally evaluated by plain X-rays, which are incapable of detecting small cartilage damage. There are some patients who have small cartilage defects on MRI with no abnormal findings on plain X-rays. In this study, the prevalence and regional characteristics of cartilage defects detected by MRI were studied in cases with normal X-ray findings (Kellgren-Lawrence grade 0 and 1). Relationships between the cartilage defects and OA risk factors such as obesity and leg alignment were also investigated. A total of 51 knees of Kellgren-Lawrence grade 0 or 1 without knee joint pain were included. Fat-suppressed spoiled-gradient recalled (SPGR) sagittal images were scanned by 3 T MRI, and the presence of cartilage damage was confirmed. Cartilage damage was visualized three-dimensionally, and its location and morphology were analyzed. On a full length standing radiograph of the lower extremities, leg alignment and other parameters were measured, and their associations with cartilage damage were analyzed. Cartilage defects were detected in 26% of women aged >50 years. Cartilage damage was located on the medial femoral condyle near the intercondylar notch, and was mostly elliptically shaped in the anteroposterior direction. Subjects with damaged cartilage were not obese and did not have abnormal leg alignment. It should be borne in mind that some elderly women may have damaged cartilage on the intercondylar notch side of the medial joint, even though plain X-rays appear normal, and this cannot be predicted by obesity or leg alignment. Copyright © 2017 The Japanese Orthopaedic Association. Published by Elsevier B.V. All rights reserved.

Is it feasible to pool funds for local children's services in England? Evidence from the national evaluation of children's trust pathfinders.

PubMed

Lorgelly, Paula; Bachmann, Max; Shreeve, Ann; Reading, Richard; Thorburn, June; Mugford, Miranda; O'Brien, Margaret; Husbands, Chris

2009-01-01

To describe how funds were pooled or otherwise jointly managed by National Health Service (NHS) primary care trusts and local authorities in England. To compare expenditure on local children's services by health, education and social services. We conducted a questionnaire survey of all 35 children's trust pathfinders, six months after they were launched, with a follow-up at 2.5 years. We also undertook an in-depth analysis of local authorities and primary care trusts, within eight pathfinder areas and three non-pathfinder areas, whereby we compared expenditure on children's services, interviewed managers and professionals and examined financial documents. Local authorities and NHS trusts coordinated expenditure in various ways, most commonly through informal agreements and aligning budgets but also by formally pooling budgets. The latter were usually for selected services such as child and adolescent mental health services, though four children's trusts pathfinders pooled (or aligned) their budgets for all children's services. Total expenditure per child was greatest for education, lowest for social services and intermediate for health. However, it was difficult to quantify education expenditure on children with health and social care needs, and health care expenditure on children. Sharing money for local children's services requires shared objectives, trust, and legal and accounting expertise. Several different mechanisms are permitted and many are feasible but programme budgeting for children's services could make them more effective.

NOVEL MEMBRANE PROCESS TO UTILIZE DILUTE METHANE STREAMS - PHASE II

EPA Science Inventory

Effect of EMIC Wave Normal Angle Distribution on Relativistic Electron Scattering in Outer RB

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Gamayunov, K. V.

2007-01-01

We present the equatorial and bounce average pitch angle diffusion coefficients for scattering of relativistic electrons by the H+ mode of EMIC waves. Both the model (prescribed) and self consistent distributions over the wave normal angle are considered. The main results of our calculation can be summarized as follows: First, in comparison with field aligned waves, the intermediate and highly oblique waves reduce the pitch angle range subject to diffusion, and strongly suppress the scattering rate for low energy electrons (E less than 2 MeV). Second, for electron energies greater than 5 MeV, the |n| = 1 resonances operate only in a narrow region at large pitch-angles, and despite their greatest contribution in case of field aligned waves, cannot cause electron diffusion into the loss cone. For those energies, oblique waves at |n| greater than 1 resonances are more effective, extending the range of pitch angle diffusion down to the loss cone boundary, and increasing diffusion at small pitch angles by orders of magnitude.

Van der Waals interaction in uniaxial anisotropic media.

PubMed

Kornilovitch, Pavel E

2013-01-23

Van der Waals interactions between flat surfaces in uniaxial anisotropic media are investigated in the nonretarded limit. The main focus is the effect of nonzero tilt between the optical axis and the surface normal on the strength of the van der Waals attraction. General expressions for the van der Waals free energy are derived using the surface mode method and the transfer-matrix formalism. To facilitate numerical calculations a temperature-dependent three-band parameterization of the dielectric tensor of the liquid crystal 5CB is developed. A solid slab immersed in a liquid crystal experiences a van der Waals torque that aligns the surface normal relative to the optical axis of the medium. The preferred orientation is different for different materials. Two solid slabs in close proximity experience a van der Waals attraction that is strongest for homeotropic alignment of the intervening liquid crystal for all the materials studied. The results have implications for the stability of plate-like colloids in liquid crystal hosts.

Effect of Oblique Electromagnetic Ion Cyclotron Waves on Relativistic Electron Scattering: CRRES Based Calculation

NASA Technical Reports Server (NTRS)

Gamayunov, K. V.; Khazanov, G. V.

2007-01-01

We consider the effect of oblique EMIC waves on relativistic electron scattering in the outer radiation belt using simultaneous observations of plasma and wave parameters from CRRES. The main findings can be s ummarized as follows: 1. In 1comparison with field-aligned waves, int ermediate and highly oblique distributions decrease the range of pitc h-angles subject to diffusion, and reduce the local scattering rate b y an order of magnitude at pitch-angles where the principle absolute value of n = 1 resonances operate. Oblique waves allow the absolute va lue of n > 1 resonances to operate, extending the range of local pitc h-angle diffusion down to the loss cone, and increasing the diffusion at lower pitch angles by orders of magnitude; 2. The local diffusion coefficients derived from CRRES data are qualitatively similar to the local results obtained for prescribed plasma/wave parameters. Conseq uently, it is likely that the bounce-averaged diffusion coefficients, if estimated from concurrent data, will exhibit the dependencies similar to those we found for model calculations; 3. In comparison with f ield-aligned waves, intermediate and highly oblique waves decrease th e bounce-averaged scattering rate near the edge of the equatorial lo ss cone by orders of magnitude if the electron energy does not excee d a threshold (approximately equal to 2 - 5 MeV) depending on specified plasma and/or wave parameters; 4. For greater electron energies_ ob lique waves operating the absolute value of n > 1 resonances are more effective and provide the same bounce_averaged diffusion rate near the loss cone as fiel_aligned waves do.

CHANGE OF MAGNETIC FIELD-GAS ALIGNMENT AT THE GRAVITY-DRIVEN ALFVÉNIC TRANSITION IN MOLECULAR CLOUDS: IMPLICATIONS FOR DUST POLARIZATION OBSERVATIONS

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

Chen, Che-Yu; King, Patrick K.; Li, Zhi-Yun

Diffuse striations in molecular clouds are preferentially aligned with local magnetic fields, whereas dense filaments tend to be perpendicular to them. When and why this transition occurs remain uncertain. To explore the physics behind this transition, we compute the histogram of relative orientation (HRO) between the density gradient and the magnetic field in three-dimensional magnetohydrodynamic (MHD) simulations of prestellar core formation in shock-compressed regions within giant molecular clouds. We find that, in the magnetically dominated (sub-Alfvénic) post-shock region, the gas structure is preferentially aligned with the local magnetic field. For overdense sub-regions with super-Alfvénic gas, their elongation becomes preferentially perpendicularmore » to the local magnetic field. The transition occurs when self-gravitating gas gains enough kinetic energy from the gravitational acceleration to overcome the magnetic support against the cross-field contraction, which results in a power-law increase of the field strength with density. Similar results can be drawn from HROs in projected two-dimensional maps with integrated column densities and synthetic polarized dust emission. We quantitatively analyze our simulated polarization properties, and interpret the reduced polarization fraction at high column densities as the result of increased distortion of magnetic field directions in trans- or super-Alfvénic gas. Furthermore, we introduce measures of the inclination and tangledness of the magnetic field along the line of sight as the controlling factors of the polarization fraction. Observations of the polarization fraction and angle dispersion can therefore be utilized in studying local magnetic field morphology in star-forming regions.« less

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes.

PubMed

Pervouchine, Dmitri D

2018-06-15

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

Detection of the Velocity Shear Effect on the Spatial Distributions of the Galactic Satellites in Isolated Systems

NASA Astrophysics Data System (ADS)

Lee, Jounghun; Choi, Yun-Young

2015-02-01

We report a detection of the effect of the large-scale velocity shear on the spatial distributions of the galactic satellites around the isolated hosts. Identifying the isolated galactic systems, each of which consists of a single host galaxy and its satellites, from the Seventh Data Release of the Sloan Digital Sky Survey and reconstructing linearly the velocity shear field in the local universe, we measure the alignments between the relative positions of the satellites from their isolated hosts and the principal axes of the local velocity shear tensors projected onto the plane of sky. We find a clear signal that the galactic satellites in isolated systems are located preferentially along the directions of the minor principal axes of the large-scale velocity shear field. Those galactic satellites that are spirals, are brighter, are located at distances larger than the projected virial radii of the hosts, and belong to the spiral hosts yield stronger alignment signals, which implies that the alignment strength depends on the formation and accretion epochs of the galactic satellites. It is also shown that the alignment strength is quite insensitive to the cosmic web environment, as well as the size and luminosity of the isolated hosts. Although this result is consistent with the numerical finding of Libeskind et al. based on an N-body experiment, owing to the very low significance of the observed signals, it remains inconclusive whether or not the velocity shear effect on the satellite distribution is truly universal.

FLASHFLOOD: A 3D Field-based similarity search and alignment method for flexible molecules

NASA Astrophysics Data System (ADS)

Pitman, Michael C.; Huber, Wolfgang K.; Horn, Hans; Krämer, Andreas; Rice, Julia E.; Swope, William C.

2001-07-01

A three-dimensional field-based similarity search and alignment method for flexible molecules is introduced. The conformational space of a flexible molecule is represented in terms of fragments and torsional angles of allowed conformations. A user-definable property field is used to compute features of fragment pairs. Features are generalizations of CoMMA descriptors (Silverman, B.D. and Platt, D.E., J. Med. Chem., 39 (1996) 2129.) that characterize local regions of the property field by its local moments. The features are invariant under coordinate system transformations. Features taken from a query molecule are used to form alignments with fragment pairs in the database. An assembly algorithm is then used to merge the fragment pairs into full structures, aligned to the query. Key to the method is the use of a context adaptive descriptor scaling procedure as the basis for similarity. This allows the user to tune the weights of the various feature components based on examples relevant to the particular context under investigation. The property fields may range from simple, phenomenological fields, to fields derived from quantum mechanical calculations. We apply the method to the dihydrofolate/methotrexate benchmark system, and show that when one injects relevant contextual information into the descriptor scaling procedure, better results are obtained more efficiently. We also show how the method works and include computer times for a query from a database that represents approximately 23 million conformers of seventeen flexible molecules.

Model of myosin node aggregation into a contractile ring: the effect of local alignment

NASA Astrophysics Data System (ADS)

Ojkic, Nikola; Wu, Jian-Qiu; Vavylonis, Dimitrios

2011-09-01

Actomyosin bundles frequently form through aggregation of membrane-bound myosin clusters. One such example is the formation of the contractile ring in fission yeast from a broad band of cortical nodes. Nodes are macromolecular complexes containing several dozens of myosin-II molecules and a few formin dimers. The condensation of a broad band of nodes into the contractile ring has been previously described by a search, capture, pull and release (SCPR) model. In SCPR, a random search process mediated by actin filaments nucleated by formins leads to transient actomyosin connections among nodes that pull one another into a ring. The SCPR model reproduces the transport of nodes over long distances and predicts observed clump-formation instabilities in mutants. However, the model does not generate transient linear elements and meshwork structures as observed in some wild-type and mutant cells during ring assembly. As a minimal model of node alignment, we added short-range aligning forces to the SCPR model representing currently unresolved mechanisms that may involve structural components, cross-linking and bundling proteins. We studied the effect of the local node alignment mechanism on ring formation numerically. We varied the new parameters and found viable rings for a realistic range of values. Morphologically, transient structures that form during ring assembly resemble those observed in experiments with wild-type and cdc25-22 cells. Our work supports a hierarchical process of ring self-organization involving components drawn together from distant parts of the cell followed by progressive stabilization.

Controlling orientational order in block copolymers using low-intensity magnetic fields

PubMed Central

Choo, Youngwoo; Kawabata, Kohsuke; Kaufman, Gilad; Feng, Xunda; Di, Xiaojun; Rokhlenko, Yekaterina; Mahajan, Lalit H.; Ndaya, Dennis; Kasi, Rajeswari M.

2017-01-01

The interaction of fields with condensed matter during phase transitions produces a rich variety of physical phenomena. Self-assembly of liquid crystalline block copolymers (LC BCPs) in the presence of a magnetic field, for example, can result in highly oriented microstructures due to the LC BCP’s anisotropic magnetic susceptibility. We show that such oriented mesophases can be produced using low-intensity fields (<0.5 T) that are accessible using permanent magnets, in contrast to the high fields (>4 T) and superconducting magnets required to date. Low-intensity field alignment is enabled by the addition of labile mesogens that coassemble with the system’s nematic and smectic A mesophases. The alignment saturation field strength and alignment kinetics have pronounced dependences on the free mesogen concentration. Highly aligned states with orientation distribution coefficients close to unity were obtained at fields as small as 0.2 T. This remarkable field response originates in an enhancement of alignment kinetics due to a reduction in viscosity, and increased magnetostatic energy due to increases in grain size, in the presence of labile mesogens. These developments provide routes for controlling structural order in BCPs, including the possibility of producing nontrivial textures and patterns of alignment by locally screening fields using magnetic nanoparticles. PMID:29078379

Accurate and robust brain image alignment using boundary-based registration.

PubMed

Greve, Douglas N; Fischl, Bruce

2009-10-15

The fine spatial scales of the structures in the human brain represent an enormous challenge to the successful integration of information from different images for both within- and between-subject analysis. While many algorithms to register image pairs from the same subject exist, visual inspection shows that their accuracy and robustness to be suspect, particularly when there are strong intensity gradients and/or only part of the brain is imaged. This paper introduces a new algorithm called Boundary-Based Registration, or BBR. The novelty of BBR is that it treats the two images very differently. The reference image must be of sufficient resolution and quality to extract surfaces that separate tissue types. The input image is then aligned to the reference by maximizing the intensity gradient across tissue boundaries. Several lower quality images can be aligned through their alignment with the reference. Visual inspection and fMRI results show that BBR is more accurate than correlation ratio or normalized mutual information and is considerably more robust to even strong intensity inhomogeneities. BBR also excels at aligning partial-brain images to whole-brain images, a domain in which existing registration algorithms frequently fail. Even in the limit of registering a single slice, we show the BBR results to be robust and accurate.

A Functional Relationship between NuMA and Kid Is Involved in Both Spindle Organization and Chromosome Alignment in Vertebrate CellsV⃞

PubMed Central

Levesque, Aime A.; Howard, Louisa; Gordon, Michael B.; Compton, Duane A.

2003-01-01

We examined spindle morphology and chromosome alignment in vertebrate cells after simultaneous perturbation of the chromokinesin Kid and either NuMA, CENP-E, or HSET. Spindle morphology and chromosome alignment after simultaneous perturbation of Kid and either HSET or CENP-E were no different from when either HSET or CENP-E was perturbed alone. However, short bipolar spindles with organized poles formed after perturbation of both Kid and NuMA in stark contrast to splayed spindle poles observed after perturbation of NuMA alone. Spindles were disorganized if Kid, NuMA, and HSET were perturbed, indicating that HSET is sufficient for spindle organization in the absence of Kid and NuMA function. In addition, chromosomes failed to align efficiently at the spindle equator after simultaneous perturbation of Kid and NuMA despite appropriate kinetochore-microtubule interactions that generated chromosome movement at normal velocities. These data indicate that a functional relationship between the chromokinesin Kid and the spindle pole organizing protein NuMA influences spindle morphology, and we propose that this occurs because NuMA forms functional linkages between kinetochore and nonkinetochore microtubules at spindle poles. In addition, these data show that both Kid and NuMA contribute to chromosome alignment in mammalian cells. PMID:12972545

The pursuit of stereopsis.

