Bellerophon: A program to detect chimeric sequences in multiple sequence alignments

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

Huber, Thomas; Faulkner, Geoffrey; Hugenholtz, Philip

2003-12-23

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments.

What to do When Scalar Invariance Fails: The Extended Alignment Method for Multi-Group Factor Analysis Comparison of Latent Means Across Many Groups.

PubMed

Marsh, Herbert W; Guo, Jiesi; Parker, Philip D; Nagengast, Benjamin; Asparouhov, Tihomir; Muthén, Bengt; Dicke, Theresa

2017-01-12

Scalar invariance is an unachievable ideal that in practice can only be approximated; often using potentially questionable approaches such as partial invariance based on a stepwise selection of parameter estimates with large modification indices. Study 1 demonstrates an extension of the power and flexibility of the alignment approach for comparing latent factor means in large-scale studies (30 OECD countries, 8 factors, 44 items, N = 249,840), for which scalar invariance is typically not supported in the traditional confirmatory factor analysis approach to measurement invariance (CFA-MI). Importantly, we introduce an alignment-within-CFA (AwC) approach, transforming alignment from a largely exploratory tool into a confirmatory tool, and enabling analyses that previously have not been possible with alignment (testing the invariance of uniquenesses and factor variances/covariances; multiple-group MIMIC models; contrasts on latent means) and structural equation models more generally. Specifically, it also allowed a comparison of gender differences in a 30-country MIMIC AwC (i.e., a SEM with gender as a covariate) and a 60-group AwC CFA (i.e., 30 countries × 2 genders) analysis. Study 2, a simulation study following up issues raised in Study 1, showed that latent means were more accurately estimated with alignment than with the scalar CFA-MI, and particularly with partial invariance scalar models based on the heavily criticized stepwise selection strategy. In summary, alignment augmented by AwC provides applied researchers from diverse disciplines considerable flexibility to address substantively important issues when the traditional CFA-MI scalar model does not fit the data. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

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

PubMed Central

Dunbrack, Roland L.

2012-01-01

Motivation: 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. Results: 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. Availability: 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. Contact: Roland.Dunbracks@fccc.edu PMID:22942020

Experimental observation of water saturation effects on shear wave splitting in synthetic rock with fractures aligned at oblique angles

NASA Astrophysics Data System (ADS)

Amalokwu, Kelvin; Chapman, Mark; Best, Angus I.; Sothcott, Jeremy; Minshull, Timothy A.; Li, Xiang-Yang

2015-01-01

Fractured rocks are known to exhibit seismic anisotropy and shear wave splitting (SWS). SWS is commonly used for fractured rock characterization and has been shown to be sensitive to fluid type. The presence of partial liquid/gas saturation is also known to affect the elastic properties of rocks. The combined effect of both fractures and partial liquid/gas saturation is still unknown. Using synthetic, silica-cemented sandstones with aligned penny-shaped voids, we conducted laboratory ultrasonic experiments to investigate the effect fractures aligned at an oblique angle to wave propagation would have on SWS under partial liquid/gas saturation conditions. The result for the fractured rock shows a saturation dependence which can be explained by combining a fractured rock model and a partial saturation model. At high to full water saturation values, SWS decreases as a result of the fluid bulk modulus effect on the quasi-shear wave. This bulk modulus effect is frequency dependent as a result of wave-induced fluid flow mechanisms, which would in turn lead to frequency dependent SWS. This result suggests the possible use of SWS for discriminating between full liquid saturation and partial liquid/gas saturation.

Planar harmonic polynomials of type B

NASA Astrophysics Data System (ADS)

Dunkl, Charles F.

1999-11-01

The hyperoctahedral group acting on icons/Journals/Common/BbbR" ALT="BbbR" ALIGN="TOP"/>N is the Weyl group of type B and is associated with a two-parameter family of differential-difference operators {Ti:1icons/Journals/Common/leq" ALT="leq" ALIGN="TOP"/> iicons/Journals/Common/leq" ALT="leq" ALIGN="TOP"/> N}. These operators are analogous to partial derivative operators. This paper finds all the polynomials h on icons/Journals/Common/BbbR" ALT="BbbR" ALIGN="TOP"/>N which are harmonic, icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/>Bh = 0 and annihilated by Ti for i>2, where the Laplacian 0305-4470/32/46/308/img1" ALT="(sum). They are given explicitly in terms of a novel basis of polynomials, defined by generating functions. The harmonic polynomials can be used to find wavefunctions for the quantum many-body spin Calogero model.

Peri-talar re-alignment osteotomy for joint preservation in asymmetrical ankle osteoarthritis

PubMed Central

Yi, Young; Lee, Woochun

2017-01-01

Various types of re-alignment surgery are used to preserve the ankle joint in cases of intermediate ankle arthritis with partial joint space narrowing. The short-term and mid-term results after re-alignment surgery are promising, with substantial post-operative pain relief and functional improvement that is reflected by high rates of patient satisfaction. In this context, re-alignment surgery can preserve the joint and reduce the pathological load that acts on the affected area. Good clinical and radiological outcomes can be achieved in asymmetrical ankle osteoarthritis by understanding the specific deformities and appropriate indications for different surgical techniques. Cite this article: EFORT Open Rev 2017;2:324-331. DOI: 10.1302/2058-5241.2.160021 PMID:28828181

Markov random field based automatic image alignment for electron tomography.

PubMed

Amat, Fernando; Moussavi, Farshid; Comolli, Luis R; Elidan, Gal; Downing, Kenneth H; Horowitz, Mark

2008-03-01

We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.

Controllable growth of vertically aligned graphene on C-face SiC

DOE PAGES

Liu, Yu; Chen, Lianlian; Hilliard, Donovan; ...

2016-10-06

We investigated how to control the growth of vertically aligned graphene on C-face SiC by varying the processing conditions. It is found that, the growth rate scales with the annealing temperature and the graphene height is proportional to the annealing time. Temperature gradient and crystalline quality of the SiC substrates influence their vaporization. The partial vapor pressure is crucial as it can interfere with further vaporization. A growth mechanism is proposed in terms of physical vapor transport. The monolayer character of vertically aligned graphene is verified by Raman and X-ray absorption spectroscopy. With the processed samples, d 0 magnetism ismore » realized and negative magnetoresistance is observed after Cu implantation. We also prove that multiple carriers exist in vertically aligned graphene.« less

Controllable growth of vertically aligned graphene on C-face SiC

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

Liu, Yu; Chen, Lianlian; Hilliard, Donovan

We investigated how to control the growth of vertically aligned graphene on C-face SiC by varying the processing conditions. It is found that, the growth rate scales with the annealing temperature and the graphene height is proportional to the annealing time. Temperature gradient and crystalline quality of the SiC substrates influence their vaporization. The partial vapor pressure is crucial as it can interfere with further vaporization. A growth mechanism is proposed in terms of physical vapor transport. The monolayer character of vertically aligned graphene is verified by Raman and X-ray absorption spectroscopy. With the processed samples, d 0 magnetism ismore » realized and negative magnetoresistance is observed after Cu implantation. We also prove that multiple carriers exist in vertically aligned graphene.« less

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.

Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns.

PubMed

Ortuño, Francisco M; Valenzuela, Olga; Rojas, Fernando; Pomares, Hector; Florido, Javier P; Urquiza, Jose M; Rojas, Ignacio

2013-09-01

Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal-Wallis test (P < 0.01). This algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P < 0.05), whereas it shows results not significantly different to 3D-COFFEE (P > 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. The source code is available at http://www.ugr.es/~fortuno/MOSAStrE/MO-SAStrE.zip.

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.

SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.

PubMed

Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver

2012-07-15

In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license.

GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D

NASA Astrophysics Data System (ADS)

Richmond, Nicola J.; Abrams, Charlene A.; Wolohan, Philippa R. N.; Abrahamian, Edmond; Willett, Peter; Clark, Robert D.

2006-09-01

Alignment of multiple ligands based on shared pharmacophoric and pharmacosteric features is a long-recognized challenge in drug discovery and development. This is particularly true when the spatial overlap between structures is incomplete, in which case no good template molecule is likely to exist. Pair-wise rigid ligand alignment based on linear assignment (the LAMDA algorithm) has the potential to address this problem (Richmond et al. in J Mol Graph Model 23:199-209, 2004). Here we present the version of LAMDA embodied in the GALAHAD program, which carries out multi-way alignments by iterative construction of hypermolecules that retain the aggregate as well as the individual attributes of the ligands. We have also generalized the cost function from being purely atom-based to being one that operates on ionic, hydrogen bonding, hydrophobic and steric features. Finally, we have added the ability to generate useful partial-match 3D search queries from the hypermolecules obtained. By running frozen conformations through the GALAHAD program, one can utilize the extended version of LAMDA to generate pharmacophores and pharmacosteres that agree well with crystal structure alignments for a range of literature datasets, with minor adjustments of the default parameters generating even better models. Allowing for inclusion of partial match constraints in the queries yields pharmacophores that are consistently a superset of full-match pharmacophores identified in previous analyses, with the additional features representing points of potentially beneficial interaction with the target.

Systems and Methods for Fabricating Carbon Nanotube-Based Vacuum Electronic Devices

NASA Technical Reports Server (NTRS)

Manohara, Harish (Inventor); Toda, Risaku (Inventor); Del Castillo, Linda Y. (Inventor); Murthy, Rakesh (Inventor)

2015-01-01

Systems and methods in accordance with embodiments of the invention proficiently produce carbon nanotube-based vacuum electronic devices. In one embodiment a method of fabricating a carbon nanotube-based vacuum electronic device includes: growing carbon nanotubes onto a substrate to form a cathode; assembling a stack that includes the cathode, an anode, and a first layer that includes an alignment slot; disposing a microsphere partially into the alignment slot during the assembling of the stack such that the microsphere protrudes from the alignment slot and can thereby separate the first layer from an adjacent layer; and encasing the stack in a vacuum sealed container.

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.

Summarizing Audiovisual Contents of a Video Program

NASA Astrophysics Data System (ADS)

Gong, Yihong

2003-12-01

In this paper, we focus on video programs that are intended to disseminate information and knowledge such as news, documentaries, seminars, etc, and present an audiovisual summarization system that summarizes the audio and visual contents of the given video separately, and then integrating the two summaries with a partial alignment. The audio summary is created by selecting spoken sentences that best present the main content of the audio speech while the visual summary is created by eliminating duplicates/redundancies and preserving visually rich contents in the image stream. The alignment operation aims to synchronize each spoken sentence in the audio summary with its corresponding speaker's face and to preserve the rich content in the visual summary. A Bipartite Graph-based audiovisual alignment algorithm is developed to efficiently find the best alignment solution that satisfies these alignment requirements. With the proposed system, we strive to produce a video summary that: (1) provides a natural visual and audio content overview, and (2) maximizes the coverage for both audio and visual contents of the original video without having to sacrifice either of them.

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.

PubMed

Huber, Thomas; Faulkner, Geoffrey; Hugenholtz, Philip

2004-09-22

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl

Fabricating cooled electronic system with liquid-cooled cold plate and thermal spreader

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

Chainer, Timothy J.; Graybill, David P.; Iyengar, Madhusudan K.

Methods are provided for facilitating cooling of an electronic component. The method includes providing a liquid-cooled cold plate and a thermal spreader associated with the cold plate. The cold plate includes multiple coolant-carrying channel sections extending within the cold plate, and a thermal conduction surface with a larger surface area than a surface area of the component to be cooled. The thermal spreader includes one or more heat pipes including multiple heat pipe sections. One or more heat pipe sections are partially aligned to a first region of the cold plate, that is, where aligned to the surface to bemore » cooled, and partially aligned to a second region of the cold plate, which is outside the first region. The one or more heat pipes facilitate distribution of heat from the electronic component to coolant-carrying channel sections of the cold plate located in the second region of the cold plate.« less

Fabricating cooled electronic system with liquid-cooled cold plate and thermal spreader

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

Chainer, Timothy J.; Graybill, David P.; Iyengar, Madhusudan K.

Methods are provided for facilitating cooling of an electronic component. The methods include providing a liquid-cooled cold plate and a thermal spreader associated with the cold plate. The cold plate includes multiple coolant-carrying channel sections extending within the cold plate, and a thermal conduction surface with a larger surface area than a surface area of the component to be cooled. The thermal spreader includes one or more heat pipes including multiple heat pipe sections. One or more heat pipe sections are partially aligned to a first region of the cold plate, that is, where aligned to the surface to bemore » cooled, and partially aligned to a second region of the cold plate, which is outside the first region. The one or more heat pipes facilitate distribution of heat from the electronic component to coolant-carrying channel sections of the cold plate located in the second region of the cold plate.« less

Cooled electronic system with liquid-cooled cold plate and thermal spreader coupled to electronic component

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

Chainer, Timothy J.; Graybill, David P.; Iyengar, Madhusudan K.

Apparatus and method are provided for facilitating cooling of an electronic component. The apparatus includes a liquid-cooled cold plate and a thermal spreader associated with the cold plate. The cold plate includes multiple coolant-carrying channel sections extending within the cold plate, and a thermal conduction surface with a larger surface area than a surface area of the component to be cooled. The thermal spreader includes one or more heat pipes including multiple heat pipe sections. One or more heat pipe sections are partially aligned to a first region of the cold plate, that is, where aligned to the surface tomore » be cooled, and partially aligned to a second region of the cold plate, which is outside the first region. The one or more heat pipes facilitate distribution of heat from the electronic component to coolant-carrying channel sections of the cold plate located in the second region of the cold plate.« less

Cooled electronic system with liquid-cooled cold plate and thermal spreader coupled to electronic component

DOEpatents

Chainer, Timothy J.; Graybill, David P.; Iyengar, Madhusudan K.; Kamath, Vinod; Kochuparambil, Bejoy J.; Schmidt, Roger R.; Steinke, Mark E.

2016-08-09

Apparatus and method are provided for facilitating cooling of an electronic component. The apparatus includes a liquid-cooled cold plate and a thermal spreader associated with the cold plate. The cold plate includes multiple coolant-carrying channel sections extending within the cold plate, and a thermal conduction surface with a larger surface area than a surface area of the component to be cooled. The thermal spreader includes one or more heat pipes including multiple heat pipe sections. One or more heat pipe sections are partially aligned to a first region of the cold plate, that is, where aligned to the surface to be cooled, and partially aligned to a second region of the cold plate, which is outside the first region. The one or more heat pipes facilitate distribution of heat from the electronic component to coolant-carrying channel sections of the cold plate located in the second region of the cold plate.

Cooled electronic system with liquid-cooled cold plate and thermal spreader coupled to electronic component

DOEpatents

Chainer, Timothy J.; Graybill, David P.; Iyengar, Madhusudan K.; Kamath, Vinod; Kochuparambil, Bejoy J.; Schmidt, Roger R.; Steinke, Mark E.

2016-04-05

Apparatus and method are provided for facilitating cooling of an electronic component. The apparatus includes a liquid-cooled cold plate and a thermal spreader associated with the cold plate. The cold plate includes multiple coolant-carrying channel sections extending within the cold plate, and a thermal conduction surface with a larger surface area than a surface area of the component to be cooled. The thermal spreader includes one or more heat pipes including multiple heat pipe sections. One or more heat pipe sections are partially aligned to a first region of the cold plate, that is, where aligned to the surface to be cooled, and partially aligned to a second region of the cold plate, which is outside the first region. The one or more heat pipes facilitate distribution of heat from the electronic component to coolant-carrying channel sections of the cold plate located in the second region of the cold plate.

Reconstruction of interatomic vectors by principle component analysis of nuclear magnetic resonance data in multiple alignments

NASA Astrophysics Data System (ADS)

Hus, Jean-Christophe; Bruschweiler, Rafael

2002-07-01

A general method is presented for the reconstruction of interatomic vector orientations from nuclear magnetic resonance (NMR) spectroscopic data of tensor interactions of rank 2, such as dipolar coupling and chemical shielding anisotropy interactions, in solids and partially aligned liquid-state systems. The method, called PRIMA, is based on a principal component analysis of the covariance matrix of the NMR parameters collected for multiple alignments. The five nonzero eigenvalues and their eigenvectors efficiently allow the approximate reconstruction of the vector orientations of the underlying interactions. The method is demonstrated for an isotropic distribution of sample orientations as well as for finite sets of orientations and internuclear vectors encountered in protein systems.

Experts' Understanding of Partial Derivatives Using the Partial Derivative Machine

ERIC Educational Resources Information Center

Roundy, David; Weber, Eric; Dray, Tevian; Bajracharya, Rabindra R.; Dorko, Allison; Smith, Emily M.; Manogue, Corinne A.

2015-01-01

Partial derivatives are used in a variety of different ways within physics. Thermodynamics, in particular, uses partial derivatives in ways that students often find especially confusing. We are at the beginning of a study of the teaching of partial derivatives, with a goal of better aligning the teaching of multivariable calculus with the needs of…

Evidence for unnatural-parity contributions to electron-impact ionization of laser-aligned atoms

DOE PAGES

Armstrong, Gregory S. J.; Colgan, James Patrick; Pindzola, M. S.; ...

2015-09-11

Recent measurements have examined the electron-impact ionization of excited-state laser-aligned Mg atoms. In this paper we show that the ionization cross section arising from the geometry where the aligned atom is perpendicular to the scattering plane directly probes the unnatural parity contributions to the ionization amplitude. The contributions from natural parity partial waves cancel exactly in this geometry. Our calculations resolve the discrepancy between the nonzero measured cross sections in this plane and the zero cross section predicted by distorted-wave approaches. Finally, we demonstrate that this is a general feature of ionization from p-state targets by additional studies of ionizationmore » from excited Ca and Na atoms.« less

Analysis of Ribosome Inactivating Protein (RIP): A Bioinformatics Approach

NASA Astrophysics Data System (ADS)

Jothi, G. Edward Gnana; Majilla, G. Sahaya Jose; Subhashini, D.; Deivasigamani, B.

2012-10-01

In spite of the medical advances in recent years, the world is in need of different sources to encounter certain health issues.Ribosome Inactivating Proteins (RIPs) were found to be one among them. In order to get easy access about RIPs, there is a need to analyse RIPs towards constructing a database on RIPs. Also, multiple sequence alignment was done towards screening for homologues of significant RIPs from rare sources against RIPs from easily available sources in terms of similarity. Protein sequences were retrieved from SWISS-PROT and are further analysed using pair wise and multiple sequence alignment.Analysis shows that, 151 RIPs have been characterized to date. Amongst them, there are 87 type I, 37 type II, 1 type III and 25 unknown RIPs. The sequence length information of various RIPs about the availability of full or partial sequence was also found. The multiple sequence alignment of 37 type I RIP using the online server Multalin, indicates the presence of 20 conserved residues. Pairwise alignment and multiple sequence alignment of certain selected RIPs in two groups namely Group I and Group II were carried out and the consensus level was found to be 98%, 98% and 90% respectively.

Capillary Printing of Highly Aligned Silver Nanowire Transparent Electrodes for High-Performance Optoelectronic Devices.

PubMed

Kang, Saewon; Kim, Taehyo; Cho, Seungse; Lee, Youngoh; Choe, Ayoung; Walker, Bright; Ko, Seo-Jin; Kim, Jin Young; Ko, Hyunhyub

2015-12-09

Percolation networks of silver nanowires (AgNWs) are commonly used as transparent conductive electrodes (TCEs) for a variety of optoelectronic applications, but there have been no attempts to precisely control the percolation networks of AgNWs that critically affect the performances of TCEs. Here, we introduce a capillary printing technique to precisely control the NW alignment and the percolation behavior of AgNW networks. Notably, partially aligned AgNW networks exhibit a greatly lower percolation threshold, which leads to the substantial improvement of optical transmittance (96.7%) at a similar sheet resistance (19.5 Ω sq(-1)) as compared to random AgNW networks (92.9%, 20 Ω sq(-1)). Polymer light-emitting diodes (PLEDs) using aligned AgNW electrodes show a 30% enhanced maximum luminance (33068 cd m(-2)) compared to that with random AgNWs and a high luminance efficiency (14.25 cd A(-1)), which is the highest value reported so far using indium-free transparent electrodes for fluorescent PLEDs. In addition, polymer solar cells (PSCs) using aligned AgNW electrodes exhibit a power conversion efficiency (PCE) of 8.57%, the highest value ever reported to date for PSCs using AgNW electrodes.

Reduction of deviation angle during occlusion therapy: in partially accommodative esotropia with moderate amblyopia.

PubMed

Chun, Bo Young; Kwon, Soon Jae; Chae, Sun Hwa; Kwon, Jung Yoon

2007-09-01

To evaluate changes in ocular alignment in partially accommodative esotropic children age ranged from 3 to 8 years during occlusion therapy for amblyopia. Angle measurements of twenty-two partially accommodative esotropic patients with moderate amblyopia were evaluated before and at 2 years after occlusion therapy. Mean deviation angle with glasses at the start of occlusion treatment was 19.45+/-5.97 PD and decreased to 12.14+/-12.96 PD at 2 years after occlusion therapy (p<0.01). After occlusion therapy, 9 (41%) cases were indications of surgery for residual deviation but if we had planned surgery before occlusion treatment, 18 (82%) of patients would have had surgery. There was a statistical relationship between increase of visual acuity ratio and decrease of deviation angle (r=-0.479, p=0.024). There was a significant reduction of deviation angle of partially accommodative esotropic patients at 2 years after occlusion therapy. Our results suggest that occlusion therapy has an influence on ocular alignment in partially accommodative esotropic patients with amblyopia.

Measuring Parameters of Massive Black Hole Binaries with Partially Aligned Spins

NASA Technical Reports Server (NTRS)

Lang, Ryan N.; Hughes, Scott A.; Cornish, Neil J.

2011-01-01

The future space-based gravitational wave detector LISA will be able to measure parameters of coalescing massive black hole binaries, often to extremely high accuracy. Previous work has demonstrated that the black hole spins can have a strong impact on the accuracy of parameter measurement. Relativistic spin-induced precession modulates the waveform in a manner which can break degeneracies between parameters, in principle significantly improving how well they are measured. Recent studies have indicated, however, that spin precession may be weak for an important subset of astrophysical binary black holes: those in which the spins are aligned due to interactions with gas. In this paper, we examine how well a binary's parameters can be measured when its spins are partially aligned and compare results using waveforms that include higher post-Newtonian harmonics to those that are truncated at leading quadrupole order. We find that the weakened precession can substantially degrade parameter estimation, particularly for the "extrinsic" parameters sky position and distance. Absent higher harmonics, LISA typically localizes the sky position of a nearly aligned binary about an order of magnitude less accurately than one for which the spin orientations are random. Our knowledge of a source's sky position will thus be worst for the gas-rich systems which are most likely to produce electromagnetic counterparts. Fortunately, higher harmonics of the waveform can make up for this degradation. By including harmonics beyond the quadrupole in our waveform model, we find that the accuracy with which most of the binary's parameters are measured can be substantially improved. In some cases, the improvement is such that they are measured almost as well as when the binary spins are randomly aligned.

Osteogenesis of human adipose-derived stem cells on hydroxyapatite-mineralized poly(lactic acid) nanofiber sheets.

PubMed

Kung, Fu-Chen; Lin, Chi-Chang; Lai, Wen-Fu T

2014-12-01

Electrospun fiber sheets with various orientations (random, partially aligned, and aligned) and smooth and roughened casted membranes were prepared. Hydroxyapatite (HA) crystals were in situ formed on these material surfaces via immersion in 10× simulated body fluid solution. The size and morphology of the resulting fibers were examined using scanning electron microscopy. The average diameter of the fibers ranged from 225±25 to 1050±150 nm depending on the electrospinning parameters. Biological experiment results show that human adipose-derived stem cells exhibit different adhesion and osteogenic differentiation on the three types of fiber. The cell proliferation and osteogenic differentiation were best on the aligned fibers. Similar results were found for phosphorylated focal adhesion kinase expression. Electrospun poly(lactic acid) aligned fibers mineralized with HA crystals provide a good environment for cell growth and osteogenic differentiation and thus have great potential in the tissue engineering field. Copyright © 2014 Elsevier B.V. All rights reserved.

Regionally variant collagen alignment correlates with viscoelastic properties of the disc of the human temporomandibular joint.

PubMed

Gutman, Shawn; Kim, Daniel; Tarafder, Solaiman; Velez, Sergio; Jeong, Julia; Lee, Chang H

2018-02-01

To determine the regionally variant quality of collagen alignment in human TMJ discs and its statistical correlation with viscoelastic properties. For quantitative analysis of the quality of collagen alignment, horizontal sections of human TMJ discs with Pricrosirius Red staining were imaged under circularly polarized microscopy. Mean angle and angular deviation of collagen fibers in each region were analyzed using a well-established automated image-processing for angular gradient. Instantaneous and relaxation moduli of each disc region were measured under stress-relaxation test both in tensile and compression. Then Spearman correlation analysis was performed between the angular deviation and the moduli. To understand the effect of glycosaminoglycans on the correlation, TMJ disc samples were treated by chondroitinase ABC (C-ABC). Our imaging processing analysis showed the region-variant direction of collagen alignment, consistently with previous findings. Interestingly, the quality of collagen alignment, not only the directions, was significantly different in between the regions. The angular deviation of fiber alignment in the anterior and intermediate regions were significantly smaller than the posterior region. Medial and lateral regions showed significantly bigger angular deviation than all the other regions. The regionally variant angular deviation values showed statistically significant correlation with the tensile instantaneous modulus and the relaxation modulus, partially dependent on C-ABC treatment. Our findings suggest the region-variant degree of collagen fiber alignment is likely attributed to the heterogeneous viscoelastic properties of TMJ disc that may have significant implications in development of regenerative therapy for TMJ disc. Copyright © 2017 Elsevier Ltd. All rights reserved.

Requirement for XLF/Cernunnos in alignment-based gap filling by DNA polymerases lambda and mu for nonhomologous end joining in human whole-cell extracts.

PubMed

Akopiants, Konstantin; Zhou, Rui-Zhe; Mohapatra, Susovan; Valerie, Kristoffer; Lees-Miller, Susan P; Lee, Kyung-Jong; Chen, David J; Revy, Patrick; de Villartay, Jean-Pierre; Povirk, Lawrence F

2009-07-01

XLF/Cernunnos is a core protein of the nonhomologous end-joining pathway of DNA double-strand break repair. To better define the role of Cernunnos in end joining, whole-cell extracts were prepared from Cernunnos-deficient human cells. These extracts effected little joining of DNA ends with cohesive 5' or 3' overhangs, and no joining at all of partially complementary 3' overhangs that required gap filling prior to ligation. Assays in which gap-filled but unligated intermediates were trapped using dideoxynucleotides revealed that there was no gap filling on aligned DSB ends in the Cernunnos-deficient extracts. Recombinant Cernunnos protein restored gap filling and end joining of partially complementary overhangs, and stimulated joining of cohesive ends more than twentyfold. XLF-dependent gap filling was nearly eliminated by immunodepletion of DNA polymerase lambda, but was restored by addition of either polymerase lambda or polymerase mu. Thus, Cernunnos is essential for gap filling by either polymerase during nonhomologous end joining, suggesting that it plays a major role in aligning the two DNA ends in the repair complex.

Effect of atelectasis changes on tissue mass and dose during lung radiotherapy.

PubMed

Guy, Christopher L; Weiss, Elisabeth; Jan, Nuzhat; Reshko, Leonid B; Christensen, Gary E; Hugo, Geoffrey D

2016-11-01

To characterize mass and density changes of lung parenchyma in non-small cell lung cancer (NSCLC) patients following midtreatment resolution of atelectasis and to quantify the impact this large geometric change has on normal tissue dose. Baseline and midtreatment CT images and contours were obtained for 18 NSCLC patients with atelectasis. Patients were classified based on atelectasis volume reduction between the two scans as having either full, partial, or no resolution. Relative mass and density changes from baseline to midtreatment were calculated based on voxel intensity and volume for each lung lobe. Patients also had clinical treatment plans available which were used to assess changes in normal tissue dose constraints from baseline to midtreatment. The midtreatment image was rigidly aligned with the baseline scan in two ways: (1) bony anatomy and (2) carina. Treatment parameters (beam apertures, weights, angles, monitor units, etc.) were transferred to each image. Then, dose was recalculated. Typical IMRT dose constraints were evaluated on all images, and the changes from baseline to each midtreatment image were investigated. Atelectatic lobes experienced mean (stdev) mass changes of -2.8% (36.6%), -24.4% (33.0%), and -9.2% (17.5%) and density changes of -66.0% (6.4%), -25.6% (13.6%), and -17.0% (21.1%) for full, partial, and no resolution, respectively. Means (stdev) of dose changes to spinal cord D max , esophagus D mean , and lungs D mean were 0.67 (2.99), 0.99 (2.69), and 0.50 Gy (2.05 Gy), respectively, for bone alignment and 0.14 (1.80), 0.77 (2.95), and 0.06 Gy (1.71 Gy) for carina alignment. Dose increases with bone alignment up to 10.93, 7.92, and 5.69 Gy were found for maximum spinal cord, mean esophagus, and mean lung doses, respectively, with carina alignment yielding similar values. 44% and 22% of patients had at least one metric change by at least 5 Gy (dose metrics) or 5% (volume metrics) for bone and carina alignments, respectively. Investigation of GTV coverage showed mean (stdev) changes in V Rx , D max , and D min of -5.5% (13.5%), 2.5% (4.2%), and 0.8% (8.9%), respectively, for bone alignment with similar results for carina alignment. Resolution of atelectasis caused mass and density decreases, on average, and introduced substantial changes in normal tissue dose metrics in a subset of the patient cohort.

Effect of atelectasis changes on tissue mass and dose during lung radiotherapy

PubMed Central

Guy, Christopher L.; Weiss, Elisabeth; Jan, Nuzhat; Reshko, Leonid B.; Christensen, Gary E.; Hugo, Geoffrey D.

2016-01-01

Purpose: To characterize mass and density changes of lung parenchyma in non-small cell lung cancer (NSCLC) patients following midtreatment resolution of atelectasis and to quantify the impact this large geometric change has on normal tissue dose. Methods: Baseline and midtreatment CT images and contours were obtained for 18 NSCLC patients with atelectasis. Patients were classified based on atelectasis volume reduction between the two scans as having either full, partial, or no resolution. Relative mass and density changes from baseline to midtreatment were calculated based on voxel intensity and volume for each lung lobe. Patients also had clinical treatment plans available which were used to assess changes in normal tissue dose constraints from baseline to midtreatment. The midtreatment image was rigidly aligned with the baseline scan in two ways: (1) bony anatomy and (2) carina. Treatment parameters (beam apertures, weights, angles, monitor units, etc.) were transferred to each image. Then, dose was recalculated. Typical IMRT dose constraints were evaluated on all images, and the changes from baseline to each midtreatment image were investigated. Results: Atelectatic lobes experienced mean (stdev) mass changes of −2.8% (36.6%), −24.4% (33.0%), and −9.2% (17.5%) and density changes of −66.0% (6.4%), −25.6% (13.6%), and −17.0% (21.1%) for full, partial, and no resolution, respectively. Means (stdev) of dose changes to spinal cord Dmax, esophagus Dmean, and lungs Dmean were 0.67 (2.99), 0.99 (2.69), and 0.50 Gy (2.05 Gy), respectively, for bone alignment and 0.14 (1.80), 0.77 (2.95), and 0.06 Gy (1.71 Gy) for carina alignment. Dose increases with bone alignment up to 10.93, 7.92, and 5.69 Gy were found for maximum spinal cord, mean esophagus, and mean lung doses, respectively, with carina alignment yielding similar values. 44% and 22% of patients had at least one metric change by at least 5 Gy (dose metrics) or 5% (volume metrics) for bone and carina alignments, respectively. Investigation of GTV coverage showed mean (stdev) changes in VRx, Dmax, and Dmin of −5.5% (13.5%), 2.5% (4.2%), and 0.8% (8.9%), respectively, for bone alignment with similar results for carina alignment. Conclusions: Resolution of atelectasis caused mass and density decreases, on average, and introduced substantial changes in normal tissue dose metrics in a subset of the patient cohort. PMID:27806593

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.

Tailorable Dielectric Material with Complex Permittivity Characteristics

NASA Technical Reports Server (NTRS)

Smith, Joseph G. (Inventor); Watson, Kent A. (Inventor); Elliott, Holly A (Inventor); Delozier, Donavon Mark (Inventor); Connell, John W. (Inventor); Ghose, Sayata (Inventor); Dudley, Kenneth L. (Inventor)

2014-01-01

A dielectric material includes a network of nanosubstrates, such as but not limited to nanotubes, nanosheets, or other nanomaterials or nanostructures, a polymer base material or matrix, and nanoparticles constructed at least partially of an elemental metal. The network has a predetermined nanosubstrate loading percentage by weight with respect to a total weight of the dielectric material, and a preferential or predetermined longitudinal alignment with respect to an orientation of an incident electrical field. A method of forming the dielectric material includes depositing the metal-based nanoparticles onto the nanosubstrates and subsequently mixing these with a polymer matrix. Once mixed, alignment can be achieved by melt extrusion or a similar mechanical shearing process. Alignment of the nanosubstrate may be in horizontal or vertical direction with respect to the orientation of an incident electrical field.

MAGNETOHYDRODYNAMIC SIMULATION OF A DISK SUBJECTED TO LENSE-THIRRING PRECESSION

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

Sorathia, Kareem A.; Krolik, Julian H.; Hawley, John F.

2013-11-01

When matter orbits around a central mass obliquely with respect to the mass's spin axis, the Lense-Thirring effect causes it to precess at a rate declining sharply with radius. Ever since the work of Bardeen and Petterson, it has been expected that when a fluid fills an orbiting disk, the orbital angular momentum at small radii should then align with the mass's spin. Nearly all previous work has studied this alignment under the assumption that a phenomenological 'viscosity' isotropically degrades fluid shears in accretion disks, even though it is now understood that internal stress in flat disks is due tomore » anisotropic MHD turbulence. In this paper we report a pair of matched simulations, one in MHD and one in pure (non-viscous) HD in order to clarify the specific mechanisms of alignment. As in the previous work, we find that disk warps induce radial flows that mix angular momentum of different orientation; however, we also show that the speeds of these flows are generically transonic and are only very weakly influenced by internal stresses other than pressure. In particular, MHD turbulence does not act in a manner consistent with an isotropic viscosity. When MHD effects are present, the disk aligns, first at small radii and then at large; alignment is only partial in the HD case. We identify the specific angular momentum transport mechanisms causing alignment and show how MHD effects permit them to operate more efficiently. Last, we relate the speed at which an alignment front propagates outward (in the MHD case) to the rate at which Lense-Thirring torques deliver angular momentum at smaller radii.« less

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.

Evaluation, development, and characterization of superconducting materials for space applications

NASA Technical Reports Server (NTRS)

Thorpe, Arthur N.

1990-01-01

The anisotropic electromagnetic features of a grain-aligned YBa2Cu3O(x) bulk sample derived from a process of long-time partial melt growth were investigated by the measurements of direct current magnetization (at 77 K) and alternating current susceptibility as a function of temperature, with the fields applied parallel and perpendicular to the c axis, respectively. The extended Bean model was further studied and applied to explain the experimental results. Upon comparison of the grain-aligned sample with pure single crystal materials, it is concluded that because of the existence of more effective pinning sites in the grain-aligned sample, not only its critical current density perpendicular to the c axis is improved, but the one parallel to the c axis is improved even more significantly. The anisotropy in the critical current densities in the grain-aligned sample at 77 K is at least one to two orders of magnitude smaller than in the pure single crystal. The measurement of anisotropy of alternating current susceptibility as a function of temperature, especially its imaginary part, shows that there are still some residues of interlayer weak links in the grain-aligned samples, but they are quite different from and far less serious than the weak links in the sintered sample.

Superporous thermo-responsive hydrogels by combination of cellulose fibers and aligned micropores.

PubMed

Halake, Kantappa S; Lee, Jonghwi

2014-05-25

In the area of artificial hydrogels, simultaneous engineering of the volume transition characteristics and mechanical properties of stimuli-responsive hydrogels is an important subject. By unrestricted architecting of hierarchical structures, natural hydrogels are able to provide a wide range of swelling and mechanical properties, beyond the limits of artificial hydrogels. Herein, a combination of nanostructures and microstructures was developed to construct superporous hydrogels. Fibers of microfibrillated cellulose (MFC), an eco-friendly reinforcing material, were used as nanostructures, aligned micropores were used as microstructures, and in situ photopolymerization was used to immobilize the two structures together within the gel networks of poly(N-isopropyl acrylamide) (PNIPAm). The introduction of MFC distinctly enhanced volume transition, mainly by decreasing the swelling ratios above the transition. The introduction of directional micropores increased the swelling ratio below the transition and decreased the swelling ratio above the transition, thereby also enhancing the volume transition. Additionally, the formation of aligned micropores achieved fast water infiltration, which is beneficial for superabsorbent applications. The introduction of aligned micropores reduced the elastic modulus, but this could partially be compensated for by reinforcement with MFC. This combination of crystalline nanofibers and aligned micropores has great potential for the development of stimuli-responsive superporous hydrogels outperforming current artificial hydrogels. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

Information Compression, Multiple Alignment, and the Representation and Processing of Knowledge in the Brain

PubMed Central

Wolff, J. Gerard

2016-01-01

The SP theory of intelligence, with its realization in the SP computer model, aims to simplify and integrate observations and concepts across artificial intelligence, mainstream computing, mathematics, and human perception and cognition, with information compression as a unifying theme. This paper describes how abstract structures and processes in the theory may be realized in terms of neurons, their interconnections, and the transmission of signals between neurons. This part of the SP theory—SP-neural—is a tentative and partial model for the representation and processing of knowledge in the brain. Empirical support for the SP theory—outlined in the paper—provides indirect support for SP-neural. In the abstract part of the SP theory (SP-abstract), all kinds of knowledge are represented with patterns, where a pattern is an array of atomic symbols in one or two dimensions. In SP-neural, the concept of a “pattern” is realized as an array of neurons called a pattern assembly, similar to Hebb's concept of a “cell assembly” but with important differences. Central to the processing of information in SP-abstract is information compression via the matching and unification of patterns (ICMUP) and, more specifically, information compression via the powerful concept of multiple alignment, borrowed and adapted from bioinformatics. Processes such as pattern recognition, reasoning and problem solving are achieved via the building of multiple alignments, while unsupervised learning is achieved by creating patterns from sensory information and also by creating patterns from multiple alignments in which there is a partial match between one pattern and another. It is envisaged that, in SP-neural, short-lived neural structures equivalent to multiple alignments will be created via an inter-play of excitatory and inhibitory neural signals. It is also envisaged that unsupervised learning will be achieved by the creation of pattern assemblies from sensory information and from the neural equivalents of multiple alignments, much as in the non-neural SP theory—and significantly different from the “Hebbian” kinds of learning which are widely used in the kinds of artificial neural network that are popular in computer science. The paper discusses several associated issues, with relevant empirical evidence. PMID:27857695

Information Compression, Multiple Alignment, and the Representation and Processing of Knowledge in the Brain.

PubMed

Wolff, J Gerard

2016-01-01

The SP theory of intelligence , with its realization in the SP computer model , aims to simplify and integrate observations and concepts across artificial intelligence, mainstream computing, mathematics, and human perception and cognition, with information compression as a unifying theme. This paper describes how abstract structures and processes in the theory may be realized in terms of neurons, their interconnections, and the transmission of signals between neurons. This part of the SP theory- SP-neural -is a tentative and partial model for the representation and processing of knowledge in the brain. Empirical support for the SP theory-outlined in the paper-provides indirect support for SP-neural. In the abstract part of the SP theory (SP-abstract), all kinds of knowledge are represented with patterns , where a pattern is an array of atomic symbols in one or two dimensions. In SP-neural, the concept of a "pattern" is realized as an array of neurons called a pattern assembly , similar to Hebb's concept of a "cell assembly" but with important differences. Central to the processing of information in SP-abstract is information compression via the matching and unification of patterns (ICMUP) and, more specifically, information compression via the powerful concept of multiple alignment , borrowed and adapted from bioinformatics. Processes such as pattern recognition, reasoning and problem solving are achieved via the building of multiple alignments, while unsupervised learning is achieved by creating patterns from sensory information and also by creating patterns from multiple alignments in which there is a partial match between one pattern and another. It is envisaged that, in SP-neural, short-lived neural structures equivalent to multiple alignments will be created via an inter-play of excitatory and inhibitory neural signals. It is also envisaged that unsupervised learning will be achieved by the creation of pattern assemblies from sensory information and from the neural equivalents of multiple alignments, much as in the non-neural SP theory-and significantly different from the "Hebbian" kinds of learning which are widely used in the kinds of artificial neural network that are popular in computer science. The paper discusses several associated issues, with relevant empirical evidence.

Instability of ocular alignment in childhood esotropia.

PubMed

Christiansen, Stephen P; Chandler, Danielle L; Holmes, Jonathan M; Arnold, Robert W; Birch, Eileen; Dagi, Linda R; Hoover, Darren L; Klimek, Deborah L; Melia, B Michele; Paysse, Evelyn; Repka, Michael X; Suh, Donny W; Ticho, Benjamin H; Wallace, David K; Weaver, Richard Grey

2008-12-01

Instability of ocular alignment may cause surgeons to delay surgical correction of childhood esotropia. The authors investigated the stability of ocular alignment over 18 weeks in children with infantile esotropia (IET), acquired nonaccommodative esotropia (ANAET), or acquired partially accommodative esotropia (APAET). Prospective, observational study. Two hundred thirty-three children aged 2 months to less than 5 years with IET, ANAET, or APAET of less than 6 months' duration. Ocular alignment was measured at baseline and at 6-week intervals for 18 weeks. Using definitions derived from a nested test-retest study and computer simulation modeling, ocular alignment was classified as unstable if there was a change of 15 prism diopters (PD) or more between any 2 of the 4 measurements, as stable if all 4 measurements were within 5 PD or less of one another, or as uncertain if neither criteria was met. Of those who completed all 3 follow-up visits within time windows for analysis, 27 (46%) of 59 subjects with IET had ocular alignment classified as unstable (95% confidence interval [CI], 33%-59%), 20% as stable (95% CI, 11%-33%), and 34% as uncertain (95% CI, 22%-47%). Thirteen (22%) of 60 subjects with ANAET had ocular alignment classified as unstable (95% CI, 12%-34%), 37% as stable (95% CI, 25%-50%), and 42% as uncertain (95% CI, 29%-55%). Six (15%) of 41 subjects with APAET had ocular alignment classified as unstable (95% CI, 6%-29%), 39% as stable (95% CI, 24%-56%), and 46% as uncertain (95% CI, 31%-63%). For IET, subjects who were older at presentation were less likely to have unstable angles than subjects who were younger at presentation (risk ratio for unstable vs stable per additional month of age, 0.85; 99% CI, 0.74-0.99). Ocular alignment instability is common in children with IET, ANAET, and APAET. The impact of this finding on the optimal timing for strabismus surgery in childhood esotropia awaits further study. The author(s) have no proprietary or commercial interest in any materials discussed in this article.

Reduction of Deviation Angle During Occlusion Therapy: In Partially Accommodative Esotropia with Moderate Amblyopia

PubMed Central

Chun, Bo Young; Kwon, Soon Jae; Chae, Sun Hwa

2007-01-01

Purpose To evaluate changes in ocular alignment in partially accommodative esotropic children age ranged from 3 to 8 years during occlusion therapy for amblyopia. Methods Angle measurements of twenty-two partially accommodative esotropic patients with moderate amblyopia were evaluated before and at 2 years after occlusion therapy. Results Mean deviation angle with glasses at the start of occlusion treatment was 19.45±5.97 PD and decreased to 12.14±12.96 PD at 2 years after occlusion therapy (p<0.01). After occlusion therapy, 9 (41%) cases were indications of surgery for residual deviation but if we had planned surgery before occlusion treatment, 18 (82%) of patients would have had surgery. There was a statistical relationship between increase of visual acuity ratio and decrease of deviation angle (r=-0.479, p=0.024). Conclusions There was a significant reduction of deviation angle of partially accommodative esotropic patients at 2 years after occlusion therapy. Our results suggest that occlusion therapy has an influence on ocular alignment in partially accommodative esotropic patients with amblyopia. PMID:17804922

Aligned and Electrospun Piezoelectric Polymer Fiber Assembly and Scaffold

NASA Technical Reports Server (NTRS)

Holloway, Nancy M. (Inventor); Scott-Carnell, Lisa A. (Inventor); Siochi, Emilie J. (Inventor); Leong, Kam W. (Inventor); Kulangara, Karina (Inventor)

2015-01-01

A scaffold assembly and related methods of manufacturing and/or using the scaffold for stem cell culture and tissue engineering applications are disclosed which at least partially mimic a native biological environment by providing biochemical, topographical, mechanical and electrical cues by using an electroactive material. The assembly includes at least one layer of substantially aligned, electrospun polymer fiber having an operative connection for individual voltage application. A method of cell tissue engineering and/or stem cell differentiation uses the assembly seeded with a sample of cells suspended in cell culture media, incubates and applies voltage to one or more layers, and thus produces cells and/or a tissue construct. In another aspect, the invention provides a method of manufacturing the assembly including the steps of providing a first pre-electroded substrate surface; electrospinning a first substantially aligned polymer fiber layer onto the first surface; providing a second pre-electroded substrate surface; electrospinning a second substantially aligned polymer fiber layer onto the second surface; and, retaining together the layered surfaces with a clamp and/or an adhesive compound.

Aligned and Electrospun Piezoelectric Polymer Fiber Assembly and Scaffold

NASA Technical Reports Server (NTRS)

Kulangara, Karina (Inventor); Scott Carnell, Lisa A. (Inventor); Holloway, Nancy M. (Inventor); Leong, Kam W. (Inventor); Siochi, Emilie J. (Inventor)

2017-01-01

A method of manufacturing and/or using a scaffold assembly for stem cell culture and tissue engineering applications is disclosed. The scaffold at least partially mimics a native biological environment by providing biochemical, topographical, mechanical and electrical cues by using an electroactive material. The assembly includes at least one layer of substantially aligned, electrospun polymer fiber having an operative connection for individual voltage application. A method of cell tissue engineering and/or stem cell differentiation that uses the assembly seeded with a sample of cells suspended in cell culture media, incubates and applies voltage to one or more layers, and thus produces cells and/or a tissue construct. In another aspect, the invention provides a method of manufacturing the assembly including the steps of providing a first pre-electroded substrate surface; electrospinning a first substantially aligned polymer fiber layer onto the first surface; providing a second pre-electroded substrate surface; electrospinning a second substantially aligned polymer fiber layer onto the second surface; and, retaining together the layered surfaces with a clamp and/or an adhesive compound.

Alignment-Independent Comparisons of Human Gastrointestinal Tract Microbial Communities in a Multidimensional 16S rRNA Gene Evolutionary Space▿

PubMed Central

Rudi, Knut; Zimonja, Monika; Kvenshagen, Bente; Rugtveit, Jarle; Midtvedt, Tore; Eggesbø, Merete

2007-01-01

We present a novel approach for comparing 16S rRNA gene clone libraries that is independent of both DNA sequence alignment and definition of bacterial phylogroups. These steps are the major bottlenecks in current microbial comparative analyses. We used direct comparisons of taxon density distributions in an absolute evolutionary coordinate space. The coordinate space was generated by using alignment-independent bilinear multivariate modeling. Statistical analyses for clone library comparisons were based on multivariate analysis of variance, partial least-squares regression, and permutations. Clone libraries from both adult and infant gastrointestinal tract microbial communities were used as biological models. We reanalyzed a library consisting of 11,831 clones covering complete colons from three healthy adults in addition to a smaller 390-clone library from infant feces. We show that it is possible to extract detailed information about microbial community structures using our alignment-independent method. Our density distribution analysis is also very efficient with respect to computer operation time, meeting the future requirements of large-scale screenings to understand the diversity and dynamics of microbial communities. PMID:17337554

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

Absence of paired crossing in the positive parity bands of 124Cs

NASA Astrophysics Data System (ADS)

Singh, A. K.; Basu, A.; Nag, Somnath; Hübel, H.; Domscheit, J.; Ragnarsson, I.; Al-Khatib, A.; Hagemann, G. B.; Herskind, B.; Elema, D. R.; Wilson, J. N.; Clark, R. M.; Cromaz, M.; Fallon, P.; Görgen, A.; Lee, I.-Y.; Ward, D.; Ma, W. C.

2018-02-01

High-spin states in 124Cs were populated in the 64Ni(64Ni,p 3 n ) reaction and the Gammasphere detector array was used to measure γ -ray coincidences. Both positive- and negative-parity bands, including bands with chiral configurations, have been extended to higher spin, where a shape change has been observed. The configurations of the bands before and after the alignment are discussed within the framework of the cranked Nilsson-Strutinsky model. The calculations suggest that the nucleus undergoes a shape transition from triaxial to prolate around spin I ≃22 of the positive-parity states. The alignment gain of 8 ℏ , observed in the positive-parity bands, is due to partial alignment of several valence nucleons. This indicates the absence of band crossing due to paired nucleons in the bands.

Real-time Optical Alignment and Diagnostic System (ROADS)

NASA Technical Reports Server (NTRS)

1972-01-01

The ultimate and most frequent usage of ROADS will be the alignment of subassemblies (collector and collimator) prior to their installation in a chamber. The system as designed has inherent associated capabilities well applied to acceptance testing of the No. 4 mirror, prediction of in-chamber performance, generation of a catalog of test results and other data, providing data for the plotting of isointensity lines, and other applications which are discussed. The ROADS system will collect, process, display, analyze, and retain data as required for components, partial subassemblies, complete subassemblies, complete modules, and multimodular arrays.

Biologically inspired EM image alignment and neural reconstruction.

PubMed

Knowles-Barley, Seymour; Butcher, Nancy J; Meinertzhagen, Ian A; Armstrong, J Douglas

2011-08-15

Three-dimensional reconstruction of consecutive serial-section transmission electron microscopy (ssTEM) images of neural tissue currently requires many hours of manual tracing and annotation. Several computational techniques have already been applied to ssTEM images to facilitate 3D reconstruction and ease this burden. Here, we present an alternative computational approach for ssTEM image analysis. We have used biologically inspired receptive fields as a basis for a ridge detection algorithm to identify cell membranes, synaptic contacts and mitochondria. Detected line segments are used to improve alignment between consecutive images and we have joined small segments of membrane into cell surfaces using a dynamic programming algorithm similar to the Needleman-Wunsch and Smith-Waterman DNA sequence alignment procedures. A shortest path-based approach has been used to close edges and achieve image segmentation. Partial reconstructions were automatically generated and used as a basis for semi-automatic reconstruction of neural tissue. The accuracy of partial reconstructions was evaluated and 96% of membrane could be identified at the cost of 13% false positive detections. An open-source reference implementation is available in the Supplementary information. seymour.kb@ed.ac.uk; douglas.armstrong@ed.ac.uk Supplementary data are available at Bioinformatics online.

Ultra-stiff large-area carpets of carbon nanotubes

NASA Astrophysics Data System (ADS)

Meysami, Seyyed Shayan; Dallas, Panagiotis; Britton, Jude; Lozano, Juan G.; Murdock, Adrian T.; Ferraro, Claudio; Gutierrez, Eduardo Saiz; Rijnveld, Niek; Holdway, Philip; Porfyrakis, Kyriakos; Grobert, Nicole

2016-06-01

Herewith, we report the influence of post-synthesis heat treatment (<=2350 °C and plasma temperatures) on the crystal structure, defect density, purity, alignment and dispersibility of free-standing large-area (several cm2) carpets of ultra-long (several mm) vertically aligned multi-wall carbon nanotubes (VA-MWCNTs). VA-MWCNTs were produced in large quantities (20-30 g per batch) using a semi-scaled-up aerosol-assisted chemical vapour deposition (AACVD) setup. Electron and X-ray diffraction showed that the heat treatment at 2350 °C under inert atmosphere purifies, removes residual catalyst particles, and partially aligns adjacent single crystals (crystallites) in polycrystalline MWCNTs. The purification and improvement in the crystallites alignment within the MWCNTs resulted in reduced dispersibility of the VA-MWCNTs in liquid media. High-resolution microscopy revealed that the crystallinity is improved in scales of few tens of nanometres while the point defects remain largely unaffected. The heat treatment also had a marked benefit on the mechanical properties of the carpets. For the first time, we report compression moduli as high as 120 MPa for VA-MWCNT carpets, i.e. an order of magnitude higher than previously reported figures. The application of higher temperatures (arc-discharge plasma, >=4000 °C) resulted in the formation of a novel graphite-matrix composite reinforced with CVD and arc-discharge-like carbon nanotubes.Herewith, we report the influence of post-synthesis heat treatment (<=2350 °C and plasma temperatures) on the crystal structure, defect density, purity, alignment and dispersibility of free-standing large-area (several cm2) carpets of ultra-long (several mm) vertically aligned multi-wall carbon nanotubes (VA-MWCNTs). VA-MWCNTs were produced in large quantities (20-30 g per batch) using a semi-scaled-up aerosol-assisted chemical vapour deposition (AACVD) setup. Electron and X-ray diffraction showed that the heat treatment at 2350 °C under inert atmosphere purifies, removes residual catalyst particles, and partially aligns adjacent single crystals (crystallites) in polycrystalline MWCNTs. The purification and improvement in the crystallites alignment within the MWCNTs resulted in reduced dispersibility of the VA-MWCNTs in liquid media. High-resolution microscopy revealed that the crystallinity is improved in scales of few tens of nanometres while the point defects remain largely unaffected. The heat treatment also had a marked benefit on the mechanical properties of the carpets. For the first time, we report compression moduli as high as 120 MPa for VA-MWCNT carpets, i.e. an order of magnitude higher than previously reported figures. The application of higher temperatures (arc-discharge plasma, >=4000 °C) resulted in the formation of a novel graphite-matrix composite reinforced with CVD and arc-discharge-like carbon nanotubes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01660j

Angular ellipticity correlations in a composite alignment model for elliptical and spiral galaxies and inference from weak lensing

NASA Astrophysics Data System (ADS)

Tugendhat, Tim M.; Schäfer, Björn Malte

2018-05-01

We investigate a physical, composite alignment model for both spiral and elliptical galaxies and its impact on cosmological parameter estimation from weak lensing for a tomographic survey. Ellipticity correlation functions and angular ellipticity spectra for spiral and elliptical galaxies are derived on the basis of tidal interactions with the cosmic large-scale structure and compared to the tomographic weak-lensing signal. We find that elliptical galaxies cause a contribution to the weak-lensing dominated ellipticity correlation on intermediate angular scales between ℓ ≃ 40 and ℓ ≃ 400 before that of spiral galaxies dominates on higher multipoles. The predominant term on intermediate scales is the negative cross-correlation between intrinsic alignments and weak gravitational lensing (GI-alignment). We simulate parameter inference from weak gravitational lensing with intrinsic alignments unaccounted; the bias induced by ignoring intrinsic alignments in a survey like Euclid is shown to be several times larger than the statistical error and can lead to faulty conclusions when comparing to other observations. The biases generally point into different directions in parameter space, such that in some cases one can observe a partial cancellation effect. Furthermore, it is shown that the biases increase with the number of tomographic bins used for the parameter estimation process. We quantify this parameter estimation bias in units of the statistical error and compute the loss of Bayesian evidence for a model due to the presence of systematic errors as well as the Kullback-Leibler divergence to quantify the distance between the true model and the wrongly inferred one.

Grain-scale alignment of melt in sheared partially molten rocks: implications for viscous anisotropy

NASA Astrophysics Data System (ADS)

Pec, Matej; Quintanilla-Terminel, Alejandra; Holtzman, Benjamin; Zimmerman, Mark; Kohlstedt, David

2016-04-01

Presence of melt significantly influences rheological properties of partially molten rocks by providing fast diffusional pathways. Under stress, melt aligns at the grain scale and this alignment induces viscous anisotropy in the deforming aggregate. One of the consequences of viscous anisotropy is melt segregation into melt-rich sheets oriented at low angle to the shear plane on much larger scales than the grain scale. The magnitude and orientation of viscous anisotropy with respect to the applied stress are important parameters for constitutive models (Takei and Holtzman 2009) that must be constrained by experimental studies. In this contribution, we analyze the shape preferred orientation (SPO) of individual grain-scale melt pockets in deformed partially molten mantle rocks. The starting materials were obtained by isostatically hot-pressing olivine + basalt and olivine + chromite + basalt powders. These partially molten rocks were deformed in general shear or torsion at a confining pressure, Pc = 300 MPa, temperature, T = 1200° - 1250° C, and strain rates of 10-3 - 10-5 s-1to finite shear strains, γ, of 0.5 - 5. After the experiment, high resolution backscattered electron images were obtained using a SEM equipped with a field emission gun. Individual melt pockets were segmented and their SPO analyzed using the paror and surfor methods and Fourier transforms (Heilbronner and Barret 2014). Melt segregation into melt-rich sheets inclined at 15° -20° antithetic with respect to the shear plane occurs in three-phase system (olivine + chromite + basalt) and in two-phase systems (olivine + basalt) twisted to high strain. The SPO of individual melt pockets within the melt-rich bands is moderately strong (b/a ≈ 0.8) and is always steeper (20° -40°) than the average melt-rich band orientation. In the two-phase system (olivine + basalt) sheared to lower strains, no distinct melt-rich sheets are observed. Individual grain-scale melt pockets are oriented at 45° -55° antithetic with respect to the shear plane (i.e., sub-perpendicular to σ3) with a strong SPO (b/a ≈ 0.7) that decreases with increasing finite strain. Our observations of melt alignment at low strains are in agreement with observations performed on analogue materials (borneol, Takei 2010) and provide further constraints for the orientation of viscous anisotropy in the Earth's mantle. The systematic difference in grain-scale melt alignment between samples in which melt segregation did and did not occur - irrespective of the deformation geometry and mineralogy - suggests that melt segregation into bands leads to local stress rotation within the samples.

An Automatic Registration Algorithm for 3D Maxillofacial Model

NASA Astrophysics Data System (ADS)

Qiu, Luwen; Zhou, Zhongwei; Guo, Jixiang; Lv, Jiancheng

2016-09-01

3D image registration aims at aligning two 3D data sets in a common coordinate system, which has been widely used in computer vision, pattern recognition and computer assisted surgery. One challenging problem in 3D registration is that point-wise correspondences between two point sets are often unknown apriori. In this work, we develop an automatic algorithm for 3D maxillofacial models registration including facial surface model and skull model. Our proposed registration algorithm can achieve a good alignment result between partial and whole maxillofacial model in spite of ambiguous matching, which has a potential application in the oral and maxillofacial reparative and reconstructive surgery. The proposed algorithm includes three steps: (1) 3D-SIFT features extraction and FPFH descriptors construction; (2) feature matching using SAC-IA; (3) coarse rigid alignment and refinement by ICP. Experiments on facial surfaces and mandible skull models demonstrate the efficiency and robustness of our algorithm.

Water saturation effects on elastic wave attenuation in porous rocks with aligned fractures

NASA Astrophysics Data System (ADS)

Amalokwu, Kelvin; Best, Angus I.; Sothcott, Jeremy; Chapman, Mark; Minshull, Tim; Li, Xiang-Yang

2014-05-01

Elastic wave attenuation anisotropy in porous rocks with aligned fractures is of interest to seismic remote sensing of the Earth's structure and to hydrocarbon reservoir characterization in particular. We investigated the effect of partial water saturation on attenuation in fractured rocks in the laboratory by conducting ultrasonic pulse-echo measurements on synthetic, silica-cemented, sandstones with aligned penny-shaped voids (fracture density of 0.0298 ± 0.0077), chosen to simulate the effect of natural fractures in the Earth according to theoretical models. Our results show, for the first time, contrasting variations in the attenuation (Q-1) of P and S waves with water saturation in samples with and without fractures. The observed Qs/Qp ratios are indicative of saturation state and the presence or absence of fractures, offering an important new possibility for remote fluid detection and characterization.

Data on partial polyhydroxyalkanoate synthase genes (phaC) mined from Aaptos aaptos marine sponge-associated bacteria metagenome.

PubMed

Amelia, Tan Suet May; Amirul, Al-Ashraf Abdullah; Bhubalan, Kesaven

2018-02-01

We report data associated with the identification of three polyhydroxyalkanoate synthase genes (phaC) isolated from the marine bacteria metagenome of Aaptos aaptos marine sponge in the waters of Bidong Island, Terengganu, Malaysia. Our data describe the extraction of bacterial metagenome from sponge tissue, measurement of purity and concentration of extracted metagenome, polymerase chain reaction (PCR)-mediated amplification using degenerate primers targeting Class I and II phaC genes, sequencing at First BASE Laboratories Sdn Bhd, and phylogenetic analysis of identified and known phaC genes. The partial nucleotide sequences were aligned, refined, compared with the Basic Local Alignment Search Tool (BLAST) databases, and released online in GenBank. The data include the identified partial putative phaC and their GenBank accession numbers, which are Rhodocista sp. phaC (MF457754), Pseudomonas sp. phaC (MF437016), and an uncultured bacterium AR5-9d_16 phaC (MF457753).

Joint Interference Alignment and Power Allocation for K-User Multicell MIMO Channel through Staggered Antenna Switching.

PubMed

Selvaprabhu, Poongundran; Chinnadurai, Sunil; Sarker, Md Abdul Latif; Lee, Moon Ho

2018-01-28

In this paper, we characterise the joint interference alignment (IA) and power allocation strategies for a K -user multicell multiple-input multiple-output (MIMO) Gaussian interference channel. We consider a MIMO interference channel with blind-IA through staggered antenna switching on the receiver. We explore the power allocation and feasibility condition for cooperative cell-edge (CE) mobile users (MUs) by assuming that the channel state information is unknown. The new insight behind the transmission strategy of the proposed scheme is premeditated (randomly generated transmission strategy) and partial cooperative CE MUs, where the transmitter is equipped with a conventional antenna, the receiver is equipped with a reconfigurable multimode antenna (staggered antenna switching pattern), and the receiver switches between preset T modes. Our proposed scheme assists and aligns the desired signals and interference signals to cancel the common interference signals because the received signal must have a corresponding independent signal subspace. The capacity for a K -user multicell MIMO Gaussian interference channel with reconfigurable multimode antennas is completely characterised. Furthermore, we show that the proposed K -user multicell MIMO scheduling and K -user L -cell CEUs partial cooperation algorithms elaborate the generalisation of K -user IA and power allocation strategies. The numerical results demonstrate that the proposed intercell interference scheme with partial-cooperative CE MUs achieves better capacity and signal-to-interference plus noise ratio (SINR) performance compared to noncooperative CE MUs and without intercell interference schemes.

Joint Interference Alignment and Power Allocation for K-User Multicell MIMO Channel through Staggered Antenna Switching

PubMed Central

2018-01-01

In this paper, we characterise the joint interference alignment (IA) and power allocation strategies for a K-user multicell multiple-input multiple-output (MIMO) Gaussian interference channel. We consider a MIMO interference channel with blind-IA through staggered antenna switching on the receiver. We explore the power allocation and feasibility condition for cooperative cell-edge (CE) mobile users (MUs) by assuming that the channel state information is unknown. The new insight behind the transmission strategy of the proposed scheme is premeditated (randomly generated transmission strategy) and partial cooperative CE MUs, where the transmitter is equipped with a conventional antenna, the receiver is equipped with a reconfigurable multimode antenna (staggered antenna switching pattern), and the receiver switches between preset T modes. Our proposed scheme assists and aligns the desired signals and interference signals to cancel the common interference signals because the received signal must have a corresponding independent signal subspace. The capacity for a K-user multicell MIMO Gaussian interference channel with reconfigurable multimode antennas is completely characterised. Furthermore, we show that the proposed K-user multicell MIMO scheduling and K-user L-cell CEUs partial cooperation algorithms elaborate the generalisation of K-user IA and power allocation strategies. The numerical results demonstrate that the proposed intercell interference scheme with partial-cooperative CE MUs achieves better capacity and signal-to-interference plus noise ratio (SINR) performance compared to noncooperative CE MUs and without intercell interference schemes. PMID:29382100

Highly uniform and vertically aligned SnO2 nanochannel arrays for photovoltaic applications

NASA Astrophysics Data System (ADS)

Kim, Jae-Yup; Kang, Jin Soo; Shin, Junyoung; Kim, Jin; Han, Seung-Joo; Park, Jongwoo; Min, Yo-Sep; Ko, Min Jae; Sung, Yung-Eun

2015-04-01

Nanostructured electrodes with vertical alignment have been considered ideal structures for electron transport and interfacial contact with redox electrolytes in photovoltaic devices. Here, we report large-scale vertically aligned SnO2 nanochannel arrays with uniform structures, without lateral cracks fabricated by a modified anodic oxidation process. In the modified process, ultrasonication is utilized to avoid formation of partial compact layers and lateral cracks in the SnO2 nanochannel arrays. Building on this breakthrough, we first demonstrate the photovoltaic application of these vertically aligned SnO2 nanochannel arrays. These vertically aligned arrays were directly and successfully applied in quasi-solid state dye-sensitized solar cells (DSSCs) as photoanodes, yielding reasonable conversion efficiency under back-side illumination. In addition, a significantly short process time (330 s) for achieving the optimal thickness (7.0 μm) and direct utilization of the anodized electrodes enable a simple, rapid and low-cost fabrication process. Furthermore, a TiO2 shell layer was coated on the SnO2 nanochannel arrays by the atomic layer deposition (ALD) process for enhancement of dye-loading and prolonging the electron lifetime in the DSSC. Owing to the presence of the ALD TiO2 layer, the short-circuit photocurrent density (Jsc) and conversion efficiency were increased by 20% and 19%, respectively, compared to those of the DSSC without the ALD TiO2 layer. This study provides valuable insight into the development of efficient SnO2-based photoanodes for photovoltaic application by a simple and rapid fabrication process.Nanostructured electrodes with vertical alignment have been considered ideal structures for electron transport and interfacial contact with redox electrolytes in photovoltaic devices. Here, we report large-scale vertically aligned SnO2 nanochannel arrays with uniform structures, without lateral cracks fabricated by a modified anodic oxidation process. In the modified process, ultrasonication is utilized to avoid formation of partial compact layers and lateral cracks in the SnO2 nanochannel arrays. Building on this breakthrough, we first demonstrate the photovoltaic application of these vertically aligned SnO2 nanochannel arrays. These vertically aligned arrays were directly and successfully applied in quasi-solid state dye-sensitized solar cells (DSSCs) as photoanodes, yielding reasonable conversion efficiency under back-side illumination. In addition, a significantly short process time (330 s) for achieving the optimal thickness (7.0 μm) and direct utilization of the anodized electrodes enable a simple, rapid and low-cost fabrication process. Furthermore, a TiO2 shell layer was coated on the SnO2 nanochannel arrays by the atomic layer deposition (ALD) process for enhancement of dye-loading and prolonging the electron lifetime in the DSSC. Owing to the presence of the ALD TiO2 layer, the short-circuit photocurrent density (Jsc) and conversion efficiency were increased by 20% and 19%, respectively, compared to those of the DSSC without the ALD TiO2 layer. This study provides valuable insight into the development of efficient SnO2-based photoanodes for photovoltaic application by a simple and rapid fabrication process. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00202h

Developments in optical modeling methods for metrology

NASA Astrophysics Data System (ADS)

Davidson, Mark P.

1999-06-01

Despite the fact that in recent years the scanning electron microscope has come to dominate the linewidth measurement application for wafer manufacturing, there are still many applications for optical metrology and alignment. These include mask metrology, stepper alignment, and overlay metrology. Most advanced non-optical lithographic technologies are also considering using topics for alignment. In addition, there have been a number of in-situ technologies proposed which use optical measurements to control one aspect or another of the semiconductor process. So optics is definitely not dying out in the semiconductor industry. In this paper a description of recent advances in optical metrology and alignment modeling is presented. The theory of high numerical aperture image simulation for partially coherent illumination is discussed. The implications of telecentric optics on the image simulation is also presented. Reciprocity tests are proposed as an important measure of numerical accuracy. Diffraction efficiencies for chrome gratings on reticles are one good way to test Kirchoff's approximation as compared to rigorous calculations. We find significant differences between the predictions of Kirchoff's approximation and rigorous methods. The methods for simulating brightfield, confocal, and coherence probe microscope imags are outlined, as are methods for describing aberrations such as coma, spherical aberration, and illumination aperture decentering.

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.

Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution.

PubMed

Brody, Thomas; Yavatkar, Amarendra S; Park, Dong Sun; Kuzin, Alexander; Ross, Jermaine; Odenwald, Ward F

2017-06-01

Flavivirus and Filovirus infections are serious epidemic threats to human populations. Multi-genome comparative analysis of these evolving pathogens affords a view of their essential, conserved sequence elements as well as progressive evolutionary changes. While phylogenetic analysis has yielded important insights, the growing number of available genomic sequences makes comparisons between hundreds of viral strains challenging. We report here a new approach for the comparative analysis of these hemorrhagic fever viruses that can superimpose an unlimited number of one-on-one alignments to identify important features within genomes of interest. We have adapted EvoPrinter alignment algorithms for the rapid comparative analysis of Flavivirus or Filovirus sequences including Zika and Ebola strains. The user can input a full genome or partial viral sequence and then view either individual comparisons or generate color-coded readouts that superimpose hundreds of one-on-one alignments to identify unique or shared identity SNPs that reveal ancestral relationships between strains. The user can also opt to select a database genome in order to access a library of pre-aligned genomes of either 1,094 Flaviviruses or 460 Filoviruses for rapid comparative analysis with all database entries or a select subset. Using EvoPrinter search and alignment programs, we show the following: 1) superimposing alignment data from many related strains identifies lineage identity SNPs, which enable the assessment of sublineage complexity within viral outbreaks; 2) whole-genome SNP profile screens uncover novel Dengue2 and Zika recombinant strains and their parental lineages; 3) differential SNP profiling identifies host cell A-to-I hyper-editing within Ebola and Marburg viruses, and 4) hundreds of superimposed one-on-one Ebola genome alignments highlight ultra-conserved regulatory sequences, invariant amino acid codons and evolutionarily variable protein-encoding domains within a single genome. EvoPrinter allows for the assessment of lineage complexity within Flavivirus or Filovirus outbreaks, identification of recombinant strains, highlights sequences that have undergone host cell A-to-I editing, and identifies unique input and database SNPs within highly conserved sequences. EvoPrinter's ability to superimpose alignment data from hundreds of strains onto a single genome has allowed us to identify unique Zika virus sublineages that are currently spreading in South, Central and North America, the Caribbean, and in China. This new set of integrated alignment programs should serve as a useful addition to existing tools for the comparative analysis of these viruses.