PubMed

Sharma, Pradeep

2018-02-01

Pediatric ophthalmologists are increasingly expected to promote, preserve, and restore binocular vision. Clinical studies on restoring alignment and stereopsis in the management of amblyopia, esotropia, exotropia, and complex strabismus are reviewed from the perspective of the author's published work and personal experiences. Treatment of amblyopia by means of optical rehabilitation, occlusion, or penalization has been reinforced by medical treatment and perceptual training with monocular or binocular video games. Studies indicate that early management of esotropia and alignment within 8 Δ is required for regaining stereopsis. In the surgical management of intermittent exotropia, distance stereopsis by Frisby Davis Distance stereotest can predict better stereopsis, with patients having preoperative distance stereopsis of <70 arcsec less likely to improve after surgery. The surgeon's armamentarium for correcting alignment and restoring binocular vision include procedures such as adjustable, partial vertical rectus muscle transposition in cases of exotropic Duane syndrome and lateral rectus palsy, periosteal fixation of the globe or of the lateral rectus muscle, and medial transposition of the split lateral rectus muscle. The goal for present-day strabismologists is not merely to correct strabismus but also to achieve alignment of eyes in time to ensure normal development of stereopsis in children and to restore alignment and stereopsis in adults. Copyright © 2017 American Association for Pediatric Ophthalmology and Strabismus. Published by Elsevier Inc. All rights reserved.

enoLOGOS: a versatile web tool for energy normalized sequence logos

PubMed Central

Workman, Christopher T.; Yin, Yutong; Corcoran, David L.; Ideker, Trey; Stormo, Gary D.; Benos, Panayiotis V.

2005-01-01

enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a set of aligned sequences. Each position of the alignment is represented by a column of stacked symbols with its total height reflecting the information content in this position. Currently, the available web servers are able to create logo images from a set of aligned sequences, but none of them generates weighted sequence logos directly from energy measurements or other sources. With the advent of high-throughput technologies for estimating the contact energy of different DNA sequences, tools that can create logos directly from binding affinity data are useful to researchers. enoLOGOS generates sequence logos from a variety of input data, including energy measurements, probability matrices, alignment matrices, count matrices and aligned sequences. Furthermore, enoLOGOS can represent the mutual information of different positions of the consensus sequence, a unique feature of this tool. Another web interface for our software, C2H2-enoLOGOS, generates logos for the DNA-binding preferences of the C2H2 zinc-finger transcription factor family members. enoLOGOS and C2H2-enoLOGOS are accessible over the web at . PMID:15980495

Lipid decorated liquid crystal pressure sensors

NASA Astrophysics Data System (ADS)

Lopatkina, Tetiana; Popov, Piotr; Honaker, Lawrence; Jakli, Antal; Mann, Elizabeth; Mann's Group Collaboration; Jakli's Group Collaboration

Surfactants usually promote the alignment of liquid crystal (LC) director parallel to the surfactant chains, and thus on average normal to the substrate (homeotropic), whereas water promotes tangential (planar) alignment. A water-LC interface is therefore very sensitive to the presence of surfactants, such as lipids: this is the principle of LC-based chemical and biological sensing introduced by Abbott et al.Using a modified configuration, we found that at higher than 10 micro molar lipid concentration, the uniformly dark texture seen for homeotropic alignment between left-, and right-handed circular polarizers becomes unstable and slowly brightens again. This texture shows extreme sensitivity to external air pressure variations offering its use for sensitive pressure sensors. Our analysis indicates an osmotic pressure induced bending of the suspended films explaining both the birefringence and pressure sensitivity. In the talk we will discuss the experimental details of these effects. This work was financially supported by NSF DMR No. DMR-0907055.

Vorticity equation for MHD fast waves in geospace environment

NASA Technical Reports Server (NTRS)

Yamauchi, M.; Lundin, R.; Lui, A. T. Y.

1993-01-01

The MHD vorticity equation is modified in order to apply it to nonlinear MHD fast waves or shocks when their extent along the magnetic field is limited. Field-aligned current (FAC) generation is also discussed on the basis of this modified vorticity equation. When the wave normal is not aligned to the finite velocity convection and the source region is spatially limited, a longitudinal polarization causes a pair of plus and minus charges inside the compressional plane waves or shocks, generating a pair of FACs. This polarization is not related to the separation between the electrons and ions caused by their difference in mass, a separation which is inherent to compressional waves. The resultant double field-aligned current structure exists both with and without the contributions from curvature drift, which is questionable in terms of its contribution to vorticity change from the viewpoint of single-particle motion.

Fast and accurate phylogeny reconstruction using filtered spaced-word matches

PubMed Central

Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

2017-01-01

Abstract Motivation: Word-based or ‘alignment-free’ algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. Results: We propose Filtered Spaced Word Matches (FSWM), a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don’t-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don’t-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don’t-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. Availability and Implementation: The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/ Contact: chris.leimeister@stud.uni-goettingen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28073754

Fast and accurate phylogeny reconstruction using filtered spaced-word matches.

PubMed

Leimeister, Chris-André; Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

2017-04-01

Word-based or 'alignment-free' algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. We propose Filtered Spaced Word Matches (FSWM) , a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don't-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don't-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don't-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/. chris.leimeister@stud.uni-goettingen.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Bi-directional signaling: Extracellular Matrix and Integrin Regulation of Breast Tumor Progression

PubMed Central

Gehler, Scott; Ponik, Suzanne M.; Riching, Kristin M; Keely, Patricia J.

2016-01-01

Cell transformation and tumor progression involves a common set of acquired capabilities, including increased proliferation, failure of cell death, self-sufficiency in growth, angiogenesis, and tumor cell invasion and metastasis (1). The stromal environment consists of many cell types, including fibroblasts, macrophages, and endothelial cells, in addition to various extracellular matrix (ECM) proteins that function to support normal tissue maintenance, but have also been implicated in tumor progression (2). Both the chemical and mechanical properties of the ECM have been shown to influence normal and malignant cell behavior. For instance, mesenchymal stem cells differentiate into specific lineages that are dependent on matrix stiffness (3), while tumor cells undergo changes in cell behavior and gene expression in response to matrix stiffness (4). ECM remodeling is implicated in tumor progression and includes changes in both the chemical and mechanical properties of the ECM (5) that can be a result of 1.) increased deposition of stromal ECM, 2.) enhanced contraction of ECM fibrils, and 3.) altered collagen alignment and ECM stiffness. In addition, remodeling of the ECM may alter whether tumor cells employ proteolytic degradation mechanisms during invasion and metastasis. Tumor cells respond to such changes in ECM remodeling through altered intracellular signaling and cell cycle control that lead to enhanced proliferation, loss of normal tissue architecture, and local tumor cell migration and invasion into the surrounding stromal tissue (6). This review will focus on the bi-directional interplay between the mechanical properties of the ECM and changes in integrin-mediated signal transduction events in an effort to elucidate cell behaviors during tumor progression. PMID:23582036

Magnetic field design for selecting and aligning immunomagnetic labeled cells.

PubMed

Tibbe, Arjan G J; de Grooth, Bart G; Greve, Jan; Dolan, Gerald J; Rao, Chandra; Terstappen, Leon W M M

2002-03-01

Recently we introduced the CellTracks cell analysis system, in which samples are prepared based on a combination of immunomagnetic selection, separation, and alignment of cells along ferromagnetic lines. Here we describe the underlying magnetic principles and considerations made in the magnetic field design to achieve the best possible cell selection and alignment of magnetically labeled cells. Materials and Methods Computer simulations, in combination with experimental data, were used to optimize the design of the magnets and Ni lines to obtain the optimal magnetic configuration. A homogeneous cell distribution on the upper surface of the sample chamber was obtained with a magnet where the pole faces were tilted towards each other. The spatial distribution of magnetically aligned objects in between the Ni lines was dependent on the ratio of the diameter of the aligned object and the line spacing, which was tested with magnetically and fluorescently labeled 6 microm polystyrene beads. The best result was obtained when the line spacing was equal to or smaller than the diameter of the aligned object. The magnetic gradient of the designed permanent magnet extracts magnetically labeled cells from any cell suspension to a desired plane, providing a homogeneous cell distribution. In addition, it magnetizes ferro-magnetic Ni lines in this plane whose additional local gradient adds to the gradient of the permanent magnet. The resultant gradient aligns the magnetically labeled cells first brought to this plane. This combination makes it possible, in a single step, to extract and align cells on a surface from any cell suspension. Copyright 2002 Wiley-Liss, Inc.

16 CFR 1512.2 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS... post center line (or the center of the seating area if no seat post exists) and the ground plane, as measured with the wheels aligned and in a plane normal to the ground plane. (d) Track bicycle means a...

Relating normal vibrational modes to local vibrational modes with the help of an adiabatic connection scheme

NASA Astrophysics Data System (ADS)

Zou, Wenli; Kalescky, Robert; Kraka, Elfi; Cremer, Dieter

2012-08-01

Information on the electronic structure of a molecule and its chemical bonds is encoded in the molecular normal vibrational modes. However, normal vibrational modes result from a coupling of local vibrational modes, which means that only the latter can provide detailed insight into bonding and other structural features. In this work, it is proven that the adiabatic internal coordinate vibrational modes of Konkoli and Cremer [Int. J. Quantum Chem. 67, 29 (1998)], 10.1002/(SICI)1097-461X(1998)67:1<29::AID-QUA3>3.0.CO;2-0 represent a unique set of local modes that is directly related to the normal vibrational modes. The missing link between these two sets of modes are the compliance constants of Decius, which turn out to be the reciprocals of the local mode force constants of Konkoli and Cremer. Using the compliance constants matrix, the local mode frequencies of any molecule can be converted into its normal mode frequencies with the help of an adiabatic connection scheme that defines the coupling of the local modes in terms of coupling frequencies and reveals how avoided crossings between the local modes lead to changes in the character of the normal modes.

Temporal and spatial adaptation of transient responses to local features

PubMed Central

O'Carroll, David C.; Barnett, Paul D.; Nordström, Karin

2012-01-01

Interpreting visual motion within the natural environment is a challenging task, particularly considering that natural scenes vary enormously in brightness, contrast and spatial structure. The performance of current models for the detection of self-generated optic flow depends critically on these very parameters, but despite this, animals manage to successfully navigate within a broad range of scenes. Within global scenes local areas with more salient features are common. Recent work has highlighted the influence that local, salient features have on the encoding of optic flow, but it has been difficult to quantify how local transient responses affect responses to subsequent features and thus contribute to the global neural response. To investigate this in more detail we used experimenter-designed stimuli and recorded intracellularly from motion-sensitive neurons. We limited the stimulus to a small vertically elongated strip, to investigate local and global neural responses to pairs of local “doublet” features that were designed to interact with each other in the temporal and spatial domain. We show that the passage of a high-contrast doublet feature produces a complex transient response from local motion detectors consistent with predictions of a simple computational model. In the neuron, the passage of a high-contrast feature induces a local reduction in responses to subsequent low-contrast features. However, this neural contrast gain reduction appears to be recruited only when features stretch vertically (i.e., orthogonal to the direction of motion) across at least several aligned neighboring ommatidia. Horizontal displacement of the components of elongated features abolishes the local adaptation effect. It is thus likely that features in natural scenes with vertically aligned edges, such as tree trunks, recruit the greatest amount of response suppression. This property could emphasize the local responses to such features vs. those in nearby texture within the scene. PMID:23087617

Hydrodynamic Equations for Flocking Models without Velocity Alignment

NASA Astrophysics Data System (ADS)

Peruani, Fernando

2017-10-01

The spontaneous emergence of collective motion patterns is usually associated with the presence of a velocity alignment mechanism that mediates the interactions among the moving individuals. Despite of this widespread view, it has been shown recently that several flocking behaviors can emerge in the absence of velocity alignment and as a result of short-range, position-based, attractive forces that act inside a vision cone. Here, we derive the corresponding hydrodynamic equations of a microscopic position-based flocking model, reviewing and extending previous reported results. In particular, we show that three distinct macroscopic collective behaviors can be observed: i) the coarsening of aggregates with no orientational order, ii) the emergence of static, elongated nematic bands, and iii) the formation of moving, locally polar structures, which we call worms. The derived hydrodynamic equations indicate that active particles interacting via position-based interactions belong to a distinct class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems.

A basic analysis toolkit for biological sequences

PubMed Central

Giancarlo, Raffaele; Siragusa, Alessandro; Siragusa, Enrico; Utro, Filippo

2007-01-01

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at under the GNU GPL. PMID:17877802

Photothermal camera port accessory for microscopic thermal diffusivity imaging

NASA Astrophysics Data System (ADS)

Escola, Facundo Zaldívar; Kunik, Darío; Mingolo, Nelly; Martínez, Oscar Eduardo

2016-06-01

The design of a scanning photothermal accessory is presented, which can be attached to the camera port of commercial microscopes to measure thermal diffusivity maps with micrometer resolution. The device is based on the thermal expansion recovery technique, which measures the defocusing of a probe beam due to the curvature induced by the local heat delivered by a focused pump beam. The beam delivery and collecting optics are built using optical fiber technology, resulting in a robust optical system that provides collinear pump and probe beams without any alignment adjustment necessary. The quasiconfocal configuration for the signal collection using the same optical fiber sets very restrictive conditions on the positioning and alignment of the optical components of the scanning unit, and a detailed discussion of the design equations is presented. The alignment procedure is carefully described, resulting in a system so robust and stable that no further alignment is necessary for the day-to-day use, becoming a tool that can be used for routine quality control, operated by a trained technician.

THE LOCAL GROUP IN THE COSMIC WEB

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

Forero-Romero, J. E.; González, R., E-mail: je.forero@uniandes.edu.co, E-mail: regonzar@astro.puc.cl

We explore the characteristics of the cosmic web around Local-Group (LG)-like pairs using a cosmological simulation in the ΛCDM cosmology. We use the Hessian of the gravitational potential to classify regions on scales of ∼2 Mpc as a peak, sheet, filament, or void. The sample of LG counterparts is represented by two samples of halo pairs. The first is a general sample composed of pairs with similar masses and isolation criteria as observed for the LG. The second is a subset with additional observed kinematic constraints such as relative pair velocity and separation. We find that the pairs in the LGmore » sample with all constraints are: (1) preferentially located in filaments and sheets, (2) located in a narrow range of local overdensity 0 < δ < 2, web ellipticity 0.1 < e < 1.0, and prolateness –0.4 < p < 0.4, (3) strongly aligned with the cosmic web. The alignments are such that the pair orbital angular momentum tends to be perpendicular to the smallest tidal eigenvector, e-hat {sub 3}, which lies along the filament direction or the sheet plane. A stronger alignment is present for the vector linking the two halos with the vector e-hat {sub 3}. Additionally, we fail to find a strong correlation between the spin of each halo in the pair with the cosmic web. All of these trends are expected to a great extent from the selection of LG total mass in the general sample. Applied to the observed LG, there is a potential conflict between the alignments of the different satellite planes and the numerical evidence for satellite accretion along filaments; the direction defined by e-hat {sub 3}. This highlights the relevance of achieving a precise characterization for the location of the LG in the cosmic web in the cosmological context provided by ΛCDM.« less

Alignment of defect levels and band edges through hybrid functionals: Effect of screening in the exchange term

NASA Astrophysics Data System (ADS)

Komsa, Hannu-Pekka; Broqvist, Peter; Pasquarello, Alfredo

2010-05-01

We investigate how various treatments of exact exchange affect defect charge transition levels and band edges in hybrid functional schemes for a variety of systems. We distinguish the effects of long-range vs short-range exchange and of local vs nonlocal exchange. This is achieved by the consideration of a set of four functionals, which comprise the semilocal Perdew-Burke-Ernzerhof (PBE) functional, the PBE hybrid (PBE0), the Heyd-Scuseria-Ernzerhof (HSE) functional, and a hybrid derived from PBE0 in which the Coulomb kernel in the exact exchange term is screened as in the HSE functional but which, unlike HSE, does not include a local expression compensating for the loss of the long-range exchange. We find that defect levels in PBE0 and in HSE almost coincide when aligned with respect to a common reference potential, due to the close total-energy differences in the two schemes. At variance, the HSE band edges determined within the same alignment scheme are found to shift significantly with respect to the PBE0 ones: the occupied and the unoccupied states undergo shifts of about +0.4eV and -0.4eV , respectively. These shifts are found to vary little among the materials considered. Through a rationale based on the behavior of local and nonlocal long-range exchange, this conclusion is generalized beyond the class of materials used in this study. Finally, we explicitly address the practice of tuning the band gap by adapting the fraction of exact exchange incorporated in the functional. When PBE0-like and HSE-like functionals are tuned to yield identical band gaps, their respective results for the positions of defect levels within the band gap and for the band alignments at interfaces are found to be very close.

INDUCED SEISMICITY MECHANISM AT THE GEYSERS, CALIFORNIA.

USGS Publications Warehouse

Oppenheimer, David

1985-01-01

Induced microearthquake activity at The Geysers geothermal reservoir is observed in the vicinity of eight geothermal steam power units. The earthquakes do not align with mapped faults but occur adjacent to steam wells. The sense of motion as deduced from focal mechanisms is strike-slip to reverse in the upper 1 km of the reservoir and changes to strike-slip to oblique normal slip at greater depth because of the increased lithostatic load. Below 1 km the reservoir is undergoing horizontal extension. Alignment of P and T axes with the regional stress field suggests that contraction of the reservoir contributes the incremental stress perturbation to the regional stress field and causes microearthquakes.

System performance conclusions

NASA Technical Reports Server (NTRS)

Arndt, G. D.

1980-01-01

The advantages and disadvantages of reducing power levels and using antennas with diameters smaller than 1 Km were evaluated if rectenna costs and land usage requirements become major factors, operating at 5800 megahertz should be considered. Three sequences (random, incoherent phasing, and concentric rings - center to edge) provided satisfactory performance in that the resultant sidelobe levels during startup/ shutdown were lower than the steady-state levels present during normal operations. Grating lobe peaks and scattered power levels were used to determine the array/subarray mechanical alignment requirements. The antenna alignment requirement is 1 min or 3 min depending on phase control configuration. System error parameters were defined to minimize scattered microwave power.

Large-scale trench-normal mantle flow beneath central South America

NASA Astrophysics Data System (ADS)

Reiss, M. C.; Rümpker, G.; Wölbern, I.

2018-01-01

We investigate the anisotropic properties of the fore-arc region of the central Andean margin between 17-25°S by analyzing shear-wave splitting from teleseismic and local earthquakes from the Nazca slab. With partly over ten years of recording time, the data set is uniquely suited to address the long-standing debate about the mantle flow field at the South American margin and in particular whether the flow field beneath the slab is parallel or perpendicular to the trench. Our measurements suggest two anisotropic layers located within the crust and mantle beneath the stations, respectively. The teleseismic measurements show a moderate change of fast polarizations from North to South along the trench ranging from parallel to subparallel to the absolute plate motion and, are oriented mostly perpendicular to the trench. Shear-wave splitting measurements from local earthquakes show fast polarizations roughly aligned trench-parallel but exhibit short-scale variations which are indicative of a relatively shallow origin. Comparisons between fast polarization directions from local earthquakes and the strike of the local fault systems yield a good agreement. To infer the parameters of the lower anisotropic layer we employ an inversion of the teleseismic waveforms based on two-layer models, where the anisotropy of the upper (crustal) layer is constrained by the results from the local splitting. The waveform inversion yields a mantle layer that is best characterized by a fast axis parallel to the absolute plate motion which is more-or-less perpendicular to the trench. This orientation is likely caused by a combination of the fossil crystallographic preferred orientation of olivine within the slab and entrained mantle flow beneath the slab. The anisotropy within the crust of the overriding continental plate is explained by the shape-preferred orientation of micro-cracks in relation to local fault zones which are oriented parallel to the overall strike of the Andean range. Our results do not provide any evidence for a significant contribution of trench-parallel mantle flow beneath the subducting slab.

Axelrod model: accepting or discussing

NASA Astrophysics Data System (ADS)

Dybiec, Bartlomiej; Mitarai, Namiko; Sneppen, Kim

2012-10-01

Agents building social systems are characterized by complex states, and interactions among individuals can align their opinions. The Axelrod model describes how local interactions can result in emergence of cultural domains. We propose two variants of the Axelrod model where local consensus is reached either by listening and accepting one of neighbors' opinion or two agents discuss their opinion and achieve an agreement with mixed opinions. We show that the local agreement rule affects the character of the transition between the single culture and the multiculture regimes.

Interpolation schemes for peptide rearrangements.

PubMed

Bauer, Marianne S; Strodel, Birgit; Fejer, Szilard N; Koslover, Elena F; Wales, David J

2010-02-07

A variety of methods (in total seven) comprising different combinations of internal and Cartesian coordinates are tested for interpolation and alignment in connection attempts for polypeptide rearrangements. We consider Cartesian coordinates, the internal coordinates used in CHARMM, and natural internal coordinates, each of which has been interfaced to the OPTIM code and compared with the corresponding results for united-atom force fields. We show that aligning the methylene hydrogens to preserve the sign of a local dihedral angle, rather than minimizing a distance metric, provides significant improvements with respect to connection times and failures. We also demonstrate the superiority of natural coordinate methods in conjunction with internal alignment. Checking the potential energy of the interpolated structures can act as a criterion for the choice of the interpolation coordinate system, which reduces failures and connection times significantly.

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

PubMed Central

Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

2016-01-01

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

NASA Astrophysics Data System (ADS)

Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

2016-03-01

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.

In silico Analysis of 2085 Clones from a Normalized Rat Vestibular Periphery 3′ cDNA Library

PubMed Central

Roche, Joseph P.; Cioffi, Joseph A.; Kwitek, Anne E.; Erbe, Christy B.; Popper, Paul

2005-01-01

The inserts from 2400 cDNA clones isolated from a normalized Rattus norvegicus vestibular periphery cDNA library were sequenced and characterized. The Wackym-Soares vestibular 3′ cDNA library was constructed from the saccular and utricular maculae, the ampullae of all three semicircular canals and Scarpa's ganglia containing the somata of the primary afferent neurons, microdissected from 104 male and female rats. The inserts from 2400 randomly selected clones were sequenced from the 5′ end. Each sequence was analyzed using the BLAST algorithm compared to the Genbank nonredundant, rat genome, mouse genome and human genome databases to search for high homology alignments. Of the initial 2400 clones, 315 (13%) were found to be of poor quality and did not yield useful information, and therefore were eliminated from the analysis. Of the remaining 2085 sequences, 918 (44%) were found to represent 758 unique genes having useful annotations that were identified in databases within the public domain or in the published literature; these sequences were designated as known characterized sequences. 1141 sequences (55%) aligned with 1011 unique sequences had no useful annotations and were designated as known but uncharacterized sequences. Of the remaining 26 sequences (1%), 24 aligned with rat genomic sequences, but none matched previously described rat expressed sequence tags or mRNAs. No significant alignment to the rat or human genomic sequences could be found for the remaining 2 sequences. Of the 2085 sequences analyzed, 86% were singletons. The known, characterized sequences were analyzed with the FatiGO online data-mining tool (http://fatigo.bioinfo.cnio.es/) to identify level 5 biological process gene ontology (GO) terms for each alignment and to group alignments with similar or identical GO terms. Numerous genes were identified that have not been previously shown to be expressed in the vestibular system. Further characterization of the novel cDNA sequences may lead to the identification of genes with vestibular-specific functions. Continued analysis of the rat vestibular periphery transcriptome should provide new insights into vestibular function and generate new hypotheses. Physiological studies are necessary to further elucidate the roles of the identified genes and novel sequences in vestibular function. PMID:16103642

Classification and localization of early-stage Alzheimer's disease in magnetic resonance images using a patch-based classifier ensemble.

PubMed

Simões, Rita; van Cappellen van Walsum, Anne-Marie; Slump, Cornelis H

2014-09-01

Classification methods have been proposed to detect Alzheimer’s disease (AD) using magnetic resonance images. Most rely on features such as the shape/volume of brain structures that need to be defined a priori. In this work, we propose a method that does not require either the segmentation of specific brain regions or the nonlinear alignment to a template. Besides classification, we also analyze which brain regions are discriminative between a group of normal controls and a group of AD patients. We perform 3D texture analysis using Local Binary Patterns computed at local image patches in the whole brain, combined in a classifier ensemble.We evaluate our method in a publicly available database including very mild-to-mild AD subjects and healthy elderly controls. For the subject cohort including only mild AD subjects, the best results are obtained using a combination of large (30×30×30 and 40×40×40 voxels) patches. A spatial analysis on the best performing patches shows that these are located in the medial-temporal lobe and in the periventricular regions. When very mild AD subjects are included in the dataset, the small (10×10×10 voxels) patches perform best, with the most discriminative ones being located near the left hippocampus. We show that our method is able not only to perform accurate classification, but also to localize dis-criminative brain regions, which are in accordance with the medical literature. This is achieved without the need to segment-specific brain structures and without performing nonlinear registration to a template, indicating that the method may be suitable for a clinical implementation that can help to diagnose AD at an earlier stage.

Electrostatic ion instabilities in the presence of parallel currents and transverse electric fields

NASA Technical Reports Server (NTRS)

Ganguli, G.; Palmadesso, P. J.

1988-01-01

The electrostatic ion instabilities are studied for oblique propagation in the presence of magnetic field-aligned currents and transverse localized electric fields in a weakly collisional plasma. The presence of transverse electric fields result in mode excitation for magnetic field aligned current values that are otherwise stable. The electron collisions enhance the growth while ion collisions have a damping effect. These results are discussed in the context of observations of low frequency ion modes in the auroral ionosphere by radar and rocket experiments.

OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.

PubMed

Verzotto, Davide; M Teo, Audrey S; Hillmer, Axel M; Nagarajan, Niranjan

2016-01-01

Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome-mapping technologies (for example, optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kilo base pairs (kbp) to 2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging because of the lack of efficient and sensitive map-alignment algorithms for robustly aligning error-prone maps to sequences. We introduce a novel seed-and-extend glocal (short for global-local) alignment method, OPTIMA (and a sliding-window extension for overlap alignment, OPTIMA-Overlap), which is the first to create indexes for continuous-valued mapping data while accounting for mapping errors. We also present a novel statistical model, agnostic with respect to technology-dependent error rates, for conservatively evaluating the significance of alignments without relying on expensive permutation-based tests. We show that OPTIMA and OPTIMA-Overlap outperform other state-of-the-art approaches (1.6-2 times more sensitive) and are more efficient (170-200 %) and precise in their alignments (nearly 99 % precision). These advantages are independent of the quality of the data, suggesting that our indexing approach and statistical evaluation are robust, provide improved sensitivity and guarantee high precision.

Highly anisotropic magneto-transport and field orientation dependent oscillations in aligned carbon nanotube/epoxy composites

NASA Astrophysics Data System (ADS)

Wells, Brian; Kumar, Raj; Reynolds, C. Lewis; Peters, Kara; Bradford, Philip D.

2017-12-01

Carbon nanotubes (CNTs) have been widely investigated as additive materials for composites with potential applications in electronic devices due to their extremely large electrical conductivity and current density. Here, highly aligned CNT composite films were created using a sequential layering fabrication technique. The degree of CNT alignment leads to anisotropic resistance values which varies >400× in orthogonal directions. Similarly, the magnetoresistance (MR) of the CNT composite differs depending upon the relative direction of current and the applied magnetic field. A suppression of negative to positive MR crossover was also observed. More importantly, an overall positive magnetoresistance behavior with localized +/- oscillations was discovered at low fields which persists up to room temperature when the current (I) and in-plane magnetic field (B) were parallel to the axis of CNT (B∥I∥CNT), which is consistent with Aharonov-Bohm oscillations in our CNT/epoxy composites. When the current, applied magnetic field, and nanotube axis are aligned, the in-plane MR is positive instead of negative as observed for all other field, current, and tube orientations. Here, we provide in-depth analysis of the conduction mechanism and anisotropy in the magneto-transport properties of these aligned CNT-epoxy composites.

Deformation field correction for spatial normalization of PET images

PubMed Central

Bilgel, Murat; Carass, Aaron; Resnick, Susan M.; Wong, Dean F.; Prince, Jerry L.

2015-01-01

Spatial normalization of positron emission tomography (PET) images is essential for population studies, yet the current state of the art in PET-to-PET registration is limited to the application of conventional deformable registration methods that were developed for structural images. A method is presented for the spatial normalization of PET images that improves their anatomical alignment over the state of the art. The approach works by correcting the deformable registration result using a model that is learned from training data having both PET and structural images. In particular, viewing the structural registration of training data as ground truth, correction factors are learned by using a generalized ridge regression at each voxel given the PET intensities and voxel locations in a population-based PET template. The trained model can then be used to obtain more accurate registration of PET images to the PET template without the use of a structural image. A cross validation evaluation on 79 subjects shows that the proposed method yields more accurate alignment of the PET images compared to deformable PET-to-PET registration as revealed by 1) a visual examination of the deformed images, 2) a smaller error in the deformation fields, and 3) a greater overlap of the deformed anatomical labels with ground truth segmentations. PMID:26142272

Neonatal Atlas Construction Using Sparse Representation

PubMed Central

Shi, Feng; Wang, Li; Wu, Guorong; Li, Gang; Gilmore, John H.; Lin, Weili; Shen, Dinggang

2014-01-01

Atlas construction generally includes first an image registration step to normalize all images into a common space and then an atlas building step to fuse the information from all the aligned images. Although numerous atlas construction studies have been performed to improve the accuracy of the image registration step, unweighted or simply weighted average is often used in the atlas building step. In this article, we propose a novel patch-based sparse representation method for atlas construction after all images have been registered into the common space. By taking advantage of local sparse representation, more anatomical details can be recovered in the built atlas. To make the anatomical structures spatially smooth in the atlas, the anatomical feature constraints on group structure of representations and also the overlapping of neighboring patches are imposed to ensure the anatomical consistency between neighboring patches. The proposed method has been applied to 73 neonatal MR images with poor spatial resolution and low tissue contrast, for constructing a neonatal brain atlas with sharp anatomical details. Experimental results demonstrate that the proposed method can significantly enhance the quality of the constructed atlas by discovering more anatomical details especially in the highly convoluted cortical regions. The resulting atlas demonstrates superior performance of our atlas when applied to spatially normalizing three different neonatal datasets, compared with other start-of-the-art neonatal brain atlases. PMID:24638883

Double-Glazing Interferometry

ERIC Educational Resources Information Center

Toal, Vincent; Mihaylova, Emilia M.

2009-01-01

This note describes how white light interference fringes can be seen by observing the Moon through a double-glazed window. White light interferometric fringes are normally observed only in a well-aligned interferometer whose optical path difference is less than the coherence length of the light source, which is approximately one micrometer for…

INTEGRATED CARBON CREDIT PROGRAMS: A BIOFUELS PROGRAM IN MADAGASCAR THAT LINKS THE ENERGY, LAND USE AND TRANSPORTATION SECTORS

EPA Science Inventory

Late Treatment of Syndesmotic Injuries.

PubMed

Swords, Michael P; Sands, Andrew; Shank, John R

2017-03-01

Normal syndesmosis anatomy and alignment are essential to ankle function. Although injuries to the syndesmosis are common with ankle injuries, accurate diagnosis and reduction continue to be a challenge. Late reconstruction for syndesmosis is reviewed. A surgical technique for late reconstruction is outlined in detail. Copyright © 2016 Elsevier Inc. All rights reserved.

36 CFR 1192.53 - Doorways.

Code of Federal Regulations, 2012 CFR

2012-07-01

... between each vehicle door at rest and the platform shall be no greater than 3 inches and the height of the vehicle floor shall be within plus or minus 5/8 inch of the platform height under all normal passenger load conditions. Vertical alignment may be accomplished by vehicle air suspension or other suitable...

36 CFR 1192.53 - Doorways.

Code of Federal Regulations, 2014 CFR

2014-07-01

... between each vehicle door at rest and the platform shall be no greater than 3 inches and the height of the vehicle floor shall be within plus or minus 5/8 inch of the platform height under all normal passenger load conditions. Vertical alignment may be accomplished by vehicle air suspension or other suitable...