TU-D-209-03: Alignment of the Patient Graphic Model Using Fluoroscopic Images for Skin Dose Mapping

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

Oines, A; Oines, A; Kilian-Meneghin, J

2016-06-15

Purpose: The Dose Tracking System (DTS) was developed to provide realtime feedback of skin dose and dose rate during interventional fluoroscopic procedures. A color map on a 3D graphic of the patient represents the cumulative dose distribution on the skin. Automated image correlation algorithms are described which use the fluoroscopic procedure images to align and scale the patient graphic for more accurate dose mapping. Methods: Currently, the DTS employs manual patient graphic selection and alignment. To improve the accuracy of dose mapping and automate the software, various methods are explored to extract information about the beam location and patient morphologymore » from the procedure images. To match patient anatomy with a reference projection image, preprocessing is first used, including edge enhancement, edge detection, and contour detection. Template matching algorithms from OpenCV are then employed to find the location of the beam. Once a match is found, the reference graphic is scaled and rotated to fit the patient, using image registration correlation functions in Matlab. The algorithm runs correlation functions for all points and maps all correlation confidences to a surface map. The highest point of correlation is used for alignment and scaling. The transformation data is saved for later model scaling. Results: Anatomic recognition is used to find matching features between model and image and image registration correlation provides for alignment and scaling at any rotation angle with less than onesecond runtime, and at noise levels in excess of 150% of those found in normal procedures. Conclusion: The algorithm provides the necessary scaling and alignment tools to improve the accuracy of dose distribution mapping on the patient graphic with the DTS. Partial support from NIH Grant R01-EB002873 and Toshiba Medical Systems Corp.« less

77 FR 71404 - Notice of Intent to License Government-Owned Inventions; Intent to License on a Partially...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-30

... DEPARTMENT OF DEFENSE Department of the Army Notice of Intent to License Government-Owned Inventions; Intent to License on a Partially-Exclusive Basis AGENCY: Department of the Army, DoD. ACTION..., issued 07/ 28/2009 and entitled ``Radiation source with self-aligning optics,'' U.S. Patent 7,852,469...

Three-dimensional computer-assisted dissection of pancreatic lymphatic anatomy on human fetuses: a step toward automatic image alignment.

PubMed

Bardol, T; Subsol, G; Perez, M-J; Genevieve, D; Lamouroux, A; Antoine, B; Captier, G; Prudhomme, M; Bertrand, M M

2018-05-01

Pancreatic cancer is the fourth cause of death by cancer worldwide. Lymph node (LN) involvement is known to be the main prognostic factor. However, lymphatic anatomy is complex and only partially characterized. The aim of the study was to study the pancreatic lymphatic system using computer-assisted anatomic dissection (CAAD) technique and also to update CAAD technique by automatizing slice alignment. We dissected three human fetuses aged from 18 to 34 WA. 5-µm serial sections of duodeno-pancreas and spleen blocks were stained (hematoxylin-eosin, hematoxylin of Mayer and Masson trichrome), scanned, aligned and modeled in three dimensions. We observed a rich, diffuse but not systematized lymphatic network in the peri-pancreatic region. There was an equal distribution of LNs between the cephalic and body-tail portions. The lymphatic vascularization appeared in continuity from the celiac trunk to the distal ends of its hepatic and splenic arterial branches parallel to the nerve ramifications of the celiac plexus. We also observed a continuity between the drainage of the pancreatic head and the para-aortic region posteriorly. In view of the wealth of peri-pancreatic LNs, the number of LNs to harvest could be increased to improve nodal staging and prognostic evaluation. Pancreatic anatomy as described does not seem to be compatible with the sentinel LN procedure in pancreatic surgery. Finally, we are now able to offer an alternative to manual alignment with a semi-automated alignment.

Analyzing and synthesizing phylogenies using tree alignment graphs.

PubMed

Smith, Stephen A; Brown, Joseph W; Hinchliff, Cody E

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

PubMed Central

Smith, Stephen A.; Brown, Joseph W.; Hinchliff, Cody E.

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe. PMID:24086118

FPFH-based graph matching for 3D point cloud registration

NASA Astrophysics Data System (ADS)

Zhao, Jiapeng; Li, Chen; Tian, Lihua; Zhu, Jihua

2018-04-01

Correspondence detection is a vital step in point cloud registration and it can help getting a reliable initial alignment. In this paper, we put forward an advanced point feature-based graph matching algorithm to solve the initial alignment problem of rigid 3D point cloud registration with partial overlap. Specifically, Fast Point Feature Histograms are used to determine the initial possible correspondences firstly. Next, a new objective function is provided to make the graph matching more suitable for partially overlapping point cloud. The objective function is optimized by the simulated annealing algorithm for final group of correct correspondences. Finally, we present a novel set partitioning method which can transform the NP-hard optimization problem into a O(n3)-solvable one. Experiments on the Stanford and UWA public data sets indicates that our method can obtain better result in terms of both accuracy and time cost compared with other point cloud registration methods.

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

Webb, Aaron P.; Carlson, Charles T.; Weaver, William T.

A mask alignment system for providing precise and repeatable alignment between ion implantation masks and workpieces. The system includes a mask frame having a plurality of ion implantation masks loosely connected thereto. The mask frame is provided with a plurality of frame alignment cavities, and each mask is provided with a plurality of mask alignment cavities. The system further includes a platen for holding workpieces. The platen may be provided with a plurality of mask alignment pins and frame alignment pins configured to engage the mask alignment cavities and frame alignment cavities, respectively. The mask frame can be lowered ontomore » the platen, with the frame alignment cavities moving into registration with the frame alignment pins to provide rough alignment between the masks and workpieces. The mask alignment cavities are then moved into registration with the mask alignment pins, thereby shifting each individual mask into precise alignment with a respective workpiece.« less

Isolation, cloning, and characterization of a partial novel aro A gene in common reed (Phragmites australis).

PubMed

Taravat, Elham; Zebarjadi, Alireza; Kahrizi, Danial; Yari, Kheirollah

2015-05-01

Among the essential amino acids, phenylalanine, tryptophan, and tyrosine are aromatic amino acids which are synthesized by the shikimate pathway in plants and bacteria. Herbicide glyphosate can inhibit the biosynthesis of these amino acids. So, identification of the gene tolerant to glyphosate is very important. It has been shown that the common reed or Phragmites australis Cav. (Poaceae) is relatively tolerant to glyphosate. The aim of the current research is identification, cloning, sequencing, and registering of partial aro A gene of the common reed P. australis. The partial aro A gene of common reed (P. australis) was cloned in Escherichia coli and the amino acid sequence was identified/determined for the first time. This is the first report for isolation, cloning, and sequencing of a part of aro A gene from the common reed. A 670 bp fragment including two introns (86 bp and 289 bp) was obtained. The open reading frame (ORF) region in part of gene was encoded for 98 amino acids. Alignment showed high similarity among this region with Zea mays (L.) (Poaceae) (94.6%), Eleusine indica L. Gaertn (Poaceae) (94.2%), and Zoysia japonica Steud. (Poaceae) (94.2%). The alignment of amino acid sequence of the investigated part of the gene showed a homology with aro A from several other plants. This conserved region forms the enzyme active site. The alignment results of nucleotide and amino acid residues with related sequences showed that there are some differences among them. The relative glyphosate tolerance in the common reed may be related to these differences.

75 FR 4528 - Certain Magnesia Carbon Bricks From the People's Republic of China: Alignment of Final...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-28

... determination. See Certain Magnesia Carbon Bricks From the People's Republic of China: Preliminary Negative... circumstances included the Department's partial or full closure during the five-day period after the CVD...

DUK - A Fast and Efficient Kmer Based Sequence Matching Tool

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

Li, Mingkun; Copeland, Alex; Han, James

2011-03-21

A new tool, DUK, is developed to perform matching task. Matching is to find whether a query sequence partially or totally matches given reference sequences or not. Matching is similar to alignment. Indeed many traditional analysis tasks like contaminant removal use alignment tools. But for matching, there is no need to know which bases of a query sequence matches which position of a reference sequence, it only need know whether there exists a match or not. This subtle difference can make matching task much faster than alignment. DUK is accurate, versatile, fast, and has efficient memory usage. It uses Kmermore » hashing method to index reference sequences and Poisson model to calculate p-value. DUK is carefully implemented in C++ in object oriented design. The resulted classes can also be used to develop other tools quickly. DUK have been widely used in JGI for a wide range of applications such as contaminant removal, organelle genome separation, and assembly refinement. Many real applications and simulated dataset demonstrate its power.« less

Strain distributions and their influence on electronic structures of WSe2-MoS2 laterally strained heterojunctions

NASA Astrophysics Data System (ADS)

Zhang, Chendong; Li, Ming-Yang; Tersoff, Jerry; Han, Yimo; Su, Yushan; Li, Lain-Jong; Muller, David A.; Shih, Chih-Kang

2018-02-01

Monolayer transition metal dichalcogenide heterojunctions, including vertical and lateral p-n junctions, have attracted considerable attention due to their potential applications in electronics and optoelectronics. Lattice-misfit strain in atomically abrupt lateral heterojunctions, such as WSe2-MoS2, offers a new band-engineering strategy for tailoring their electronic properties. However, this approach requires an understanding of the strain distribution and its effect on band alignment. Here, we study a WSe2-MoS2 lateral heterojunction using scanning tunnelling microscopy and image its moiré pattern to map the full two-dimensional strain tensor with high spatial resolution. Using scanning tunnelling spectroscopy, we measure both the strain and the band alignment of the WSe2-MoS2 lateral heterojunction. We find that the misfit strain induces type II to type I band alignment transformation. Scanning transmission electron microscopy reveals the dislocations at the interface that partially relieve the strain. Finally, we observe a distinctive electronic structure at the interface due to hetero-bonding.

Higher Order Lagrange Finite Elements In M3D

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

J. Chen; H.R. Strauss; S.C. Jardin

The M3D code has been using linear finite elements to represent multilevel MHD on 2-D poloidal planes. Triangular higher order elements, up to third order, are constructed here in order to provide M3D the capability to solve highly anisotropic transport problems. It is found that higher order elements are essential to resolve the thin transition layer characteristic of the anisotropic transport equation, particularly when the strong anisotropic direction is not aligned with one of the Cartesian coordinates. The transition layer is measured by the profile width, which is zero for infinite anisotropy. It is shown that only higher order schemesmore » have the ability to make this layer converge towards zero when the anisotropy gets stronger and stronger. Two cases are considered. One has the strong transport direction partially aligned with one of the element edges, the other doesn't have any alignment. Both cases have the strong transport direction misaligned with the grid line by some angles.« less

Effect of wall pattern configurations on Stokes flow through a microchannel with superhydrophobic slip

NASA Astrophysics Data System (ADS)

Mak, H. M.; Ng, C. O.

2010-11-01

The present work aims to study low-Reynolds-number flow through a microchannel with superhydrophobic surfaces, which contain a periodic array of parallel ribs on the upper and lower walls. Mimicking impregnation, the liquid is allowed to penetrate the grooves between the ribs which are filled with an inviscid gas. The array of ribs and grooves gives a heterogeneous wall boundary condition to the channel flow, with partial-slip boundary condition on the solid surface and no-shear boundary condition on the liquid-gas interface. Using the method of eigenfunction expansions and domain decomposition, semi-analytical models are developed for four configurations. Two of them are for longitudinal flow and the others are for transverse flow. For each flow orientation, in-phase and out-phase alignments of ribs between the upper and lower walls are analyzed. The effect of the phase alignments of ribs is appreciable when the channel height is sufficiently small. In-phase alignment gives rise to a larger effective slip length in longitudinal flow. On the contrary, out-phase alignment will yield a larger effective slip length in transverse flow. This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region, China, through Project HKU 7156/09E.

Diagnosis and treatment of movement system impairment syndromes.

PubMed

Sahrmann, Shirley; Azevedo, Daniel C; Dillen, Linda Van

Diagnoses and treatments based on movement system impairment syndromes were developed to guide physical therapy treatment. This masterclass aims to describe the concepts on that are the basis of the syndromes and treatment and to provide the current research on movement system impairment syndromes. The conceptual basis of the movement system impairment syndromes is that sustained alignment in a non-ideal position and repeated movements in a specific direction are thought to be associated with several musculoskeletal conditions. Classification into movement system impairment syndromes and treatment has been described for all body regions. The classification involves interpreting data from standardized tests of alignments and movements. Treatment is based on correcting the impaired alignment and movement patterns as well as correcting the tissue adaptations associated with the impaired alignment and movement patterns. The reliability and validity of movement system impairment syndromes have been partially tested. Although several case reports involving treatment using the movement system impairment syndromes concept have been published, efficacy of treatment based on movement system impairment syndromes has not been tested in randomized controlled trials, except in people with chronic low back pain. Copyright © 2017 Associação Brasileira de Pesquisa e Pós-Graduação em Fisioterapia. Publicado por Elsevier Editora Ltda. All rights reserved.

Data preprocessing method for liquid chromatography-mass spectrometry based metabolomics.

PubMed

Wei, Xiaoli; Shi, Xue; Kim, Seongho; Zhang, Li; Patrick, Jeffrey S; Binkley, Joe; McClain, Craig; Zhang, Xiang

2012-09-18

A set of data preprocessing algorithms for peak detection and peak list alignment are reported for analysis of liquid chromatography-mass spectrometry (LC-MS)-based metabolomics data. For spectrum deconvolution, peak picking is achieved at the selected ion chromatogram (XIC) level. To estimate and remove the noise in XICs, each XIC is first segmented into several peak groups based on the continuity of scan number, and the noise level is estimated by all the XIC signals, except the regions potentially with presence of metabolite ion peaks. After removing noise, the peaks of molecular ions are detected using both the first and the second derivatives, followed by an efficient exponentially modified Gaussian-based peak deconvolution method for peak fitting. A two-stage alignment algorithm is also developed, where the retention times of all peaks are first transferred into the z-score domain and the peaks are aligned based on the measure of their mixture scores after retention time correction using a partial linear regression. Analysis of a set of spike-in LC-MS data from three groups of samples containing 16 metabolite standards mixed with metabolite extract from mouse livers demonstrates that the developed data preprocessing method performs better than two of the existing popular data analysis packages, MZmine2.6 and XCMS(2), for peak picking, peak list alignment, and quantification.

A Data Pre-processing Method for Liquid Chromatography Mass Spectrometry-based Metabolomics

PubMed Central

Wei, Xiaoli; Shi, Xue; Kim, Seongho; Zhang, Li; Patrick, Jeffrey S.; Binkley, Joe; McClain, Craig; Zhang, Xiang

2012-01-01

A set of data pre-processing algorithms for peak detection and peak list alignment are reported for analysis of LC-MS based metabolomics data. For spectrum deconvolution, peak picking is achieved at selected ion chromatogram (XIC) level. To estimate and remove the noise in XICs, each XIC is first segmented into several peak groups based on the continuity of scan number, and the noise level is estimated by all the XIC signals, except the regions potentially with presence of metabolite ion peaks. After removing noise, the peaks of molecular ions are detected using both the first and the second derivatives, followed by an efficient exponentially modified Gaussian-based peak deconvolution method for peak fitting. A two-stage alignment algorithm is also developed, where the retention times of all peaks are first transferred into z-score domain and the peaks are aligned based on the measure of their mixture scores after retention time correction using a partial linear regression. Analysis of a set of spike-in LC-MS data from three groups of samples containing 16 metabolite standards mixed with metabolite extract from mouse livers, demonstrates that the developed data pre-processing methods performs better than two of the existing popular data analysis packages, MZmine2.6 and XCMS2, for peak picking, peak list alignment and quantification. PMID:22931487

COACH: profile-profile alignment of protein families using hidden Markov models.

PubMed

Edgar, Robert C; Sjölander, Kimmen

2004-05-22

Alignments of two multiple-sequence alignments, or statistical models of such alignments (profiles), have important applications in computational biology. The increased amount of information in a profile versus a single sequence can lead to more accurate alignments and more sensitive homolog detection in database searches. Several profile-profile alignment methods have been proposed and have been shown to improve sensitivity and alignment quality compared with sequence-sequence methods (such as BLAST) and profile-sequence methods (e.g. PSI-BLAST). Here we present a new approach to profile-profile alignment we call Comparison of Alignments by Constructing Hidden Markov Models (HMMs) (COACH). COACH aligns two multiple sequence alignments by constructing a profile HMM from one alignment and aligning the other to that HMM. We compare the alignment accuracy of COACH with two recently published methods: Yona and Levitt's prof_sim and Sadreyev and Grishin's COMPASS. On two sets of reference alignments selected from the FSSP database, we find that COACH is able, on average, to produce alignments giving the best coverage or the fewest errors, depending on the chosen parameter settings. COACH is freely available from www.drive5.com/lobster

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.

IUS prerelease alignment

NASA Technical Reports Server (NTRS)

Evans, F. A.

1978-01-01

Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

PubMed

Tong, Jing; Pei, Jimin; Grishin, Nick V

2015-09-03

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

Books Noted

NASA Astrophysics Data System (ADS)

Walsh, Edward J.

1999-10-01

The Colloidal Domain: Where Physics, Chemistry, Biology, and Technology Meet, 2nd edition

D. Fennell Evans and Hakan Wennerstroem. Advances in Interfacial Engineering Series. Wiley-VCH: New York, 1999. xl + 632 pp. ISBN 0-471-24247-0. 89.95.

Commercial Nuclear Power: Assuring Safety for the Future

Charles B. Ramsey and Mohammed Modarres. Wiley-Interscience: New York, 1998. xxviii + 508 pp. ISBN 0-471-29186-2. 79.95.

Advances in Medicinal Chemistry, Vol. 4

Bruce E. Maryanoff and Allen B. Reitz, Eds. JAI Press: Stamford, CT, 1999. ISBN 1-7623-0064-7. 109.50.

Advances in Strained and Interesting Organic Molecules, Vol. 7

Brian Halton, Ed. JAI Press: Stamford, CT, 1999. xii + 259 pp. ISBN 0-7623-0530-4. 109.50.

Advances in Electron Transfer Chemistry, Vol. 6

Patrick S. Mariano, Ed. JAI Press: Stamford, CT, 1999. x + 171 pp. ISBN 0-7623-0213-5. 109.50.

Automating Science and Engineering Laboratories with Visual Basic

Mark F. Russo and Martin M. Echols. Wiley-Interscience Series on Laboratory Automation. Wiley-Interscience: New York, 1999. xx + 355 pp. ISBN 0-471-25493-2. 49.95.

Plantwide Process Control

Kelvin T. Erickson and John L. Hedrick. Wiley Series in Chemical Engineering. Wiley-Interscience: New York, 1999. xii + 547 pp. ISBN 0-471-17835-7. 89.95.

Heme Peroxidases

H. Brian Dunford. Wiley-VCH: New York, 1999. xiii + 507 pp. ISBN 0-471-24244-6. 195.00.

Industrial Ecology: Environmental Chemistry and Hazardous Wastes

Stanley E. Manahan. Lewis: Boca Raton, FL, 1999. 318 pp. ISBN 1-56670-381-6. 69.95.

Reviews in Computational Chemistry, Vol. 13

Kenny B. Lipkowitz and Donald B. Boyd. Wiley-VCH: New York, 1999. xxxiii + 426 pp. ISBN 0-471-33135-x. 135.00.

Surfaces, Interfaces, and Colloids: Principles and Applications, 2nd edition

Drew Myers. Wiley-VCH: New York, 1999. xx + 501 pp. ISBN 0-471-33060-4. 94.95.

Onium Ions

George A. Olah, Kenneth K. Laali, Qi Wang, and G. K. Surya Prakash. Wiley-Interscience: New York, 1998. xv + 509 pp. ISBN 0-471-14877-6. 110.00.

Environmental Soil and Water Chemistry: Principles and Applications V. P. Evangelou. Wiley-Interscience: New York, 1998. xix + 564 pp. ISBN 0-471-16515-8. 79.95.

1001 Chemicals in Everyday Products, 2nd edition

Grace Ross Lewis. Wiley-Interscience: New York, 1999. x + 388 pp. ISBN 0-471-29212-5. 39.95.

Organic Coatings: Science and Technology, 2nd edition

Zeno W. Wicks Jr., Frank N. Jones, and S. Peter Pappas. Wiley-Interscience: New York, 1999. xxi + 630 pp. ISBN 0-471-24507-0. 125.00.

Progress in Inorganic Chemistry, Vol. 48

Kenneth D. Karlin, Ed. Wiley-Interscience: New York, 1999. vi + 603 pp. ISBN 0-471-32623-2. 145.00.

Occupational Biomechanics, 3rd edition

Don B. Chaffin, Gunnar B. Andersson, and Bernard J. Martin. Wiley-Interscience: New York, 1999. xvii + 579 pp. ISBN 0-471-24697-2. 69.95.

Advances in Photochemistry, Vol. 25

Douglas C. Neckers, David H. Volman, and Gunther Von Bünau. Wiley-Interscience: New York, 1999. xi + 238 pp. ISBN 0-471-32708-5. 110.00.

Distillation

Johann G. Stichlmair and James R. Fair. Wiley-VCH: New York, 1998. xiii + 524 pp. ISBN 0-471-25241-7. 94.95.

Ammonia - Principles and Industrial Practice

Maz Appl. Wiley-VCH: New York, 1999. ix + 301 pp. ISBN 3-527-29593-3. 160.00.

Precursor-Derived Ceramics: Synthesis, Structure, and High-Temperature Mechanical Properties

Fritz Aldinger, Fumihiro Wakai, and Joachim Bill, Eds. Wiley-VCH: New York, 1999. xv + 298 pp. ISBN 3-527-29814-2. 180.00.

Advances in Sonochemisty, Vol. 5

Timothy J. Mason. JAI Press: Stamford, CT, 1999. xi + 311 pp. ISBN 0-7623-0331-x. 109.50.

Fluid Metals: The Liquid-Vapor Transition of Metals

Friedrich Hensel and William W. Warren Jr. Princeton University Press: Princeton, NJ. 1999. xvii + 243 pp. ISBN 0-691-05830-x. 69.50.

Direct Phasing in Crystallography: Fundamentals and Applications

Carmelo Giacovazzo. Oxford University Press: New York, 1999. xxiii + 767 pp. ISBN 0-19-850072-6. 140.00.

Practical Environmental Analysis

M. Radojevic and V. N. Bashkin. Royal Society of Chemistry: Cambridge, UK. 1999. xx + 466 pp. ISBN 0-85404-594-5. £32.00.

Advances in Dendritic Macromolecules, Vol. 4 George R. Newkome, Ed. JAI Press: Stamford, CT, 1999. x + 207 pp. ISBN 0-7623-0347-6. 109.50.

Advances in Quantitative Structure-Property Relationships, Vol. 2

Marvin Charton. JAI Press: Stamford, CT, 1999. ix + 257 pp. ISBN 0-7623-0067-1. 109.50.

Pesticide Residues in Foods: Methods, Techniques, and Regulations

W. George Fong, H. Anson Moye, James N. Seiber, and John P. Toth. Chemical Analysis, Vol. 151.Wiley-Interscience: New York, 1999. xiv + 358 pp. ISBN 0-471-57400-7. $84.95.

A novel approach to multiple sequence alignment using hadoop data grids.

PubMed

Sudha Sadasivam, G; Baktavatchalam, G

2010-01-01

Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences.

Fabrication of high temperature superconductors

DOEpatents

Balachandran, Uthamalingam; Dorris, Stephen E.; Ma, Beihai; Li, Meiya

2003-06-17

A method of forming a biaxially aligned superconductor on a non-biaxially aligned substrate substantially chemically inert to the biaxially aligned superconductor comprising is disclosed. A non-biaxially aligned substrate chemically inert to the superconductor is provided and a biaxially aligned superconductor material is deposited directly on the non-biaxially aligned substrate. A method forming a plume of superconductor material and contacting the plume and the non-biaxially aligned substrate at an angle greater than 0.degree. and less than 90.degree. to deposit a biaxially aligned superconductor on the non-biaxially aligned substrate is also disclosed. Various superconductors and substrates are illustrated.

Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

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

Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G.

2015-11-01

Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangularmore » AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.« less

Unified Alignment of Protein-Protein Interaction Networks.

PubMed

Malod-Dognin, Noël; Ban, Kristina; Pržulj, Nataša

2017-04-19

Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others.

Accelerating large-scale protein structure alignments with graphics processing units

PubMed Central

2012-01-01

Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs). As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU. PMID:22357132

AlignMe—a membrane protein sequence alignment web server

PubMed Central

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement

NASA Astrophysics Data System (ADS)

Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.

2016-03-01

Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

MaxAlign: maximizing usable data in an alignment.

PubMed

Gouveia-Oliveira, Rodrigo; Sackett, Peter W; Pedersen, Anders G

2007-08-28

The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand-alone package.

Alignment methods: strategies, challenges, benchmarking, and comparative overview.

PubMed

Löytynoja, Ari

2012-01-01

Comparative evolutionary analyses of molecular sequences are solely based on the identities and differences detected between homologous characters. Errors in this homology statement, that is errors in the alignment of the sequences, are likely to lead to errors in the downstream analyses. Sequence alignment and phylogenetic inference are tightly connected and many popular alignment programs use the phylogeny to divide the alignment problem into smaller tasks. They then neglect the phylogenetic tree, however, and produce alignments that are not evolutionarily meaningful. The use of phylogeny-aware methods reduces the error but the resulting alignments, with evolutionarily correct representation of homology, can challenge the existing practices and methods for viewing and visualising the sequences. The inter-dependency of alignment and phylogeny can be resolved by joint estimation of the two; methods based on statistical models allow for inferring the alignment parameters from the data and correctly take into account the uncertainty of the solution but remain computationally challenging. Widely used alignment methods are based on heuristic algorithms and unlikely to find globally optimal solutions. The whole concept of one correct alignment for the sequences is questionable, however, as there typically exist vast numbers of alternative, roughly equally good alignments that should also be considered. This uncertainty is hidden by many popular alignment programs and is rarely correctly taken into account in the downstream analyses. The quest for finding and improving the alignment solution is complicated by the lack of suitable measures of alignment goodness. The difficulty of comparing alternative solutions also affects benchmarks of alignment methods and the results strongly depend on the measure used. As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended.

System and method for 2D workpiece alignment

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

Weaver, William T.; Carlson, Charles T.; Smith, Scott A.

2015-07-14

A carrier capable of holding one or more workpieces is disclosed. The carrier includes movable projections located along the sides of each cell in the carrier. This carrier, in conjunction with a separate alignment apparatus, aligns each workpiece within its respective cell against several alignment pins, using a multiple step alignment process to guarantee proper positioning of the workpiece in the cell. First, the workpieces are moved toward one side of the cell. Once the workpieces have been aligned against this side, the workpieces are then moved toward an adjacent orthogonal side such that the workpieces are aligned to twomore » sides of the cell. Once aligned, the workpiece is held in place by the projections located along each side of each cell. In addition, the alignment pins are also used to align the associated mask, thereby guaranteeing that the mask is properly aligned to the workpiece.« less

The power of change: interpersonal attraction as a function of attitude similarity and attitude alignment.

PubMed

Reid, Chelsea A; Davis, Jody L; Green, Jeffrey D

2013-01-01

Does attitude alignment predict attraction? Would you like a stranger more who shifts her/his attitudes to more closely align with yours? In pairs, participants (N = 77) discussed social issues about which they disagreed and received false feedback on whether the partner engaged in attitude alignment (shifted her/his attitudes toward the participant's attitude) following discussion. Participants also received false feedback about the proportion of similarity to the partner on a set of issues (i.e., 25%, 50%, or 75%). Participants reported greater attraction to partners who engaged in attitude alignment and who were more similar. Moreover, similarity and attitude alignment interacted. Similarity predicted attraction when attitude alignment did not occur, but did not predict attraction when attitude alignment did occur. Finally, partner attitude alignment led to participant attitude alignment, and perceived reasoning ability mediated the attitude alignment-attraction relationship.

Aligned Single Wall Carbon Nanotube Polymer Composites Using an Electric Field

NASA Technical Reports Server (NTRS)

Park, Cheol; Wiklinson, John; Banda, Sumanth; Ounaies, Zoubeida; Wise, Kristopher E.; Sauti, Godfrey; Lillehei, Peter T.; Harrison, Joycelyn S.

2005-01-01

While high shear alignment has been shown to improve the mechanical properties of single wall carbon nanotubes (SWNT)-polymer composites, it is difficult to control and often results in degradation of the electrical and dielectric properties of the composite. Here, we report a novel method to actively align SWNTs in a polymer matrix, which allows for control over the degree of alignment of SWNTs without the side effects of shear alignment. In this process, SWNTs are aligned via field-induced dipolar interactions among the nanotubes under an AC electric field in a liquid matrix followed by immobilization by photopolymerization while maintaining the electric field. Alignment of SWNTs was controlled as a function of magnitude, frequency, and application time of the applied electric field. The degree of SWNT alignment was assessed using optical microscopy and polarized Raman spectroscopy and the morphology of the aligned nanocomposites was investigated by high resolution scanning electron microscopy. The structure of the field induced aligned SWNTs is intrinsically different from that of shear aligned SWNTs. In the present work, SWNTs are not only aligned along the field, but also migrate laterally to form thick, aligned SWNT percolative columns between the electrodes. The actively aligned SWNTs amplify the electrical and dielectric properties in addition to improving the mechanical properties of the composite. All of these properties of the aligned nanocomposites exhibited anisotropic characteristics, which were controllable by tuning the applied field conditions.

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

PubMed

Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan; Brent, Michael R

2009-07-01

The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

Image-based quantification of fiber alignment within electrospun tissue engineering scaffolds is related to mechanical anisotropy.

PubMed

Fee, Timothy; Downs, Crawford; Eberhardt, Alan; Zhou, Yong; Berry, Joel

2016-07-01

It is well documented that electrospun tissue engineering scaffolds can be fabricated with variable degrees of fiber alignment to produce scaffolds with anisotropic mechanical properties. Several attempts have been made to quantify the degree of fiber alignment within an electrospun scaffold using image-based methods. However, these methods are limited by the inability to produce a quantitative measure of alignment that can be used to make comparisons across publications. Therefore, we have developed a new approach to quantifying the alignment present within a scaffold from scanning electron microscopic (SEM) images. The alignment is determined by using the Sobel approximation of the image gradient to determine the distribution of gradient angles with an image. This data was fit to a Von Mises distribution to find the dispersion parameter κ, which was used as a quantitative measure of fiber alignment. We fabricated four groups of electrospun polycaprolactone (PCL) + Gelatin scaffolds with alignments ranging from κ = 1.9 (aligned) to κ = 0.25 (random) and tested our alignment quantification method on these scaffolds. It was found that our alignment quantification method could distinguish between scaffolds of different alignments more accurately than two other published methods. Additionally, the alignment parameter κ was found to be a good predictor the mechanical anisotropy of our electrospun scaffolds. The ability to quantify fiber alignment within and make direct comparisons of scaffold fiber alignment across publications can reduce ambiguity between published results where cells are cultured on "highly aligned" fibrous scaffolds. This could have important implications for characterizing mechanics and cellular behavior on aligned tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1680-1686, 2016. © 2016 Wiley Periodicals, Inc.

Aligning for accountable care: Strategic practices for change in accountable care organizations.

PubMed

Hilligoss, Brian; Song, Paula H; McAlearney, Ann Scheck

Alignment within accountable care organizations (ACOs) is crucial if these new entities are to achieve their lofty goals. However, the concept of alignment remains underexamined, and we know little about the work entailed in creating alignment. The aim of this study was to develop the concept of aligning by identifying and describing the strategic practices administrators use to align the structures, processes, and behaviors of their organizations and individual providers in pursuit of accountable care. We conducted 2-year qualitative case studies of four ACOs that have assumed full risk for the costs and quality of care for defined populations. Five strategic aligning practices were used by all four ACOs. Informing both aligns providers' understandings with the goals and value proposition of the ACO and aligns the providers' attention with the drivers of performance. Involving both aligns ACO leaders' understandings with the realities facing providers and aligns the policies of the ACO with the needs of providers. Enhancing both aligns the operations of individual provider practices with the operations of the ACO and aligns the trust of providers with the ACO. Motivating aligns what providers value with the goals of the ACO. Finally, evolving is a metapractice of learning and adapting that guides the execution of the other four practices. Our findings suggest that there are second-order cognitive (e.g., understandings and attention) and cultural (e.g., trust and values) levels of alignment, as well as a first-order operational level (organizational structures, processes, and incentives). A well-aligned organization may require ongoing repositioning at each of these levels, as well as attention to both cooperative and coordinative dimensions of alignment. Implications for research and practice are discussed.

Using structure to explore the sequence alignment space of remote homologs.

PubMed

Kuziemko, Andrew; Honig, Barry; Petrey, Donald

2011-10-01

Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

Partial slip effect on non-aligned stagnation point nanofluid over a stretching convective surface

NASA Astrophysics Data System (ADS)

Nadeem, S.; Rashid, Mehmood; Noreen Sher, Akbar

2015-01-01

The present study inspects the non-aligned stagnation point nano fluid over a convective surface in the presence of partial slip.Two types of base fluids namely water and kerosene are selected with Cu nanoparticles. The governing physical problem is presented and transformed into a system of coupled nonlinear differential equations using suitable similarity transformations. These equations are then solved numerically using midpoint integration scheme along with Richardson extrapolation via Maple. Impact of relevant physical parameters on the dimensionless velocity and temperature profiles are portrayed through graphs. Physical quantities such as local skin frictions co-efficient and Nusselt numbers are tabularized. It is detected from numerical computations that kerosene-based nano fluids have better heat transfer capability compared with water-based nanofluids. Moreover it is found that water-based nanofluids offer less resistance in terms of skin friction than kerosene-based fluid. In order to authenticate our present study, the calculated results are compared with the prevailing literature and a considerable agreement is perceived for the limiting case.

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.

Cyclic mechanical stretch contributes to network development of osteocyte-like cells with morphological change and autophagy promotion but without preferential cell alignment in rat.

PubMed

Inaba, Nao; Kuroshima, Shinichiro; Uto, Yusuke; Sasaki, Muneteru; Sawase, Takashi

2017-09-01

Osteocytes play important roles in controlling bone quality as well as preferential alignment of biological apatite c -axis/collagen fibers. However, the relationship between osteocytes and mechanical stress remains unclear due to the difficulty of three-dimensional (3D) culture of osteocytes in vitro . The aim of this study was to investigate the effect of cyclic mechanical stretch on 3D-cultured osteocyte-like cells. Osteocyte-like cells were established using rat calvarial osteoblasts cultured in a 3D culture system. Cyclic mechanical stretch (8% amplitude at a rate of 2 cycles min -1 ) was applied for 24, 48 and 96 consecutive hours. Morphology, cell number and preferential cell alignment were evaluated. Apoptosis- and autophagy-related gene expression levels were measured using quantitative PCR. 3D-cultured osteoblasts became osteocyte-like cells that expressed osteocyte-specific genes such as Dmp1 , Cx43 , Sost , Fgf23 and RANKL , with morphological changes similar to osteocytes. Cell number was significantly decreased in a time-dependent manner under non-loaded conditions, whereas cyclic mechanical stretch significantly prevented decreased cell numbers with increased expression of anti-apoptosis-related genes. Moreover, cyclic mechanical stretch significantly decreased cell size and ellipticity with increased expression of autophagy-related genes, LC3b and atg7 . Interestingly, preferential cell alignment did not occur, irrespective of mechanical stretch. These findings suggest that an anti-apoptotic effect contributes to network development of osteocyte-like cells under loaded condition. Spherical change of osteocyte-like cells induced by mechanical stretch may be associated with autophagy upregulation. Preferential alignment of osteocytes induced by mechanical load in vivo may be partially predetermined before osteoblasts differentiate into osteocytes and embed into bone matrix.