OP17MICRORNA PROFILING USING SMALL RNA-SEQ IN PAEDIATRIC LOW GRADE GLIOMAS

PubMed Central

Jeyapalan, Jennie N.; Jones, Tania A.; Tatevossian, Ruth G.; Qaddoumi, Ibrahim; Ellison, David W.; Sheer, Denise

2014-01-01

INTRODUCTION: MicroRNAs regulate gene expression by targeting mRNAs for translational repression or degradation at the post-transcriptional level. In paediatric low-grade gliomas a few key genetic mutations have been identified, including BRAF fusions, FGFR1 duplications and MYB rearrangements. Our aim in the current study is to profile aberrant microRNA expression in paediatric low-grade gliomas and determine the role of epigenetic changes in the aetiology and behaviour of these tumours. METHOD: MicroRNA profiling of tumour samples (6 pilocytic, 2 diffuse, 2 pilomyxoid astrocytomas) and normal brain controls (4 adult normal brain samples and a primary glial progenitor cell-line) was performed using small RNA sequencing. Bioinformatic analysis included sequence alignment, analysis of the number of reads (CPM, counts per million) and differential expression. RESULTS: Sequence alignment identified 695 microRNAs, whose expression was compared in tumours v. normal brain. PCA and hierarchical clustering showed separate groups for tumours and normal brain. Computational analysis identified approximately 400 differentially expressed microRNAs in the tumours compared to matched location controls. Our findings will then be validated and integrated with extensive genetic and epigenetic information we have previously obtained for the full tumour cohort. CONCLUSION: We have identified microRNAs that are differentially expressed in paediatric low-grade gliomas. As microRNAs are known to target genes involved in the initiation and progression of cancer, they provide critical information on tumour pathogenesis and are an important class of biomarkers.

Human Corneal Limbal-Epithelial Cell Response to Varying Silk Film Geometric Topography In Vitro

PubMed Central

Lawrence, Brian D.; Pan, Zhi; Liu, Aihong; Kaplan, David L.; Rosenblatt, Mark I.

2012-01-01

Silk fibroin films are a promising class of biomaterials that have a number of advantages for use in ophthalmic applications due to their transparent nature, mechanical properties and minimal inflammatory response upon implantation. Freestanding silk films with parallel line and concentric ring topographies were generated for in vitro characterization of human corneal limbal-epithelial (HCLE) cell response upon differing geometric patterned surfaces. Results indicated that silk film topography significantly affected initial HCLE culture substrate attachment, cellular alignment, cell-to-cell contact formation, actin cytoskeleton alignment, and focal adhesion (FA) localization. Most notably, parallel line patterned surfaces displayed a 36%–54% increase on average in initial cell attachment, which corresponded to an over 2-fold increase in FA localization when compared to other silk film surfaces and controls. In addition, distinct localization of FA formation was observed along the edges for all patterned silk film topographies. In conclusion, silk film feature topography appears to help direct corneal epithelial cell response and cytoskeleton development, especially in regards to FA distribution, in vitro. PMID:22705042

Correlation between failure and local material property in chopped carbon fiber chip-reinforced sheet molding compound composites under tensile load

DOE PAGES

Tang, Haibin; Chen, Zhangxing; Zhou, Guowei; ...

2018-02-06

To develop further understanding towards the role of a heterogeneous microstructure on tensile crack initiation and failure behavior in chopped carbon fiber chip-reinforced composites, uni-axial tensile tests are performed on coupons cut from compression molded plaque with varying directions. Our experimental results indicate that failure initiation is relevant to the strain localization, and a new criterion with the nominal modulus to predict the failure location is proposed based on the strain analysis. Furthermore, optical microscopic images show that the nominal modulus is determined by the chip orientation distribution. At the area with low nominal modulus, it is found that chipsmore » are mostly aligning along directions transverse to loading direction and/or less concentrated, while at the area with high nominal modulus, more chips are aligning to tensile direction. On the basis of failure mechanism analysis, it is concluded that transversely-oriented chips or resin-rich regions are easier for damage initiation, while longitudinally-oriented chips postpone the fracture. Good agreement is found among failure mechanism, strain localization and chip orientation distribution.« less

Correlation between failure and local material property in chopped carbon fiber chip-reinforced sheet molding compound composites under tensile load

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

Tang, Haibin; Chen, Zhangxing; Zhou, Guowei

To develop further understanding towards the role of a heterogeneous microstructure on tensile crack initiation and failure behavior in chopped carbon fiber chip-reinforced composites, uni-axial tensile tests are performed on coupons cut from compression molded plaque with varying directions. Our experimental results indicate that failure initiation is relevant to the strain localization, and a new criterion with the nominal modulus to predict the failure location is proposed based on the strain analysis. Furthermore, optical microscopic images show that the nominal modulus is determined by the chip orientation distribution. At the area with low nominal modulus, it is found that chipsmore » are mostly aligning along directions transverse to loading direction and/or less concentrated, while at the area with high nominal modulus, more chips are aligning to tensile direction. On the basis of failure mechanism analysis, it is concluded that transversely-oriented chips or resin-rich regions are easier for damage initiation, while longitudinally-oriented chips postpone the fracture. Good agreement is found among failure mechanism, strain localization and chip orientation distribution.« less

SU-E-J-33: Comparison Between Soft Tissue Alignment and Bony Alignment for Pancreatic Cancer Radiotherapy

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

Suh, Y; Crane, C; Krishnan, S

Purpose An IGRT modality for pancreatic cancer treatment with dose escalation at our institution is in-room daily CT imaging. The purpose of this study is to assess the difference between soft tissue alignment and bony alignment for pancreatic tumor localization. Methods Eighteen patients with pancreatic tumors who underwent IMRT treatment with an inspiration breath-hold technique between July 2012 and February 2015 are included in this study. Prior to each treatment, a CT scan was acquired. The CT image guidance started with auto-alignment to either the bony anatomy (vertebral bodies) or fiducials (for the six patients with the stent in/near themore » tumor) and then, when necessary, manual adjustments were made based on soft tissue alignment using clinical software (CT-Assisted Targeting system). The difference between soft tissue alignment and bony/fiducial alignment was evaluated. Results Of all 380 treatments, manual adjustment was made in 225 treatments, ranging from 11% (3 treatments out of 28) to 96% (27 treatments out of 28) per patient. The mean of the difference between soft tissue alignment and bony/fiducial alignment per patient ranged from −3.6 to 0.3 mm, −1.5 to 2.8 mm, and −3.3 to 3.4 mm in the AP, SI, and RL directions, respectively. The maximum difference over all treatments was −9.5, −14.6, and −14.6 mm in the AP, SI, and RL directions, respectively. Conclusion About 60% of the time, manual adjustment based on soft tissue alignment was required. The extent of manual adjustment was usually small but varied significantly from patient to patient. The ultimate goal of the IGRT modality using daily CT imaging is not to fully cover the target but to spare organs-at-risk as much as possible to avoid them moving into higher dose gradients than accepted in the treatment plan. To this end, manual adjustment based on soft tissue alignment is critically important.« less

Orientation and Order in Shear-Aligned Thin Films of Cylinder-Forming Block Copolymers

NASA Astrophysics Data System (ADS)

Register, Richard

The regularity and tunability of the nanoscale structure in block copolymers makes their thin films attractive as nanolithographic templates; however, in the absence of a guiding field, self-assembly produces a polygrain structure with no particular orientation and a high density of defects. As demonstrated in the elegant studies of Ed Kramer and coworkers, graphoepitaxy can provide local control over domain orientation, with a dramatic reduction in defect density. Alternatively, cylindrical microdomains lying in the plane of the film can be aligned over macroscopic areas by applying shear stress at the film surface. In non-sheared films of polystyrene-poly(n-hexylmethacrylate) diblocks, PS-PHMA, the PS cylinder axis orientation relative to the surface switches from parallel to perpendicular as a function of film thickness; this oscillation is damped out as the fraction of the PS block increases, away from the sphere-cylinder phase boundary. In aligned films, thicknesses which possess the highest coverage of parallel cylinders prior to shear show the highest quality of alignment post-shear, as measured by the in-plane orientational order parameter. In well-aligned samples of optimal thickness, the quality of alignment is limited by isolated dislocations, whose density is highest at high PS contents, and by undulations in the cylinders' trajectories, whose impact is most severe at low PS contents; consequently, polymers whose compositions lie in the middle of the cylinder-forming region exhibit the highest quality of alignment. The dynamics of the alignment process are also investigated, and fit to a melting-recrystallization model which allows for the determination of two key alignment parameters: the critical stress needed for alignment, and an orientation rate constant. For films containing a monolayer of cylindrical domains, as PS weight fraction or overall molecular weight increases, the critical stress increases moderately, while the rate of alignment drastically decreases. As the number of layers of cylinders in the film increases, the critical stress decreases modestly, while the rate remains unchanged; substrate wetting condition has no measurable influence on alignment response. [Work of Raleigh Davis, in collaboration with Paul Chaikin.

An association of magnetospheric whistler dispersion characteristics with changes in local plasma density.

NASA Technical Reports Server (NTRS)

Scarf, F. L.; Chappell, C. R.

1973-01-01

We use OGO 5 measurements made within the plasmapause on May 15, 1969, to investigate the possible association between changes in lightning whistler dispersion characteristics and local density fluctuations. It is shown that groups of whistlers with relatively constant dispersions tended to be detected in regions where the local ion concentration was significantly enhanced. It is assumed that these local density fluctuations represent characteristics of large-scale field-aligned variations. The results are then compared with ray refraction estimates appropriate for low-frequency whistler mode propagation (wave components with frequencies comparable to the local lower hybrid frequency) in a nonuniform medium.

Evaluation of Changes in Morphology and Function of Human Induced Pluripotent Stem Cell Derived Cardiomyocytes (HiPSC-CMs) Cultured on an Aligned-Nanofiber Cardiac Patch

PubMed Central

Khan, Mahmood; Xu, Yanyi; Hua, Serena; Johnson, Jed; Belevych, Andriy; Janssen, Paul M. L.; Gyorke, Sandor; Guan, Jianjun; Angelos, Mark G.

2015-01-01

Introduction Dilated cardiomyopathy is a major cause of progressive heart failure. Utilization of stem cell therapy offers a potential means of regenerating viable cardiac tissue. However, a major obstacle to stem cell therapy is the delivery and survival of implanted stem cells in the ischemic heart. To address this issue, we have developed a biomimetic aligned nanofibrous cardiac patch and characterized the alignment and function of human inducible pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) cultured on this cardiac patch. This hiPSC-CMs seeded patch was compared with hiPSC-CMs cultured on standard flat cell culture plates. Methods hiPSC-CMs were cultured on; 1) a highly aligned polylactide-co-glycolide (PLGA) nanofiber scaffold (~50 microns thick) and 2) on a standard flat culture plate. Scanning electron microscopy (SEM) was used to determine alignment of PLGA nanofibers and orientation of the cells on the respective surfaces. Analysis of gap junctions (Connexin-43) was performed by confocal imaging in both the groups. Calcium cycling and patch-clamp technique were performed to measure calcium transients and electrical coupling properties of cardiomyocytes. Results SEM demonstrated >90% alignment of the nanofibers in the patch which is similar to the extracellular matrix of decellularized rat myocardium. Confocal imaging of the cardiomyocytes demonstrated symmetrical alignment in the same direction on the aligned nanofiber patch in sharp contrast to the random appearance of cardiomyocytes cultured on a tissue culture plate. The hiPSC-CMs cultured on aligned nanofiber cardiac patches showed more efficient calcium cycling compared with cells cultured on standard flat surface culture plates. Quantification of mRNA with qRT-PCR confirmed that these cardiomyocytes expressed α-actinin, troponin-T and connexin-43 in-vitro. Conclusions Overall, our results demonstrated changes in morphology and function of human induced pluripotent derived cardiomyocytes cultured in an anisotropic environment created by an aligned nanofiber patch. In this environment, these cells better approximate normal cardiac tissue compared with cells cultured on flat surface and can serve as the basis for bioengineering of an implantable cardiac patch. PMID:25993466

Evaluation of Changes in Morphology and Function of Human Induced Pluripotent Stem Cell Derived Cardiomyocytes (HiPSC-CMs) Cultured on an Aligned-Nanofiber Cardiac Patch.

PubMed

Khan, Mahmood; Xu, Yanyi; Hua, Serena; Johnson, Jed; Belevych, Andriy; Janssen, Paul M L; Gyorke, Sandor; Guan, Jianjun; Angelos, Mark G

2015-01-01

Dilated cardiomyopathy is a major cause of progressive heart failure. Utilization of stem cell therapy offers a potential means of regenerating viable cardiac tissue. However, a major obstacle to stem cell therapy is the delivery and survival of implanted stem cells in the ischemic heart. To address this issue, we have developed a biomimetic aligned nanofibrous cardiac patch and characterized the alignment and function of human inducible pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) cultured on this cardiac patch. This hiPSC-CMs seeded patch was compared with hiPSC-CMs cultured on standard flat cell culture plates. hiPSC-CMs were cultured on; 1) a highly aligned polylactide-co-glycolide (PLGA) nanofiber scaffold (~50 microns thick) and 2) on a standard flat culture plate. Scanning electron microscopy (SEM) was used to determine alignment of PLGA nanofibers and orientation of the cells on the respective surfaces. Analysis of gap junctions (Connexin-43) was performed by confocal imaging in both the groups. Calcium cycling and patch-clamp technique were performed to measure calcium transients and electrical coupling properties of cardiomyocytes. SEM demonstrated >90% alignment of the nanofibers in the patch which is similar to the extracellular matrix of decellularized rat myocardium. Confocal imaging of the cardiomyocytes demonstrated symmetrical alignment in the same direction on the aligned nanofiber patch in sharp contrast to the random appearance of cardiomyocytes cultured on a tissue culture plate. The hiPSC-CMs cultured on aligned nanofiber cardiac patches showed more efficient calcium cycling compared with cells cultured on standard flat surface culture plates. Quantification of mRNA with qRT-PCR confirmed that these cardiomyocytes expressed α-actinin, troponin-T and connexin-43 in-vitro. Overall, our results demonstrated changes in morphology and function of human induced pluripotent derived cardiomyocytes cultured in an anisotropic environment created by an aligned nanofiber patch. In this environment, these cells better approximate normal cardiac tissue compared with cells cultured on flat surface and can serve as the basis for bioengineering of an implantable cardiac patch.

Does Kinematic Alignment and Flexion of a Femoral Component Designed for Mechanical Alignment Reduce the Proximal and Lateral Reach of the Trochlea?

PubMed

Brar, Abheetinder S; Howell, Stephen M; Hull, Maury L; Mahfouz, Mohamed R

2016-08-01

Kinematically aligned total knee arthroplasty uses a femoral component designed for mechanical alignment (MA) and sets the component in more internal, valgus, and flexion rotation than MA. It is unknown how much kinematic alignment (KA) and flexion of the femoral component reduce the proximal and lateral reach of the trochlea; two reductions that could increase the risk of abnormal patella tracking. We simulated MA and KA of the femoral component in 0° of flexion on 20 3-dimensional bone models of normal femurs. The mechanically and kinematically aligned components were then aligned in 5°, 10°, and 15° of flexion and downsized until the flange contacted the anterior femur. The reductions in the proximal and lateral reach from the proximal point of the trochlea of the MA component set in 0° of flexion were computed. KA at 0° of flexion did not reduce the proximal reach and reduced the lateral reach an average of 3 mm. Flexion of the MA and KA femoral component 5°, 10°, and 15° reduced the proximal reach an average of 4 mm, 8 mm, and 12 mm, respectively (0.8 mm/degree of flexion), and reduced the lateral reach an average of 1 mm and 4 mm regardless of the degree of flexion, respectively. Arthroplasty surgeons and biomechanical engineers striving to optimize patella tracking might consider developing surgical techniques to minimize flexion of the femoral component when performing KA and MA total knee arthroplasty to promote early patella engagement and consider designing a femoral component with a trochlea shaped specifically for KA. Copyright © 2016 Elsevier Inc. All rights reserved.

Millimeter-Wave Localizers for Aircraft-to-Aircraft Approach Navigation

NASA Technical Reports Server (NTRS)

Tang, Adrian J.

2013-01-01

Aerial refueling technology for both manned and unmanned aircraft is critical for operations where extended aircraft flight time is required. Existing refueling assets are typically manned aircraft, which couple to a second aircraft through the use of a refueling boom. Alignment and mating of the two aircraft continues to rely on human control with use of high-resolution cameras. With the recent advances in unmanned aircraft, it would be highly advantageous to remove/reduce human control from the refueling process, simplifying the amount of remote mission management and enabling new operational scenarios. Existing aerial refueling uses a camera, making it non-autonomous and prone to human error. Existing commercial localizer technology has proven robust and reliable, but not suited for aircraft-to-aircraft approaches like in aerial refueling scenarios since the resolution is too coarse (approximately one meter). A localizer approach system for aircraft-to-aircraft docking can be constructed using the same modulation with a millimeterwave carrier to provide high resolution. One technology used to remotely align commercial aircraft on approach to a runway are ILS (instrument landing systems). ILS have been in service within the U.S. for almost 50 years. In a commercial ILS, two partially overlapping beams of UHF (109 to 126 MHz) are broadcast from an antenna array so that their overlapping region defines the centerline of the runway. This is called a localizer system and is responsible for horizontal alignment of the approach. One beam is modulated with a 150-Hz tone, while the other with a 90-Hz tone. Through comparison of the modulation depths of both tones, an autopilot system aligns the approaching aircraft with the runway centerline. A similar system called a glide-slope (GS) exists in the 320-to-330MHz band for vertical alignment of the approach. While this technology has been proven reliable for millions of commercial flights annually, its UHF nature limits its ability to operate beyond the 1-to-2-meter precisions associated with commercial runway width. A prototype ILS-type system operates at millimeter-wave frequencies to provide automatic and robust approach control for aerial refueling. The system allows for the coupling process to remain completely autonomous, as a boom operator is no longer required. Operating beyond 100 GHz provides enough resolution and a narrow enough beamwidth that an approach corridor of centimeter scales can be maintained. Two modules were used to accomplish this task. The first module is a localizer/glide-slope module that can be fitted on a refueling aircraft. This module provides the navigation beams for aligning the approaching aircraft. The second module is navigational receiver fitted onto the approaching aircraft to be re fueled that can detect the approach beams. Since unmanned aircraft have a limited payload size and limited electrical power, the receiver portion was implemented in CMOS (complementary metal oxide semiconductor) technology based on a super-regenerative receiver (SRR) architecture. The SRR achieves mW-level power consumption and chip sizes less than l mm2. While super-regenerative techniques have small bandwidths that limit use in communication systems, their advantages of high sensitivity, low complexity, and low power make them ideal in this situation where modulating tones of less than 1 kHz are used.

The Alignment of the Mean Wind and Stress Vectors in the Unstable Surface Layer

NASA Astrophysics Data System (ADS)

Bernardes, M.; Dias, N. L.

2010-01-01

A significant non-alignment between the mean horizontal wind vector and the stress vector was observed for turbulence measurements both above the water surface of a large lake, and over a land surface (soybean crop). Possible causes for this discrepancy such as flow distortion, averaging times and the procedure used for extracting the turbulent fluctuations (low-pass filtering and filter widths etc.), were dismissed after a detailed analysis. Minimum averaging times always less than 30 min were established by calculating ogives, and error bounds for the turbulent stresses were derived with three different approaches, based on integral time scales (first-crossing and lag-window estimates) and on a bootstrap technique. It was found that the mean absolute value of the angle between the mean wind and stress vectors is highly related to atmospheric stability, with the non-alignment increasing distinctively with increasing instability. Given a coordinate rotation that aligns the mean wind with the x direction, this behaviour can be explained by the growth of the relative error of the u- w component with instability. As a result, under more unstable conditions the u- w and the v- w components become of the same order of magnitude, and the local stress vector gives the impression of being non-aligned with the mean wind vector. The relative error of the v- w component is large enough to make it undistinguishable from zero throughout the range of stabilities. Therefore, the standard assumptions of Monin-Obukhov similarity theory hold: it is fair to assume that the v- w stress component is actually zero, and that the non-alignment is a purely statistical effect. An analysis of the dimensionless budgets of the u- w and the v- w components confirms this interpretation, with both shear and buoyant production of u- w decreasing with increasing instability. In the v- w budget, shear production is zero by definition, while buoyancy displays very low-intensity fluctuations around zero. As local free convection is approached, the turbulence becomes effectively axisymetrical, and a practical limit seems to exist beyond which it is not possible to measure the u- w component accurately.

Localized temperature and chemical reaction control in nanoscale space by nanowire array.

PubMed

Jin, C Yan; Li, Zhiyong; Williams, R Stanley; Lee, K-Cheol; Park, Inkyu

2011-11-09

We introduce a novel method for chemical reaction control with nanoscale spatial resolution based on localized heating by using a well-aligned nanowire array. Numerical and experimental analysis shows that each individual nanowire could be selectively and rapidly Joule heated for local and ultrafast temperature modulation in nanoscale space (e.g., maximum temperature gradient 2.2 K/nm at the nanowire edge; heating/cooling time < 2 μs). By taking advantage of this capability, several nanoscale chemical reactions such as polymer decomposition/cross-linking and direct and localized hydrothermal synthesis of metal oxide nanowires were demonstrated.

Optimized graph-based mosaicking for virtual microscopy

NASA Astrophysics Data System (ADS)

Steckhan, Dirk G.; Wittenberg, Thomas

2009-02-01

Virtual microscopy has the potential to partially replace traditional microscopy. For virtualization, the slide is scanned once by a fully automatized robotic microscope and saved digitally. Typically, such a scan results in several hundreds to thousands of fields of view. Since robotic stages have positioning errors, these fields of view have to be registered locally and globally in an additional step. In this work we propose a new global mosaicking method for the creation of virtual slides based on sub-pixel exact phase correlation for local alignment in combination with Prim's minimum spanning tree algorithm for global alignment. Our algorithm allows for a robust reproduction of the original slide even in the presence of views with little to no information content. This makes it especially suitable for the mosaicking of cervical smears. These smears often exhibit large empty areas, which do not contain enough information for common stitching approaches.

MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids.

PubMed

Andreini, Claudia; Cavallaro, Gabriele; Rosato, Antonio; Valasatava, Yana

2013-11-25

We developed a new software tool, MetalS(2), for the structural alignment of Minimal Functional Sites (MFSs) in metal-binding biological macromolecules. MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. On our example data sets, MetalS(2) unveiled structural similarities that other programs for protein structure comparison do not consistently point out and overall identified a larger number of structurally similar MFSs. MetalS(2) supports the comparison of MFSs harboring different metals and/or with different nuclearity and is available both as a stand-alone program and a Web tool ( http://metalweb.cerm.unifi.it/tools/metals2/).

Use of market research data by state chronic disease programs, Illinois, 2012-2014.

PubMed

Amerson, Nancy L; Arbise, Benjamin S; Kelly, Nora K; Traore, Elizabeth

2014-09-25

Market research data complement traditional epidemiologic data by allowing users to examine health behavior and patterns by census block or census tract. Market research data can identify products and behaviors that align or do not align with public health program goals. Illinois is a recipient of an award from the Directors of Health Promotion and Education to use industry market research data collected by The Nielsen Company for public health purposes. Illinois creates customized community profiles using market research data on tobacco use characteristics to describe the demographics, habits, and media preferences of smokers in certain locations. Local agencies use profiles to plan and target marketing initiatives, reach disparate groups within overall community populations, and restructure program objectives and policy initiatives. Local market research data provide detailed information on the characteristics of smokers, allowing Illinois communities to design public health programs without having to collect data on their own.

Use of Market Research Data by State Chronic Disease Programs, Illinois, 2012–2014

PubMed Central

Arbise, Benjamin S.; Kelly, Nora K.; Traore, Elizabeth

2014-01-01

Market research data complement traditional epidemiologic data by allowing users to examine health behavior and patterns by census block or census tract. Market research data can identify products and behaviors that align or do not align with public health program goals. Illinois is a recipient of an award from the Directors of Health Promotion and Education to use industry market research data collected by The Nielsen Company for public health purposes. Illinois creates customized community profiles using market research data on tobacco use characteristics to describe the demographics, habits, and media preferences of smokers in certain locations. Local agencies use profiles to plan and target marketing initiatives, reach disparate groups within overall community populations, and restructure program objectives and policy initiatives. Local market research data provide detailed information on the characteristics of smokers, allowing Illinois communities to design public health programs without having to collect data on their own. PMID:25254983

Weightbearing CT in normal hindfoot alignment - Presence of a constitutional valgus?

PubMed

Burssens, A; Van Herzele, E; Leenders, T; Clockaerts, S; Buedts, K; Vandeputte, G; Victor, J

2017-02-16

The normal hindfoot angle is estimated between 2° and 6° of valgus in the general population. These results are solely based on clinical findings and plain radiographs. The purpose of this study is to assess the hindfoot alignment using weightbear CT. Forty-eight patients, mean age of 39.6±13.2 years, with clinical and radiological absence of hindfoot pathology were included. A weightbear CT was obtained and allowed to measure the anatomical tibia axis (TAx) and the hindfoot alignment (HA). The HA was firstly determined using the inferior point of the calcaneus (HA IC ). A density measurement of this area was subsequently performed to analyze if this point concurred with an increased ossification, indicating a higher load exposure. Secondly the HA was determined by dividing the calcaneus in the long axial view (HALA) and compared to the (HA IC ) to point out any possible differences attributed to the measurement method. Reliability was assessed using an intra class correlation coefficient (ICC). The mean HA IC equaled 0.79° of valgus±3.2 (ICC HA IC =0.73) with a mean TAx of 2.7° varus±2.1 (ICCTA=0.76). The HALA equaled 9.1° of valgus±4.8 (ICCHA LA=0.71) and differed significantly by a P<0.001 from the HA IC , which showed a more neutral alignment. Correlation between both was shown to be good by a Spearman's correlation coefficient of 0.74. The mean density of the inferior calcaneal area equaled 271.3±84.1 and was significantly higher than the regional calcaneal area (P<0.001). These results show a more neutral alignment of the hindfoot in this group of non-symptomatic feet as opposed to the generally accepted constitutional valgus. This could have repercussion on hindfoot position during fusion or in quantifying the correction of a malalignment. The inferior calcaneus point in this can be used during pre-operative planning of a hindfoot correction as an anatomical landmark due to its shown influence on load transfer. Copyright © 2017 European Foot and Ankle Society. Published by Elsevier Ltd. All rights reserved.

Influence of tumor location on the intensity-modulated radiation therapy plan of helical tomotherapy.

PubMed

Xu, Yingjie; Yan, Hui; Hu, Zhihui; Ma, Pan; Men, Kuo; Huang, Peng; Ren, Wenting; Dai, Jianrong; Li, Yexiong

2017-01-01

Given the design of the Helical TomoTherapy device, the patient's central axis is routinely aligned with the machine's rotational axis to prevent the patient's body from colliding with the machine walls. However, for treatment of tumors located away from the patient's central axis, this position may not be optimal as the adequate radiation dose may not reach the affected site. Our study aimed to investigate the influence of tumor location on dose quality and delivery efficiency of tomotherapy plans. A phantom and 15 patients were selected for this study. Two plans, A and B, were implemented for each case. In plan A, the patient's central axis was aligned with the machine's rotational axis, whereas in plan B, the center of the planning target volume (PTV) was aligned with the machine's rotational axis. Both plans were optimized with the same planning parameters, and the dose quality of the plans was evaluated using dosimetrics. The delivery efficiency was determined from delivery time and monitor units (MUs). A paired t-test or nonparametric Wilcoxon signed-rank test was performed for statistical comparison. In the phantom study, the median delivery times were 358 and 336 seconds for plans A and B, respectively, and this difference was significant (p = 0.005). In the patient study, the median delivery times were 348 and 317 seconds for plans A and B, respectively, and this difference was also significant (p = 0.001). The dose qualities of both plans for each patient were nearly identical. No significant differences were found in the conformal index, heterogeneity index, and mean dose delivered to normal tissue between the plans. Both phantom and patient studies showed that for normal-sized patients, the delivery time reduced as the distance between the PTV and the patient's central axis increased when the PTV center was aligned with the machine axis. In conclusion, aligning the PTV center with the machine's rotational axis by shifting the patient during tomotherapy reduces the delivery time without compromising the dose quality of intensity-modulated radiation therapy. Copyright © 2017 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights reserved.

Measures of three-dimensional anisotropy and intermittency in strong Alfvénic turbulence

NASA Astrophysics Data System (ADS)

Mallet, A.; Schekochihin, A. A.; Chandran, B. D. G.; Chen, C. H. K.; Horbury, T. S.; Wicks, R. T.; Greenan, C. C.

2016-06-01

We measure the local anisotropy of numerically simulated strong Alfvénic turbulence with respect to two local, physically relevant directions: along the local mean magnetic field and along the local direction of one of the fluctuating Elsasser fields. We find significant scaling anisotropy with respect to both these directions: the fluctuations are `ribbon-like' - statistically, they are elongated along both the mean magnetic field and the fluctuating field. The latter form of anisotropy is due to scale-dependent alignment of the fluctuating fields. The intermittent scalings of the nth-order conditional structure functions in the direction perpendicular to both the local mean field and the fluctuations agree well with the theory of Chandran, Schekochihin & Mallet, while the parallel scalings are consistent with those implied by the critical-balance conjecture. We quantify the relationship between the perpendicular scalings and those in the fluctuation and parallel directions, and find that the scaling exponent of the perpendicular anisotropy (I.e. of the aspect ratio of the Alfvénic structures in the plane perpendicular to the mean magnetic field) depends on the amplitude of the fluctuations. This is shown to be equivalent to the anticorrelation of fluctuation amplitude and alignment at each scale. The dependence of the anisotropy on amplitude is shown to be more significant for the anisotropy between the perpendicular and fluctuation-direction scales than it is between the perpendicular and parallel scales.

Investigations of the local environment and macroscopic alignment behavior of novel polymerizeable lyotropic liquid crystals using nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Juang, Elizabeth

In this dissertation, a variety of NMR techniques were used to explore the local environment of novel polymerizeable lyotropic liquid crystals (LLC). The LLC monomers examined in this study self-assemble in the presence of a small amount of water to form uniform, nanometer-scale tubes with aqueous interiors. The phase architecture is retained upon photopolymerization to yield the resulting nanoporous material. By dissolving reactive precursors into the aqueous phase, well- structured nancomposite materials have also been formed. Proposed uses for these novel polymerizeable LLCs are as porous water filtration membranes, as heterogeneous organic catalysts, and as nanocomposite materials for load bearing and optical applications. In order to better exploit these polymerizeable LLCs for materials development, the local environment must be examined. In addition, the macroscopic orientation of these materials remains an important step in their advancement. Various NMR studies were conducted on these novel LLCs. NMR T1 relaxation measurements were conducted to elucidate the local environment and dynamics of the 23Na counterions located inside the aqueous channels. 2H NMR line shape analyses were used to characterize the local structure and dynamics near the hydrophilic headgroup. 29 Si NMR studies were performed on silica nanocomposites formed with these LLC structures. Finally, the macroscopic alignment behavior of these novel LLCs using shear and magnetic fields was examined.

Magnetic field alignment of coil-coil diblock copolymers and blends via intrinsic chain anisotropy

NASA Astrophysics Data System (ADS)

Rokhlenko, Yekaterina; Majewski, Pawel; Larson, Steven; Yager, Kevin; Gopalan, Padma; Avgeropoulos, Apostolos; Chan, Edwin; Osuji, Chinedum

Magnetic fields can control alignment of self-assembled soft materials such as block copolymers provided there is a suitably large magnetic susceptibility anisotropy present in the system. Recent results have highlighted the existence of a non-trivial intrinsic anisotropy in coil-coil diblock copolymers, specifically in lamellar-forming PS-b-P4VP, which enables alignment at field strengths of a few tesla in systems lacking mesogenic components. Alignment is predicated on correlation in the orientation of end-end vectors implied by the localization of block junctions at the microdomain interface and is observed on cooling across the order-disorder transition in the presence of the field. For appropriate combinations of field strength and grain size, we can leverage intrinsic chain anisotropy to magnetically direct self-assembly of many non-mesogenic systems, including other coil-coil BCPs like PS-b-PDMS and PS-b-PMMA, blends of BCPs of disparate morphologies and MWs, and blends of BCPs with homopolymers. This is noteworthy as blends of PS-b-P4VP with PEO provide a route to form functional materials such as nanoporous films by dissolution of PEO, or aligned ion conduction materials. We survey these various systems using TEM and in-situ X-ray scattering to study the phase behavior and temperature-, time- and field- dependent dynamics of alignment.

A rib-specific multimodal registration algorithm for fused unfolded rib visualization using PET/CT

NASA Astrophysics Data System (ADS)

Kaftan, Jens N.; Kopaczka, Marcin; Wimmer, Andreas; Platsch, Günther; Declerck, Jérôme

2014-03-01

Respiratory motion affects the alignment of PET and CT volumes from PET/CT examinations in a non-rigid manner. This becomes particularly apparent if reviewing fine anatomical structures such as ribs when assessing bone metastases, which frequently occur in many advanced cancers. To make this routine diagnostic task more efficient, a fused unfolded rib visualization for 18F-NaF PET/CT is presented. It allows to review the whole rib cage in a single image. This advanced visualization is enabled by a novel rib-specific registration algorithm that rigidly optimizes the local alignment of each individual rib in both modalities based on a matched filter response function. More specifically, rib centerlines are automatically extracted from CT and subsequently individually aligned to the corresponding bone-specific PET rib uptake pattern. The proposed method has been validated on 20 PET/CT scans acquired at different clinical sites. It has been demonstrated that the presented rib- specific registration method significantly improves the rib alignment without having to run complex deformable registration algorithms. At the same time, it guarantees that rib lesions are not further deformed, which may otherwise affect quantitative measurements such as SUVs. Considering clinically relevant distance thresholds, the centerline portion with good alignment compared to the ground truth improved from 60:6% to 86:7% after registration while approximately 98% can be still considered as acceptably aligned.