Computational analysis of electrical conduction in hybrid nanomaterials with embedded non-penetrating conductive particles

NASA Astrophysics Data System (ADS)

Cai, Jizhe; Naraghi, Mohammad

2016-08-01

In this work, a comprehensive multi-resolution two-dimensional (2D) resistor network model is proposed to analyze the electrical conductivity of hybrid nanomaterials made of insulating matrix with conductive particles such as CNT reinforced nanocomposites and thick film resistors. Unlike existing approaches, our model takes into account the impenetrability of the particles and their random placement within the matrix. Moreover, our model presents a detailed description of intra-particle conductivity via finite element analysis, which to the authors’ best knowledge has not been addressed before. The inter-particle conductivity is assumed to be primarily due to electron tunneling. The model is then used to predict the electrical conductivity of electrospun carbon nanofibers as a function of microstructural parameters such as turbostratic domain alignment and aspect ratio. To simulate the microstructure of single CNF, randomly positioned nucleation sites were seeded and grown as turbostratic particles with anisotropic growth rates. Particle growth was in steps and growth of each particle in each direction was stopped upon contact with other particles. The study points to the significant contribution of both intra-particle and inter-particle conductivity to the overall conductivity of hybrid composites. Influence of particle alignment and anisotropic growth rate ratio on electrical conductivity is also discussed. The results show that partial alignment in contrast to complete alignment can result in maximum electrical conductivity of whole CNF. High degrees of alignment can adversely affect conductivity by lowering the probability of the formation of a conductive path. The results demonstrate approaches to enhance electrical conductivity of hybrid materials through controlling their microstructure which is applicable not only to carbon nanofibers, but also many other types of hybrid composites such as thick film resistors.

Intrinsic alignments of galaxies in the EAGLE and cosmo-OWLS simulations

NASA Astrophysics Data System (ADS)

Velliscig, Marco; Cacciato, Marcello; Schaye, Joop; Hoekstra, Henk; Bower, Richard G.; Crain, Robert A.; van Daalen, Marcel P.; Furlong, Michelle; McCarthy, I. G.; Schaller, Matthieu; Theuns, Tom

2015-12-01

We report results for the alignments of galaxies in the EAGLE and cosmo-OWLS hydrodynamical cosmological simulations as a function of galaxy separation (-1 ≤ log10(r/[ h-1 Mpc]) ≤ 2) and halo mass (10.7 ≤ log10(M200/[h-1 M⊙]) ≤ 15). We focus on two classes of alignments: the orientations of galaxies with respect to either the directions to, or the orientations of, surrounding galaxies. We find that the strength of the alignment is a strongly decreasing function of the distance between galaxies. For galaxies hosted by the most massive haloes in our simulations the alignment can remain significant up to ˜100 Mpc. Galaxies hosted by more massive haloes show stronger alignment. At a fixed halo mass, more aspherical or prolate galaxies exhibit stronger alignments. The spatial distribution of satellites is anisotropic and significantly aligned with the major axis of the main host halo. The major axes of satellite galaxies, when all stars are considered, are preferentially aligned towards the centre of the main host halo. The predicted projected direction-orientation alignment, ɛg+(rp), is in broad agreement with recent observations. We find that the orientation-orientation alignment is weaker than the orientation-direction alignment on all scales. Overall, the strength of galaxy alignments depends strongly on the subset of stars that are used to measure the orientations of galaxies and it is always weaker than the alignment of dark matter haloes. Thus, alignment models that use halo orientation as a direct proxy for galaxy orientation overestimate the impact of intrinsic galaxy alignments.

Connecting Interface Structure to Energy Level Alignment at Aqueous Semiconductor Interfaces

NASA Astrophysics Data System (ADS)

Hybertsen, Mark

Understanding structure-function relationships at aqueous semiconductor interfaces presents fundamental challenges, including the discovery of the key interface structure motifs themselves. Important examples include the alignment of electrochemical redox levels with the semiconductor band edges and the identification of catalytic active sites. We have developed a multistep approach, initially demonstrated for GaN, ZnO and their alloys, motivated by measured high efficiency for photocatalytic water oxidation. The interface structure is simulated using ab initio molecular dynamics (AIMD). The calculated, average interface dipole is combined with the GW approach from many-body perturbation theory to calculate the energy level alignment between the semiconductor band edges and the centroid of the occupied 1b1 energy level of water and thus, the electrochemical levels. Cluster models are used to study reaction pathways. The emergent interface motif is the full (GaN) or partial (ZnO) dissociated interface water layer. Here I will focus on the aqueous interfaces to the stable TiO2 anatase (101) and rutile (110) facets. The AIMD calculations reveal interface water dissociation and reassociation processes through distinct pathways: one direct at the interface and the other via a spectator water molecule from the hydration layer. Comparisons between the two interfaces shows that the energy landscape for these pathways depends on the local hydrogen bonding patterns and the interplay with the interface template. Combined results from different initial conditions and AIMD temperatures demonstrate a partially dissociated interface water layer in both cases. Specifically for rutile, structure and the GW-based analysis of the interface energy level alignment agree with experiment. Finally, hole localization at different interface structure motifs will be discussed. Work performed in collaboration with J. Lyons, N. Kharche, M. Ertem and J. Muckerman, done in part at the CFN, which is a U.S. DOE Office of Science Facility, at BNL under Contract No. DE-SC0012704 and with resources from NERSC under Contract No. DE-AC02-05CH11231.

Alignment method for parabolic trough solar concentrators

DOEpatents

Diver, Richard B [Albuquerque, NM

2010-02-23

A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

Anisotropic thermal conductive MWCNT/polymer composites prepared with an immiscible PS/LDPE blend.

PubMed

Kwon, Younghwan

2014-08-01

This study focuses on MWCNT/polymer composites with flexible, anisotropic heat transporting properties. For this study, an immiscible polymer blend of MWCNT/PS and LDPE (13.5:86.5 v:v) were used as a template. MWCNT/PS composites were first prepared by a solution process, and then melt-blended with LDPE using a brabender mixer. For achieving an alignment of MWCNT/PS in LDPE matrix, the blends of MWCNT/PS and LDPE were continuously treated under a fixed shear rate of 10 s(-1) at 210 °C. With partial extraction of PS in the aligned blends, FE-SEM images of the aligned blends revealed morphology of MWCNT in the PS/LDPE matrix, indicating local distribution of MWCNT selectively inside PS, where PS was elongated parallel to shear direction in LDPE matrix. The prepared MWCNT/PS and LDPE blends showed an anisotropic heat transporting behavior with anisotropic ratio of thermal conductivity (AR = λx/λz) up to 1.330 at 10 wt% of MWCNT in PS (equivalent to 1.50 wt% of MWCNT in PS/LDPE).

The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences.

PubMed

Fourment, Mathieu; Gibbs, Mark J

2008-02-05

Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically.

Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation.

PubMed

Sharma, Virag; Hiller, Michael

2017-08-21

Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0.75 substitutions per neutral site, like human and other non-placental vertebrates, benefit from increased sensitivity. To systematically test if increased sensitivity improves comparative gene annotations, we built a multiple alignment of 144 vertebrate genomes and used this alignment to map human genes to the other 143 vertebrates with CESAR. We found that higher alignment sensitivity substantially improves the completeness of comparative gene annotations by adding on average 2382 and 7440 novel exons and 117 and 317 novel genes for mammalian and non-mammalian species, respectively. Our results suggest a more sensitive alignment strategy that should generally be used for genome alignments between distantly-related species. Our 144-vertebrate genome alignment and the comparative gene annotations (https://bds.mpi-cbg.de/hillerlab/144VertebrateAlignment_CESAR/) are a valuable resource for comparative genomics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks.

PubMed

Hashemifar, Somaye; Xu, Jinbo

2014-09-01

High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene

PubMed Central

2017-01-01

The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data. We use a taxonomic gold standard to compare the accuracy of alignment-free phylogenetic inference with that of common microbiome-wide phylogenetic inference pipelines based on PyNAST and MUSCLE alignments with FastTree and RAxML. We re-simulate fecal communities from Human Microbiome Project data to evaluate the performance of the methods on datasets with properties of real data. Our comparisons show that alignment-free methods are not inferior to alignment-based methods in giving accurate and robust phylogenic trees. Moreover, consensus ensembles of alignment-free phylogenies are superior to those built from alignment-based methods in their ability to highlight community differences in low power settings. In addition, the overall running times of alignment-based and alignment-free phylogenetic inference are comparable. Taken together our empirical results suggest that alignment-free methods provide a viable approach for microbiome-wide phylogenetic inference. PMID:29136663

Constraints on Martian Aerosol Particles Using MGS/TES and HST Data: Shapes

NASA Astrophysics Data System (ADS)

Wolff, M. J.; Clancy, R. T.; Pitman, K. M.; Bell, J. F.; James, P. B.

2001-12-01

In order to constrain the shape of water ice and dust aerosols, we have combined a numerical approach for axisymmetric particle shapes, i.e., cylinders, disks, spheroids (Waterman's T-Matrix approach as improved by Mishchenko and collaborators; cf., Mishchenko et al. 1997, JGR, 102, D14, 16,831), with a multiple-scattering radiative transfer algorithm. We utilize a two-stage iterative process. First, we empirically derive a scattering phase function for each aerosol component from radiative transfer models of Mars Global Surveyor Thermal Emission Spectrometer Emission Phase Function (EPF) sequences. Next, we perform a series of scattering calculations, adjusting our parameters to arrive at a ``best-fit'' theoretical phase function. It is important to note that in addition to randomly-oriented particles, we explicitly consider the possibility of (partially) aligned aerosol particles as well. Thus far, we have been analyzing the three empirically-derived presented by Clancy et al. (this meeting): dust, Type I ice particles (effective radii ~ 1-2 microns), and Type II ice particles (effective radii ~ 3-4 microns). We find that the ``dust'' phase function is best fit by randomly-oriented cylinders with an axial ratio (D/L = diameter-to-length) of either 2.3 or 0.6. Similarly, the shape of the Type II ice curve is reasonably reproduced by randomly-oriented spheroids with an axial ratio of either 0.7 or 1.4. However, neither of the two shapes (nor that of spheres or randomly-oriented hexagonal prisms) can reproduce the phase function derived for the Type I ice. This led to the direct consideration of oriented or aligned particles. which, at least qualitatively, have the ability to account for the phase function shapes for both Type I and II ice particles. The difference between these two phase functions may represent the degree of alignment, with the Type II particles being much less-aligned. The calculations for partially aligned particles is quite numerically intensive and this avenue of research is currently in progress. Additional work is also being done to further constrain the dust aerosol properties using both TES visible/IR and Hubble Space Telescope UV-NIR spectroscopy/imaging data of the recent (and ongoing) Martian global dust storm. Our work has been supported through NASA (MDAP) grant NAG5-9820, (MED) JPL contract 961471, STScI GO programs #8577 and #9052.

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

Health care's new game changer. Thinking like a health plan.

PubMed

Eggbeer, Bill; Bowers, Krista

2014-10-01

The transition for hospitals from having only a provider's perspective to thinking more like a health plan will require strategic alignment on four fronts: Health plan alignment. Hospital and physician alignment. Leadership alignment. Organizational alignment.

Iterative non-sequential protein structural alignment.

PubMed

Salem, Saeed; Zaki, Mohammed J; Bystroff, Christopher

2009-06-01

Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs.rpi.edu/~zaki/software/SNAP.

Electric-field-induced flow-aligning state in a nematic liquid crystal.

PubMed

Fatriansyah, Jaka Fajar; Orihara, Hiroshi

2015-04-01

The response of shear stress to a weak ac electric field as a probe is measured in a nematic liquid crystal under shear flow and dc electric fields. Two states with different responses are clearly observed when the dc electric field is changed at a constant shear rate: the flow aligning and non-flow aligning states. The director lies in the shear plane in the flow aligning state and out of the plane in the non-flow aligning state. Through application of dc electric field, the non-flow aligning state can be changed to the flow aligning state. In the transition from the flow aligning state to the non-flow aligning state, it is found that the response increases and the relaxation time becomes longer. Here, the experimental results in the flow aligning state are discussed on the basis of the Ericksen-Leslie theory.

A similarity measure for partially folded proteins: application to unfolded and native-like conformational fluctuations

NASA Astrophysics Data System (ADS)

Larios, Edgar; Yang, Wei Y.; Schulten, K.; Gruebele, M.

2004-12-01

Computing the root-mean-square deviation (RMSD) of a partially folded protein structure from the folded state requires the two structures to be translationally and rotationally aligned. We examine the constraint matrix L that preserves orthogonality of the rotation matrix during minimization of the RMSD. L is proportional to the sensitivity of the RMSD to the rotational alignment matrix. Its trace yields an isotropic reaction coordinate, while its off-diagonal matrix elements are related to the moment of inertia derivative tensor that encodes anisotropic information about the structure. We use L to compare λ-repressor fragment 6-85 (λ 6-85) to several partially folded structures obtained from molecular dynamics simulation (MD), and find that L as a reaction coordinate indeed encodes some information about protein topology. We also apply C α RMSD, L and tryptophan sidechain mobility as criteria for native state structural fluctuations of several λ 6-85 mutants. The mutants' denaturation curves and fluorescence quenching are measured experimentally for comparison. The results are in accord with a recent proposal that structural fluctuations near the chromophore can induce increased native state fluorescence or hyperfluorescence during unfolding of proteins.

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

PubMed

Zheng, Qi; Grice, Elizabeth A

2016-10-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

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

Alignment of the femoral component in a mobile-bearing unicompartmental knee arthroplasty: a study in 10 cadaver femora.

PubMed

Kort, N P; van Raay, J J A M; Thomassen, B J W

2007-08-01

Use of an intramedullary rod is advised for the alignment of the femoral component of an Oxford phase-III prosthesis. There are users moving toward extramedullary alignment, which is merely an indicator of frustration with accuracy of intramedullary alignment. The results of our study with 10 cadaver femora demonstrate that use of a short and long intramedullary femoral rod may result in excessive flexion alignment error of the femoral component. Understanding of the extramedullary alignment possibility and experience with the visual alignment of the femoral drill guide is essential toward minimizing potential errors in the alignment of the femoral component.

Desktop aligner for fabrication of multilayer microfluidic devices.

PubMed

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-07-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm(-1). To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices.

Desktop aligner for fabrication of multilayer microfluidic devices

PubMed Central

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-01-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm−1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices. PMID:26233409

Iterative refinement of structure-based sequence alignments by Seed Extension

PubMed Central

Kim, Changhoon; Tai, Chin-Hsien; Lee, Byungkook

2009-01-01

Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available, but current structure-based sequence alignment procedures still mis-align substantial numbers of residues. In order to correct such errors, we previously explored the possibility of replacing the residue-based dynamic programming algorithm in structure alignment procedures with the Seed Extension algorithm, which does not use a gap penalty. Here, we describe a new procedure called RSE (Refinement with Seed Extension) that iteratively refines a structure-based sequence alignment. Results RSE uses SE (Seed Extension) in its core, which is an algorithm that we reported recently for obtaining a sequence alignment from two superimposed structures. The RSE procedure was evaluated by comparing the correctly aligned fractions of residues before and after the refinement of the structure-based sequence alignments produced by popular programs. CE, DaliLite, FAST, LOCK2, MATRAS, MATT, TM-align, SHEBA and VAST were included in this analysis and the NCBI's CDD root node set was used as the reference alignments. RSE improved the average accuracy of sequence alignments for all programs tested when no shift error was allowed. The amount of improvement varied depending on the program. The average improvements were small for DaliLite and MATRAS but about 5% for CE and VAST. More substantial improvements have been seen in many individual cases. The additional computation times required for the refinements were negligible compared to the times taken by the structure alignment programs. Conclusion RSE is a computationally inexpensive way of improving the accuracy of a structure-based sequence alignment. It can be used as a standalone procedure following a regular structure-based sequence alignment or to replace the traditional iterative refinement procedures based on residue-level dynamic programming algorithm in many structure alignment programs. PMID:19589133

Torsional stress impedance and magneto-impedance in (Co0.95Fe0.05)72.5 Si12.5B15 amorphous wire with helical induced anisotropy

NASA Astrophysics Data System (ADS)

Blanco, J. M.; Zhukov, A. P.; González, J.

1999-12-01

The magneto-impedance effect icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/ZH = [Z(H)-Z(Hmax)]/Z(Hmax) has been measured in (Fe0.95Co0.05)72.5B15Si12.5 wire under torsion stress, icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/> (torsion angle per unit length) with axial magnetic field (H) as parameter. Without stress (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)H(H) dependence has a non-monotonous shape with first an increase of total impedance Z and then a decrease, i.e. shows a maximum at certain axial magnetic field Hm. It was found that the torsion stress dependence of electrical impedance (torsion impedance), (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> = [Z(icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/>)-Z(icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/>max)]/Z(icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/>max), has asymmetric character with a clear maximum at torsion angle, icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/> around 7icons/Journals/Common/pi" ALT="pi" ALIGN="TOP"/> rad m-1 in as-cast wire, while (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> reaches a maximum around 170%. Thermal treatments under torsion stress (without and with a previous annealing stage) develop a helical anisotropy on the amorphous wire, which drastically modifies the (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> response. Such treatments were carried out by using current annealing which resulted in a drastic increase of the maximum (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> up to 225%, and a change of torsion dependence of icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z with a tendency to a finally symmetric dependence of (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/>(icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/>). The maximum (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> ratio, (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/> m, was obtained under torsion stress of icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/> = 20icons/Journals/Common/pi" ALT="pi" ALIGN="TOP"/> rad m-1 (in a torsion annealed sample) and = 11 rad m-1 (with pre-annealing and torsion annealing). Observed dependences were explained taking into account the frozen-in magneto-elastic anisotropy owing to the internal stress distribution during the fabrication process, the helical anisotropies induced by the torsion strain and that developed by thermal treatment under torsion stress (torsion annealing). The differences in the shape and intensity of the maximum ( Z/Z) m between the torsion annealed and pre-annealed and torsion annealed samples should be ascribed to the visco-elastic character of the helical anisotropy induced by torsion stress.

Reverse alignment "mirror image" visualization as a laparoscopic training tool improves task performance.

PubMed

Dunnican, Ward J; Singh, T Paul; Ata, Ashar; Bendana, Emma E; Conlee, Thomas D; Dolce, Charles J; Ramakrishnan, Rakesh

2010-06-01

Reverse alignment (mirror image) visualization is a disconcerting situation occasionally faced during laparoscopic operations. This occurs when the camera faces back at the surgeon in the opposite direction from which the surgeon's body and instruments are facing. Most surgeons will attempt to optimize trocar and camera placement to avoid this situation. The authors' objective was to determine whether the intentional use of reverse alignment visualization during laparoscopic training would improve performance. A standard box trainer was configured for reverse alignment, and 34 medical students and junior surgical residents were randomized to train with either forward alignment (DIRECT) or reverse alignment (MIRROR) visualization. Enrollees were tested on both modalities before and after a 4-week structured training program specific to their modality. Student's t test was used to determine differences in task performance between the 2 groups. Twenty-one participants completed the study (10 DIRECT, 11 MIRROR). There were no significant differences in performance time between DIRECT or MIRROR participants during forward or reverse alignment initial testing. At final testing, DIRECT participants had improved times only in forward alignment performance; they demonstrated no significant improvement in reverse alignment performance. MIRROR participants had significant time improvement in both forward and reverse alignment performance at final testing. Reverse alignment imaging for laparoscopic training improves task performance for both reverse alignment and forward alignment tasks. This may be translated into improved performance in the operating room when faced with reverse alignment situations. Minimal lab training can account for drastic adaptation to this environment.

Sensory Subtypes in Preschool Aged Children with Autism Spectrum Disorder.

PubMed

Tomchek, Scott D; Little, Lauren M; Myers, John; Dunn, Winnie

2018-06-01

Given the heterogeneity of autism spectrum disorder (ASD), research has investigated how sensory features elucidate subtypes that enhance our understanding of etiology and tailored treatment approaches. Previous studies, however, have not integrated core developmental behaviors with sensory features in investigations of subtypes in ASD. Therefore, we used latent profile analysis to examine subtypes in a preschool aged sample considering sensory processing patterns in combination with social-communication skill, motor performance, and adaptive behavior. Results showed four subtypes that differed by degree and quality of sensory features, age and differential presentation of developmental skills. Findings partially align with previous literature on sensory subtypes and extends our understanding of how sensory processing aligns with other developmental domains in young children with ASD.

Photoresist thin-film effects on alignment process capability

NASA Astrophysics Data System (ADS)

Flores, Gary E.; Flack, Warren W.

1993-08-01

Two photoresists were selected for alignment characterization based on their dissimilar coating properties and observed differences on alignment capability. The materials are Dynachem OFPR-800 and Shipley System 8. Both photoresists were examined on two challenging alignment levels in a submicron CMOS process, a nitride level and a planarized second level metal. An Ultratech Stepper model 1500 which features a darkfield alignment system with a broadband green light for alignment signal detection was used for this project. Initially, statistically designed linear screening experiments were performed to examine six process factors for each photoresist: viscosity, spin acceleration, spin speed, spin time, softbake time, and softbake temperature. Using the results derived from the screening experiments, a more thorough examination of the statistically significant process factors was performed. A full quadratic experimental design was conducted to examine viscosity, spin speed, and spin time coating properties on alignment. This included a characterization of both intra and inter wafer alignment control and alignment process capability. Insight to the different alignment behavior is analyzed in terms of photoresist material properties and the physical nature of the alignment detection system.

A Polar Initial Alignment Algorithm for Unmanned Underwater Vehicles

PubMed Central

Yan, Zheping; Wang, Lu; Wang, Tongda; Zhang, Honghan; Zhang, Xun; Liu, Xiangling

2017-01-01

Due to its highly autonomy, the strapdown inertial navigation system (SINS) is widely used in unmanned underwater vehicles (UUV) navigation. Initial alignment is crucial because the initial alignment results will be used as the initial SINS value, which might affect the subsequent SINS results. Due to the rapid convergence of Earth meridians, there is a calculation overflow in conventional initial alignment algorithms, making conventional initial algorithms are invalid for polar UUV navigation. To overcome these problems, a polar initial alignment algorithm for UUV is proposed in this paper, which consists of coarse and fine alignment algorithms. Based on the principle of the conical slow drift of gravity, the coarse alignment algorithm is derived under the grid frame. By choosing the velocity and attitude as the measurement, the fine alignment with the Kalman filter (KF) is derived under the grid frame. Simulation and experiment are realized among polar, conventional and transversal initial alignment algorithms for polar UUV navigation. Results demonstrate that the proposed polar initial alignment algorithm can complete the initial alignment of UUV in the polar region rapidly and accurately. PMID:29168735

Relation between film character and wafer alignment: critical alignment issues on HV device for VLSI manufacturing

NASA Astrophysics Data System (ADS)

Lo, Yi-Chuan; Lee, Chih-Hsiung; Lin, Hsun-Peng; Peng, Chiou-Shian

1998-06-01

Several continuous splits for wafer alignment target topography conditions to improve epitaxy film alignment were applied. The alignment evaluation among former layer pad oxide thickness (250 angstrom - 500 angstrom), drive oxide thickness (6000 angstrom - 10000 angstrom), nitride film thickness (600 angstrom - 1500 angstrom), initial oxide etch (fully wet etch, fully dry etch and dry plus wet etch) will be split to this experiment. Also various epitaxy deposition recipe such as: epitaxy source (SiHCl2 or SiCHCl3) and growth rate (1.3 micrometer/min approximately 2.0 micrometer/min) will be used to optimize the process window for alignment issue. All the reflectance signal and cross section photography of alignment target during NIKON stepper alignment process will be examined. Experimental results show epitaxy recipe plays an important role to wafer alignment. Low growth rate with good performance conformity epitaxy lead to alignment target avoid washout, pattern shift and distortion. All the results (signal monitor and film character) combined with NIKON's stepper standard laser scanning alignment system will be discussed in this paper.

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

PubMed

Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

2013-07-01

The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

How genome complexity can explain the difficulty of aligning reads to genomes.

PubMed

Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S

2015-01-01

Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes.

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework

PubMed Central

Zheng, Qi; Grice, Elizabeth A.

2016-01-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost’s algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost. PMID:27706155

Multiple DNA and protein sequence alignment on a workstation and a supercomputer.

PubMed

Tajima, K

1988-11-01

This paper describes a multiple alignment method using a workstation and supercomputer. The method is based on the alignment of a set of aligned sequences with the new sequence, and uses a recursive procedure of such alignment. The alignment is executed in a reasonable computation time on diverse levels from a workstation to a supercomputer, from the viewpoint of alignment results and computational speed by parallel processing. The application of the algorithm is illustrated by several examples of multiple alignment of 12 amino acid and DNA sequences of HIV (human immunodeficiency virus) env genes. Colour graphic programs on a workstation and parallel processing on a supercomputer are discussed.

Alignment system for SGII-Up laser facility

NASA Astrophysics Data System (ADS)

Gao, Yanqi; Cui, Yong; Li, Hong; Gong, Lei; Lin, Qiang; Liu, Daizhong; Zhu, Baoqiang; Ma, Weixin; Zhu, Jian; Lin, Zunqi

2018-03-01

The SGII-Up laser facility in Shanghai is one of the most important high-power laser facilities in China. It is designed to obtain 24 kJ (3ω) of energy with a square pulse of 3 ns using eight laser beams (two bundles). To satisfy the requirements for the safety, efficiency, and quality, an alignment system is developed for this facility. This alignment system can perform automatic alignment of the preamplifier system, main amplifier system, and harmonic conversion system within 30 min before every shot during the routine operation of the facility. In this article, an overview of the alignment system is first presented. Then, its alignment characteristics are discussed, along with the alignment process. Finally, experimental results, including the alignment results and the facility performance, are reported. The results show that the far-field beam pointing alignment accuracy is better than 3 μrad, and the alignment error of the near-field beam centering is no larger than 1 mm. These satisfy the design requirements very well.

Fine-tuning structural RNA alignments in the twilight zone.

PubMed

Bremges, Andreas; Schirmer, Stefanie; Giegerich, Robert

2010-04-30

A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

PubMed

Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

2012-09-01

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Modified alignment CGHs for aspheric surface test

NASA Astrophysics Data System (ADS)

Song, Jae-Bong; Yang, Ho-Soon; Rhee, Hyug-Gyo; Lee, Yun-Woo

2009-08-01

Computer Generated Holograms (CGH) for optical test are commonly consisted of one main pattern for testing aspheric surface and some alignment patterns for aligning the interferometer, CGH, and the test optics. To align the CGH plate and the test optics, we designed the alignment CGHs modified from the cat's eye alignment method, which are consisted of a couple of CGH patterns. The incident beam passed through the one part of the alignment CGH pattern is focused onto the one radius position of the test aspheric surface, and is reflected to the other part, and vice versa. This method has several merits compared to the conventional cat's eye alignment method. First, this method can be used in testing optics with a center hole, and the center part of CGH plate can be assigned to the alignment pattern. Second, the alignment pattern becomes a concentric circular arc pattern. The whole CGH patterns including the main pattern and alignment patterns are consisted of only concentric circular fringes. This concentric circular pattern can be easily made by the polar coordinated writer with circular scanning. The required diffraction angle becomes relatively small, so the 1st order diffraction beams instead of the 3rd order diffraction beam can be used as alignment beams, and the visibility can be improved. This alignment method also is more sensitive to the tilt and the lateral shift of the test aspheric surface. Using this alignment pattern, a 200 mm diameter F/0.5 aspheric mirror and a 600 mm diameter F/0.9 mirror were tested.

Effects of whole spine alignment patterns on neck responses in rear end impact.

PubMed

Sato, Fusako; Odani, Mamiko; Miyazaki, Yusuke; Yamazaki, Kunio; Östh, Jonas; Svensson, Mats

2017-02-17

The aim of this study was to investigate the whole spine alignment in automotive seated postures for both genders and the effects of the spinal alignment patterns on cervical vertebral motion in rear impact using a human finite element (FE) model. Image data for 8 female and 7 male subjects in a seated posture acquired by an upright open magnetic resonance imaging (MRI) system were utilized. Spinal alignment was determined from the centers of the vertebrae and average spinal alignment patterns for both genders were estimated by multidimensional scaling (MDS). An occupant FE model of female average size (162 cm, 62 kg; the AF 50 size model) was developed by scaling THUMS AF 05. The average spinal alignment pattern for females was implemented in the model, and model validation was made with respect to female volunteer sled test data from rear end impacts. Thereafter, the average spinal alignment pattern for males and representative spinal alignments for all subjects were implemented in the validated female model, and additional FE simulations of the sled test were conducted to investigate effects of spinal alignment patterns on cervical vertebral motion. The estimated average spinal alignment pattern was slight kyphotic, or almost straight cervical and less-kyphotic thoracic spine for the females and lordotic cervical and more pronounced kyphotic thoracic spine for the males. The AF 50 size model with the female average spinal alignment exhibited spine straightening from upper thoracic vertebra level and showed larger intervertebral angular displacements in the cervical spine than the one with the male average spinal alignment. The cervical spine alignment is continuous with the thoracic spine, and a trend of the relationship between cervical spine and thoracic spinal alignment was shown in this study. Simulation results suggested that variations in thoracic spinal alignment had a potential impact on cervical spine motion as well as cervical spinal alignment in rear end impact condition.

Kinematically aligned TKA can align knee joint line to horizontal.

PubMed

Ji, Hyung-Min; Han, Jun; Jin, Dong San; Seo, Hyunseok; Won, Ye-Yeon

2016-08-01

The joint line of the native knee is horizontal to the floor and perpendicular to the vertical weight-bearing axis of the patient in a bipedal stance. The purposes of this study were as follows: (1) to find out the distribution of the native joint line in a population of normal patients with normal knees; (2) to compare the native joint line orientation between patients receiving conventional mechanically aligned total knee arthroplasty (TKA), navigated mechanically aligned TKA, and kinematically aligned TKA; and (3) to determine which of the three TKA methods aligns the postoperative knee joint perpendicular to the weight-bearing axis of the limb in bipedal stance. To determine the joint line orientation of a native knee, 50 full-length standing hip-to-ankle digital radiographs were obtained in 50 young, healthy individuals. The angle between knee joint line and the line parallel to the floor was measured and defined as joint line orientation angle (JLOA). JLOA was also measured prior to and after conventional mechanically aligned TKA (65 knees), mechanically aligned TKA using imageless navigation (65 knees), and kinematically aligned TKA (65 knees). The proportion of the knees similar to the native joint line was calculated for each group. The mean JLOA in healthy individuals was parallel to the floor (0.2° ± 1.1°). The pre-operative JLOA of all treatment groups slanted down to the lateral side. Postoperative JLOA slanted down to the lateral side in conventional mechanically aligned TKA (-3.3° ± 2.2°) and in navigation mechanically aligned TKA (-2.6° ± 1.8°), while it was horizontal to the floor in kinematically aligned TKA (0.6° ± 1.7°). Only 6.9 % of the conventional mechanically aligned TKA and 16.9 % of the navigation mechanically aligned TKA were within one SD of the mean JLOA of the native knee, while the proportion was significantly higher (50.8 %) in kinematically aligned TKA. The portion was statistically greater in mechanically aligned TKA group than the other two. Postoperative joint line orientation after kinematically aligned TKA was more similar to that of native knees than that of mechanically aligned TKA and horizontal to the floor. Kinematically aligned TKA can restore pre-arthritic knee joint line orientation, while mechanically aligned TKA is inefficient in achieving the purpose even if navigation TKA is employed. III.

Analyzing the Curriculum Alignment of Teachers

ERIC Educational Resources Information Center

Turan-Özpolat, Esen; Bay, Erdal

2017-01-01

The purpose of this research was to analyze the curriculum alignment of teachers in secondary education 5th grade Science course. Alignment levels of teachers in dimensions of acquisition, content, teaching methods and techniques, activity, material and measurement - assessment, and the reasons for their alignment/non-alignment to the curriculum…

Alignment of Standards and Assessments as an Accountability Criterion.

ERIC Educational Resources Information Center

La Marca, Paul M.

2001-01-01

Provides an overview of the concept of alignment and the role it plays in assessment and accountability systems. Discusses some methodological issues affecting the study of alignment and explores the relationship between alignment and test score interpretation. Alignment is not only a methodological requirement but also an ethical requirement.…

Sandia Corporation (Albuquerque, NM)

DOEpatents

Diver, Richard B.

2010-02-23

A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

The post-genomic era of biological network alignment.

PubMed

Faisal, Fazle E; Meng, Lei; Crawford, Joseph; Milenković, Tijana

2015-12-01

Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological knowledge from well-studied model species to less well-studied species between conserved (aligned) network regions, thus complementing valuable insights that have already been provided by genomic sequence alignment. Here, we review computational challenges behind the network alignment problem, existing approaches for solving the problem, ways of evaluating their alignment quality, and the approaches' biomedical applications. We discuss recent innovative efforts of improving the existing view of network alignment. We conclude with open research questions in comparative biological network research that could further our understanding of principles of life, evolution, disease, and therapeutics.

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

PubMed Central

Di Tommaso, Paolo; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

2014-01-01

This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee. PMID:24972831

Implementation of a parallel protein structure alignment service on cloud.

PubMed

Hung, Che-Lun; Lin, Yaw-Ling

2013-01-01

Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

Nuclear reactor alignment plate configuration

DOEpatents

Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

2014-01-28

An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

Implementation of a Parallel Protein Structure Alignment Service on Cloud

PubMed Central

Hung, Che-Lun; Lin, Yaw-Ling

2013-01-01

Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

Diffractive optics for precision alignment of Euclid space telescope optics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Asfour, Jean-Michel; Weidner, Frank; Bodendorf, Christof; Bode, Andreas; Poleshchuk, Alexander G.; Nasyrov, Ruslan K.; Grupp, Frank; Bender, Ralf

2017-09-01

We present a method for precise alignment of lens elements using specific Computer Generated Hologram (CGH) with an integrated Fizeau reference flat surface and a Fizeau interferometer. The method is used for aligning the so called Camera Lens Assembly for ESAs Euclid telescope. Each lens has a corresponding annular area on the diffractive optics, which is used to control the position of each lens. The lenses are subsequently positioned using individual annular rings of the CGH. The overall alignment accuracy is below 1 µm, the alignment sensitivity is in the range of 0.1 µm. The achieved alignment accuracy of the lenses relative to each other is mainly depending on the stability in time of the alignment tower. Error budgets when using computer generated holograms and physical limitations are explained. Calibration measurements of the alignment system and the typically reached alignment accuracies will be shown and discussed.

SIM Lite: Ground Alignment of the Instrument

NASA Technical Reports Server (NTRS)

Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

2010-01-01

We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

SIM Lite: ground alignment of the instrument

NASA Astrophysics Data System (ADS)

Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

2010-07-01

We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

Multiple network alignment via multiMAGNA+.