Assessing the statistical robustness of inter- and intra-basinal carbon isotope chemostratigraphic correlation

NASA Astrophysics Data System (ADS)

Hay, C.; Creveling, J. R.; Huybers, P. J.

2016-12-01

Excursions in the stable carbon isotopic composition of carbonate rocks (δ13Ccarb) can facilitate correlation of Precambrian and Phanerozoic sedimentary successions at a higher temporal resolution than radiometric and biostratigraphic frameworks typically afford. Within the bounds of litho- and biostratigraphic constraints, stratigraphers often correlate isotopic patterns between distant stratigraphic sections through visual alignment of local maxima and minima of isotopic values. The reproducibility of this method can prove challenging and, thus, evaluating the statistical robustness of intrabasinal composite carbon isotope curves, and global correlations to these reference curves, remains difficult. To assess the reproducibility of stratigraphic alignment of δ13Ccarb data, and correlations between carbon isotope excursions, we employ a numerical dynamic time warping methodology that stretches and squeezes the time axis of a record to obtain an optimal correlation (in a least-squares sense) between time-uncertain series of data. In particular, we assess various alignments between series of Early Cambrian δ13Ccarb data with respect to plausible matches. We first show that an alignment of these records obtained visually, and published previously, is broadly reproducible using dynamic time warping. Alternative alignments with similar goodness of fits are also obtainable, and their stratigraphic plausibility are discussed. This approach should be generalizable to an algorithm for the purposes of developing a library of plausible alignments between multiple time-uncertain stratigraphic records.

Effect of Alignment on Transport Properties of Carbon Nanotube/Metallic Junctions

NASA Technical Reports Server (NTRS)

Wincheski, Buzz; Namkung, Min; Smits, Jan; Williams, Phillip; Harvey, Robert

2003-01-01

Ballistic and spin coherent transport in single walled carbon nanotubes (SWCNT) are predicted to enable high sensitivity single-nanotube devices for strain and magnetic field sensing. Based upon these phenomena, electron beam lithography procedures have been developed to study the transport properties of purified HiPCO single walled carbon nanotubes for development into sensory materials for nondestructive evaluation. Purified nanotubes are dispersed in solvent suspension and then deposited on the device substrate before metallic contacts are defined and deposited through electron beam lithography. This procedure produces randomly dispersed ropes, typically 2 - 20 nm in diameter, of single walled carbon nanotubes. Transport and scanning probe microscopy studies have shown a good correlation between the junction resistance and tube density, alignment, and contact quality. In order to improve transport properties of the junctions a technique has been developed to align and concentrate nanotubes at specific locations on the substrate surface. Lithographic techniques are used to define local areas where high frequency electric fields are to be concentrated. Application of the fields while the substrate is exposed to nanotube-containing solution results in nanotube arrays aligned with the electric field lines. A second electron beam lithography layer is then used to deposit metallic contacts across the aligned tubes. Experimental measurements are presented showing the increased tube alignment and improvement in the transport properties of the junctions.

Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks

PubMed Central

Wadhwab, Gulshan; Upadhyayaa, K. C.

2016-01-01

The amount of data on molecular interactions is growing at an enormous pace, whereas the progress of methods for analysing this data is still lacking behind. Particularly, in the area of comparative analysis of biological networks, where one wishes to explore the similarity between two biological networks, this holds a potential problem. In consideration that the functionality primarily runs at the network level, it advocates the need for robust comparison methods. In this paper, we describe Net2Align, an algorithm for pairwise global alignment that can perform node-to-node correspondences as well as edge-to-edge correspondences into consideration. The uniqueness of our algorithm is in the fact that it is also able to detect the type of interaction, which is essential in case of directed graphs. The existing algorithm is only able to identify the common nodes but not the common edges. Another striking feature of the algorithm is that it is able to remove duplicate entries in case of variable datasets being aligned. This is achieved through creation of a local database which helps exclude duplicate links. In a pervasive computational study on gene regulatory network, we establish that our algorithm surpasses its counterparts in its results. Net2Align has been implemented in Java 7 and the source code is available as supplementary files. PMID:28356678

Climatology of the relationship of cusp-related density anomaly with zonal wind and large-scale FAC based on CHAMP observations: IMF By and solar cycle dependence

NASA Astrophysics Data System (ADS)

Kervalishvili, Guram; Lühr, Hermann

2014-05-01

We present climatology of the relationship of cusp-related density enhancement with the neutral zonal wind velocity, large-scale field-aligned current (FAC), small-scale FAC, and electron temperature using the superposed epoch analysis (SEA) method. The dependence of these variables on the interplanetary magnetic field (IMF) By component orientation and solar cycle are of particular interest. In addition, the obtained results of relative density enhancement (ρrel), zonal wind, electron temperature and FAC are subdivided into three local seasons of 130 days each: local winter (1 January ±65 days), combined equinoxes (1 April ±32 days and 1 October ±32 days), and local summer (1 July ±65 days). Our investigation is based on CHAMP satellite observations and NASA/GSFC's OMNI online data set for solar maximum (Mar/2002-2007) and minimum (Mar/2004-2009) conditions in the Northern Hemisphere. The SEA technique uses the time and location of the thermospheric mass density anomaly peaks as reference parameters. The relative amplitude of cusp-related density enhancement does on average not depend on the IMF By orientation, solar cycle phase, and local season. Also, it is apparent that the IMF By amplitude does not have a big influence on the relative amplitude of the density anomaly. Conversely, there exists a good correlation between ρrel and the negative amplitude of IMF Bz prevailing about half an hour earlier. In the cusp region, both large-scale FAC distribution and thermospheric zonal wind velocity exhibit a clear dependence on the IMF By orientation. In the case of positive (negative) IMF By there is a systematic imbalance between downward (upward) and upward (downward) FACs peaks equatorward and poleward of the reference point, respectively. The zonal wind velocity is directed towards west i.e. towards dawn in a geomagnetic latitude-magnetic local time (MLat-MLT) frame. This is true for all local seasons and solar conditions. The thermospheric density enhancements appear half way between Region 1 (R1) and Region 0 (R0) field-aligned currents, in closer proximity to the upward FAC region. In our case R0 currents are systematically weaker than R1 ones. Also, around the cusp region we find no sign of Region 2 field-aligned currents. We can conclude that there is a close spatial relationship between FACs and cusp-related density enhancements, but we cannot offer any simple functional relation between field-aligned current strength and density anomaly amplitude. There seem to be other quantities (e.g. precipitating electrons) controlling this relation. All the conclusions drawn above are true for the Northern Hemisphere. There may be differences in the Southern Hemisphere.

Perturbation of cytosolic calcium by 2-aminoethoxydiphenyl borate and caffeine affects zebrafish myofibril alignment.

PubMed

Wu, Hsin-Ju; Fong, Tsorng-Harn; Chen, Shen-Liang; Wei, Jen-Cheng; Wang, I-Jong; Wen, Chi-Chung; Chang, Chao-Yuan; Chen, Xing-Guang; Chen, Wei-Yu; Chen, Hui-Min; Horng, Juin-Lin; Wang, Yun-Hsin; Chen, Yau-Hung

2015-03-01

The objective of the current study was to investigate the effects of Ca(2+) levels on myofibril alignment during zebrafish embryogenesis. To investigate how altered cytoplasmic Ca(2+) levels affect myofibril alignment, we exposed zebrafish embryos to 2-aminothoxyldiphenyl borate (2-APB; an inositol 1,4,5-trisphosphate receptor inhibitor that reduces cytosolic Ca(2+) levels) and caffeine (a ryanodine receptor activator that enhances cytosolic Ca(2+) levels). The results demonstrated that the most evident changes in zebrafish embryos treated with 2-APB were shorter body length, curved trunk and malformed somite boundary. In contrast, such malformed phenotypes were evident neither in untreated controls nor in caffeine-treated embryos. Subtle morphological changes, including changes in muscle fibers, F-actin and ultrastructures were easily observed by staining with specific monoclonal antibodies (F59 and α-laminin), fluorescent probes (phalloidin) and by transmission electron microscopy. Our data suggested that: (1) the exposure to 2-APB and/or caffeine led to myofibril misalignment; (2) 2-APB-treated embryos displayed split and short myofibril phenotypes, whereas muscle fibers from caffeine-treated embryos were twisted and wavy; and (3) zebrafish embryos co-exposed to 2-APB and caffeine resulted in normal myofibril alignment. In conclusion, we proposed that cytosolic Ca(2+) is important for myogenesis, particularly for myofibril alignment. Copyright © 2014 John Wiley & Sons, Ltd.

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

Barnes, Jason W., E-mail: jwbarnes@uidaho.ed

Main-sequence stars earlier than spectral-type approxF6 or so are expected to rotate rapidly due to their radiative exteriors. This rapid rotation leads to an oblate stellar figure. It also induces the photosphere to be hotter (by up to several thousand kelvin) at the pole than at the equator as a result of a process called gravity darkening that was first predicted by von Zeipel. Transits of extrasolar planets across such a non-uniform, oblate disk yield unusual and distinctive lightcurves that can be used to determine the relative alignment of the stellar rotation pole and the planet orbit normal. This spin-orbitmore » alignment can be used to constrain models of planet formation and evolution. Orderly planet formation and migration within a disk that is coplanar with the stellar equator will result in spin-orbit alignment. More violent planet-planet scattering events should yield spin-orbit misaligned planets. Rossiter-McLaughlin measurements of transits of lower-mass stars show that some planets are spin-orbit aligned, and some are not. Since Rossiter-McLaughlin measurements are difficult around rapid rotators, lightcurve photometry may be the best way to determine the spin-orbit alignment of planets around massive stars. The Kepler mission will monitor approx10{sup 4} of these stars within its sample. The lightcurves of any detected planets will allow us to probe the planet formation process around high-mass stars for the first time.« less

Quantitative analysis of three-dimensional fibrillar collagen microstructure within the normal, aged and glaucomatous human optic nerve head

PubMed Central

Jones, H. J.; Girard, M. J.; White, N.; Fautsch, M. P.; Morgan, J. E.; Ethier, C. R.; Albon, J.

2015-01-01

The aim of this study was to quantify connective tissue fibre orientation and alignment in young, old and glaucomatous human optic nerve heads (ONH) to understand ONH microstructure and predisposition to glaucomatous optic neuropathy. Transverse (seven healthy, three glaucomatous) and longitudinal (14 healthy) human ONH cryosections were imaged by both second harmonic generation microscopy and small angle light scattering (SALS) in order to quantify preferred fibre orientation (PFO) and degree of fibre alignment (DOFA). DOFA was highest within the peripapillary sclera (ppsclera), with relatively low values in the lamina cribrosa (LC). Elderly ppsclera DOFA was higher than that in young ppsclera (p < 0.00007), and generally higher than in glaucoma ppsclera. In all LCs, a majority of fibres had preferential orientation horizontally across the nasal–temporal axis. In all glaucomatous LCs, PFO was significantly different from controls in a minimum of seven out of 12 LC regions (p < 0.05). Additionally, higher fibre alignment was observed in the glaucomatous inferior–temporal LC (p < 0.017). The differences between young and elderly ONH fibre alignment within regions suggest that age-related microstructural changes occur within the structure. The additional differences in fibre alignment observed within the glaucomatous LC may reflect an inherent susceptibility to glaucomatous optic neuropathy, or may be a consequence of ONH remodelling and/or collapse. PMID:25808336

Quantitative analysis of three-dimensional fibrillar collagen microstructure within the normal, aged and glaucomatous human optic nerve head.

PubMed

Jones, H J; Girard, M J; White, N; Fautsch, M P; Morgan, J E; Ethier, C R; Albon, J

2015-05-06

The aim of this study was to quantify connective tissue fibre orientation and alignment in young, old and glaucomatous human optic nerve heads (ONH) to understand ONH microstructure and predisposition to glaucomatous optic neuropathy. Transverse (seven healthy, three glaucomatous) and longitudinal (14 healthy) human ONH cryosections were imaged by both second harmonic generation microscopy and small angle light scattering (SALS) in order to quantify preferred fibre orientation (PFO) and degree of fibre alignment (DOFA). DOFA was highest within the peripapillary sclera (ppsclera), with relatively low values in the lamina cribrosa (LC). Elderly ppsclera DOFA was higher than that in young ppsclera (p < 0.00007), and generally higher than in glaucoma ppsclera. In all LCs, a majority of fibres had preferential orientation horizontally across the nasal-temporal axis. In all glaucomatous LCs, PFO was significantly different from controls in a minimum of seven out of 12 LC regions (p < 0.05). Additionally, higher fibre alignment was observed in the glaucomatous inferior-temporal LC (p < 0.017). The differences between young and elderly ONH fibre alignment within regions suggest that age-related microstructural changes occur within the structure. The additional differences in fibre alignment observed within the glaucomatous LC may reflect an inherent susceptibility to glaucomatous optic neuropathy, or may be a consequence of ONH remodelling and/or collapse.

Angular spectra of the intrinsic galaxy ellipticity field, their observability and their impact on lensing in tomographic surveys

NASA Astrophysics Data System (ADS)

Schäfer, Björn Malte; Merkel, Philipp M.

2017-09-01

This paper describes intrinsic ellipticity correlations between galaxies, their statistical properties, their observability with future surveys and their interference with weak gravitational lensing measurements. Using an angular-momentum-based, quadratic intrinsic alignment model we derive correlation functions of the ellipticity components and project them to yield the four non-zero angular ellipticity spectra C^ɛ _E(ℓ), C^ɛ _B(ℓ), C^ɛ _C(ℓ) and C^ɛ _S(ℓ) in their generalization to tomographic surveys. For a Euclid-like survey, these spectra would have amplitudes smaller than the weak lensing effect on non-linear structures, but would constitute an important systematics. Computing estimation biases for cosmological parameters derived from an alignment-contaminated survey suggests biases of +5σw for the dark energy equation of state parameter w, -20σ _{Ω _m} for the matter density Ωm and -12σ _{σ _8} for the spectrum normalization σ8. Intrinsic alignments yield a signal that is easily observable with a survey similar to Euclid: while not independent, significances for estimates of each of the four spectra reach values of tens of σ if weak lensing and shape noise are considered as noise sources, which suggests relative uncertainties on alignment parameters at the percent level, implying that galaxy alignment mechanisms can be investigated by future surveys.

Ionospheric electron heating, optical emissions, and striations induced by powerful HF radio waves at high latitudes: Aspect angle dependence

NASA Astrophysics Data System (ADS)

Rietveld, M. T.; Kosch, M. J.; Blagoveshchenskaya, N. F.; Kornienko, V. A.; Leyser, T. B.; Yeoman, T. K.

2003-04-01

In recent years, large electron temperature increases of 300% (3000 K above background) caused by powerful HF-radio wave injection have been observed during nighttime using the EISCAT incoherent scatter radar near Tromsø in northern Norway. In a case study we examine the spatial structure of the modified region. The electron heating is accompanied by ion heating of about 100 degrees and magnetic field-aligned measurements show ion outflows increasing with height up to 300 m s-1 at 582 km. The electron density decreases by up to 20%. When the radar antenna was scanned between three elevations from near field-aligned to vertical, the strongest heating effects were always obtained in the field-aligned position. When the HF-pump beam was scanned between the same three positions, the heating was still almost always strongest in the field-aligned direction. Simultaneous images of the 630 nm O(1D) line in the radio-induced aurora showed that the enhancement caused by the HF radio waves also remained localized near the field-aligned position. Coherent HF radar backscatter also appeared strongest when the pump beam was pointed field-aligned. These results are similar to some Langmuir turbulence phenomena which also show a strong preference for excitation by HF rays launched in the field-aligned direction. The correlation of the position of largest temperature enhancement with the position of the radio-induced aurora suggests that a common mechanism, upper-hybrid wave turbulence, is responsible for both effects. Why the strongest heating effects occur for HF rays directed along the magnetic field is still unclear, but self-focusing on field-aligned striations is a candidate mechanism, and possibly ionospheric tilts may be important.