PubMed

Vijayan, Vipin; Milenkovic, Tijana

2017-08-21

Network alignment (NA) aims to find a node mapping that identifies topologically or functionally similar network regions between molecular networks of different species. Analogous to genomic sequence alignment, NA can be used to transfer biological knowledge from well- to poorly-studied species between aligned network regions. Pairwise NA (PNA) finds similar regions between two networks while multiple NA (MNA) can align more than two networks. We focus on MNA. Existing MNA methods aim to maximize total similarity over all aligned nodes (node conservation). Then, they evaluate alignment quality by measuring the amount of conserved edges, but only after the alignment is constructed. Directly optimizing edge conservation during alignment construction in addition to node conservation may result in superior alignments. Thus, we present a novel MNA method called multiMAGNA++ that can achieve this. Indeed, multiMAGNA++ outperforms or is on par with existing MNA methods, while often completing faster than existing methods. That is, multiMAGNA++ scales well to larger network data and can be parallelized effectively. During method evaluation, we also introduce new MNA quality measures to allow for more fair MNA method comparison compared to the existing alignment quality measures. MultiMAGNA++ code is available on the method's web page at http://nd.edu/~cone/multiMAGNA++/.

Rapid Quantification of 3D Collagen Fiber Alignment and Fiber Intersection Correlations with High Sensitivity

PubMed Central

Sun, Meng; Bloom, Alexander B.; Zaman, Muhammad H.

2015-01-01

Metastatic cancers aggressively reorganize collagen in their microenvironment. For example, radially orientated collagen fibers have been observed surrounding tumor cell clusters in vivo. The degree of fiber alignment, as a consequence of this remodeling, has often been difficult to quantify. In this paper, we present an easy to implement algorithm for accurate detection of collagen fiber orientation in a rapid pixel-wise manner. This algorithm quantifies the alignment of both computer generated and actual collagen fiber networks of varying degrees of alignment within 5°°. We also present an alternative easy method to calculate the alignment index directly from the standard deviation of fiber orientation. Using this quantitative method for determining collagen alignment, we demonstrate that the number of collagen fiber intersections has a negative correlation with the degree of fiber alignment. This decrease in intersections of aligned fibers could explain why cells move more rapidly along aligned fibers than unaligned fibers, as previously reported. Overall, our paper provides an easier, more quantitative and quicker way to quantify fiber orientation and alignment, and presents a platform in studying effects of matrix and cellular properties on fiber alignment in complex 3D environments. PMID:26158674

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.

Simultaneous phylogeny reconstruction and multiple sequence alignment

PubMed Central

Yue, Feng; Shi, Jian; Tang, Jijun

2009-01-01

Background A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstruction, they must be aligned, and the quality of the multiple sequence alignment has been shown to affect the quality of the inferred phylogeny. At the same time, all the current multiple sequence alignment programs use a guide tree to produce the alignment and experiments showed that good guide trees can significantly improve the multiple alignment quality. Results We devise a new algorithm to simultaneously align multiple sequences and search for the phylogenetic tree that leads to the best alignment. We also implemented the algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM250 or BLOSUM62. The performance of the new method are compared with those from other popular multiple sequence alignment tools, including the widely used programs such as ClustalW and T-Coffee. Experimental results suggest that this method has good performance in terms of both phylogeny accuracy and alignment quality. Conclusion We present an algorithm to align multiple sequences and reconstruct the phylogenies that minimize the alignment score, which is based on an efficient algorithm to solve the median problems for three sequences. Our extensive experiments suggest that this method is very promising and can produce high quality phylogenies and alignments. PMID:19208110

Structural re-alignment in an immunologic surface region of ricin A chain

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

Zemla, A T; Zhou, C E

2007-07-24

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connectingmore » the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.« less

Evolution of physician-hospital alignment models: a case study of comanagement.

PubMed

Sowers, Kevin W; Newman, Paul R; Langdon, Jeffrey C

2013-06-01

Recently, quality, financial, and regulatory demands have driven physicians to seek alignment opportunities with hospitals. The motivation for alignment on the part of physicians and hospitals is now accelerating because the new paradigm under healthcare reform requires an increased focus on improving quality, cost, and efficiency. We (1) identify the key drivers for physician-hospital alignment models; (2) summarize comanagement as a physician-hospital alignment model; and (3) explore a detailed case study of comanagement as an option to better align physicians with hospital goals on quality, safety, and outcomes. A Medline abstract review was performed that identified 45 references that discuss options for physician-hospital alignment. None of the articles identified provide a detailed example of successful alignment structures. A detailed case study of a successful comanagement alignment program is reviewed. The key drivers for alignment are inpatient growth rates, declining reimbursements, and the opportunity to improve quality, decrease costs, and increase efficiency. Two general strategies of alignment involve noneconomic and/or economic integration. In our example, comanagement with economic integration was chosen as the preferred structure for physician-hospital alignment. The choice of structure will vary depending on the existing relationships and governance of the hospital and the physicians in the targeted area of focus. The measure of success in building physician-hospital alignment is measured in improvements in care for the patient, reduced cost of care delivery, and improved relations between physicians and hospital leadership.

Matt: local flexibility aids protein multiple structure alignment.

PubMed

Menke, Matthew; Berger, Bonnie; Cowen, Lenore

2008-01-01

Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these "bent" alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of alpha-helices and beta-strands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse protein-folding problem. The related question of whether Matt alignments can be used to distinguish distantly homologous structure pairs from pairs of proteins that are not homologous is also considered. For this purpose, a p-value score based on the length of the common core and average root mean squared deviation (RMSD) of Matt alignments is shown to largely separate decoys from homologous protein structures in the SABmark benchmark dataset. We postulate that Matt's strong performance comes from its ability to model proteins in different conformational states and, perhaps even more important, its ability to model backbone distortions in more distantly related proteins.

USDA snack food and beverage standards: how big of a stretch for the states?

PubMed

Chriqui, Jamie F; Piekarz, Elizabeth; Chaloupka, Frank J

2014-06-01

The USDA snack food and beverage standards take effect in school year (SY) 2014-2015. Although the USDA standards will provide nationwide requirements, concerns exist about compliance. This study examined whether existing state laws are aligned with the USDA standards to determine whether some states may be better positioned to facilitate compliance. Codified state statutory and regulatory laws effective for SY 2012-2013 for each of the 50 states and the District of Columbia were identified through Boolean keyword searches using the Westlaw and LexisNexis databases. Laws were analyzed for alignment with 18 snack food and beverage provisions contained within the USDA standards. Thirty-eight states had snack food and beverage standards; 33 states' laws exceeded restrictions on foods of minimal nutritional value. Of the 33 states, no states' laws fully met the USDA's standards, 16 states' laws fully met and 10 states' laws partially met at least one USDA provision, and seven states' laws met no USDA provisions. One state's law met 9 of 18 provisions. On average, states met 4 of 18 provisions. States were more likely to meet individual USDA beverage than snack provisions. Implementation and compliance with the USDA standards may be facilitated in states with laws already containing provisions aligned with the USDA standards and may be more difficult in states with fewer or no provisions in alignment, suggesting possible geographic areas for the USDA to target with technical assistance and training efforts and for advocates to work in to facilitate compliance.

Highly Enhanced Gas Adsorption Properties in Vertically Aligned MoS2 Layers.

PubMed

Cho, Soo-Yeon; Kim, Seon Joon; Lee, Youhan; Kim, Jong-Seon; Jung, Woo-Bin; Yoo, Hae-Wook; Kim, Jihan; Jung, Hee-Tae

2015-09-22

In this work, we demonstrate that gas adsorption is significantly higher in edge sites of vertically aligned MoS2 compared to that of the conventional basal plane exposed MoS2 films. To compare the effect of the alignment of MoS2 on the gas adsorption properties, we synthesized three distinct MoS2 films with different alignment directions ((1) horizontally aligned MoS2 (basal plane exposed), (2) mixture of horizontally aligned MoS2 and vertically aligned layers (basal and edge exposed), and (3) vertically aligned MoS2 (edge exposed)) by using rapid sulfurization method of CVD process. Vertically aligned MoS2 film shows about 5-fold enhanced sensitivity to NO2 gas molecules compared to horizontally aligned MoS2 film. Vertically aligned MoS2 has superior resistance variation compared to horizontally aligned MoS2 even with same surface area exposed to identical concentration of gas molecules. We found that electrical response to target gas molecules correlates directly with the density of the exposed edge sites of MoS2 due to high adsorption of gas molecules onto edge sites of vertically aligned MoS2. Density functional theory (DFT) calculations corroborate the experimental results as stronger NO2 binding energies are computed for multiple configurations near the edge sites of MoS2, which verifies that electrical response to target gas molecules (NO2) correlates directly with the density of the exposed edge sites of MoS2 due to high adsorption of gas molecules onto edge sites of vertically aligned MoS2. We believe that this observation extends to other 2D TMD materials as well as MoS2 and can be applied to significantly enhance the gas sensor performance in these materials.

What can the past of pay-for-performance tell us about the future of Value-Based Purchasing in Medicare?

PubMed

Ryan, Andrew M; Damberg, Cheryl L

2013-06-01

The Medicare program has implemented pay-for-performance (P4P), or Value-Based Purchasing, for inpatient care and for Medicare Advantage plans, and plans to implement a program for physicians in 2015. In this paper, we review evidence on the effectiveness of P4P and identify design criteria deemed to be best practice in P4P. We then assess the extent to which Medicare's existing and planned Value-Based Purchasing programs align with these best practices. Of the seven identified best practices in P4P program design, the Hospital Value-Based Purchasing program is strongly aligned with two of the best practices, moderately aligned with three, weakly aligned with one, and has unclear alignment with one best practice. The Physician Value-Based Purchasing Modifier is strongly aligned with two of the best practices, moderately aligned with one, weakly aligned with three, and has unclear alignment with one of the best practices. The Medicare Advantage Quality Bonus Program is strongly aligned with four of the best practices, moderately aligned with two, and weakly aligned with one of the best practices. We identify enduring gaps in P4P literature as it relates to Medicare's plans for Value-Based Purchasing and discuss important issues in the future of these implementations in Medicare. Copyright © 2013 Elsevier Inc. All rights reserved.

Fine-tuning structural RNA alignments in the twilight zone

PubMed Central

2010-01-01

Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index. PMID:20433706

On-command on/off switching of progenitor cell and cancer cell polarized motility and aligned morphology via a cytocompatible shape memory polymer scaffold.

PubMed

Wang, Jing; Quach, Andy; Brasch, Megan E; Turner, Christopher E; Henderson, James H

2017-09-01

In vitro biomaterial models have enabled advances in understanding the role of extracellular matrix (ECM) architecture in the control of cell motility and polarity. Most models are, however, static and cannot mimic dynamic aspects of in vivo ECM remodeling and function. To address this limitation, we present an electrospun shape memory polymer scaffold that can change fiber alignment on command under cytocompatible conditions. Cellular response was studied using the human fibrosarcoma cell line HT-1080 and the murine mesenchymal stem cell line C3H/10T1/2. The results demonstrate successful on-command on/off switching of cell polarized motility and alignment. Decrease in fiber alignment causes a change from polarized motility along the direction of fiber alignment to non-polarized motility and from aligned to unaligned morphology, while increase in fiber alignment causes a change from non-polarized to polarized motility along the direction of fiber alignment and from unaligned to aligned morphology. In addition, the findings are consistent with the hypothesis that increased fiber alignment causes increased cell velocity, while decreased fiber alignment causes decreased cell velocity. On-command on/off switching of cell polarized motility and alignment is anticipated to enable new study of directed cell motility in tumor metastasis, in cell homing, and in tissue engineering. Copyright © 2017 Elsevier Ltd. All rights reserved.

Self-Alignment MEMS IMU Method Based on the Rotation Modulation Technique on a Swing Base

PubMed Central

Chen, Zhiyong; Yang, Haotian; Wang, Chengbin; Lin, Zhihui; Guo, Meifeng

2018-01-01

The micro-electro-mechanical-system (MEMS) inertial measurement unit (IMU) has been widely used in the field of inertial navigation due to its small size, low cost, and light weight, but aligning MEMS IMUs remains a challenge for researchers. MEMS IMUs have been conventionally aligned on a static base, requiring other sensors, such as magnetometers or satellites, to provide auxiliary information, which limits its application range to some extent. Therefore, improving the alignment accuracy of MEMS IMU as much as possible under swing conditions is of considerable value. This paper proposes an alignment method based on the rotation modulation technique (RMT), which is completely self-aligned, unlike the existing alignment techniques. The effect of the inertial sensor errors is mitigated by rotating the IMU. Then, inertial frame-based alignment using the rotation modulation technique (RMT-IFBA) achieved coarse alignment on the swing base. The strong tracking filter (STF) further improved the alignment accuracy. The performance of the proposed method was validated with a physical experiment, and the results of the alignment showed that the standard deviations of pitch, roll, and heading angle were 0.0140°, 0.0097°, and 0.91°, respectively, which verified the practicality and efficacy of the proposed method for the self-alignment of the MEMS IMU on a swing base. PMID:29649150

Score distributions of gapped multiple sequence alignments down to the low-probability tail

NASA Astrophysics Data System (ADS)

Fieth, Pascal; Hartmann, Alexander K.

2016-08-01

Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are exponentially small. For gapless local alignments of infinitely long sequences this distribution is known analytically to follow a Gumbel distribution. Distributions for gapped local alignments and global alignments of finite lengths can only be obtained numerically. To obtain result for the small-probability region, specific statistical mechanics-based rare-event algorithms can be applied. In previous studies, this was achieved for pairwise alignments. They showed that, contrary to results from previous simple sampling studies, strong deviations from the Gumbel distribution occur in case of finite sequence lengths. Here we extend the studies to multiple sequence alignments with gaps, which are much more relevant for practical applications in molecular biology. We study the distributions of scores over a large range of the support, reaching probabilities as small as 10-160, for global and local (sum-of-pair scores) multiple alignments. We find that even after suitable rescaling, eliminating the sequence-length dependence, the distributions for multiple alignment differ from the pairwise alignment case. Furthermore, we also show that the previously discussed Gaussian correction to the Gumbel distribution needs to be refined, also for the case of pairwise alignments.

Improving SPAWAR PEO C4I Organizational Alignment to Better Enable Enterprise Technical Risk Management

DTIC Science & Technology

2017-03-01

possible. The thesis also utilized organizational alignment literature to include organizational alignment principles in the evaluation. Key principles ...thesis also utilized organizational alignment literature to include organizational alignment principles in the evaluation. Key principles include 1...39 A. CORE PRINCIPLES ...............................................................................39 B. RELATIONSHIP OF CORE PRINCIPLES

Alignment of Standards and Assessments as an Accountability Criterion. ERIC Digest.

ERIC Educational Resources Information Center

La Marca, Paul M.

This digest provides an overview of the concept of alignment and the role it plays in assessment and accountability systems. It also discusses methodological issues affecting the study of alignment and explores the relationship between alignment and test score interpretation. Alignment refers to the degree of match between test content and subject…

Homeotropic alignment of multiple bent-core liquid crystal phases using a polydimethylsiloxane alignment layer

NASA Astrophysics Data System (ADS)

Carlson, Eric D.; Foley, Lee M.; Guzman, Edward; Korblova, Eva D.; Visvanathan, Rayshan; Ryu, SeongHo; Gim, Min-Jun; Tuchband, Michael R.; Yoon, Dong Ki; Clark, Noel A.; Walba, David M.

2017-08-01

The control of the molecular orientation of liquid crystals (LCs) is important in both understanding phase properties and the continuing development of new LC technologies including displays, organic transistors, and electro-optic devices. Many techniques have been developed for successfully inducing alignment of calamitic LCs, though these techniques typically do not translate to the alignment of bent-core liquid crystals (BCLCs). Some techniques have been utilized to align various phases of BCLCs, but these techniques are often unsuccessful for general alignment of multiple materials and/or multiple phases. Here, we demonstrate that glass cells treated with polydimethylsiloxane (PDMS) thin films induce high quality homeotropic alignment of multiple mesophases of four BCLCs. On cooling to the lowest temperature phase the homeotropic alignment is lost, and spherulitic growth is seen in crystal and crystal-like phases including the dark conglomerate (DC) and helical nanofilament (HNF) phases. Evidence of homeotropic alignment is observed using polarized optical microscopy. We speculate that the methyl groups on the surface of the PDMS films strongly interact with the aliphatic tails of each mesogens, resulting in homeotropic alignment.

Some aspects of SR beamline alignment

NASA Astrophysics Data System (ADS)

Gaponov, Yu. A.; Cerenius, Y.; Nygaard, J.; Ursby, T.; Larsson, K.

2011-09-01

Based on the Synchrotron Radiation (SR) beamline optical element-by-element alignment with analysis of the alignment results an optimized beamline alignment algorithm has been designed and developed. The alignment procedures have been designed and developed for the MAX-lab I911-4 fixed energy beamline. It has been shown that the intermediate information received during the monochromator alignment stage can be used for the correction of both monochromator and mirror without the next stages of alignment of mirror, slits, sample holder, etc. Such an optimization of the beamline alignment procedures decreases the time necessary for the alignment and becomes useful and helpful in the case of any instability of the beamline optical elements, storage ring electron orbit or the wiggler insertion device, which could result in the instability of angular and positional parameters of the SR beam. A general purpose software package for manual, semi-automatic and automatic SR beamline alignment has been designed and developed using the developed algorithm. The TANGO control system is used as the middle-ware between the stand-alone beamline control applications BLTools, BPMonitor and the beamline equipment.

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

PubMed

Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

2012-01-01

Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of those sequences that maximize likelihood under the Jukes-Cantor model is uninformative in the worst possible sense. For all inputs, all trees optimize the likelihood score. Second, we show that a greedy heuristic that uses GTR+Gamma ML to optimize the alignment and the tree can produce very poor alignments and trees. Therefore, the excellent performance of SATé-II and SATé-I is not because ML is used as an optimization criterion for choosing the best tree/alignment pair but rather due to the particular divide-and-conquer realignment techniques employed.

Alignment method for solar collector arrays

DOEpatents

Driver, Jr., Richard B

2012-10-23

The present invention is directed to an improved method for establishing camera fixture location for aligning mirrors on a solar collector array (SCA) comprising multiple mirror modules. The method aligns the mirrors on a module by comparing the location of the receiver image in photographs with the predicted theoretical receiver image location. To accurately align an entire SCA, a common reference is used for all of the individual module images within the SCA. The improved method can use relative pixel location information in digital photographs along with alignment fixture inclinometer data to calculate relative locations of the fixture between modules. The absolute locations are determined by minimizing alignment asymmetry for the SCA. The method inherently aligns all of the mirrors in an SCA to the receiver, even with receiver position and module-to-module alignment errors.

NO2 sensing at room temperature using vertically aligned MoS2 flakes network

NASA Astrophysics Data System (ADS)

Kumar, Rahul; Goel, Neeraj; Kumar, Mahesh

2018-04-01

To exploit the role of alignment of MoS2 flake in chemical sensing, here, we have synthesized the horizontally and vertically aligned MoS2 flake network using conventional chemical vapor deposition technique. The morphology and number of layers were confirmed by SEM and Raman spectroscopy, respectively. The sensing performance of horizontally aligned and vertically aligned flake network was investigated to NO2 at room temperature. Vertically aligned MoS2 based sensor showed higher sensitivity 51.54 % and 63.2 % compared to horizontally aligned MoS2 sensor' sensitivity of 35.32 % and 45.2 % to 50 ppm and 100 ppm NO2, respectively. This high sensitivity attributed to the high aspect ratio and high adsorption energy on the edge site of vertically aligned MoS2.

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees.

PubMed

Kück, Patrick; Meusemann, Karen; Dambach, Johannes; Thormann, Birthe; von Reumont, Björn M; Wägele, Johann W; Misof, Bernhard

2010-03-31

Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS) which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE) based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict. Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment profiling, alignment masking should routinely be used to improve tree reconstructions. Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements.

Colour stabilities of three types of orthodontic clear aligners exposed to staining agents

PubMed Central

Liu, Chen-Lu; Sun, Wen-Tian; Liao, Wen; Lu, Wen-Xin; Li, Qi-Wen; Jeong, Yunho; Liu, Jun; Zhao, Zhi-He

2016-01-01

The aim of this study was to evaluate and compare the colour stabilities of three types of orthodontic clear aligners exposed to staining agents in vitro. Sixty clear orthodontic aligners produced by three manufacturers (Invisalign, Angelalign, and Smartee) were immersed in three staining solutions (coffee, black tea, and red wine) and one control solution (distilled water). After 12-h and 7-day immersions, the aligners were washed in an ultrasonic cleaner and measured with a colourimeter. The colour changes (ΔE*) were calculated on the basis of the Commission Internationale de I'Eclairage L*a*b* colour system (CIE L*a*b*), and the results were then converted into National Bureau of Standards (NBS) units. Fourier transformation infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM) were conducted to observe the molecular and morphologic alterations to the aligner surfaces, respectively. The three types of aligners exhibited slight colour changes after 12 h of staining, with the exception of the Invisalign aligners stained with coffee. The Invisalign aligners exhibited significantly higher ΔE* values (ranging from 0.30 to 27.81) than those of the Angelalign and Smartee aligners (ΔE* values ranging from 0.33 to 1.89 and 0.32 to 1.61, respectively, P<0.05). FT-IR analysis confirmed that the polymer-based structure of aligners did not exhibit significant chemical differences before and after the immersions. The SEM results revealed different surface alterations to the three types of aligner materials after the 7-day staining. The three types of aesthetic orthodontic appliances exhibited colour stability after the 12-h immersion, with the exception of the Invisalign aligners stained by coffee. The Invisalign aligners were more prone than the Angelalign and Smartee aligners to pigmentation. Aligner materials may be improved by considering aesthetic colour stability properties. PMID:27660048

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.

PubMed

Hu, Jun; Liu, Zi; Yu, Dong-Jun; Zhang, Yang

2018-02-15

Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1,415,871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. http://zhanglab.ccmb.med.umich.edu/LS-align/. njyudj@njust.edu.cn or zhng@umich.edu. Supplementary data are available at Bioinformatics online.

Colour stabilities of three types of orthodontic clear aligners exposed to staining agents.

PubMed

Liu, Chen-Lu; Sun, Wen-Tian; Liao, Wen; Lu, Wen-Xin; Li, Qi-Wen; Jeong, Yunho; Liu, Jun; Zhao, Zhi-He

2016-12-16

The aim of this study was to evaluate and compare the colour stabilities of three types of orthodontic clear aligners exposed to staining agents in vitro. Sixty clear orthodontic aligners produced by three manufacturers (Invisalign, Angelalign, and Smartee) were immersed in three staining solutions (coffee, black tea, and red wine) and one control solution (distilled water). After 12-h and 7-day immersions, the aligners were washed in an ultrasonic cleaner and measured with a colourimeter. The colour changes (ΔE*) were calculated on the basis of the Commission Internationale de I'Eclairage L*a*b* colour system (CIE L*a*b*), and the results were then converted into National Bureau of Standards (NBS) units. Fourier transformation infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM) were conducted to observe the molecular and morphologic alterations to the aligner surfaces, respectively. The three types of aligners exhibited slight colour changes after 12 h of staining, with the exception of the Invisalign aligners stained with coffee. The Invisalign aligners exhibited significantly higher ΔE* values (ranging from 0.30 to 27.81) than those of the Angelalign and Smartee aligners (ΔE* values ranging from 0.33 to 1.89 and 0.32 to 1.61, respectively, P<0.05). FT-IR analysis confirmed that the polymer-based structure of aligners did not exhibit significant chemical differences before and after the immersions. The SEM results revealed different surface alterations to the three types of aligner materials after the 7-day staining. The three types of aesthetic orthodontic appliances exhibited colour stability after the 12-h immersion, with the exception of the Invisalign aligners stained by coffee. The Invisalign aligners were more prone than the Angelalign and Smartee aligners to pigmentation. Aligner materials may be improved by considering aesthetic colour stability properties.

StructAlign, a Program for Alignment of Structures of DNA-Protein Complexes.

PubMed

Popov, Ya V; Galitsyna, A A; Alexeevski, A V; Karyagina, A S; Spirin, S A

2015-11-01

Comparative analysis of structures of complexes of homologous proteins with DNA is important in the analysis of DNA-protein recognition. Alignment is a necessary stage of the analysis. An alignment is a matching of amino acid residues and nucleotides of one complex to residues and nucleotides of the other. Currently, there are no programs available for aligning structures of DNA-protein complexes. We present the program StructAlign, which should fill this gap. The program inputs a pair of complexes of DNA double helix with proteins and outputs an alignment of DNA chains corresponding to the best spatial fit of the protein chains.

Interference Alignment With Partial CSI Feedback in MIMO Cellular Networks

NASA Astrophysics Data System (ADS)

Rao, Xiongbin; Lau, Vincent K. N.

2014-04-01

Interference alignment (IA) is a linear precoding strategy that can achieve optimal capacity scaling at high SNR in interference networks. However, most existing IA designs require full channel state information (CSI) at the transmitters, which would lead to significant CSI signaling overhead. There are two techniques, namely CSI quantization and CSI feedback filtering, to reduce the CSI feedback overhead. In this paper, we consider IA processing with CSI feedback filtering in MIMO cellular networks. We introduce a novel metric, namely the feedback dimension, to quantify the first order CSI feedback cost associated with the CSI feedback filtering. The CSI feedback filtering poses several important challenges in IA processing. First, there is a hidden partial CSI knowledge constraint in IA precoder design which cannot be handled using conventional IA design methodology. Furthermore, existing results on the feasibility conditions of IA cannot be applied due to the partial CSI knowledge. Finally, it is very challenging to find out how much CSI feedback is actually needed to support IA processing. We shall address the above challenges and propose a new IA feasibility condition under partial CSIT knowledge in MIMO cellular networks. Based on this, we consider the CSI feedback profile design subject to the degrees of freedom requirements, and we derive closed-form trade-off results between the CSI feedback cost and IA performance in MIMO cellular networks.

Anarchic Yukawas and top partial compositeness: the flavour of a successful marriage

NASA Astrophysics Data System (ADS)

Cacciapaglia, Giacomo; Cai, Haiying; Flacke, Thomas; Lee, Seung J.; Parolini, Alberto; Serôdio, Hugo

2015-06-01

The top quark can be naturally singled out from other fermions in the Standard Model due to its large mass, of the order of the electroweak scale. We follow this reasoning in models of pseudo Nambu Goldstone Boson composite Higgs, which may derive from an underlying confining dynamics. We consider a new class of flavour models, where the top quark obtains its mass via partial compositeness, while the lighter fermions acquire their masses by a deformation of the dynamics generated at a high flavour scale. One interesting feature of such scenario is that it can avoid all the flavour constraints without the need of flavour symmetries, since the flavour scale can be pushed high enough. We show that both flavour conserving and violating constraints can be satisfied with top partial compositeness without invoking any flavour symmetry for the up-type sector, in the case of the minimal SO(5)/SO(4) coset with top partners in the four-plet and singlet of SO(4). In the down-type sector, some degree of alignment is required if all down-type quarks are elementary. We show that taking the bottom quark partially composite provides a dynamical explanation for the hierarchy causing this alignment. We present explicit realisations of this mechanism which do not require to include additional bottom partner fields. Finally, these conclusions are generalised to scenarios with non-minimal cosets and top partners in larger representations.

SANA NetGO: a combinatorial approach to using Gene Ontology (GO) terms to score network alignments.

PubMed

Hayes, Wayne B; Mamano, Nil

2018-04-15

Gene Ontology (GO) terms are frequently used to score alignments between protein-protein interaction (PPI) networks. Methods exist to measure GO similarity between proteins in isolation, but proteins in a network alignment are not isolated: each pairing is dependent on every other via the alignment itself. Existing measures fail to take into account the frequency of GO terms across networks, instead imposing arbitrary rules on when to allow GO terms. Here we develop NetGO, a new measure that naturally weighs infrequent, informative GO terms more heavily than frequent, less informative GO terms, without arbitrary cutoffs, instead downweighting GO terms according to their frequency in the networks being aligned. This is a global measure applicable only to alignments, independent of pairwise GO measures, in the same sense that the edge-based EC or S3 scores are global measures of topological similarity independent of pairwise topological similarities. We demonstrate the superiority of NetGO in alignments of predetermined quality and show that NetGO correlates with alignment quality better than any existing GO-based alignment measures. We also demonstrate that NetGO provides a measure of taxonomic similarity between species, consistent with existing taxonomic measuresa feature not shared with existing GObased network alignment measures. Finally, we re-score alignments produced by almost a dozen aligners from a previous study and show that NetGO does a better job at separating good alignments from bad ones. Available as part of SANA. whayes@uci.edu. Supplementary data are available at Bioinformatics online.

Precision alignment and mounting apparatus

NASA Technical Reports Server (NTRS)

Preston, Dennis R. (Inventor)

1993-01-01

An alignment and mounting apparatus for mounting two modules (10,12) includes a first portion having a cylindrical alignment pin (16) projecting normal to a module surface, a second portion having a three-stage alignment guide (18) including a shoehorn flange (34), a Y-slot (42) and a V-block (22) which sequentially guide the alignment pin (16) with successively finer precision and a third portion in the form of a spring-loaded captive fastener (20) for connecting the two modules after alignment is achieved.

Mobile and replicated alignment of arrays in data-parallel programs

NASA Technical Reports Server (NTRS)

Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

1993-01-01

When a data-parallel language like FORTRAN 90 is compiled for a distributed-memory machine, aggregate data objects (such as arrays) are distributed across the processor memories. The mapping determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: first, an alignment that maps all the objects to an abstract template, and then a distribution that maps the template to the processors. We solve two facets of the problem of finding alignments that reduce residual communication: we determine alignments that vary in loops, and objects that should have replicated alignments. We show that loop-dependent mobile alignment is sometimes necessary for optimum performance, and we provide algorithms with which a compiler can determine good mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself (via spread operations) or can be used to improve performance. We propose an algorithm based on network flow that determines which objects to replicate so as to minimize the total amount of broadcast communication in replication. This work on mobile and replicated alignment extends our earlier work on determining static alignment.

Theory of grain alignment in molecular clouds

NASA Technical Reports Server (NTRS)

Roberge, Wayne G.

1993-01-01

Research accomplishments are presented and include the following: (1) mathematical theory of grain alignment; (2) super-paramagnetic alignment of molecular cloud grains; and (3) theory of grain alignment by ambipolar diffusion.

Attenuation-emission alignment in cardiac PET∕CT based on consistency conditions

PubMed Central

Alessio, Adam M.; Kinahan, Paul E.; Champley, Kyle M.; Caldwell, James H.

2010-01-01

Purpose: In cardiac PET and PET∕CT imaging, misaligned transmission and emission images are a common problem due to respiratory and cardiac motion. This misalignment leads to erroneous attenuation correction and can cause errors in perfusion mapping and quantification. This study develops and tests a method for automated alignment of attenuation and emission data. Methods: The CT-based attenuation map is iteratively transformed until the attenuation corrected emission data minimize an objective function based on the Radon consistency conditions. The alignment process is derived from previous work by Welch et al. [“Attenuation correction in PET using consistency information,” IEEE Trans. Nucl. Sci. 45, 3134–3141 (1998)] for stand-alone PET imaging. The process was evaluated with the simulated data and measured patient data from multiple cardiac ammonia PET∕CT exams. The alignment procedure was applied to simulations of five different noise levels with three different initial attenuation maps. For the measured patient data, the alignment procedure was applied to eight attenuation-emission combinations with initially acceptable alignment and eight combinations with unacceptable alignment. The initially acceptable alignment studies were forced out of alignment a known amount and quantitatively evaluated for alignment and perfusion accuracy. The initially unacceptable studies were compared to the proposed aligned images in a blinded side-by-side review. Results: The proposed automatic alignment procedure reduced errors in the simulated data and iteratively approaches global minimum solutions with the patient data. In simulations, the alignment procedure reduced the root mean square error to less than 5 mm and reduces the axial translation error to less than 1 mm. In patient studies, the procedure reduced the translation error by >50% and resolved perfusion artifacts after a known misalignment for the eight initially acceptable patient combinations. The side-by-side review of the proposed aligned attenuation-emission maps and initially misaligned attenuation-emission maps revealed that reviewers preferred the proposed aligned maps in all cases, except one inconclusive case. Conclusions: The proposed alignment procedure offers an automatic method to reduce attenuation correction artifacts in cardiac PET∕CT and provides a viable supplement to subjective manual realignment tools. PMID:20384256

SU-G-JeP3-02: Comparison of Magnitude and Frequency of Patient Positioning Errors in Breast Irradiation Using AlignRT 3D Optical Surface Imaging and Skin Mark Techniques

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

Yao, R; Chisela, W; Dorbu, G

2016-06-15

Purpose: To evaluate clinical usefulness of AlignRT (Vision RT Ltd., London, UK) in reducing patient positioning errors in breast irradiation. Methods: 60 patients undergoing whole breast irradiation were selected for this study. Patients were treated to the left or right breast lying on Qfix Access breast board (Qfix, Avondale, PA) in supine position for 28 fractions using tangential fields. 30 patients were aligned using AlignRT by aligning a breast surface region of interest (ROI) to the same area from a reference surface image extracted from planning CT. When the patient’s surface image deviated from the reference by more than 3mmmore » on one or more translational and rotational directions, a new reference was acquired using AlignRT in-room cameras. The other 30 patients were aligned to the skin marks with room lasers. On-Board MV portal images of medial field were taken daily and matched to the DRRs. The magnitude and frequency of positioning errors were determined from measured translational shifts. Kolmogorov-Smirnov test was used to evaluate statistical differences of positional accuracy and precision between AlignRT and non-AlignRT patients. Results: The percentage of port images with no shift required was 46.5% and 27.0% in vertical, 49.8% and 25.8% in longitudinal, 47.6% and 28.5% in lateral for AlignRT and non-AlignRT patients, respectively. The percentage of port images requiring more than 3mm shifts was 18.1% and 35.1% in vertical, 28.6% and 50.8% in longitudinal, 11.3% and 24.2% in lateral for AlignRT and non-AlignRT patients, respectively. Kolmogorov-Smirnov test showed that there were significant differences between the frequency distributions of AlignRT and non-AlignRT in vertical, longitudinal, and lateral shifts. Conclusion: As confirmed by port images, AlignRT-assisted patient positioning can significantly reduce the frequency and magnitude of patient setup errors in breast irradiation compared to the use of lasers and skin marks.« less

Optical Device for Converting a Laser Beam into Two Co-aligned but Oppositely Directed Beams

NASA Technical Reports Server (NTRS)

Jennings, Donald

2013-01-01

Optical systems consisting of a series of optical elements require alignment from the input end to the output end. The optical elements can be mirrors, lenses, sources, detectors, or other devices. Complex optical systems are often difficult to align from end-to-end because the alignment beam must be inserted at one end in order for the beam to traverse the entire optical path to the other end. The ends of the optical train may not be easily accessible to the alignment beam. Typically, when a series of optical elements is to be aligned, an alignment laser beam is inserted into the optical path with a pick-off mirror at one end of the series of elements. But it may be impossible to insert the beam at an end-point. It can be difficult to locate the pick-off mirror at the desired position because there is not enough space, there is no mounting surface, or the location is occupied by a source, detector, or other component. Alternatively, the laser beam might be inserted at an intermediate location (not at an end-point) and sent, first in one direction and then the other, to the opposite ends of the optical system for alignment. However, in this case, alignment must be performed in two directions and extra effort is required to co-align the two beams to make them parallel and coincident, i.e., to follow the same path as an end-to-end beam. An optical device has been developed that accepts a laser beam as input and produces two co-aligned, but counter-propagating beams. In contrast to a conventional alignment laser placed at one end of the optical path, this invention can be placed at a convenient position within the optical train and aligned to send its two beams simultaneously along precisely opposite paths that, taken together, trace out exactly the same path as the conventional alignment laser. This invention allows the user the freedom to choose locations within the optical train for placement of the alignment beam. It is also self-aligned by design and requires almost no adjustment.

Impact of alignment to gravito-inertial force on motion sickness and cardiopulmonary variables.

PubMed

Mert, Agali; Bles, Willem

2011-07-01

In tilting trains partial alignment to the gravito-inertial force (GIF) in the curves seems to be the best tilt compensation to reduce the incidence of motion sickness. We investigated the effect of alignment to the GIF on the development of motion sickness during low-frequency horizontal motion. There were 12 healthy subjects who participated. The design was a three-period, single-blind, crossover trial, counterbalanced for order. Cardiopulmonary measurements, Misery SCores (MISC), and questionnaire data (Motion Sickness Susceptibility Questionnaire, Nijmegen Questionnaire for Hyperventilation) were obtained. The stimulus was a sinusoidal movement (0.176 Hz, 0.2 g peak acceleration) on the ESA-sled. The cabin was compensated for 0% (A-0), 50% (A-50), and 100% (A-100) to the GIF. Runs were 1 wk apart. The A-50 condition may delay the development of motion sickness. Based on the survival curves the possible effect seems temporary. However, MISC 2 early in the runs resulted in high positive and negative predictive values for dropout and survival during the runs. No synchronization of the respiratory frequency with the sled motion was observed. There was a significant (P = 0.002) drop in relative end-tidal CO2 levels. There seems to be a rationale for partially compensating to the GIF while trying to prevent motion sickness in tilting trains. Sitting comfort is just better than without compensation at all and Coriolis effects are not as nauseating as with complete tilt compensation. Also, a drop in end-tidal CO2 levels might be a sign of pulmonary compensation for the nauseating stimulus.

Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM)☆

PubMed Central

Parson, Walther; Strobl, Christina; Huber, Gabriela; Zimmermann, Bettina; Gomes, Sibylle M.; Souto, Luis; Fendt, Liane; Delport, Rhena; Langit, Reina; Wootton, Sharon; Lagacé, Robert; Irwin, Jodi

2013-01-01

Insights into the human mitochondrial phylogeny have been primarily achieved by sequencing full mitochondrial genomes (mtGenomes). In forensic genetics (partial) mtGenome information can be used to assign haplotypes to their phylogenetic backgrounds, which may, in turn, have characteristic geographic distributions that would offer useful information in a forensic case. In addition and perhaps even more relevant in the forensic context, haplogroup-specific patterns of mutations form the basis for quality control of mtDNA sequences. The current method for establishing (partial) mtDNA haplotypes is Sanger-type sequencing (STS), which is laborious, time-consuming, and expensive. With the emergence of Next Generation Sequencing (NGS) technologies, the body of available mtDNA data can potentially be extended much more quickly and cost-efficiently. Customized chemistries, laboratory workflows and data analysis packages could support the community and increase the utility of mtDNA analysis in forensics. We have evaluated the performance of mtGenome sequencing using the Personal Genome Machine (PGM) and compared the resulting haplotypes directly with conventional Sanger-type sequencing. A total of 64 mtGenomes (>1 million bases) were established that yielded high concordance with the corresponding STS haplotypes (<0.02% differences). About two-thirds of the differences were observed in or around homopolymeric sequence stretches. In addition, the sequence alignment algorithm employed to align NGS reads played a significant role in the analysis of the data and the resulting mtDNA haplotypes. Further development of alignment software would be desirable to facilitate the application of NGS in mtDNA forensic genetics. PMID:23948325

Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin.

PubMed

Guzzi, Pietro Hiram; Milenkovic, Tijana

2018-05-01

Analogous to genomic sequence alignment that allows for across-species transfer of biological knowledge between conserved sequence regions, biological network alignment can be used to guide the knowledge transfer between conserved regions of molecular networks of different species. Hence, biological network alignment can be used to redefine the traditional notion of a sequence-based homology to a new notion of network-based homology. Analogous to genomic sequence alignment, there exist local and global biological network alignments. Here, we survey prominent and recent computational approaches of each network alignment type and discuss their (dis)advantages. Then, as it was recently shown that the two approach types are complementary, in the sense that they capture different slices of cellular functioning, we discuss the need to reconcile the two network alignment types and present a recent first step in this direction. We conclude with some open research problems on this topic and comment on the usefulness of network alignment in other domains besides computational biology.

Four-quadrant gratings moiré fringe alignment measurement in proximity lithography.

PubMed

Zhu, Jiangping; Hu, Song; Yu, Junsheng; Zhou, Shaolin; Tang, Yan; Zhong, Min; Zhao, Lixin; Chen, Minyong; Li, Lanlan; He, Yu; Jiang, Wei

2013-02-11

This paper aims to deal with a four-quadrant gratings alignment method benefiting from phase demodulation for proximity lithography, which combines the advantages of interferometry with image processing. Both the mask alignment mark and the wafer alignment mark consist of four sets of gratings, which bring the convenience and simplification of realization for coarse alignment and fine alignment. Four sets of moiré fringes created by superposing the mask alignment mark and the wafer alignment mark are highly sensitive to the misalignment between them. And the misalignment can be easily determined through demodulating the phase of moiré fringe without any external reference. Especially, the period and phase distribution of moiré fringes are unaffected by the gap between the mask and the wafer, not excepting the wavelength of alignment illumination. Disturbance from the illumination can also be negligible, which enhances the technological adaptability. The experimental results bear out the feasibility and rationality of our designed approach.

A generalized global alignment algorithm.

PubMed

Huang, Xiaoqiu; Chao, Kun-Mao

2003-01-22

Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions. We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity. The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.

Fast Response and Spontaneous Alignment in Liquid Crystals Doped with 12-Hydroxystearic Acid Gelators.

PubMed

Lin, Hui-Chi; Wang, Chih-Hung; Wang, Jyun-Kai; Tsai, Sheng-Feng

2018-05-07

The spontaneous vertical alignment of liquid crystals (LCs) in gelator (12-hydroxystearic acid)-doped LC cells was studied. Gelator-induced alignment can be used in both positive and negative LC cells. The electro-optical characteristics of the gelator-doped negative LC cell were similar to those of an LC cell that contained a vertically aligned (VA) host. The rise time of the gelator-doped LC cell was two orders of magnitude shorter than that of the VA host LC cell. The experimental results indicate that the gelator-induced vertical alignment of LC molecules occurred not only on the surface of the indium tin oxide (ITO) but also on the homogeneous alignment layer. Various LC alignments (planar, hybrid, multistable hybrid, and vertical alignments) were achieved by modulating the doped gelator concentrations. The multistable characteristic of LCs doped with the gelator is also presented. The alignment by doping with a gelator reduces the manufacturing costs and provides a means of fabricating fast-responding, flexible LC displays using a low-temperature process.

A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law.

PubMed

Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

2015-11-01

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. Copyright © 2015 Elsevier Inc. All rights reserved.

A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law

PubMed Central

Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

2015-01-01

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. PMID:26455556

Origins and challenges of viral dark matter.

PubMed

Krishnamurthy, Siddharth R; Wang, David

2017-07-15

The accurate classification of viral dark matter - metagenomic sequences that originate from viruses but do not align to any reference virus sequences - is one of the major obstacles in comprehensively defining the virome. Depending on the sample, viral dark matter can make up from anywhere between 40 and 90% of sequences. This review focuses on the specific nature of dark matter as it relates to viral sequences. We identify three factors that contribute to the existence of viral dark matter: the divergence and length of virus sequences, the limitations of alignment based classification, and limited representation of viruses in reference sequence databases. We then discuss current methods that have been developed to at least partially circumvent these limitations and thereby reduce the extent of viral dark matter. Copyright © 2017 Elsevier B.V. All rights reserved.

77 FR 35870 - Approval of Air Quality Implementation Plans; Wisconsin; Partial Disapproval of “Infrastructure...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-15

... alignment of the State and Federal definition for ``major modification'' occurs as expeditiously as possible... disapproves a state rule implementing a Federal Standard. National Technology Transfer Advancement Act In..., the requirements of section 12(d) of the National Technology Transfer and Advancement Act of 1995 (15...

Slider--maximum use of probability information for alignment of short sequence reads and SNP detection.

PubMed

Malhis, Nawar; Butterfield, Yaron S N; Ester, Martin; Jones, Steven J M

2009-01-01

A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce a new alignment approach (Slider) that reduces the alignment problem space by utilizing each read base's probabilities given in the prb files. Compared with other aligners, Slider has higher alignment accuracy and efficiency. In addition, given that Slider matches bases with probabilities other than the most probable, it significantly reduces the percentage of base mismatches. The result is that its SNP predictions are more accurate than other SNP prediction approaches used today that start from the most probable sequence, including those using base quality.

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

A statistically harmonized alignment-classification in image space enables accurate and robust alignment of noisy images in single particle analysis.

PubMed

Kawata, Masaaki; Sato, Chikara

2007-06-01

In determining the three-dimensional (3D) structure of macromolecular assemblies in single particle analysis, a large representative dataset of two-dimensional (2D) average images from huge number of raw images is a key for high resolution. Because alignments prior to averaging are computationally intensive, currently available multireference alignment (MRA) software does not survey every possible alignment. This leads to misaligned images, creating blurred averages and reducing the quality of the final 3D reconstruction. We present a new method, in which multireference alignment is harmonized with classification (multireference multiple alignment: MRMA). This method enables a statistical comparison of multiple alignment peaks, reflecting the similarities between each raw image and a set of reference images. Among the selected alignment candidates for each raw image, misaligned images are statistically excluded, based on the principle that aligned raw images of similar projections have a dense distribution around the correctly aligned coordinates in image space. This newly developed method was examined for accuracy and speed using model image sets with various signal-to-noise ratios, and with electron microscope images of the Transient Receptor Potential C3 and the sodium channel. In every data set, the newly developed method outperformed conventional methods in robustness against noise and in speed, creating 2D average images of higher quality. This statistically harmonized alignment-classification combination should greatly improve the quality of single particle analysis.

Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search

NASA Technical Reports Server (NTRS)

Wheeler, Ward C.

2003-01-01

A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

Using confidence intervals to evaluate the focus alignment of spectrograph detector arrays.

PubMed

Sawyer, Travis W; Hawkins, Kyle S; Damento, Michael

2017-06-20

High-resolution spectrographs extract detailed spectral information of a sample and are frequently used in astronomy, laser-induced breakdown spectroscopy, and Raman spectroscopy. These instruments employ dispersive elements such as prisms and diffraction gratings to spatially separate different wavelengths of light, which are then detected by a charge-coupled device (CCD) or complementary metal-oxide-semiconductor (CMOS) detector array. Precise alignment along the optical axis (focus position) of the detector array is critical to maximize the instrumental resolution; however, traditional approaches of scanning the detector through focus lack a quantitative measure of precision, limiting the repeatability and relying on one's experience. Here we propose a method to evaluate the focus alignment of spectrograph detector arrays by establishing confidence intervals to measure the alignment precision. We show that propagation of uncertainty can be used to estimate the variance in an alignment, thus providing a quantitative and repeatable means to evaluate the precision and confidence of an alignment. We test the approach by aligning the detector array of a prototype miniature echelle spectrograph. The results indicate that the procedure effectively quantifies alignment precision, enabling one to objectively determine when an alignment has reached an acceptable level. This quantitative approach also provides a foundation for further optimization, including automated alignment. Furthermore, the procedure introduced here can be extended to other alignment techniques that rely on numerically fitting data to a model, providing a general framework for evaluating the precision of alignment methods.

The perception of verticality in lunar and Martian gravity conditions.

PubMed

de Winkel, Ksander N; Clément, Gilles; Groen, Eric L; Werkhoven, Peter J

2012-10-31

Although the mechanisms of neural adaptation to weightlessness and re-adaptation to Earth-gravity have received a lot of attention since the first human space flight, there is as yet little knowledge about how spatial orientation is affected by partial gravity, such as lunar gravity of 0.16 g or Martian gravity of 0.38 g. Up to now twelve astronauts have spent a cumulated time of approximately 80 h on the lunar surface, but no psychophysical experiments were conducted to investigate their perception of verticality. We investigated how the subjective vertical (SV) was affected by reduced gravity levels during the first European Parabolic Flight Campaign of Partial Gravity. In normal and hypergravity, subjects accurately aligned their SV with the gravitational vertical. However, when gravity was below a certain threshold, subjects aligned their SV with their body longitudinal axis. The value of the threshold varied considerably between subjects, ranging from 0.03 to 0.57 g. Despite the small number of subjects, there was a significant positive correlation of the threshold with subject age, which calls for further investigation. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Field-Aligned Current Systems at Mercury

NASA Astrophysics Data System (ADS)

Heyner, Daniel; Exner, Willi

2017-04-01

Mercury exhibits a very dynamic magnetosphere, which is partially due to strong dayside reconnection and fast magnetospheric convection. It has been shown that dayside reconnection occurs even on low magnetic shear angles across the magnetopause. This drives quasi-steady region 1 field-aligned currents (FAC) that are observable in in-situ MESSENGER data. Here, the structure of the Hermean FAC-system is discussed and compared to the terrestrial counterpart. Due to the lack of a significant ionosphere at Mercury, it has to be examined how much of the poloidal FAC is reflected back to the magnetosphere, closed via toroidal currents in the planetary interior or via Pedersen currents in the tenuous exosphere. This investigation gives insights into the planetary conductivity structure as well as the exospheric plasma densities. Furthermore, it will be examined how much the only partially developed ring current at Mercury produces possible region 2 FAC signatures. We conclude with requirements to simulations that are needed to forecast the FAC structure on the southern hemisphere that will be closely studied with the upcoming BepiColombo mission.

Shear rupture of a directionally solidified eutectic gamma/gamma prime - alpha (Mo) alloy

NASA Technical Reports Server (NTRS)

Harf, F. H.

1978-01-01

Directionally solidified Mo alloys are evaluated to determine the shear rupture strength and to possibly improve it by microstructural and heat treatment variations. Bars of the alloy containing nominally 5.7% Al and 33.5% Mo by weight with balance Ni were directionally solidified at rates between 10 and 100 mm per hour in furnaces with thermal gradients at the liquid-solid interface of 250 or 100 C per cm. A limited number of longitudinal shear rupture tests were conducted at 760 C and 207 MPa in the as - solidified and in several heat treated conditions. It is shown that shear rupture failures are partly transgranular and that resistance to failure is prompted by good fiber alignment and a matrix structure consisting mainly of gamma prime. Well aligned as - solidified specimens sustained the shear stress for an average of 81 hours. A simulated coating heat treatment appeared to increase the transformation of gamma to gamma prime and raised the average shear life of aligned specimens to 111 hours. However, heat treatments at 1245 C and especially at 1190 C appeared to be detrimental by causing partial solutioning of the gamma prime, and reducing lives to 47 and 10 hours, respectively.

The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences

PubMed Central

Fourment, Mathieu; Gibbs, Mark J

2008-01-01

Background Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. Results The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. Conclusion VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically. PMID:18251994

Controlled growth of periodically aligned copper-silicide nanocrystal arrays on silicon directed by laser-induced periodic surface structures (LIPSS)

NASA Astrophysics Data System (ADS)

Nürnberger, Philipp; Reinhardt, Hendrik M.; Rhinow, Daniel; Riedel, René; Werner, Simon; Hampp, Norbert A.

2017-10-01

In this paper we introduce a versatile tool for the controlled growth and alignment of copper-silicide nanocrystals. The method takes advantage of a unique self-organization phenomenon denoted as laser-induced periodic surface structures (LIPSS). Copper films (3 ± 0.2 nm) are sputter-deposited onto single crystal silicon (100) substrates with a thin oxide layer (4 ± 0.2 nm), and subsequently exposed to linearly polarized nanosecond laser pulses (τ ≈ 6 ns) at a central wavelength of 532 nm. The irradiation triggers dewetting of the Cu film and simultaneous formation of periodic Cu nanowires (LIPSS), which partially penetrate the oxide layer to the Si substrate. These LIPSS act as nucleation centers for the growth of Cu-Si crystals during thermal processing at 500 °C under forming gas 95/5 atmosphere. Exemplified by our model system Cu/SiO2/Si, LIPSS are demonstrated to facilitate the diffusion reaction between Cu and underlying Si. Moreover, adjustment of the laser polarization allows us to precisely control the nanocrystal alignment with respect to the LIPSS orientation. Potential applications and conceivable alternatives of this process are discussed.

Grasping Beer Mugs: On the Dynamics of Alignment Effects Induced by Handled Objects

ERIC Educational Resources Information Center

Bub, Daniel N.; Masson, Michael E. J.

2010-01-01

We examined automatic spatial alignment effects evoked by handled objects. Using color as the relevant cue carried by an irrelevant handled object aligned or misaligned with the response hand, responses to color were faster when the handle aligned with the response hand. Alignment effects were observed only when the task was to make a reach and…

Jig Aligns Shadow Mask On CCD

NASA Technical Reports Server (NTRS)

Matus, Carlos V.

1989-01-01

Alignment viewed through microscope. Alignment jig positions shadow mask on charge-coupled device (CCD) so metal film deposited on it precisely. Allows CCD package to be inserted and removed without disturbing alignment of mask. Holds CCD packages securely and isolates it electrostatically while providing electrical contact to each of its pins. When alignment jig assembled with CCD, used to move mask under micrometer control.

Information Technology Governance Maturity: Examining the Moderating Effect on the Relationship between Strategic Alignment Maturity and Information Technology Effectiveness

ERIC Educational Resources Information Center

Kouakou, Claude N.

2013-01-01

The positive contribution of information technology (IT) in an organization is undeniable. Most organizations take advantage of that contributive benefit by aligning their business strategy with their IT strategy. This alignment is known as IT-business strategic alignment. Strategic alignment involves making the best possible use of corporate IT…

Global Network Alignment in the Context of Aging.

PubMed

Faisal, Fazle Elahi; Zhao, Han; Milenkovic, Tijana

2015-01-01

Analogous to sequence alignment, network alignment (NA) can be used to transfer biological knowledge across species between conserved network regions. NA faces two algorithmic challenges: 1) Which cost function to use to capture "similarities" between nodes in different networks? 2) Which alignment strategy to use to rapidly identify "high-scoring" alignments from all possible alignments? We "break down" existing state-of-the-art methods that use both different cost functions and different alignment strategies to evaluate each combination of their cost functions and alignment strategies. We find that a combination of the cost function of one method and the alignment strategy of another method beats the existing methods. Hence, we propose this combination as a novel superior NA method. Then, since human aging is hard to study experimentally due to long lifespan, we use NA to transfer aging-related knowledge from well annotated model species to poorly annotated human. By doing so, we produce novel human aging-related knowledge, which complements currently available knowledge about aging that has been obtained mainly by sequence alignment. We demonstrate significant similarity between topological and functional properties of our novel predictions and those of known aging-related genes. We are the first to use NA to learn more about aging.

The twilight zone of cis element alignments.

PubMed

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-02-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.

The twilight zone of cis element alignments

PubMed Central

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-01-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein–DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein–DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments. PMID:23268451

Nurses' Satisfaction With Using Nursing Information Systems From Technology Acceptance Model and Information Systems Success Model Perspectives: A Reductionist Approach.

PubMed

Lin, Hsien-Cheng

2017-02-01

Nursing information systems can enhance nursing practice and the efficiency and quality of administrative affairs within the nursing department and thus have been widely considered for implementation. Close alignment of human-computer interaction can advance optimal clinical performance with the use of information systems. However, a lack of introduction of the concept of alignment between users' perceptions and technological functionality has caused dissatisfaction, as shown in the existing literature. This study provides insight into the alignment between nurses' perceptions and how technological functionality affects their satisfaction with Nursing Information System use through a reductionist perspective of alignment. This cross-sectional study collected data from 531 registered nurses in Taiwan. The results indicated that "perceived usefulness in system quality alignment," "perceived usefulness in information quality alignment," "perceived ease of use in system quality alignment," "perceived ease of use in information quality alignment," and "perceived ease of use in service quality alignment" have significantly affected nurses' satisfaction with Nursing Information System use. However, "perceived usefulness in service quality alignment" had no significant effect on nurses' satisfaction. This study also provides some meaningful implications for theoretical and practical aspects of design.

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

Wilbur, Jeffrey D.; Gomez, Enrique D.; Ellsworth, Mark W.

A procedure for creating samples that can be repeatedly cycled between weakly aligned and strongly aligned states is described. Poly(styrene-b-isoprene) block copolymer samples were first shear-aligned and then cross-linked using a high energy electron beam. Samples with more than 1.0 cross-links per chain on average showed almost complete recovery of their initial alignment state even after 20 cycles of heating above the order–disorder transition temperature of the un-cross-linked block copolymer. Samples with 1.1 cross-links per chain, which showed over 90% loss of alignment on heating and almost 100% recovery of alignment on cooling, provided the best example of a reversiblemore » aligned-to-unaligned transition. Samples with lower cross-linking densities exhibited irreversible loss of alignment upon heating, while those with higher cross-linking densities exhibited less than 90% loss of alignment upon heating. Alignment was quantified by a technique that we call two color depolarized light scattering (TCDLS), an extension of the traditional depolarized light scattering experiment used to determine the state of order in block copolymers. Qualitative confirmation of our interpretation of TCDLS data was obtained by small-angle X-ray scattering and transmission electron microscopy.« less

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

PubMed

Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

2016-02-01

The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A new statistical framework to assess structural alignment quality using information compression

PubMed Central

Collier, James H.; Allison, Lloyd; Lesk, Arthur M.; Garcia de la Banda, Maria; Konagurthu, Arun S.

2014-01-01

Motivation: Progress in protein biology depends on the reliability of results from a handful of computational techniques, structural alignments being one. Recent reviews have highlighted substantial inconsistencies and differences between alignment results generated by the ever-growing stock of structural alignment programs. The lack of consensus on how the quality of structural alignments must be assessed has been identified as the main cause for the observed differences. Current methods assess structural alignment quality by constructing a scoring function that attempts to balance conflicting criteria, mainly alignment coverage and fidelity of structures under superposition. This traditional approach to measuring alignment quality, the subject of considerable literature, has failed to solve the problem. Further development along the same lines is unlikely to rectify the current deficiencies in the field. Results: This paper proposes a new statistical framework to assess structural alignment quality and significance based on lossless information compression. This is a radical departure from the traditional approach of formulating scoring functions. It links the structural alignment problem to the general class of statistical inductive inference problems, solved using the information-theoretic criterion of minimum message length. Based on this, we developed an efficient and reliable measure of structural alignment quality, I-value. The performance of I-value is demonstrated in comparison with a number of popular scoring functions, on a large collection of competing alignments. Our analysis shows that I-value provides a rigorous and reliable quantification of structural alignment quality, addressing a major gap in the field. Availability: http://lcb.infotech.monash.edu.au/I-value Contact: arun.konagurthu@monash.edu Supplementary information: Online supplementary data are available at http://lcb.infotech.monash.edu.au/I-value/suppl.html PMID:25161241

Using Quasi-Horizontal Alignment in the absence of the actual alignment.

PubMed

Banihashemi, Mohamadreza

2016-10-01

Horizontal alignment is a major roadway characteristic used in safety and operational evaluations of many facility types. The Highway Safety Manual (HSM) uses this characteristic in crash prediction models for rural two-lane highways, freeway segments, and freeway ramps/C-D roads. Traffic simulation models use this characteristic in their processes on almost all types of facilities. However, a good portion of roadway databases do not include horizontal alignment data; instead, many contain point coordinate data along the roadways. SHRP 2 Roadway Information Database (RID) is a good example of this type of data. Only about 5% of this geodatabase contains alignment information and for the rest, point data can easily be produced. Even though the point data can be used to extract actual horizontal alignment data but, extracting horizontal alignment is a cumbersome and costly process, especially for a database of miles and miles of highways. This research introduces a so called "Quasi-Horizontal Alignment" that can be produced easily and automatically from point coordinate data and can be used in the safety and operational evaluations of highways. SHRP 2 RID for rural two-lane highways in Washington State is used in this study. This paper presents a process through which Quasi-Horizontal Alignments are produced from point coordinates along highways by using spreadsheet software such as MS EXCEL. It is shown that the safety and operational evaluations of the highways with Quasi-Horizontal Alignments are almost identical to the ones with the actual alignments. In the absence of actual alignment the Quasi-Horizontal Alignment can easily be produced from any type of databases that contain highway coordinates such geodatabases and digital maps. Copyright © 2016 Elsevier Ltd. All rights reserved.

Laser beam alignment apparatus and method

DOEpatents

Gruhn, C.R.; Hammond, R.B.

The disclosure related to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

Laser beam alignment apparatus and method

DOEpatents

Gruhn, Charles R.; Hammond, Robert B.

1981-01-01

The disclosure relates to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

ARYANA: Aligning Reads by Yet Another Approach

PubMed Central

2014-01-01

Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. Contribution We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. Availability ARYANA with complete source code can be obtained from http://github.com/aryana-aligner PMID:25252881

The ties that bind: an integrative framework of physician-hospital alignment

PubMed Central

2011-01-01

Background Alignment between physicians and hospitals is of major importance to the health care sector. Two distinct approaches to align the medical staff with the hospital have characterized previous research. The first approach, economic integration, is rooted in the economic literature, in which alignment is realized by financial means. The second approach, noneconomic integration, represents a sociological perspective emphasizing the cooperative nature of their relationship. Discussion Empirical studies and management theory (agency theory and social exchange theory) are used to increase holistic understanding of physician hospital alignment. On the one hand, noneconomic integration is identified as a means to realize a cooperative relationship. On the other hand, economic integration is studied as a way to align financial incentives. The framework is developed around two key antecedent factors which play an important role in aligning the medical staff. First, provider financial risk bearing is identified as a driving force towards closer integration. Second, organizational trust is believed to be important in explaining the causal relation between noneconomic and economic integration. Summary Hospital financial risk bearing creates a greater need for closer cooperation with the medical staff and alignment of financial incentives. Noneconomic integration lies at the very basis of alignment. It contributes directly to alignment through the norm of reciprocity and indirectly by building trust with the medical staff, laying the foundation for alignment of financial incentives. PMID:21324128

The ties that bind: an integrative framework of physician-hospital alignment.

PubMed

Trybou, Jeroen; Gemmel, Paul; Annemans, Lieven

2011-02-15

Alignment between physicians and hospitals is of major importance to the health care sector. Two distinct approaches to align the medical staff with the hospital have characterized previous research. The first approach, economic integration, is rooted in the economic literature, in which alignment is realized by financial means. The second approach, noneconomic integration, represents a sociological perspective emphasizing the cooperative nature of their relationship. Empirical studies and management theory (agency theory and social exchange theory) are used to increase holistic understanding of physician hospital alignment. On the one hand, noneconomic integration is identified as a means to realize a cooperative relationship. On the other hand, economic integration is studied as a way to align financial incentives. The framework is developed around two key antecedent factors which play an important role in aligning the medical staff. First, provider financial risk bearing is identified as a driving force towards closer integration. Second, organizational trust is believed to be important in explaining the causal relation between noneconomic and economic integration. Hospital financial risk bearing creates a greater need for closer cooperation with the medical staff and alignment of financial incentives. Noneconomic integration lies at the very basis of alignment. It contributes directly to alignment through the norm of reciprocity and indirectly by building trust with the medical staff, laying the foundation for alignment of financial incentives.

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.

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

PubMed Central

Satija, Rahul; Novák, Ádám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-01-01

Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. Results We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the α-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. Conclusion BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from PMID:19715598

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.

PubMed

Satija, Rahul; Novák, Adám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-08-28

We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the alpha-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from http://www.stats.ox.ac.uk/~satija/BigFoot/

ARYANA: Aligning Reads by Yet Another Approach.

PubMed

Gholami, Milad; Arbabi, Aryan; Sharifi-Zarchi, Ali; Chitsaz, Hamidreza; Sadeghi, Mehdi

2014-01-01

Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $10(6) prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. ARYANA with complete source code can be obtained from http://github.com/aryana-aligner.

AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis

PubMed Central

Aniba, Mohamed Radhouene; Poch, Olivier; Marchler-Bauer, Aron; Thompson, Julie Dawn

2010-01-01

Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently outperforms the rest. This has led to the development of a number of ‘meta-methods’ that systematically run several aligners and merge the output into one single solution. Although these methods generally produce more accurate alignments, they are inefficient because all the aligners need to be run first and the choice of the best solution is made a posteriori. Here, we describe the development of a new expert system, AlexSys, for the multiple alignment of protein sequences. AlexSys incorporates an intelligent inference engine to automatically select an appropriate aligner a priori, depending only on the nature of the input sequences. The inference engine was trained on a large set of reference multiple alignments, using a novel machine learning approach. Applying AlexSys to a test set of 178 alignments, we show that the expert system represents a good compromise between alignment quality and running time, making it suitable for high throughput projects. AlexSys is freely available from http://alnitak.u-strasbg.fr/∼aniba/alexsys. PMID:20530533

Design of practical alignment device in KSTAR Thomson diagnostic

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

Lee, J. H., E-mail: jhlee@nfri.re.kr; University of Science and Technology; Lee, S. H.

2016-11-15

The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak’s Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broadmore » wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR’s Thomson scattering diagnostics.« less

Design of practical alignment device in KSTAR Thomson diagnostic.

PubMed

Lee, J H; Lee, S H; Yamada, I

2016-11-01

The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak's Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broad wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR's Thomson scattering diagnostics.

Studies on in situ magnetic alignment of bonded anisotropic Nd-Fe-B alloy powders

DOE PAGES

Nlebedim, I. C.; Ucar, Huseyin; Hatter, Christine B.; ...

2016-08-30

We presented some considerations for achieving high degree of alignment in polymer bonded permanent magnets via the results of a study on in situ magnetic alignment of anisotropic Nd-Fe-B magnet powders. Contributions from effect of the alignment temperature, alignment magnetic field and the properties of the polymer on the hard magnetic properties of the bonded magnet were considered. Moreover, the thermo-rheological properties of the polymer and the response of the magnet powders to the applied magnetic field indicate that hard magnetic properties were optimized at an alignment temperature just above the melting temperature of the EVA co-polymer. This agrees withmore » an observed correlation between the change in magnetization due to improved magnetic alignment of the anisotropic powders and the change in viscosity of the binder. Finally, manufacturing cost can be minimized by identifying optimum alignment temperatures and magnetic field strengths.« less

Unaligned instruction relocation

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

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unalignedmore » ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.« less

Mechanical design of multiple zone plates precision alignment apparatus for hard X-ray focusing in twenty-nanometer scale

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

Shu, Deming; Liu, Jie; Gleber, Sophie C.

An enhanced mechanical design of multiple zone plates precision alignment apparatus for hard x-ray focusing in a twenty-nanometer scale is provided. The precision alignment apparatus includes a zone plate alignment base frame; a plurality of zone plates; and a plurality of zone plate holders, each said zone plate holder for mounting and aligning a respective zone plate for hard x-ray focusing. At least one respective positioning stage drives and positions each respective zone plate holder. Each respective positioning stage is mounted on the zone plate alignment base frame. A respective linkage component connects each respective positioning stage and the respectivemore » zone plate holder. The zone plate alignment base frame, each zone plate holder and each linkage component is formed of a selected material for providing thermal expansion stability and positioning stability for the precision alignment apparatus.« less

ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.

PubMed

Hoffmann, Nils; Stoye, Jens

2009-08-15

We describe ChromA, a web-based alignment tool for chromatography-mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location.

QUASAR--scoring and ranking of sequence-structure alignments.

PubMed

Birzele, Fabian; Gewehr, Jan E; Zimmer, Ralf

2005-12-15

Sequence-structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence-structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence-structure alignments ranking) provides a unifying framework for scoring sequence-structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against 'standard-of-truth' structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.

Spatio-temporal alignment of multiple sensors

NASA Astrophysics Data System (ADS)

Zhang, Tinghua; Ni, Guoqiang; Fan, Guihua; Sun, Huayan; Yang, Biao

2018-01-01

Aiming to achieve the spatio-temporal alignment of multi sensor on the same platform for space target observation, a joint spatio-temporal alignment method is proposed. To calibrate the parameters and measure the attitude of cameras, an astronomical calibration method is proposed based on star chart simulation and collinear invariant features of quadrilateral diagonal between the observed star chart. In order to satisfy a temporal correspondence and spatial alignment similarity simultaneously, the method based on the astronomical calibration and attitude measurement in this paper formulates the video alignment to fold the spatial and temporal alignment into a joint alignment framework. The advantage of this method is reinforced by exploiting the similarities and prior knowledge of velocity vector field between adjacent frames, which is calculated by the SIFT Flow algorithm. The proposed method provides the highest spatio-temporal alignment accuracy compared to the state-of-the-art methods on sequences recorded from multi sensor at different times.

Unaligned instruction relocation

DOEpatents

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.; Sura, Zehra N.

2018-01-23

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unaligned ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.

Projected power iteration for network alignment

NASA Astrophysics Data System (ADS)

Onaran, Efe; Villar, Soledad

2017-08-01

The network alignment problem asks for the best correspondence between two given graphs, so that the largest possible number of edges are matched. This problem appears in many scientific problems (like the study of protein-protein interactions) and it is very closely related to the quadratic assignment problem which has graph isomorphism, traveling salesman and minimum bisection problems as particular cases. The graph matching problem is NP-hard in general. However, under some restrictive models for the graphs, algorithms can approximate the alignment efficiently. In that spirit the recent work by Feizi and collaborators introduce EigenAlign, a fast spectral method with convergence guarantees for Erd-s-Renyí graphs. In this work we propose the algorithm Projected Power Alignment, which is a projected power iteration version of EigenAlign. We numerically show it improves the recovery rates of EigenAlign and we describe the theory that may be used to provide performance guarantees for Projected Power Alignment.

Studies on in situ magnetic alignment of bonded anisotropic Nd-Fe-B alloy powders

NASA Astrophysics Data System (ADS)

Nlebedim, I. C.; Ucar, Huseyin; Hatter, Christine B.; McCallum, R. W.; McCall, Scott K.; Kramer, M. J.; Paranthaman, M. Parans

2017-01-01

Considerations for achieving high degree of alignment in polymer bonded permanent magnets are presented via the results of a study on in situ magnetic alignment of anisotropic Nd-Fe-B magnet powders. Contributions from effect of the alignment temperature, alignment magnetic field and the properties of the polymer on the hard magnetic properties of the bonded magnet were considered. The thermo-rheological properties of the polymer and the response of the magnet powders to the applied magnetic field indicate that hard magnetic properties were optimized at an alignment temperature just above the melting temperature of the EVA co-polymer. This agrees with an observed correlation between the change in magnetization due to improved magnetic alignment of the anisotropic powders and the change in viscosity of the binder. Manufacturing cost can be minimized by identifying optimum alignment temperatures and magnetic field strengths.

The geometry and volume of melt beneath Ethiopia

NASA Astrophysics Data System (ADS)

Kendall, J. M.; Hammond, J. O. S.