A survey and evaluations of histogram-based statistics in alignment-free sequence comparison.

PubMed

Luczak, Brian B; James, Benjamin T; Girgis, Hani Z

2017-12-06

Since the dawn of the bioinformatics field, sequence alignment scores have been the main method for comparing sequences. However, alignment algorithms are quadratic, requiring long execution time. As alternatives, scientists have developed tens of alignment-free statistics for measuring the similarity between two sequences. We surveyed tens of alignment-free k-mer statistics. Additionally, we evaluated 33 statistics and multiplicative combinations between the statistics and/or their squares. These statistics are calculated on two k-mer histograms representing two sequences. Our evaluations using global alignment scores revealed that the majority of the statistics are sensitive and capable of finding similar sequences to a query sequence. Therefore, any of these statistics can filter out dissimilar sequences quickly. Further, we observed that multiplicative combinations of the statistics are highly correlated with the identity score. Furthermore, combinations involving sequence length difference or Earth Mover's distance, which takes the length difference into account, are always among the highest correlated paired statistics with identity scores. Similarly, paired statistics including length difference or Earth Mover's distance are among the best performers in finding the K-closest sequences. Interestingly, similar performance can be obtained using histograms of shorter words, resulting in reducing the memory requirement and increasing the speed remarkably. Moreover, we found that simple single statistics are sufficient for processing next-generation sequencing reads and for applications relying on local alignment. Finally, we measured the time requirement of each statistic. The survey and the evaluations will help scientists with identifying efficient alternatives to the costly alignment algorithm, saving thousands of computational hours. The source code of the benchmarking tool is available as Supplementary Materials. © The Author 2017. Published by Oxford University Press.

a Robust Registration Algorithm for Point Clouds from Uav Images for Change Detection

NASA Astrophysics Data System (ADS)

Al-Rawabdeh, A.; Al-Gurrani, H.; Al-Durgham, K.; Detchev, I.; He, F.; El-Sheimy, N.; Habib, A.

2016-06-01

Landslides are among the major threats to urban landscape and manmade infrastructure. They often cause economic losses, property damages, and loss of lives. Temporal monitoring data of landslides from different epochs empowers the evaluation of landslide progression. Alignment of overlapping surfaces from two or more epochs is crucial for the proper analysis of landslide dynamics. The traditional methods for point-cloud-based landslide monitoring rely on using a variation of the Iterative Closest Point (ICP) registration procedure to align any reconstructed surfaces from different epochs to a common reference frame. However, sometimes the ICP-based registration can fail or may not provide sufficient accuracy. For example, point clouds from different epochs might fit to local minima due to lack of geometrical variability within the data. Also, manual interaction is required to exclude any non-stable areas from the registration process. In this paper, a robust image-based registration method is introduced for the simultaneous evaluation of all registration parameters. This includes the Interior Orientation Parameters (IOPs) of the camera and the Exterior Orientation Parameters (EOPs) of the involved images from all available observation epochs via a bundle block adjustment with self-calibration. Next, a semi-global dense matching technique is implemented to generate dense 3D point clouds for each epoch using the images captured in a particular epoch separately. The normal distances between any two consecutive point clouds can then be readily computed, because the point clouds are already effectively co-registered. A low-cost DJI Phantom II Unmanned Aerial Vehicle (UAV) was customised and used in this research for temporal data collection over an active soil creep area in Lethbridge, Alberta, Canada. The customisation included adding a GPS logger and a Large-Field-Of-View (LFOV) action camera which facilitated capturing high-resolution geo-tagged images in two epochs over the period of one year (i.e., May 2014 and May 2015). Note that due to the coarse accuracy of the on-board GPS receiver (e.g., +/- 5-10 m) the geo-tagged positions of the images were only used as initial values in the bundle block adjustment. Normal distances, signifying detected changes, varying from 20 cm to 4 m were identified between the two epochs. The accuracy of the co-registered surfaces was estimated by comparing non-active patches within the monitored area of interest. Since these non-active sub-areas are stationary, the computed normal distances should theoretically be close to zero. The quality control of the registration results showed that the average normal distance was approximately 4 cm, which is within the noise level of the reconstructed surfaces.

Alignment and Calibration of an Airborne Infrared Spectrometer

NASA Astrophysics Data System (ADS)

Vira, A.

2017-12-01

The airborne infrared spectrometer (AIR-Spec) will measure the coronal plasma emission lines in the infrared at high spatial and spectral resolution. These results will enhance our understanding of the coronal dynamics and improve solar forecasting models. To measure the infrared coronal emission lines, the airborne system will fly on the NSF/NCAR High-Performance Instrumented Airborne Platform for Environmental Research (HIAPER) during the total solar eclipse in August 2017. The flight path was calculated to maximize the observation time. A detailed analysis of our flight path will be reported. The optical system consists of a fast steering mirror, telescope, grating spectrometer, and slit-jaw imager. Light from the sun is directed into the f/15 telescope by a fast steering mirror. The telescope focuses the light on the slitjaw and the remaining light enters the grating spectrometer through the slit. The poster will include a discussion of the alignment procedures for the telescope and spectrograph. All of the spectrometer optics are cooled to cryogenic temperatures, which complicates the alignment process. After the telescope and spectrometer are aligned independently, the telescope needs to be precisely aligned to the spectrometer. Several alignment methods were used to ensure that the telescope is focused at the slitjaw and normal to the spectrometer. In addition to the optical alignment, there are a few calibrations to complete: 1) flat field, 2) spectral, and 3) radiometric. The flat field gives us a measure of the pixel to pixel variations. The spectral calibration is used to determine the conversion factor between wavelength and pixel. The radiometric calibration is used to map the camera output to radiance. All these calibrations are necessary for processing our data from the solar eclipse. We will report on our methods and results for the optical alignment and calibration for AIR-Spec. AIR-Spec is supported by NSF and Smithsonian Institution through the Major Research Instrumentation program. This work is supported by the NSF-REU solar physics program at SAO, grant number AGS-1560313.

Long-wavelength asymptotics of unstable crossflow modes, including the effect of surface curvature

NASA Technical Reports Server (NTRS)

Choudhari, Meelan

1994-01-01

Stationary vortex instabilities with wavelengths significantly larger than the thickness of the underlying three-dimensional boundary layer are studied with asymptotic methods. The long-wavelength Rayleigh modes are locally neutral and are aligned with the direction of the local inviscid streamline. For a spanwise wave number Beta much less than 1, the spatial growth rate of these vortices is O(Beta(exp 3/2)). When Beta becomes O(R(exp -1/7)), the viscous correction associated with a thin sublayer near the surface modifies the inviscid growth rate to the leading order. As Beta is further decreased through this regime, viscous effects assume greater significance and dominate the growth-rate behavior. The spatial growth rate becomes comparable to the real part of the wave number when Beta = O(R(exp -1/4)). At this stage, the disturbance structure becomes fully viscous-inviscid interactive and is described by the triple-deck theory. For even smaller values of Beta, the vortex modes become nearly neutral again and align themselves with the direction of the wall-shear stress. Thus, the study explains the progression of the crossflow-vortex structure from the inflectional upper branch mode to nearly neutral long-wavelength modes that are aligned with the wall-shear direction.

Accelerated Profile HMM Searches

PubMed Central

Eddy, Sean R.

2011-01-01

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call “sparse rescaling”. These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches. PMID:22039361

Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

DOE PAGES

Wang, Xu; Le, Anh -Thu; Yu, Chao; ...

2016-03-30

We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. Lastly, amore » simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.« less

Sequence analysis of Leukemia DNA

NASA Astrophysics Data System (ADS)

Nacong, Nasria; Lusiyanti, Desy; Irawan, Muhammad. Isa

2018-03-01

Cancer is a very deadly disease, one of which is leukemia disease or better known as blood cancer. The cancer cell can be detected by taking DNA in laboratory test. This study focused on local alignment of leukemia and non leukemia data resulting from NCBI in the form of DNA sequences by using Smith-Waterman algorithm. SmithWaterman algorithm was invented by TF Smith and MS Waterman in 1981. These algorithms try to find as much as possible similarity of a pair of sequences, by giving a negative value to the unequal base pair (mismatch), and positive values on the same base pair (match). So that will obtain the maximum positive value as the end of the alignment, and the minimum value as the initial alignment. This study will use sequences of leukemia and 3 sequences of non leukemia.

MSuPDA: A Memory Efficient Algorithm for Sequence Alignment.

PubMed

Khan, Mohammad Ibrahim; Kamal, Md Sarwar; Chowdhury, Linkon

2016-03-01

Space complexity is a million dollar question in DNA sequence alignments. In this regard, memory saving under pushdown automata can help to reduce the occupied spaces in computer memory. Our proposed process is that anchor seed (AS) will be selected from given data set of nucleotide base pairs for local sequence alignment. Quick splitting techniques will separate the AS from all the DNA genome segments. Selected AS will be placed to pushdown automata's (PDA) input unit. Whole DNA genome segments will be placed into PDA's stack. AS from input unit will be matched with the DNA genome segments from stack of PDA. Match, mismatch and indel of nucleotides will be popped from the stack under the control unit of pushdown automata. During the POP operation on stack, it will free the memory cell occupied by the nucleotide base pair.

Simulation of electrostatic ion instabilities in the presence of parallel currents and transverse electric fields

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Ganguli, G.; Lee, Y. C.; Palmadesso, P. J.

1989-01-01

A spatially two-dimensional electrostatic PIC simulation code was used to study the stability of a plasma equilibrium characterized by a localized transverse dc electric field and a field-aligned drift for L is much less than Lx, where Lx is the simulation length in the x direction and L is the scale length associated with the dc electric field. It is found that the dc electric field and the field-aligned current can together play a synergistic role to enable the excitation of electrostatic waves even when the threshold values of the field aligned drift and the E x B drift are individually subcritical. The simulation results show that the growing ion waves are associated with small vortices in the linear stage, which evolve to the nonlinear stage dominated by larger vortices with lower frequencies.

Cell Guidance on Nanogratings: A Computational Model of the Interplay between PC12 Growth Cones and Nanostructures

PubMed Central

Tonazzini, Ilaria; Cecchini, Marco; Micera, Silvestro

2013-01-01

Background Recently, the effects of nanogratings have been investigated on PC12 with respect to cell polarity, neuronal differentiation, migration, maturation of focal adhesions and alignment of neurites. Methodology/Principal Findings A synergistic procedure was used to study the mechanism of alignment of PC12 neurites with respect to the main direction of nanogratings. Finite Element simulations were used to qualitatively assess the distribution of stresses at the interface between non-spread growth cones and filopodia, and to study their dependence on filopodial length and orientation. After modelling all adhesions under non-spread growth cone and filopodial protrusions, the values of local stress maxima resulted from the length of filopodia. Since the stress was assumed to be the main triggering cause leading to the increase and stabilization of filopodia, the position of the local maxima was directly related to the orientation of neurites. An analytic closed form equation was then written to quantitatively assess the average ridge width needed to achieve a given neuritic alignment (R2 = 0.96), and the alignment course, when the ridge depth varied (R2 = 0.97). A computational framework was implemented within an improved free Java environment (CX3D) and in silico simulations were carried out to reproduce and predict biological experiments. No significant differences were found between biological experiments and in silico simulations (alignment, p = 0.3571; tortuosity, p = 0.2236) with a standard level of confidence (95%). Conclusions/Significance A mechanism involved in filopodial sensing of nanogratings is proposed and modelled through a synergistic use of FE models, theoretical equations and in silico simulations. This approach shows the importance of the neuritic terminal geometry, and the key role of the distribution of the adhesion constraints for the cell/substrate coupling process. Finally, the effects of the geometry of nanogratings were explicitly considered in cell/surface interactions thanks to the analytic framework presented in this work. PMID:23936404

Boundary layer polarization and voltage in the 14 MLT region

NASA Astrophysics Data System (ADS)

Lundin, R.; Yamauchi, M.; Woch, J.; Marklund, G.

1995-05-01

Viking midlatitude observations of ions and electrons in the postnoon auroral region show that field-aligned acceleration of electrons and ions with energies up to a few kiloelectron volts takes place. The characteristics of the upgoing ion beams and the local transverse electric field observed by Viking indicate that parallel ion acceleration is primarily due to a quasi-electrostatic field-aligned acceleration process below Viking altitudes, i.e., below 10,000-13,500 km. A good correlation is found between the maximum upgoing ion beam energy and the depth of the local potential well determined by the Viking electric field experiment within dayside 'ion inverted Vs.' The total transverse potential throughout the entire region near the ion inverted Vs. is generally much higher than the field-aligned potential and may reach well above 10 kV. However, the detailed mapping of the transverse potential out to the boundary layer, a fundamental issue which remains controversial, was not attempted here. An important finding in this study is the strong correlation between the maximum up going ion beam energy of dayside ion inverted Vs and the solar wind velocity. This suggests a direct coupling of the solar wind plasma dynamo/voltage generator to the region of field-aligned particle acceleration. The fact that the center of dayside ion inverted Vs coincide with convection reversals/flow stagnation and upward Birkeland currents on what appears to be closed field lines (Woch et al., 1993), suggests that field-aligned potential structures connect to the inner part of an MHD dyanmo in the low-latitude boundary layer. Thus the Viking observations substantiate the idea of a solar wind induced boundary layer polarization where negatively charged perturbations in the postnoon sector persistently develops along the magnetic field lines, establishing accelerating potential drops along the geomagnetic field lines in the 0.5-10 kV range.

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.

PubMed

Zemla, Adam T; Lang, Dorothy M; Kostova, Tanya; Andino, Raul; Ecale Zhou, Carol L

2011-06-02

Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory--still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could help overcome these difficulties by facilitating the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV (structure-alignment sequence variability), a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus, and we demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique, or that share structural similarity with proteins that would be considered distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local structural alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. StralSV is provided as a web service at http://proteinmodel.org/AS2TS/STRALSV/.

Fully automated calculation of cardiothoracic ratio in digital chest radiographs

NASA Astrophysics Data System (ADS)

Cong, Lin; Jiang, Luan; Chen, Gang; Li, Qiang

2017-03-01

The calculation of Cardiothoracic Ratio (CTR) in digital chest radiographs would be useful for cardiac anomaly assessment and heart enlargement related disease indication. The purpose of this study was to develop and evaluate a fully automated scheme for calculation of CTR in digital chest radiographs. Our automated method consisted of three steps, i.e., lung region localization, lung segmentation, and CTR calculation. We manually annotated the lung boundary with 84 points in 100 digital chest radiographs, and calculated an average lung model for the subsequent work. Firstly, in order to localize the lung region, generalized Hough transform was employed to identify the upper, lower, and outer boundaries of lung by use of Sobel gradient information. The average lung model was aligned to the localized lung region to obtain the initial lung outline. Secondly, we separately applied dynamic programming method to detect the upper, lower, outer and inner boundaries of lungs, and then linked the four boundaries to segment the lungs. Based on the identified outer boundaries of left lung and right lung, we corrected the center and the declination of the original radiography. Finally, CTR was calculated as a ratio of the transverse diameter of the heart to the internal diameter of the chest, based on the segmented lungs. The preliminary results on 106 digital chest radiographs showed that the proposed method could obtain accurate segmentation of lung based on subjective observation, and achieved sensitivity of 88.9% (40 of 45 abnormalities), and specificity of 100% (i.e. 61 of 61 normal) for the identification of heart enlargements.

Chronobiology, endocrinology, and energy- and food-reward homeostasis.

PubMed

Gonnissen, H K J; Hulshof, T; Westerterp-Plantenga, M S

2013-05-01

Energy- and food-reward homeostasis is the essential component for maintaining energy balance and its disruption may lead to metabolic disorders, including obesity and diabetes. Circadian alignment, quality sleep and sleep architecture in relation to energy- and food-reward homeostasis are crucial. A reduced sleep duration, quality sleep and rapid-eye movement sleep affect substrate oxidation, leptin and ghrelin concentrations, sleeping metabolic rate, appetite, food reward, hypothalamic-pituitary-adrenal (HPA)-axis activity, and gut-peptide concentrations, enhancing a positive energy balance. Circadian misalignment affects sleep architecture and the glucose-insulin metabolism, substrate oxidation, homeostasis model assessment of insulin resistance (HOMA-IR) index, leptin concentrations and HPA-axis activity. Mood disorders such as depression occur; reduced dopaminergic neuronal signaling shows decreased food reward. A good sleep hygiene, together with circadian alignment of food intake, a regular meal frequency, and attention for protein intake or diets, contributes in curing sleep abnormalities and overweight/obesity features by preventing overeating; normalizing substrate oxidation, stress, insulin and glucose metabolism including HOMA-IR index, and leptin, GLP-1 concentrations, lipid metabolism, appetite, energy expenditure and substrate oxidation; and normalizing food reward. Synchrony between circadian and metabolic processes including meal patterns plays an important role in the regulation of energy balance and body-weight control. Additive effects of circadian alignment including meal patterns, sleep restoration, and protein diets in the treatment of overweight and obesity are suggested. © 2013 The Authors. obesity reviews © 2013 International Association for the Study of Obesity.

Usefulness of anterior cervical fusion using titanium interbody cage for treatment of cervical degenerative disease with preoperative segmental kyphosis

PubMed Central

Hosoi, Kunihiko; Tonomura, Hitoshi; Takatori, Ryota; Nagae, Masateru; Mikami, Yasuo; Osawa, Toru; Arai, Yuji; Fujiwara, Hiroyoshi; Kubo, Toshikazu

2017-01-01

Abstract Favorable bone fusion and clinical results have been reported for anterior cervical fusion (ACF) using titanium interbody cage (TIC). This method might induce postoperative subsidence and local kyphosis, but the relationship between radiological changes and preoperative local alignment is not known. The purpose of the present study is to investigate the impact of preoperative local alignment on the clinical and radiological outcomes of ACF using TIC. The study enrolled 36 patients (mean age 49.8 years) who underwent single-level ACF using TIC for cervical degenerative diseases. Patients were divided into 2 groups by preoperative segmental lordotic angle at the operative level: group L, ≥0° (n = 16); group K, <0° (n = 20). Clinical outcomes included recovery rate according to the Japanese Orthopaedic Association score and complication rates. Radiological assessment was conducted for the cervical and segmental lordotic angles, subsidence, and bone fusion. Mann–Whitney test and chi-square test were applied to compare the outcomes. The Japanese Orthopaedic Association score recovery rate was 77.2% in group L and 87.6% in group K, with no significant difference. No obvious complications were observed in any of the subjects. Mean cervical lordotic angles preoperatively and at last follow-up were 9.2 ± 9.5° and 11.3 ± 11.7°, respectively, in group L, and −1.3 ± 12.8° and 4.6 ± 13.3°, respectively, in group K. The mean segmental lordotic angles preoperatively and at last follow-up were 2.5 ± 2.2° and 2.6 ± 5.7°, respectively, in group L, and −4.5 ± 2.8° and −1.4 ± 5.8°, respectively, in group K. In group K, the cervical and segmental lordotic angles at the last follow-up were significantly greater than the preoperative angles. The change observed in group L was not significant. Subsidence of ≥3 mm was observed in 3 patients in group L and 4 patients in group K. None of the patients showed nonunion. Anterior cervical fusion using TIC provided favorable clinical results regardless of preoperative segmental alignment. Although postoperative subsidence and kyphotic changes are concerns in patients presenting segmental kyphosis, ACF using TIC corrected both the entire cervical spine and segmental alignment. The TIC is useful for correction of the cervical alignment for patients with cervical degenerative disease with local kyphotic changes. PMID:28796062

Absolute Measurement of Tilts via Fourier Analysis of Interferograms

NASA Technical Reports Server (NTRS)

Toland, Ronald W.

2004-01-01

The Fourier method of interferogram analysis requires the introduction of a constant tilt into the inteferogram to serve as a 'carrier signal' for information on the figure of the surface under test. This tilt is usually removed in the first steps of analysis and ignored thereafter. However, in the problem of aligning optical components and systems, knowledge of part orientation is crucial to proper instrument performance. This paper outlines an algorithm which uses the normally ignored carrier signal in Fourier analysis to compute an absolute tilt (orientation) of the test surface. We also provide a brief outline of how this technique, incorporated in a rotating Twyman-Green interferometer, can be used in alignment and metrology of optical systems.

Absolute Measurement of Tilts via Fourier Analysis of Interferograms

NASA Technical Reports Server (NTRS)

Toland, Ronald W.

2004-01-01

The Fourier method of interferogram analysis requires the introduction of a constant tilt into the interferogram to serve as a carrier signal for information on the figure of the surface under test. This tilt is usually removed in the first steps of analysis and ignored thereafter. However, in the problem of aligning optical components and systems, knowledge of part orientation is crucial to proper instrument performance. This paper outlines an algorithm which uses the normally ignored carrier signal in Fourier analysis to compute an absolute tilt (orientation) of the test surface. We also provide a brief outline of how this technique, incorporated in a rotating Twyman-Green interferometer, can be used in alignment and metrology of optical systems.

Research on the method of precise alignment technology of atmospheric laser communication

NASA Astrophysics Data System (ADS)

Chen, Wen-jian; Gao, Wei; Duan, Yuan-yuan; Ma, Shi-wei; Chen, Jian

2016-10-01

Atmosphere laser communication takes advantage of laser as the carrier transmitting the voice, data, and image information in the atmosphere. Because of its high reliability, strong anti-interference ability, the advantages of easy installation, it has great potential and development space in the communications field. In the process of establish communication, the capture, targeting and tracking of the communication signal is the key technology. This paper introduce a method of targeting the signal spot in the process of atmosphere laser communication, which through the way of making analog signal addition and subtraction directly and normalized to obtain the target azimuth information to drive the servo system to achieve precise alignment of tracking.

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB.

PubMed

Xu, Qifang; Dunbrack, Roland L

2012-11-01

Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed. We have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM-HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains >50 residues. The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly.

Undoing Diversity: Knowledge and Neoliberal Discourses in Colleges of Education

ERIC Educational Resources Information Center

Matus, Claudia; Infante, Marta

2011-01-01

In this article we analyze discourses of "diversity" in colleges of education in Chile. We contend that the use of discourses of diversity, as reproducing the separation between mainstream subjectivities and those uncontained by the category of normal, is one of the ways universities align themselves with the rules of a democratic…

49 CFR 38.53 - Doorways.

Code of Federal Regulations, 2011 CFR

2011-10-01

... shall be no greater than 3 inches and the height of the vehicle floor shall be within plus or minus 5/8 inch of the platform height under all normal passenger load conditions. Vertical alignment may be... vehicles operating in existing stations may have a floor height within plus or minus 11/2 inches of the...

36 CFR § 1192.53 - Doorways.

Code of Federal Regulations, 2013 CFR

2013-07-01

... between each vehicle door at rest and the platform shall be no greater than 3 inches and the height of the vehicle floor shall be within plus or minus 5/8 inch of the platform height under all normal passenger load conditions. Vertical alignment may be accomplished by vehicle air suspension or other suitable...

49 CFR 38.53 - Doorways.

Code of Federal Regulations, 2014 CFR

2014-10-01

... shall be no greater than 3 inches and the height of the vehicle floor shall be within plus or minus 5/8 inch of the platform height under all normal passenger load conditions. Vertical alignment may be... vehicles operating in existing stations may have a floor height within plus or minus 11/2 inches of the...

49 CFR 38.53 - Doorways.

Code of Federal Regulations, 2013 CFR

2013-10-01

... shall be no greater than 3 inches and the height of the vehicle floor shall be within plus or minus 5/8 inch of the platform height under all normal passenger load conditions. Vertical alignment may be... vehicles operating in existing stations may have a floor height within plus or minus 11/2 inches of the...

49 CFR 38.53 - Doorways.

Code of Federal Regulations, 2012 CFR

2012-10-01

... shall be no greater than 3 inches and the height of the vehicle floor shall be within plus or minus 5/8 inch of the platform height under all normal passenger load conditions. Vertical alignment may be... vehicles operating in existing stations may have a floor height within plus or minus 11/2 inches of the...

Engineered plant biomass feedstock particles

DOEpatents

Dooley, James H [Federal Way, WA; Lanning, David N [Federal Way, WA; Broderick, Thomas F [Lake Forest Park, WA

2011-10-11

A novel class of flowable biomass feedstock particles with unusually large surface areas that can be manufactured in remarkably uniform sizes using low-energy comminution techniques. The feedstock particles are roughly parallelepiped in shape and characterized by a length dimension (L) aligned substantially with the grain direction and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. The particles exhibit a disrupted grain structure with prominent end and surface checks that greatly enhances their skeletal surface area as compared to their envelope surface area. The L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers. The W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers. The L.times.W dimensions define a pair of substantially parallel top surfaces characterized by some surface checking between longitudinally arrayed fibers. The feedstock particles are manufactured from a variety of plant biomass materials including wood, crop residues, plantation grasses, hemp, bagasse, and bamboo.

Focusing and alignment of erythrocytes in a viscoelastic medium

NASA Astrophysics Data System (ADS)

Go, Taesik; Byeon, Hyeokjun; Lee, Sang Joon

2017-01-01

Viscoelastic fluid flow-induced cross-streamline migration has recently received considerable attention because this process provides simple focusing and alignment over a wide range of flow rates. The lateral migration of particles depends on the channel geometry and physicochemical properties of particles. In this study, digital in-line holographic microscopy (DIHM) is employed to investigate the lateral migration of human erythrocytes induced by viscoelastic fluid flow in a rectangular microchannel. DIHM provides 3D spatial distributions of particles and information on particle orientation in the microchannel. The elastic forces generated in the pressure-driven flows of a viscoelastic fluid push suspended particles away from the walls and enforce erythrocytes to have a fixed orientation. Blood cell deformability influences the lateral focusing and fixed orientation in the microchannel. Different from rigid spheres and hardened erythrocytes, deformable normal erythrocytes disperse from the channel center plane, as the flow rate increases. Furthermore, normal erythrocytes have a higher angle of inclination than hardened erythrocytes in the region near the side-walls of the channel. These results may guide the label-free diagnosis of hematological diseases caused by abnormal erythrocyte deformability.

Collagen and the myocardium: fibrillar structure, biosynthesis and degradation in relation to hypertrophy and its regression.

PubMed

Eghbali, M; Weber, K T

1990-07-17

The extracellular matrix of the myocardium contains an elaborate structural matrix composed mainly of fibrillar types I and III collagen. This matrix is responsible for the support and alignment of myocytes and capillaries. Because of its alignment, location, configuration and tensile strength, relative to cardiac myocytes, the collagen matrix represents a major determinant of myocardial stiffness. Cardiac fibroblasts, not myocytes, contain the mRNA for these fibrillar collagens. In the hypertrophic remodeling of the myocardium that accompanies arterial hypertension, a progressive structural and biochemical remodeling of the matrix follows enhanced collagen gene expression. The resultant significant accumulation of collagen in the interstitium and around intramyocardial coronary arteries, or interstitial and perivascular fibrosis, represents a pathologic remodeling of the myocardium that compromises this normally efficient pump. This report reviews the structural nature, biosynthesis and degradation of collagen in the normal and hypertrophied myocardium. It suggests that interstitial heart disease, or the disproportionate growth of the extracellular matrix relative to myocyte hypertrophy, is an entity that merits greater understanding, particularly the factors regulating types I and III collagen gene expression and their degradation.

Valve for controlling solids flow

DOEpatents

Feldman, David K.

1980-01-01

A fluidized solids control valve is disclosed that is particularly well adapted for use with a flow of coal or char that includes both large particles and fines. The particles may or may not be fluidized at various times during the operation. The valve includes a tubular body that terminates in a valve seat covered by a normally closed closure plate. The valve body at the seat and the closure plate is provided with aligned longitudinal slots that receive a pivotally supported key plate. The key plate is positionable by an operator in inserted, intermediate and retracted positions respecting the longitudinal slot in the valve body. The key plate normally closes the slot within the closure plate but is shaped and aligned obliquely to the longitudinal slot within the valve body to provide progressively increasing slot openings between the inserted and retracted positions. Transfer members are provided between the operator, key plate and closure plate to move the closure plate into an open position only when the key plate is retracted from the longitudinal slot within the valve body.

Polyad breaking phenomenon associated with a local-to-normal mode transition and suitability to estimate force constants

NASA Astrophysics Data System (ADS)

Bermúdez-Montaña, M.; Lemus, R.; Castaños, O.

2017-12-01

In a system of two interacting harmonic oscillators a local-to-normal mode transition is manifested as a polyad breaking phenomenon. This phenomenon is associated with the suitability to estimate zeroth-order force constants in the framework of a local mode description. This transition is also exhibited in two interacting Morse oscillators. To study this case, an appropriate parameterisation going from a molecule with local mode behaviour (H2O) to a molecule presenting a normal mode behaviour (CO2) is introduced. Concepts from quantum mechanics like fidelity, entropy and probability density, as well from nonlinear classical mechanics like Poincaré sections are used to detect the transition region. It is found that fidelity and entropy are sensitive complementary properties to detect the local-to-normal transition. Poincaré sections allow the local-to-normal transition to be detected through the appearance of chaos as a consequence of the polyad breaking phenomenon. In addition, two kinds of avoided energy crossings are identified in accordance with the different regions of the spectrum.

Dipolar correlations and the dielectric permittivity of water.

PubMed

Sharma, Manu; Resta, Raffaele; Car, Roberto

2007-06-15

The static dielectric properties of liquid and solid water are investigated within linear response theory in the context of ab initio molecular dynamics. Using maximally localized Wannier functions to treat the macroscopic polarization we formulate a first-principles, parameter-free, generalization of Kirkwood's phenomenological theory. Our calculated static permittivity is in good agreement with experiment. Two effects of the hydrogen bonds, i.e., a significant increase of the average local moment and a local alignment of the molecular dipoles, contribute in almost equal measure to the unusually large dielectric constant of water.

Studying internal and external magnetic fields in Japan using MAGSAT data

NASA Technical Reports Server (NTRS)

Fukushima, N. (Principal Investigator); Maeda, H.; Yukutake, T.; Tanaka, M.; Oshima, S.; Ogawa, K.; Kawamura, M.; Miyazaki, Y.; Uyeda, S.; Kobayashi, K.

1980-01-01

Examination of the total intensity data of CHRONIT on a few paths over Japan and its neighboring sea shows MAGSAT is extremely useful for studying the local magnetic anomaly. In high latitudes, the signatures of field aligned currents are clearly recognized. These include (1) the persistent basic pattern of current flow; (2) the more intense currents in the summer hemisphere than in the winter hemisphere; (3) more fluctuations in current intensities in summer dawn hours; and (4) apparent dawn-dusk asymmetry in the field-aligned current intensity between the north and south polar regions.

Manifold alignment with Schroedinger eigenmaps

NASA Astrophysics Data System (ADS)

Johnson, Juan E.; Bachmann, Charles M.; Cahill, Nathan D.

2016-05-01

The sun-target-sensor angle can change during aerial remote sensing. In an attempt to compensate BRDF effects in multi-angular hyperspectral images, the Semi-Supervised Manifold Alignment (SSMA) algorithm pulls data from similar classes together and pushes data from different classes apart. SSMA uses Laplacian Eigenmaps (LE) to preserve the original geometric structure of each local data set independently. In this paper, we replace LE with Spatial-Spectral Schoedinger Eigenmaps (SSSE) which was designed to be a semisupervised enhancement to the to extend the SSMA methodology and improve classification of multi-angular hyperspectral images captured over Hog Island in the Virginia Coast Reserve.

Electro-optic characteristics of 4-domain vertical alignment nematic liquid crystal display with interdigital electrode

NASA Astrophysics Data System (ADS)

Hong, S. H.; Jeong, Y. H.; Kim, H. Y.; Cho, H. M.; Lee, W. G.; Lee, S. H.

2000-06-01

We have fabricated a vertically aligned 4-domain nematic liquid crystal display cell with thin film transistor. Unlike the conventional method constructing 4-domain, i.e., protrusion and surrounding electrode which needs additional processes, in this study the pixel design forming 4-domain with interdigital electrodes is suggested. In the device, one pixel is divided into two parts. One part has a horizontal electric field in the vertical direction and the other part has a horizontal one in the horizontal direction. Such fields in the horizontal and vertical direction drive the liquid crystal director to tilt down in four directions. In this article, the electro-optic characteristics of cells with 2 and 4 domain have been studied. The device with 4 domain shows faster response time than normal twisted-nematic and in-plane switching cells, wide viewing angle with optical compensation film, and more stable color characteristics than 2-domain vertical alignment cell with similar structure.