2016-12-01

A range of seismic measurements can be used to map melt distribution in the crust and uppermost mantle. These include seismic P- and S-wave velocities derived from surface- and body-wave tomography, Vp/Vs ratios obtained from receiver functions, and estimates of seismic anisotropy and attenuation. The most obvious melt parameter that seismic data might be sensitive to is volume fraction. However, such data are more sensitive to the aspect ratio of melt inclusions, which is controlled by the melt wetting angle or in other words the shape of the melt inclusion. To better understand this we perform numerical modelling, varying the shape and amount of melt, to show how various seismic phases are effected by melt. To consider the effects on seismic anisotropy we assume that the melt can be stored in pockets of melt that are either horizontally or vertically aligned (e.g., sills versus dykes). We then consider a range of seismic observations from the rifting environment of Ethiopia. Recent studies of P- and S-wave tomography, Rayleigh and Love waves, and Pn or wide angle P-wave refractions provide provide complimentary constraints on melt volume, orientation and inclusion aspect ratio. Furthermore, receiver functions and shear-wave splitting in body waves show strong anisotropy in this region and can be used to constrain the strike of vertically-aligned partial melt. We show that melt in the mantle beneath Ethiopia is likely stored in low aspect ratio disk-like inclusions, suggesting melt is not in textural equilibrium. We estimate that 2-7% vertically aligned melt is stored beneath the Main Ethiopian Rift, >6% horizontally and vertically aligned melt is stored beneath the Afar-region of the Red Sea Rift and 1-6% horizontally aligned melt is stored beneath the Danakil microplate. This supports ideas of strong shear-derived segregation of melt in narrow parts of the rift and large volumes of melt beneath Afar.

Validation of Splicing Events in Transcriptome Sequencing Data

PubMed Central

Kaisers, Wolfgang; Ptok, Johannes; Schwender, Holger; Schaal, Heiner

2017-01-01

Genomic alignments of sequenced cellular messenger RNA contain gapped alignments which are interpreted as consequence of intron removal. The resulting gap-sites, genomic locations of alignment gaps, are landmarks representing potential splice-sites. As alignment algorithms report gap-sites with a considerable false discovery rate, validations are required. We describe two quality scores, gap quality score (gqs) and weighted gap information score (wgis), developed for validation of putative splicing events: While gqs solely relies on alignment data wgis additionally considers information from the genomic sequence. FASTQ files obtained from 54 human dermal fibroblast samples were aligned against the human genome (GRCh38) using TopHat and STAR aligner. Statistical properties of gap-sites validated by gqs and wgis were evaluated by their sequence similarity to known exon-intron borders. Within the 54 samples, TopHat identifies 1,000,380 and STAR reports 6,487,577 gap-sites. Due to the lack of strand information, however, the percentage of identified GT-AG gap-sites is rather low. While gap-sites from TopHat contain ≈89% GT-AG, gap-sites from STAR only contain ≈42% GT-AG dinucleotide pairs in merged data from 54 fibroblast samples. Validation with gqs yields 156,251 gap-sites from TopHat alignments and 166,294 from STAR alignments. Validation with wgis yields 770,327 gap-sites from TopHat alignments and 1,065,596 from STAR alignments. Both alignment algorithms, TopHat and STAR, report gap-sites with considerable false discovery rate, which can drastically be reduced by validation with gqs and wgis. PMID:28545234

Nuclear reactor internals alignment configuration

DOEpatents

Gilmore, Charles B [Greensburg, PA; Singleton, Norman R [Murrysville, PA

2009-11-10

An alignment system that employs jacking block assemblies and alignment posts around the periphery of the top plate of a nuclear reactor lower internals core shroud to align an upper core plate with the lower internals and the core shroud with the core barrel. The distal ends of the alignment posts are chamfered and are closely received within notches machined in the upper core plate at spaced locations around the outer circumference of the upper core plate. The jacking block assemblies are used to center the core shroud in the core barrel and the alignment posts assure the proper orientation of the upper core plate. The alignment posts may alternately be formed in the upper core plate and the notches may be formed in top plate.

X-ray verification of an optically aligned off-plane grating module

NASA Astrophysics Data System (ADS)

Donovan, Benjamin D.; McEntaffer, Randall L.; Tutt, James H.; DeRoo, Casey T.; Allured, Ryan; Gaskin, Jessica A.; Kolodziejczak, Jeffery J.

2018-01-01

Off-plane x-ray reflection gratings are theoretically capable of achieving high resolution and high diffraction efficiencies over the soft x-ray bandpass, making them an ideal technology to implement on upcoming x-ray spectroscopy missions. To achieve high effective area, these gratings must be aligned into grating modules. X-ray testing was performed on an aligned grating module to assess the current optical alignment methods. Results indicate that the grating module achieved the desired alignment for an upcoming x-ray spectroscopy suborbital rocket payload with modest effective area and resolving power. These tests have also outlined a pathway towards achieving the stricter alignment tolerances of future x-ray spectrometer payloads, which require improvements in alignment metrology, grating fabrication, and testing techniques.

Optical alignment of the JWST ISIM to the OTE simulator (OSIM): current concept and design studies

NASA Astrophysics Data System (ADS)

Frey, Bradley J.; Davila, Pamela S.; Hagopian, John G.; Marsh, James M.; Ohl, Raymond G.; Wilson, Mark E.; Young, Philip J.

2007-09-01

The James Webb Space Telescope's (JWST) Integrated Science Instrument Module (ISIM) contains the observatory's four science instruments and their support subsystems. During alignment and test of the integrated ISIM at NASA's Goddard Space Flight Center (GSFC), the Optical telescope element SIMulator (OSIM) will be used to optically stimulate the science instruments to verify their operation and performance. In this paper we present the design of two cryogenic alignment fixtures that will be used to align the OSIM to the ISIM during testing at GSFC. These fixtures, the Master Alignment Target Fixture (MATF) and the ISIM Alignment Target Fixture (IATF), will provide continuous, six degree of freedom feedback to OSIM during initial ambient alignment as well as during cryogenic vacuum testing. These fixtures will allow us to position the OSIM and detect OSIM-ISIM absolute alignment to better than 180 microns in translation and 540 micro-radians in rotation. We will provide a brief overview of the OSIM system and we will also discuss the relevance of these fixtures in the context of the overall ISIM alignment and test plan.

Node fingerprinting: an efficient heuristic for aligning biological networks.

PubMed

Radu, Alex; Charleston, Michael

2014-10-01

With the continuing increase in availability of biological data and improvements to biological models, biological network analysis has become a promising area of research. An emerging technique for the analysis of biological networks is through network alignment. Network alignment has been used to calculate genetic distance, similarities between regulatory structures, and the effect of external forces on gene expression, and to depict conditional activity of expression modules in cancer. Network alignment is algorithmically complex, and therefore we must rely on heuristics, ideally as efficient and accurate as possible. The majority of current techniques for network alignment rely on precomputed information, such as with protein sequence alignment, or on tunable network alignment parameters, which may introduce an increased computational overhead. Our presented algorithm, which we call Node Fingerprinting (NF), is appropriate for performing global pairwise network alignment without precomputation or tuning, can be fully parallelized, and is able to quickly compute an accurate alignment between two biological networks. It has performed as well as or better than existing algorithms on biological and simulated data, and with fewer computational resources. The algorithmic validation performed demonstrates the low computational resource requirements of NF.

BatMis: a fast algorithm for k-mismatch mapping.

PubMed

Tennakoon, Chandana; Purbojati, Rikky W; Sung, Wing-Kin

2012-08-15

Second-generation sequencing (SGS) generates millions of reads that need to be aligned to a reference genome allowing errors. Although current aligners can efficiently map reads allowing a small number of mismatches, they are not well suited for handling a large number of mismatches. The efficiency of aligners can be improved using various heuristics, but the sensitivity and accuracy of the alignments are sacrificed. In this article, we introduce Basic Alignment tool for Mismatches (BatMis)--an efficient method to align short reads to a reference allowing k mismatches. BatMis is a Burrows-Wheeler transformation based aligner that uses a seed and extend approach, and it is an exact method. Benchmark tests show that BatMis performs better than competing aligners in solving the k-mismatch problem. Furthermore, it can compete favorably even when compared with the heuristic modes of the other aligners. BatMis is a useful alternative for applications where fast k-mismatch mappings, unique mappings or multiple mappings of SGS data are required. BatMis is written in C/C++ and is freely available from http://code.google.com/p/batmis/

Efficient and robust model-to-image alignment using 3D scale-invariant features.

PubMed

Toews, Matthew; Wells, William M

2013-04-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. Copyright © 2012 Elsevier B.V. All rights reserved.

Fast Response and Spontaneous Alignment in Liquid Crystals Doped with 12-Hydroxystearic Acid Gelators

PubMed Central

Lin, Hui-Chi; Wang, Chih-Hung; Wang, Jyun-Kai; Tsai, Sheng-Feng

2018-01-01

The spontaneous vertical alignment of liquid crystals (LCs) in gelator (12-hydroxystearic acid)-doped LC cells was studied. Gelator-induced alignment can be used in both positive and negative LC cells. The electro-optical characteristics of the gelator-doped negative LC cell were similar to those of an LC cell that contained a vertically aligned (VA) host. The rise time of the gelator-doped LC cell was two orders of magnitude shorter than that of the VA host LC cell. The experimental results indicate that the gelator-induced vertical alignment of LC molecules occurred not only on the surface of the indium tin oxide (ITO) but also on the homogeneous alignment layer. Various LC alignments (planar, hybrid, multistable hybrid, and vertical alignments) were achieved by modulating the doped gelator concentrations. The multistable characteristic of LCs doped with the gelator is also presented. The alignment by doping with a gelator reduces the manufacturing costs and provides a means of fabricating fast-responding, flexible LC displays using a low-temperature process. PMID:29735937

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

PubMed Central

Budavari, Tamas; Langmead, Ben; Wheelan, Sarah J.; Salzberg, Steven L.; Szalay, Alexander S.

2015-01-01

When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected. We formulated this task as a series of list-processing operations that can be efficiently performed on graphics processing unit (GPU) hardware.We followed this approach in implementing a read aligner called Arioc that uses GPU-based parallel sort and reduction techniques to identify high-priority locations where potential alignments may be found. We then carried out a read-by-read comparison of Arioc’s reported alignments with the alignments found by several leading read aligners. With simulated reads, Arioc has comparable or better accuracy than the other read aligners we tested. With human sequencing reads, Arioc demonstrates significantly greater throughput than the other aligners we evaluated across a wide range of sensitivity settings. The Arioc software is available at https://github.com/RWilton/Arioc. It is released under a BSD open-source license. PMID:25780763

Efficient and Robust Model-to-Image Alignment using 3D Scale-Invariant Features

PubMed Central

Toews, Matthew; Wells, William M.

2013-01-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a-posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. PMID:23265799

Optical tools and techniques for aligning solar payloads with the SPARCS control system. [Solar Pointing Aerobee Rocket Control System

NASA Technical Reports Server (NTRS)

Thomas, N. L.; Chisel, D. M.

1976-01-01

The success of a rocket-borne experiment depends not only on the pointing of the attitude control system, but on the alignment of the attitude control system to the payload. To ensure proper alignment, special optical tools and alignment techniques are required. Those that were used in the SPARCS program are described and discussed herein. These tools include theodolites, autocollimators, a 38-cm diameter solar simulator, a high-performance 1-m heliostat to provide a stable solar source during the integration of the rocket payload, a portable 75-cm sun tracker for use at the launch site, and an innovation called the Solar Alignment Prism. Using the real sun as the primary reference under field conditions, the Solar Alignment Prism facilitates the coalignment of the attitude sun sensor with the payload. The alignment techniques were developed to ensure the precise alignment of the solar payloads to the SPARCS attitude sensors during payload integration and to verify the required alignment under field conditions just prior to launch.

Alignment displacements of the solar optical telescope primary mirror

NASA Technical Reports Server (NTRS)

Medenica, W. V.

1978-01-01

Solar optical telescope is a space shuttle payload which is at the present time (1978) being planned. The selected alignment method for the telescope's primary mirror is such that the six inclined legs supporting the mirror are at the same time motorized alignment actuators, changing their own length according to the alignment requirement and command. The alignment displacements were described, including circumvention of some apparent NASTRAN limitations.

Automatic target alignment of the Helios laser system

NASA Astrophysics Data System (ADS)

Liberman, I.; Viswanathan, V. K.; Klein, M.; Seery, B. D.

1980-05-01

An automatic target-alignment technique for the Helios laser facility is reported and verified experimentally. The desired alignment condition is completely described by an autocollimation test. A computer program examines the autocollimated return pattern from the surrogate target and correctly describes any changes required in mirror orientation to yield optimum target alignment with either aberrated or misaligned beams. Automated on-line target alignment is thus shown to be feasible.

Development of a method of alignment between various SOLAR MAXIMUM MISSION experiments

NASA Technical Reports Server (NTRS)

1977-01-01

Results of an engineering study of the methods of alignment between various experiments for the solar maximum mission are described. The configuration studied consists of the instruments, mounts and instrument support platform located within the experiment module. Hardware design, fabrication methods and alignment techniques were studied with regard to optimizing the coalignment between the experiments and the fine sun sensor. The proposed hardware design was reviewed with regard to loads, stress, thermal distortion, alignment error budgets, fabrication techniques, alignment techniques and producibility. Methods of achieving comparable alignment accuracies on previous projects were also reviewed.

Electric-Field-Induced Alignment of Block Copolymer/Nanoparticle Blends

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

Liedel, Clemens; Schindler, Kerstin; Pavan, Mariela J.

External electric fi elds readily align birefringent block-copolymer mesophases. In this study the effect of gold nanoparticles on the electric-fi eld-induced alignment of a lamellae-forming polystyrene- block -poly(2-vinylpyridine) copolymer is assessed. Nanoparticles are homogeneously dispersed in the styrenic phase and promote the quantitative alignment of lamellar domains by substantially lowering the critical field strength above which alignment proceeds. The results suggest that the electric-fi eldassisted alignment of nanostructured block copolymer/nanoparticle composites may offer a simple way to greatly mitigate structural and orientational defects of such fi lms under benign experimental conditions.

Alignments of Dark Matter Halos with Large-scale Tidal Fields: Mass and Redshift Dependence

NASA Astrophysics Data System (ADS)

Chen, Sijie; Wang, Huiyuan; Mo, H. J.; Shi, Jingjing

2016-07-01

Large-scale tidal fields estimated directly from the distribution of dark matter halos are used to investigate how halo shapes and spin vectors are aligned with the cosmic web. The major, intermediate, and minor axes of halos are aligned with the corresponding tidal axes, and halo spin axes tend to be parallel with the intermediate axes and perpendicular to the major axes of the tidal field. The strengths of these alignments generally increase with halo mass and redshift, but the dependence is only on the peak height, ν \\equiv {δ }{{c}}/σ ({M}{{h}},z). The scaling relations of the alignment strengths with the value of ν indicate that the alignment strengths remain roughly constant when the structures within which the halos reside are still in a quasi-linear regime, but decreases as nonlinear evolution becomes more important. We also calculate the alignments in projection so that our results can be compared directly with observations. Finally, we investigate the alignments of tidal tensors on large scales, and use the results to understand alignments of halo pairs separated at various distances. Our results suggest that the coherent structure of the tidal field is the underlying reason for the alignments of halos and galaxies seen in numerical simulations and in observations.

Halo Intrinsic Alignment: Dependence on Mass, Formation Time, and Environment

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

Xia, Qianli; Kang, Xi; Wang, Peng

In this paper we use high-resolution cosmological simulations to study halo intrinsic alignment and its dependence on mass, formation time, and large-scale environment. In agreement with previous studies using N -body simulations, it is found that massive halos have stronger alignment. For the first time, we find that for a given halo mass older halos have stronger alignment and halos in cluster regions also have stronger alignment than those in filaments. To model these dependencies, we extend the linear alignment model with inclusion of halo bias and find that the halo alignment with its mass and formation time dependence canmore » be explained by halo bias. However, the model cannot account for the environment dependence, as it is found that halo bias is lower in clusters and higher in filaments. Our results suggest that halo bias and environment are independent factors in determining halo alignment. We also study the halo alignment correlation function and find that halos are strongly clustered along their major axes and less clustered along the minor axes. The correlated halo alignment can extend to scales as large as 100 h {sup −1} Mpc, where its feature is mainly driven by the baryon acoustic oscillation effect.« less

Enhanced critical-current in P-doped BaFe2As2 thin films on metal substrates arising from poorly aligned grain boundaries.

PubMed

Sato, Hikaru; Hiramatsu, Hidenori; Kamiya, Toshio; Hosono, Hideo

2016-11-11

Thin films of the iron-based superconductor BaFe 2 (As 1-x P x ) 2 (Ba122:P) were fabricated on polycrystalline metal-tape substrates with two kinds of in-plane grain boundary alignments (well aligned (4°) and poorly aligned (8°)) by pulsed laser deposition. The poorly aligned substrate is not applicable to cuprate-coated conductors because the in-plane alignment >4° results in exponential decay of the critical current density (J c ). The Ba122:P film exhibited higher J c at 4 K when grown on the poorly aligned substrate than on the well-aligned substrate even though the crystallinity was poorer. It was revealed that the misorientation angles of the poorly aligned samples were less than 6°, which are less than the critical angle of an iron-based superconductor, cobalt-doped BaFe 2 As 2 (~9°), and the observed strong pinning in the Ba122:P is attributed to the high-density grain boundaries with the misorientation angles smaller than the critical angle. This result reveals a distinct advantage over cuprate-coated conductors because well-aligned metal-tape substrates are not necessary for practical applications of the iron-based superconductors.

Effect of alignment perturbations in a trans-tibial prosthesis user: A pilot study.

PubMed

Courtney, Anna; Orendurff, Michael S; Buis, Arjan

2016-04-01

A recurring complication in trans-tibial prosthetic limb users is "poor socket fit" with painful residuum-socket interfaces, a consequence of excess pressure. This is due to both poor socket fit and poor socket alignment; however, the interaction of these factors has not been quantified. Through evaluation of kinetic data this study aimed to articulate an interaction uniting socket design, alignment and interface pressures. The results will help to refine future studies and will hopefully help determine whether sockets can be designed, fitted and aligned to maximize mobility whilst minimizing injurious forces. Interface pressures were recorded throughout ambulation in one user with "optimal (reference) alignment" followed by 5 malalignments in a patellar tendon-bearing and a hydrocast socket. Marked differences in pressure distribution were discovered when equating the patellar tendon-bearing against the hydrocast socket and when comparing interface pressures from reference with offset alignment. Patellar tendon-bearing sockets were found to be more sensitive to alignment perturbations than hydrocast sockets. A complex interaction was found, with the most prominent finding demonstrating the requisite for attainment of optimal alignment: a translational alignment error of 10 mm can increase maximum peak pressures by 227% (mean 17.5%). Refinements for future trials are described and the necessity for future research into socket design, alignment and interface pressures has been estabilished.

Engineering survey planning for the alignment of a particle accelerator: part I. Proposition of an assessment method

NASA Astrophysics Data System (ADS)

Junqueira Leão, Rodrigo; Raffaelo Baldo, Crhistian; Collucci da Costa Reis, Maria Luisa; Alves Trabanco, Jorge Luiz

2018-03-01

The performance of particle accelerators depends highly on the relative alignment between their components. The position and orientation of the magnetic lenses that form the trajectory of the charged beam is kept to micrometric tolerances in a range of hundreds of meters of the length of the machines. Therefore, the alignment problem is fundamentally of a dimensional metrology nature. There is no common way of expressing these tolerances in terms of terminology and alignment concept. The alignment needs for a certain machine is normally given in terms of deviations between the position of any magnet in the accelerator and the fitted line that relates the actual position of the magnets’ assembly. Root mean square errors and standard deviations are normally used interchangeably and measurement uncertainty is often neglected. Although some solutions have been employed successfully in several accelerators, there is no off-the-shelf solution to perform the alignment. Also, each alignment campaign makes use of different measuring instruments to achieve the desired results, which makes the alignment process a complex measurement chain. This paper explores these issues by reviewing the tolerances specified for the alignment of particle accelerators, and proposes a metric to assess the quality of the alignment. The metric has the advantage of fully integrating the measurement uncertainty in the process.

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics

PubMed Central

Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M.

2015-01-01

Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system. PMID:26710335

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

PubMed

Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M

2015-01-01

Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

PubMed

Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

2018-05-21

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies.

PubMed

Zeng, Lu; Kortschak, R Daniel; Raison, Joy M; Bertozzi, Terry; Adelson, David L

2018-01-01

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package.

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

PubMed Central

Zeng, Lu; Kortschak, R. Daniel; Raison, Joy M.

2018-01-01

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package. PMID:29538441

Understanding performance management in primary care.

PubMed

Rogan, Lisa; Boaden, Ruth

2017-02-13

Purpose Principal-agent theory (PAT) has been used to understand relationships among different professional groups and explain performance management between organisations, but is rarely used for research within primary care. The purpose of this paper is to explore whether PAT can be used to attain a better understanding of performance management in primary care. Design/methodology/approach Purposive sampling was used to identify a range of general practices in the North-west of England. Interviews were carried out with directors, managers and clinicians in commissioning and regional performance management organisations and within general practices, and the data analysed using matrix analysis techniques to produce a case study of performance management. Findings There are various elements of the principal-agent framework that can be applied in primary care. Goal alignment is relevant, but can only be achieved through clear, strategic direction and consistent interpretation of objectives at all levels. There is confusion between performance measurement and performance management and a tendency to focus on things that are easy to measure whilst omitting aspects of care that are more difficult to capture. Appropriate use of incentives, good communication, clinical engagement, ownership and trust affect the degree to which information asymmetry is overcome and goal alignment achieved. Achieving the right balance between accountability and clinical autonomy is important to ensure governance and financial balance without stifling innovation. Originality/value The principal-agent theoretical framework can be used to attain a better understanding of performance management in primary care; although it is likely that only partial goal alignment will be achieved, dependent on the extent and level of alignment of a range of factors.

Delineating slowly and rapidly evolving fractions of the Drosophila genome.

PubMed

Keith, Jonathan M; Adams, Peter; Stephen, Stuart; Mattick, John S

2008-05-01

Evolutionary conservation is an important indicator of function and a major component of bioinformatic methods to identify non-protein-coding genes. We present a new Bayesian method for segmenting pairwise alignments of eukaryotic genomes while simultaneously classifying segments into slowly and rapidly evolving fractions. We also describe an information criterion similar to the Akaike Information Criterion (AIC) for determining the number of classes. Working with pairwise alignments enables detection of differences in conservation patterns among closely related species. We analyzed three whole-genome and three partial-genome pairwise alignments among eight Drosophila species. Three distinct classes of conservation level were detected. Sequences comprising the most slowly evolving component were consistent across a range of species pairs, and constituted approximately 62-66% of the D. melanogaster genome. Almost all (>90%) of the aligned protein-coding sequence is in this fraction, suggesting much of it (comprising the majority of the Drosophila genome, including approximately 56% of non-protein-coding sequences) is functional. The size and content of the most rapidly evolving component was species dependent, and varied from 1.6% to 4.8%. This fraction is also enriched for protein-coding sequence (while containing significant amounts of non-protein-coding sequence), suggesting it is under positive selection. We also classified segments according to conservation and GC content simultaneously. This analysis identified numerous sub-classes of those identified on the basis of conservation alone, but was nevertheless consistent with that classification. Software, data, and results available at www.maths.qut.edu.au/-keithj/. Genomic segments comprising the conservation classes available in BED format.

Anisotropic piezoresistivity characteristics of aligned carbon nanotube-polymer nanocomposites

NASA Astrophysics Data System (ADS)

Sengezer, Engin C.; Seidel, Gary D.; Bodnar, Robert J.

2017-09-01

Dielectrophoresis under the application of AC electric fields is one of the primary fabrication techniques for obtaining aligned carbon nanotube (CNT)-polymer nanocomposites, and is used here to generate long range alignment of CNTs at the structural level. The degree of alignment of CNTs within this long range architecture is observed via polarized Raman spectroscopy so that its influence on the electrical conductivity and piezoresistive response in both the alignment and transverse to alignment directions can be assessed. Nanocomposite samples consisting of randomly oriented, well dispersed single-wall carbon nanotubes (SWCNTs) and of long range electric field aligned SWCNTs in a photopolymerizable monomer blend (urethane dimethacrylate and 1,6-hexanediol dimethacrylate) are quantitatively and qualitatively evaluated. Piezoresistive sensitivities in form of gauge factors were measured for randomly oriented, well dispersed specimens with 0.03, 0.1 and 0.5 wt% SWCNTs and compared with gauge factors in both the axial and transverse to SWCNT alignment directions for electric field aligned 0.03 wt% specimens under both quasi-static monotonic and cyclic tensile loading. Gauge factors in the axial direction were observed to be on the order of 2, while gauge factors in the transverse direction demonstrated a 5 fold increase with values on the order of 10 for aligned specimens. Based on Raman analysis, it is believed the higher sensitivity of the transverse direction is related to architectural evolution of misaligned bridging structures which connect alignment structures under load due to Poisson’s contraction.

Alignment as a Teacher Variable

ERIC Educational Resources Information Center

Porter, Andrew C.; Smithson, John; Blank, Rolf; Zeidner, Timothy

2007-01-01

With the exception of the procedures developed by Porter and colleagues (Porter, 2002), other methods of defining and measuring alignment are essentially limited to alignment between tests and standards. Porter's procedures have been generalized to investigating the alignment between content standards, tests, textbooks, and even classroom…

The number of reduced alignments between two DNA sequences

PubMed Central

2014-01-01

Background In this study we consider DNA sequences as mathematical strings. Total and reduced alignments between two DNA sequences have been considered in the literature to measure their similarity. Results for explicit representations of some alignments have been already obtained. Results We present exact, explicit and computable formulas for the number of different possible alignments between two DNA sequences and a new formula for a class of reduced alignments. Conclusions A unified approach for a wide class of alignments between two DNA sequences has been provided. The formula is computable and, if complemented by software development, will provide a deeper insight into the theory of sequence alignment and give rise to new comparison methods. AMS Subject Classification Primary 92B05, 33C20, secondary 39A14, 65Q30 PMID:24684679

Beam alignment based on two-dimensional power spectral density of a near-field image.

PubMed

Wang, Shenzhen; Yuan, Qiang; Zeng, Fa; Zhang, Xin; Zhao, Junpu; Li, Kehong; Zhang, Xiaolu; Xue, Qiao; Yang, Ying; Dai, Wanjun; Zhou, Wei; Wang, Yuanchen; Zheng, Kuixing; Su, Jingqin; Hu, Dongxia; Zhu, Qihua

2017-10-30

Beam alignment is crucial to high-power laser facilities and is used to adjust the laser beams quickly and accurately to meet stringent requirements of pointing and centering. In this paper, a novel alignment method is presented, which employs data processing of the two-dimensional power spectral density (2D-PSD) for a near-field image and resolves the beam pointing error relative to the spatial filter pinhole directly. Combining this with a near-field fiducial mark, the operation of beam alignment is achieved. It is experimentally demonstrated that this scheme realizes a far-field alignment precision of approximately 3% of the pinhole size. This scheme adopts only one near-field camera to construct the alignment system, which provides a simple, efficient, and low-cost way to align lasers.

Functional Alignment of Metabolic Networks.

PubMed

Mazza, Arnon; Wagner, Allon; Ruppin, Eytan; Sharan, Roded

2016-05-01

Network alignment has become a standard tool in comparative biology, allowing the inference of protein function, interaction, and orthology. However, current alignment techniques are based on topological properties of networks and do not take into account their functional implications. Here we propose, for the first time, an algorithm to align two metabolic networks by taking advantage of their coupled metabolic models. These models allow us to assess the functional implications of genes or reactions, captured by the metabolic fluxes that are altered following their deletion from the network. Such implications may spread far beyond the region of the network where the gene or reaction lies. We apply our algorithm to align metabolic networks from various organisms, ranging from bacteria to humans, showing that our alignment can reveal functional orthology relations that are missed by conventional topological alignments.

Integrative network alignment reveals large regions of global network similarity in yeast and human.

PubMed

Kuchaiev, Oleksii; Przulj, Natasa

2011-05-15

High-throughput methods for detecting molecular interactions have produced large sets of biological network data with much more yet to come. Analogous to sequence alignment, efficient and reliable network alignment methods are expected to improve our understanding of biological systems. Unlike sequence alignment, network alignment is computationally intractable. Hence, devising efficient network alignment heuristics is currently a foremost challenge in computational biology. We introduce a novel network alignment algorithm, called Matching-based Integrative GRAph ALigner (MI-GRAAL), which can integrate any number and type of similarity measures between network nodes (e.g. proteins), including, but not limited to, any topological network similarity measure, sequence similarity, functional similarity and structural similarity. Hence, we resolve the ties in similarity measures and find a combination of similarity measures yielding the largest contiguous (i.e. connected) and biologically sound alignments. MI-GRAAL exposes the largest functional, connected regions of protein-protein interaction (PPI) network similarity to date: surprisingly, it reveals that 77.7% of proteins in the baker's yeast high-confidence PPI network participate in such a subnetwork that is fully contained in the human high-confidence PPI network. This is the first demonstration that species as diverse as yeast and human contain so large, continuous regions of global network similarity. We apply MI-GRAAL's alignments to predict functions of un-annotated proteins in yeast, human and bacteria validating our predictions in the literature. Furthermore, using network alignment scores for PPI networks of different herpes viruses, we reconstruct their phylogenetic relationship. This is the first time that phylogeny is exactly reconstructed from purely topological alignments of PPI networks. Supplementary files and MI-GRAAL executables: http://bio-nets.doc.ic.ac.uk/MI-GRAAL/.

Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.

PubMed

Neuwald, Andrew F

2009-08-01

The patterns of sequence similarity and divergence present within functionally diverse, evolutionarily related proteins contain implicit information about corresponding biochemical similarities and differences. A first step toward accessing such information is to statistically analyze these patterns, which, in turn, requires that one first identify and accurately align a very large set of protein sequences. Ideally, the set should include many distantly related, functionally divergent subgroups. Because it is extremely difficult, if not impossible for fully automated methods to align such sequences correctly, researchers often resort to manual curation based on detailed structural and biochemical information. However, multiply-aligning vast numbers of sequences in this way is clearly impractical. This problem is addressed using Multiply-Aligned Profiles for Global Alignment of Protein Sequences (MAPGAPS). The MAPGAPS program uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences. It relies on Karlin-Altschul statistics for sensitivity and on PSI-BLAST (and other) heuristics for speed. Using as input a carefully curated multiple-profile alignment for P-loop GTPases, MAPGAPS correctly aligned weakly conserved sequence motifs within 33 distantly related GTPases of known structure. By comparison, the sequence- and structurally based alignment methods hmmalign and PROMALS3D misaligned at least 11 and 23 of these regions, respectively. When applied to a dataset of 65 million protein sequences, MAPGAPS identified, classified and aligned (with comparable accuracy) nearly half a million putative P-loop GTPase sequences. A C++ implementation of MAPGAPS is available at http://mapgaps.igs.umaryland.edu. Supplementary data are available at Bioinformatics online.

Effect of alignment changes on sagittal and coronal socket reaction moment interactions in transtibial prostheses.

PubMed

Kobayashi, Toshiki; Orendurff, Michael S; Zhang, Ming; Boone, David A

2013-04-26

Alignment is important for comfortable and stable gait of lower-limb prosthesis users. The magnitude of socket reaction moments in the multiple planes acting simultaneously upon the residual limb may be related to perception of comfort in individuals using prostheses through socket interface pressures. The aim of this study was to investigate the effect of prosthetic alignment changes on sagittal and coronal socket reaction moment interactions (moment-moment curves) and to characterize the curves in 11 individuals with transtibial amputation using novel moment-moment interaction parameters measured by plotting sagittal socket reaction moments versus coronal ones under various alignment conditions. A custom instrumented prosthesis alignment component was used to measure socket reaction moments during walking. Prosthetic alignment was tuned to a nominally aligned condition by a prosthetist, and from this position, angular (3° and 6° of flexion, extension, abduction or adduction of the socket) and translational (5mm and 10mm of anterior, posterior, medial or lateral translation of the socket) alignment changes were performed in either the sagittal or the coronal plane in a randomized manner. A total of 17 alignment conditions were tested. Coronal angulation and translation alignment changes demonstrated similar consistent changes in the moment-moment curves. Sagittal alignment changes demonstrated more complex changes compared to the coronal alignment changes. Effect of sagittal angulations and translations on the moment-moment curves was different during 2nd rocker (mid-stance) with extension malalignment appearing to cause medio-lateral instability. Presentation of coronal and sagittal socket reaction moment interactions may provide useful visual information for prosthetists to understand the biomechanical effects of malalignment of transtibial prostheses. Copyright © 2013 Elsevier Ltd. All rights reserved.

Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines.

PubMed

Oliveira, Francisco P M; Tavares, João Manuel R S

2013-03-01

This article presents an enhanced methodology to align plantar pressure image sequences simultaneously in time and space. The temporal alignment of the sequences is accomplished using B-splines in the time modeling, and the spatial alignment can be attained using several geometric transformation models. The methodology was tested on a dataset of 156 real plantar pressure image sequences (3 sequences for each foot of the 26 subjects) that was acquired using a common commercial plate during barefoot walking. In the alignment of image sequences that were synthetically deformed both in time and space, an outstanding accuracy was achieved with the cubic B-splines. This accuracy was significantly better (p < 0.001) than the one obtained using the best solution proposed in our previous work. When applied to align real image sequences with unknown transformation involved, the alignment based on cubic B-splines also achieved superior results than our previous methodology (p < 0.001). The consequences of the temporal alignment on the dynamic center of pressure (COP) displacement was also assessed by computing the intraclass correlation coefficients (ICC) before and after the temporal alignment of the three image sequence trials of each foot of the associated subject at six time instants. The results showed that, generally, the ICCs related to the medio-lateral COP displacement were greater when the sequences were temporally aligned than the ICCs of the original sequences. Based on the experimental findings, one can conclude that the cubic B-splines are a remarkable solution for the temporal alignment of plantar pressure image sequences. These findings also show that the temporal alignment can increase the consistency of the COP displacement on related acquired plantar pressure image sequences.

Solving the problem of Trans-Genomic Query with alignment tables.

PubMed

Parker, Douglass Stott; Hsiao, Ruey-Lung; Xing, Yi; Resch, Alissa M; Lee, Christopher J

2008-01-01

The trans-genomic query (TGQ) problem--enabling the free query of biological information, even across genomes--is a central challenge facing bioinformatics. Solutions to this problem can alter the nature of the field, moving it beyond the jungle of data integration and expanding the number and scope of questions that can be answered. An alignment table is a binary relationship on locations (sequence segments). An important special case of alignment tables are hit tables ? tables of pairs of highly similar segments produced by alignment tools like BLAST. However, alignment tables also include general binary relationships, and can represent any useful connection between sequence locations. They can be curated, and provide a high-quality queryable backbone of connections between biological information. Alignment tables thus can be a natural foundation for TGQ, as they permit a central part of the TGQ problem to be reduced to purely technical problems involving tables of locations.Key challenges in implementing alignment tables include efficient representation and indexing of sequence locations. We define a location datatype that can be incorporated naturally into common off-the-shelf database systems. We also describe an implementation of alignment tables in BLASTGRES, an extension of the open-source POSTGRESQL database system that provides indexing and operators on locations required for querying alignment tables. This paper also reviews several successful large-scale applications of alignment tables for Trans-Genomic Query. Tables with millions of alignments have been used in queries about alternative splicing, an area of genomic analysis concerning the way in which a single gene can yield multiple transcripts. Comparative genomics is a large potential application area for TGQ and alignment tables.

Standard versus physiologic bone preparation in total knee arthroplasty and the effect on joint space opening.

PubMed

Burkhart, Timothy A; Herman, Benjamin V; Perry, Kevin; Vandekerckhove, Pieter-Jan; Howard, James; Lanting, Brent

2017-11-01

Total knee arthroplasty is an effective treatment for osteoarthritis. Restoration of physiologic varus alignment may restore the native soft tissue tension and improve outcomes. Six paired fresh-frozen knee specimens were used to perform total knee arthroplastys. The left and right sides of were randomly assigned to have either a physiologic alignment cut or a standard of care neutral alignment bony cut prior to the implantation. Loads of 100 and 200N were applied at 0, 30, 60, and 90° of flexion and the magnitude of the medial and lateral compartment distraction was measured. The loads were applied with the knee specimen intact and post arthroplasty. The physiologic alignment had no difference between medial and lateral gaps at either load. With 100N of load the physiologic alignment had a greater gap at 90° than at full extension while the standard alignment had significantly more gap at 60° of flexion than full extension. The physiologic alignment had a significantly greater gap with the implant compared to the intact condition at both loads. The standard alignment had no significant difference in overall gap between the implant and intact condition with any load. Although performing a physiologic aligned TKA resulted in medial-lateral soft tissue balance, the flexion gap was found to have greater magnitude than the intact knee. Notably, a neutral aligned TKA was found to be balanced, but also was found to recreate the intact knee flexion gaps. These results suggest that coronal plane stability can be achieved with physiologic alignment objectives, but the clinician needs to be aware of the potential to have greater laxity than the intact and neutral alignment surgical objectives. Copyright © 2017 Elsevier Ltd. All rights reserved.

Automatic alignment of double optical paths in excimer laser amplifier

NASA Astrophysics Data System (ADS)

Wang, Dahui; Zhao, Xueqing; Hua, Hengqi; Zhang, Yongsheng; Hu, Yun; Yi, Aiping; Zhao, Jun

2013-05-01

A kind of beam automatic alignment method used for double paths amplification in the electron pumped excimer laser system is demonstrated. In this way, the beams from the amplifiers can be transferred along the designated direction and accordingly irradiate on the target with high stabilization and accuracy. However, owing to nonexistence of natural alignment references in excimer laser amplifiers, two cross-hairs structure is used to align the beams. Here, one crosshair put into the input beam is regarded as the near-field reference while the other put into output beam is regarded as the far-field reference. The two cross-hairs are transmitted onto Charge Coupled Devices (CCD) by image-relaying structures separately. The errors between intersection points of two cross-talk images and centroid coordinates of actual beam are recorded automatically and sent to closed loop feedback control mechanism. Negative feedback keeps running until preset accuracy is reached. On the basis of above-mentioned design, the alignment optical path is built and the software is compiled, whereafter the experiment of double paths automatic alignment in electron pumped excimer laser amplifier is carried through. Meanwhile, the related influencing factors and the alignment precision are analyzed. Experimental results indicate that the alignment system can achieve the aiming direction of automatic aligning beams in short time. The analysis shows that the accuracy of alignment system is 0.63μrad and the beam maximum restoration error is 13.75μm. Furthermore, the bigger distance between the two cross-hairs, the higher precision of the system is. Therefore, the automatic alignment system has been used in angular multiplexing excimer Main Oscillation Power Amplification (MOPA) system and can satisfy the requirement of beam alignment precision on the whole.

Rotation of intramedullary alignment rods affects distal femoral cutting plane in total knee arthroplasty.

PubMed

Maderbacher, Günther; Matussek, Jan; Keshmiri, Armin; Greimel, Felix; Baier, Clemens; Grifka, Joachim; Maderbacher, Hermann

2018-02-17

Intramedullary rods are widely used to align the distal femoral cut in total knee arthroplasty. We hypothesised that both coronal (varus/valgus) and sagittal (extension/flexion) cutting plane are affected by rotational changes of intramedullary femoral alignment guides. Distal femoral cuts using intramedullary alignment rods were simulated by means of a computer-aided engineering software in 4°, 6°, 8°, 10°, and 12° of valgus in relation to the femoral anatomical axis and 4° extension, neutral, as well as 4°, 8°, and 12° of flexion in relation to the femoral mechanical axis. This reflects the different angles between anatomical and mechanical axis in coronal and sagittal planes. To assess the influence of rotation of the alignment guide on the effective distal femoral cutting plane, all combinations were simulated with the rod gradually aligned from 40° of external to 40° of internal rotation. Rotational changes of the distal femoral alignment guides affect both the coronal and sagittal cutting planes. When alignment rods are intruded neutrally with regards to sagittal alignment, external rotation causes flexion, while internal rotation causes extension of the sagittal cutting plane. Simultaneously the coronal effect (valgus) decreases resulting in an increased varus of the cutting plane. However, when alignment rods are intruded in extension or flexion partly contradictory effects are observed. Generally the effect increases with the degree of valgus preset, rotation and flexion. As incorrect rotation of intramedullary alignment guides for distal femoral cuts causes significant cutting errors, exact rotational alignment is crucial. Coronal cutting errors in the distal femoral plane might result in overall leg malalignment, asymmetric extension gaps and subsequent sagittal cutting errors.

Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading.

PubMed

Rahn, René; Budach, Stefan; Costanza, Pascal; Ehrhardt, Marcel; Hancox, Jonny; Reinert, Knut

2018-05-03

Pairwise sequence alignment is undoubtedly a central tool in many bioinformatics analyses. In this paper, we present a generically accelerated module for pairwise sequence alignments applicable for a broad range of applications. In our module, we unified the standard dynamic programming kernel used for pairwise sequence alignments and extended it with a generalized inter-sequence vectorization layout, such that many alignments can be computed simultaneously by exploiting SIMD (Single Instruction Multiple Data) instructions of modern processors. We then extended the module by adding two layers of thread-level parallelization, where we a) distribute many independent alignments on multiple threads and b) inherently parallelize a single alignment computation using a work stealing approach producing a dynamic wavefront progressing along the minor diagonal. We evaluated our alignment vectorization and parallelization on different processors, including the newest Intel® Xeon® (Skylake) and Intel® Xeon Phi™ (KNL) processors, and use cases. The instruction set AVX512-BW (Byte and Word), available on Skylake processors, can genuinely improve the performance of vectorized alignments. We could run single alignments 1600 times faster on the Xeon Phi™ and 1400 times faster on the Xeon® than executing them with our previous sequential alignment module. The module is programmed in C++ using the SeqAn (Reinert et al., 2017) library and distributed with version 2.4. under the BSD license. We support SSE4, AVX2, AVX512 instructions and included UME::SIMD, a SIMD-instruction wrapper library, to extend our module for further instruction sets. We thoroughly test all alignment components with all major C++ compilers on various platforms. rene.rahn@fu-berlin.de.

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.

A UNIFIED MODEL OF GRAIN ALIGNMENT: RADIATIVE ALIGNMENT OF INTERSTELLAR GRAINS WITH MAGNETIC INCLUSIONS

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

Hoang, Thiem; Lazarian, A.

The radiative torque (RAT) alignment of interstellar grains with ordinary paramagnetic susceptibilities has been supported by earlier studies. The alignment of such grains depends on the so-called RAT parameter q {sup max}, which is determined by the grain shape. In this paper, we elaborate on our model of RAT alignment for grains with enhanced magnetic susceptibility due to iron inclusions, such that RAT alignment is magnetically enhanced, which we term the MRAT mechanism. Such grains can be aligned with high angular momentum at the so-called high- J attractor points, achieving a high degree of alignment. Using our analytical model ofmore » RATs, we derive the critical value of the magnetic relaxation parameter δ {sub m} to produce high- J attractor points as functions of q {sup max} and the anisotropic radiation angle relative to the magnetic field ψ . We find that if about 10% of the total iron abundance present in silicate grains is forming iron clusters, this is sufficient to produce high- J attractor points for all reasonable values of q {sup max}. To calculate the degree of grain alignment, we carry out numerical simulations of MRAT alignment by including stochastic excitations from gas collisions and magnetic fluctuations. We show that large grains can achieve perfect alignment when the high- J attractor point is present, regardless of the values of q {sup max}. Our obtained results pave the way for the physical modeling of polarized thermal dust emission as well as magnetic dipole emission. We also find that millimeter-sized grains in accretion disks may be aligned with the magnetic field if they are incorporated with iron nanoparticles.« less

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

PubMed Central

Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H.

2008-01-01

A novel method is presented for joint prediction of alignment and common secondary structures of two RNA sequences. The joint consideration of common secondary structures and alignment is accomplished by structural alignment over a search space defined by the newly introduced motif called matched helical regions. The matched helical region formulation generalizes previously employed constraints for structural alignment and thereby better accommodates the structural variability within RNA families. A probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities is utilized for scoring structural alignments. Maximum a posteriori (MAP) common secondary structures, sequence alignment and joint posterior probabilities of base pairing are obtained from the model via a dynamic programming algorithm called PARTS. The advantage of the more general structural alignment of PARTS is seen in secondary structure predictions for the RNase P family. For this family, the PARTS MAP predictions of secondary structures and alignment perform significantly better than prior methods that utilize a more restrictive structural alignment model. For the tRNA and 5S rRNA families, the richer structural alignment model of PARTS does not offer a benefit and the method therefore performs comparably with existing alternatives. For all RNA families studied, the posterior probability estimates obtained from PARTS offer an improvement over posterior probability estimates from a single sequence prediction. When considering the base pairings predicted over a threshold value of confidence, the combination of sensitivity and positive predictive value is superior for PARTS than for the single sequence prediction. PARTS source code is available for download under the GNU public license at http://rna.urmc.rochester.edu. PMID:18304945

Knots in Thinking and the Problem of Enactment: Exploring the Classroom Thinking of Three Novice Teachers

ERIC Educational Resources Information Center

Zimmerman, Aaron Samuel

2017-01-01

Novice teachers begin their careers with certain instructional ideals; however, in practice, novice teachers tend to enact classroom practices that only partially align with these ideals--a phenomenon referred to as the problem of enactment. This article explores this phenomenon by investigating the classroom thinking of three novice teachers.…

ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

PubMed

Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

2006-12-15

We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

Alternative alignments development and evaluation for the US 220 project in Maryland.

DOT National Transportation Integrated Search

2011-06-01

This project aims to find the preferred alternative alignments for the Maryland section of existing US 220, using the highway : alignment optimization (HAO) model. The model was used to explore alternative alignments within a 4,000 foot-wide buffer o...

Alignment of gold nanorods by angular photothermal depletion

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

Taylor, Adam B.; Chow, Timothy T. Y.; Chon, James W. M., E-mail: jchon@swin.edu.au

2014-02-24

In this paper, we demonstrate that a high degree of alignment can be imposed upon randomly oriented gold nanorod films by angular photothermal depletion with linearly polarized laser irradiation. The photothermal reshaping of gold nanorods is observed to follow quadratic melting model rather than the threshold melting model, which distorts the angular and spectral hole created on 2D distribution map of nanorods to be an open crater shape. We have accounted these observations to the alignment procedures and demonstrated good agreement between experiment and simulations. The use of multiple laser depletion wavelengths allowed alignment criteria over a large range ofmore » aspect ratios, achieving 80% of the rods in the target angular range. We extend the technique to demonstrate post-alignment in a multilayer of randomly oriented gold nanorod films, with arbitrary control of alignment shown across the layers. Photothermal angular depletion alignment of gold nanorods is a simple, promising post-alignment method for creating future 3D or multilayer plasmonic nanorod based devices and structures.« less

Galaxy Alignments: Theory, Modelling & Simulations

NASA Astrophysics Data System (ADS)

Kiessling, Alina; Cacciato, Marcello; Joachimi, Benjamin; Kirk, Donnacha; Kitching, Thomas D.; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Brown, Michael L.; Rassat, Anais

2015-11-01

The shapes of galaxies are not randomly oriented on the sky. During the galaxy formation and evolution process, environment has a strong influence, as tidal gravitational fields in the large-scale structure tend to align nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of both the shapes and angular momenta of galaxies throughout their history. These "intrinsic galaxy alignments" are known to exist, but are still poorly understood. This review will offer a pedagogical introduction to the current theories that describe intrinsic galaxy alignments, including the apparent difference in intrinsic alignment between early- and late-type galaxies and the latest efforts to model them analytically. It will then describe the ongoing efforts to simulate intrinsic alignments using both N-body and hydrodynamic simulations. Due to the relative youth of this field, there is still much to be done to understand intrinsic galaxy alignments and this review summarises the current state of the field, providing a solid basis for future work.

Comparison of two on-orbit attitude sensor alignment methods

NASA Technical Reports Server (NTRS)

Krack, Kenneth; Lambertson, Michael; Markley, F. Landis

1990-01-01

Compared here are two methods of on-orbit alignment of vector attitude sensors. The first method uses the angular difference between simultaneous measurements from two or more sensors. These angles are compared to the angular differences between the respective reference positions of the sensed objects. The alignments of the sensors are adjusted to minimize the difference between the two sets of angles. In the second method, the sensor alignment is part of a state vector that includes the attitude. The alignments are adjusted along with the attitude to minimize all observation residuals. It is shown that the latter method can result in much less alignment uncertainty when gyroscopes are used for attitude propagation during the alignment estimation. The additional information for this increased accuracy comes from knowledge of relative attitude obtained from the spacecraft gyroscopes. The theoretical calculations of this difference in accuracy are presented. Also presented are numerical estimates of the alignment uncertainties of the fixed-head star trackers on the Extreme Ultraviolet Explorer spacecraft using both methods.

Optimizing Mechanical Alignment With Modular Stems in Revision TKA.

PubMed

Fleischman, Andrew N; Azboy, Ibrahim; Restrepo, Camilo; Maltenfort, Mitchell G; Parvizi, Javad

2017-09-01

Although mechanical alignment is critical for optimal function and long-term implant durability, the role of modular stems in achieving ideal alignment is unclear. We identified 319 revision total knee arthroplasty from 2003-2013, for which stem length, stem diameter, and stem fixation method were recorded prospectively. Three-dimensional canal-filling ratio, the product of canal-filling ratio at the stem tip in both the anteroposterior and lateral planes, and alignment were measured radiographically. Ideal alignment of the femur was considered to be 95° in the anteroposterior (AP) plane and from 1° of extension to 4° of flexion in the lateral plane, and ideal tibial alignment was considered to be 90° in the AP plane. Even after accounting for difference in stem size and canal-fill, ideal AP alignment was more reliably achieved with press-fit stems. Furthermore, increased engagement of the diaphysis and its anatomical axis with canal-filling stems facilitates accurate alignment. Copyright © 2017 Elsevier Inc. All rights reserved.

Dissipation dynamics of field-free molecular alignment for symmetric-top molecules: Ethane (C2H6)

NASA Astrophysics Data System (ADS)

Zhang, H.; Billard, F.; Yu, X.; Faucher, O.; Lavorel, B.

2018-03-01

The field-free molecular alignment of symmetric-top molecules, ethane, induced by intense non-resonant linearly polarized femtosecond laser pulses is investigated experimentally in the presence of collisional relaxation. The dissipation dynamics of field-free molecular alignment are measured by the balanced detection of ultrafast molecular birefringence of ethane gas samples at high pressures. By separating the molecular alignment into the permanent alignment and the transient alignment, the decay time-constants of both components are quantified at the same pressure. It is observed that the permanent alignment always decays slower compared to the transient alignment within the measured pressure range. This demonstrates that the propensity of molecules to conserve the orientation of angular momentum during collisions, previously observed for linear species, is also applicable to symmetric-top molecules. The results of this work provide valuable information for further theoretical understanding of collisional relaxation within nonlinear polyatomic molecules, which are expected to present interesting and nontrivial features due to an extra rotational degree of freedom.

Concurrent and Accurate Short Read Mapping on Multicore Processors.

PubMed

Martínez, Héctor; Tárraga, Joaquín; Medina, Ignacio; Barrachina, Sergio; Castillo, Maribel; Dopazo, Joaquín; Quintana-Ortí, Enrique S

2015-01-01

We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA (HPG Aligner SA is an open-source application. The software is available at http://www.opencb.org, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100-400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR.

Implant alignment in total elbow arthroplasty: conventional vs. navigated techniques

NASA Astrophysics Data System (ADS)

McDonald, Colin P.; Johnson, James A.; King, Graham J. W.; Peters, Terry M.

2009-02-01

Incorrect selection of the native flexion-extension axis during implant alignment in elbow replacement surgery is likely a significant contributor to failure of the prosthesis. Computer and image-assisted surgery is emerging as a useful surgical tool in terms of improving the accuracy of orthopaedic procedures. This study evaluated the accuracy of implant alignment using an image-based navigation technique compared against a conventional non-navigated approach. Implant alignment error was 0.8 +/- 0.3 mm in translation and 1.1 +/- 0.4° in rotation for the navigated alignment, compared with 3.1 +/- 1.3 mm and 5.0 +/- 3.8° for the non-navigated alignment. Five (5) of the 11 non-navigated alignments were malaligned greater than 5° while none of the navigated alignments were placed with an error of greater than 2.0°. It is likely that improved implant positioning will lead to reduced implant loading and wear, resulting in fewer implantrelated complications and revision surgeries.

ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

PubMed Central

Hoffmann, Nils; Stoye, Jens

2009-01-01

Summary: We describe ChromA, a web-based alignment tool for chromatography–mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. Availability: ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location. Contact: stoye@techfak.uni-bielefeld.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19505941

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos.

PubMed

Roca, Alberto I

2014-01-01

The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org.

Improving scanner wafer alignment performance by target optimization

NASA Astrophysics Data System (ADS)

Leray, Philippe; Jehoul, Christiane; Socha, Robert; Menchtchikov, Boris; Raghunathan, Sudhar; Kent, Eric; Schoonewelle, Hielke; Tinnemans, Patrick; Tuffy, Paul; Belen, Jun; Wise, Rich

2016-03-01

In the process nodes of 10nm and below, the patterning complexity along with the processing and materials required has resulted in a need to optimize alignment targets in order to achieve the required precision, accuracy and throughput performance. Recent industry publications on the metrology target optimization process have shown a move from the expensive and time consuming empirical methodologies, towards a faster computational approach. ASML's Design for Control (D4C) application, which is currently used to optimize YieldStar diffraction based overlay (DBO) metrology targets, has been extended to support the optimization of scanner wafer alignment targets. This allows the necessary process information and design methodology, used for DBO target designs, to be leveraged for the optimization of alignment targets. In this paper, we show how we applied this computational approach to wafer alignment target design. We verify the correlation between predictions and measurements for the key alignment performance metrics and finally show the potential alignment and overlay performance improvements that an optimized alignment target could achieve.

Amperometric Detection in Microchip Electrophoresis Devices: Effect of Electrode Material and Alignment on Analytical Performance

PubMed Central

Fischer, David J.; Hulvey, Matthew K.; Regel, Anne R.; Lunte, Susan M.

2012-01-01

The fabrication and evaluation of different electrode materials and electrode alignments for microchip electrophoresis with electrochemical (EC) detection is described. The influences of electrode material, both metal and carbon-based, on sensitivity and limits of detection (LOD) were examined. In addition, the effects of working electrode alignment on analytical performance (in terms of peak shape, resolution, sensitivity, and LOD) were directly compared. Using dopamine (DA), norepinephrine (NE), and catechol (CAT) as test analytes, it was found that pyrolyzed photoresist electrodes with end-channel alignment yielded the lowest limit of detection (35 nM for DA). In addition to being easier to implement, end-channel alignment also offered better analytical performance than off-channel alignment for the detection of all three analytes. In-channel electrode alignment resulted in a 3.6-fold reduction in peak skew and reduced peak tailing by a factor of 2.1 for catechol in comparison to end-channel alignment. PMID:19802847

Unsupervised parameter optimization for automated retention time alignment of severely shifted gas chromatographic data using the piecework alignment algorithm.

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

Pierce, Karisa M.; Wright, Bob W.; Synovec, Robert E.

2007-02-02

First, simulated chromatographic separations with declining retention time precision were used to study the performance of the piecewise retention time alignment algorithm and to demonstrate an unsupervised parameter optimization method. The average correlation coefficient between the first chromatogram and every other chromatogram in the data set was used to optimize the alignment parameters. This correlation method does not require a training set, so it is unsupervised and automated. This frees the user from needing to provide class information and makes the alignment algorithm more generally applicable to classifying completely unknown data sets. For a data set of simulated chromatograms wheremore » the average chromatographic peak was shifted past two neighboring peaks between runs, the average correlation coefficient of the raw data was 0.46 ± 0.25. After automated, optimized piecewise alignment, the average correlation coefficient was 0.93 ± 0.02. Additionally, a relative shift metric and principal component analysis (PCA) were used to independently quantify and categorize the alignment performance, respectively. The relative shift metric was defined as four times the standard deviation of a given peak’s retention time in all of the chromatograms, divided by the peak-width-at-base. The raw simulated data sets that were studied contained peaks with average relative shifts ranging between 0.3 and 3.0. Second, a “real” data set of gasoline separations was gathered using three different GC methods to induce severe retention time shifting. In these gasoline separations, retention time precision improved ~8 fold following alignment. Finally, piecewise alignment and the unsupervised correlation optimization method were applied to severely shifted GC separations of reformate distillation fractions. The effect of piecewise alignment on peak heights and peak areas is also reported. Piecewise alignment either did not change the peak height, or caused it to slightly decrease. The average relative difference in peak height after piecewise alignment was –0.20%. Piecewise alignment caused the peak areas to either stay the same, slightly increase, or slightly decrease. The average absolute relative difference in area after piecewise alignment was 0.15%.« less

Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers.

PubMed

Galpert, Deborah; Fernández, Alberto; Herrera, Francisco; Antunes, Agostinho; Molina-Ruiz, Reinaldo; Agüero-Chapin, Guillermin

2018-05-03

The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were alignment-free features related to amino acid composition. The incorporation of alignment-free features in supervised big data models did not significantly improve ortholog detection in yeast proteomes regarding the classification qualities achieved with just alignment-based similarity measures. However, the similarity of their classification performance to that of traditional ortholog detection methods encourages the evaluation of other alignment-free protein pair descriptors in future research.

Towards a Unified Framework for Pose, Expression, and Occlusion Tolerant Automatic Facial Alignment.

PubMed

Seshadri, Keshav; Savvides, Marios

2016-10-01

We propose a facial alignment algorithm that is able to jointly deal with the presence of facial pose variation, partial occlusion of the face, and varying illumination and expressions. Our approach proceeds from sparse to dense landmarking steps using a set of specific models trained to best account for the shape and texture variation manifested by facial landmarks and facial shapes across pose and various expressions. We also propose the use of a novel l1-regularized least squares approach that we incorporate into our shape model, which is an improvement over the shape model used by several prior Active Shape Model (ASM) based facial landmark localization algorithms. Our approach is compared against several state-of-the-art methods on many challenging test datasets and exhibits a higher fitting accuracy on all of them.

FASMA: a service to format and analyze sequences in multiple alignments.

PubMed

Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

2007-12-01

Multiple sequence alignments are successfully applied in many studies for under- standing the structural and functional relations among single nucleic acids and protein sequences as well as whole families. Because of the rapid growth of sequence databases, multiple sequence alignments can often be very large and difficult to visualize and analyze. We offer a new service aimed to visualize and analyze the multiple alignments obtained with different external algorithms, with new features useful for the comparison of the aligned sequences as well as for the creation of a final image of the alignment. The service is named FASMA and is available at http://bioinformatica.isa.cnr.it/FASMA/.

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

PubMed

Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong; Warnow, Tandy

2015-05-01

We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.

Alignment and focus of mirrored facets of a heliosat

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

Yellowhair, Julius E; Ho, Clifford Kuofei; Diver, Richard B

2013-11-12

Various technologies pertaining to aligning and focusing mirrored facets of a heliostat are described herein. Updating alignment and/or focus of mirrored facets is undertaken through generation of a theoretical image, wherein the theoretical image is indicative of a reflection of the target via the mirrored facets when the mirrored facets are properly aligned. This theoretical image includes reference points that are overlaid on an image of the target as reflected by the mirrored facets of the heliostat. A technician adjusts alignment/focus of a mirrored facet by causing reflected reference markings to become aligned with the reference points in the theoreticalmore » image.« less

Business-IT Alignment in Trade Facilitation: A Case Study

NASA Astrophysics Data System (ADS)

Adaba, Godfried; Rusu, Lazar; El-Mekawy, Mohamed

In the information age, no organization can thrive without harnessing the power of IT. The effective deployment of IT to achieve business goals and gain competitive advantage requires the alignment of business and IT strategies of organizations. Using the Strategic Alignment Maturity model, this paper evaluates strategic alignment maturity of Customs Excise Preventive service, a frontline public organization charged with trade facilitation in Ghana. Strategic alignment maturity is at level 3; which implies the existence of an established process to leverage IT for efficiency and effectiveness. Efforts are required to strengthen alignment and fully harness the potential of IT to facilitate trade in Ghana.

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.

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

PubMed

Rajan, Vaibhav

2013-03-01

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

YAHA: fast and flexible long-read alignment with optimal breakpoint detection.

PubMed

Faust, Gregory G; Hall, Ira M

2012-10-01

With improved short-read assembly algorithms and the recent development of long-read sequencers, split mapping will soon be the preferred method for structural variant (SV) detection. Yet, current alignment tools are not well suited for this. We present YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints. YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from http://faculty.virginia.edu/irahall/YAHA. imh4y@virginia.edu.

STELLAR: fast and exact local alignments

PubMed Central

2011-01-01

Background Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches. Results We present here the local pairwise aligner STELLAR that has full sensitivity for ε-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments. Conclusions STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de. PMID:22151882

Vector correlation between the alignment of reactant N2 (A 3Σu+) and the alignment of product NO (A 2Σ+) rotation in the energy transfer reaction of aligned N2 (A 3Σu+) + NO (X 2Π) → NO (A 2Σ+) + N2 (X 1Σg+).

PubMed

Ohoyama, H

2013-12-21

The vector correlation between the alignment of reactant N2 (A (3)Σu(+)) and the alignment of product NO (A (2)Σ(+)) rotation has been studied in the energy transfer reaction of aligned N2 (A (3)Σu(+)) + NO (X (2)Π) → NO (A (2)Σ(+)) + N2 (X (1)Σg(+)) under the crossed beam condition at a collision energy of ~0.07 eV. NO (A (2)Σ(+)) emission in the two linear polarization directions (i.e., parallel and perpendicular with respect to the relative velocity vector v(R)) has been measured as a function of the alignment of N2 (A (3)Σu(+)) along its molecular axis in the collision frame. The degree of polarization of NO (A (2)Σ(+)) emission is found to depend on the alignment angle (θ(v(R))) of N2 (A (3)Σu(+)) in the collision frame. The shape of the steric opacity function at the two polarization conditions turns out to be extremely different from each other: The steric opacity function at the parallel polarization condition is more favorable for the oblique configuration of N2 (A (3)Σu(+)) at an alignment angle of θ(v(R)) ~ 45° as compared with that at the perpendicular polarization condition. The alignment of N2 (A (3)Σu(+)) is found to give a significant effect on the alignment of NO (A (2)Σ(+)) rotation in the collision frame: The N2 (A (3)Σu(+)) configuration at an oblique alignment angle θ(v(R)) ~ 45° leads to a parallel alignment of NO (A (2)Σ(+)) rotation (J-vector) with respect to v(R), while the axial and sideways configurations of N2 (A (3)Σu(+)) lead to a perpendicular alignment of NO (A (2)Σ(+)) rotation with respect to vR. These stereocorrelated alignments of the product rotation have a good correlation with the stereocorrelated reactivity observed in the multi-dimensional steric opacity function [H. Ohoyama and S. Maruyama, J. Chem. Phys. 137, 064311 (2012)].

Some Alignment Considerations for the Next Linear Collider

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

Ruland, R

Next Linear Collider type accelerators require a new level of alignment quality. The relative alignment of these machines is to be maintained in an error envelope dimensioned in micrometers and for certain parts in nanometers. In the nanometer domain our terra firma cannot be considered monolithic but compares closer to jelly. Since conventional optical alignment methods cannot deal with the dynamics and cannot approach the level of accuracy, special alignment and monitoring techniques must be pursued.

Aligning Plasma-Arc Welding Oscillations

NASA Technical Reports Server (NTRS)

Norris, Jeff; Fairley, Mike

1989-01-01

Tool aids in alignment of oscillator probe on variable-polarity plasma-arc welding torch. Probe magnetically pulls arc from side to side as it moves along joint. Tensile strength of joint depends on alignment of weld bead and on alignment of probe. Operator installs new tool on front of torch body, levels it with built-in bubble glass, inserts probe in slot on tool, and locks probe in place. Procedure faster and easier and resulting alignment more accurate and repeatable.

Optimal network alignment with graphlet degree vectors.

PubMed

Milenković, Tijana; Ng, Weng Leong; Hayes, Wayne; Przulj, Natasa

2010-06-30

Important biological information is encoded in the topology of biological networks. Comparative analyses of biological networks are proving to be valuable, as they can lead to transfer of knowledge between species and give deeper insights into biological function, disease, and evolution. We introduce a new method that uses the Hungarian algorithm to produce optimal global alignment between two networks using any cost function. We design a cost function based solely on network topology and use it in our network alignment. Our method can be applied to any two networks, not just biological ones, since it is based only on network topology. We use our new method to align protein-protein interaction networks of two eukaryotic species and demonstrate that our alignment exposes large and topologically complex regions of network similarity. At the same time, our alignment is biologically valid, since many of the aligned protein pairs perform the same biological function. From the alignment, we predict function of yet unannotated proteins, many of which we validate in the literature. Also, we apply our method to find topological similarities between metabolic networks of different species and build phylogenetic trees based on our network alignment score. The phylogenetic trees obtained in this way bear a striking resemblance to the ones obtained by sequence alignments. Our method detects topologically similar regions in large networks that are statistically significant. It does this independent of protein sequence or any other information external to network topology.

Retention time alignment of LC/MS data by a divide-and-conquer algorithm.

PubMed

Zhang, Zhongqi

2012-04-01

Liquid chromatography-mass spectrometry (LC/MS) has become the method of choice for characterizing complex mixtures. These analyses often involve quantitative comparison of components in multiple samples. To achieve automated sample comparison, the components of interest must be detected and identified, and their retention times aligned and peak areas calculated. This article describes a simple pairwise iterative retention time alignment algorithm, based on the divide-and-conquer approach, for alignment of ion features detected in LC/MS experiments. In this iterative algorithm, ion features in the sample run are first aligned with features in the reference run by applying a single constant shift of retention time. The sample chromatogram is then divided into two shorter chromatograms, which are aligned to the reference chromatogram the same way. Each shorter chromatogram is further divided into even shorter chromatograms. This process continues until each chromatogram is sufficiently narrow so that ion features within it have a similar retention time shift. In six pairwise LC/MS alignment examples containing a total of 6507 confirmed true corresponding feature pairs with retention time shifts up to five peak widths, the algorithm successfully aligned these features with an error rate of 0.2%. The alignment algorithm is demonstrated to be fast, robust, fully automatic, and superior to other algorithms. After alignment and gap-filling of detected ion features, their abundances can be tabulated for direct comparison between samples.

B-MIC: An Ultrafast Three-Level Parallel Sequence Aligner Using MIC.

PubMed

Cui, Yingbo; Liao, Xiangke; Zhu, Xiaoqian; Wang, Bingqiang; Peng, Shaoliang

2016-03-01

Sequence alignment is the central process for sequence analysis, where mapping raw sequencing data to reference genome. The large amount of data generated by NGS is far beyond the process capabilities of existing alignment tools. Consequently, sequence alignment becomes the bottleneck of sequence analysis. Intensive computing power is required to address this challenge. Intel recently announced the MIC coprocessor, which can provide massive computing power. The Tianhe-2 is the world's fastest supercomputer now equipped with three MIC coprocessors each compute node. A key feature of sequence alignment is that different reads are independent. Considering this property, we proposed a MIC-oriented three-level parallelization strategy to speed up BWA, a widely used sequence alignment tool, and developed our ultrafast parallel sequence aligner: B-MIC. B-MIC contains three levels of parallelization: firstly, parallelization of data IO and reads alignment by a three-stage parallel pipeline; secondly, parallelization enabled by MIC coprocessor technology; thirdly, inter-node parallelization implemented by MPI. In this paper, we demonstrate that B-MIC outperforms BWA by a combination of those techniques using Inspur NF5280M server and the Tianhe-2 supercomputer. To the best of our knowledge, B-MIC is the first sequence alignment tool to run on Intel MIC and it can achieve more than fivefold speedup over the original BWA while maintaining the alignment precision.

Galaxy-halo alignments in the Horizon-AGN cosmological hydrodynamical simulation

NASA Astrophysics Data System (ADS)

Chisari, N. E.; Koukoufilippas, N.; Jindal, A.; Peirani, S.; Beckmann, R. S.; Codis, S.; Devriendt, J.; Miller, L.; Dubois, Y.; Laigle, C.; Slyz, A.; Pichon, C.

2017-11-01

Intrinsic alignments of galaxies are a significant astrophysical systematic affecting cosmological constraints from weak gravitational lensing. Obtaining numerical predictions from hydrodynamical simulations of expected survey volumes is expensive, and a cheaper alternative relies on populating large dark matter-only simulations with accurate models of alignments calibrated on smaller hydrodynamical runs. This requires connecting the shapes and orientations of galaxies to those of dark matter haloes and to the large-scale structure. In this paper, we characterize galaxy-halo alignments in the Horizon-AGN cosmological hydrodynamical simulation. We compare the shapes and orientations of galaxies in the redshift range of 0 < z < 3 to those of their embedding dark matter haloes, and to the matching haloes of a twin dark-matter only run with identical initial conditions. We find that galaxy ellipticities, in general, cannot be predicted directly from halo ellipticities. The mean misalignment angle between the minor axis of a galaxy and its embedding halo is a function of halo mass, with residuals arising from the dependence of alignment on galaxy type, but not on environment. Haloes are much more strongly aligned among themselves than galaxies, and they decrease their alignment towards low redshift. Galaxy alignments compete with this effect, as galaxies tend to increase their alignment with haloes towards low redshift. We discuss the implications of these results for current halo models of intrinsic alignments and suggest several avenues for improvement.

Alignment of Irregular Grains by Mechanical Torques

NASA Astrophysics Data System (ADS)

Hoang, Thiem; Cho, Jungyeon; Lazarian, A.

2018-01-01

We study the alignment of irregular dust grains by mechanical torques due to the drift of grains through the ambient gas. We first calculate mechanical alignment torques (MATs) resulting from specular reflection of gas atoms for seven irregular shapes: one shape of mirror symmetry, three highly irregular shapes (HIS), and three weakly irregular shapes (WIS). We find that the grain with mirror symmetry experiences negligible MATs due to its mirror-symmetry geometry. Three HIS can produce strong MATs, which exhibit some generic properties as radiative torques (RATs), while three WIS produce less efficient MATs. We then study grain alignment by MATs for the different angles between the drift velocity and the ambient magnetic field, for paramagnetic and superparamagnetic grains assuming efficient internal relaxation. We find that for HIS grains, MATs can align subsonically drifting grains in the same way as RATs, with low-J and high-J attractors. For supersonic drift, MATs can align grains with low-J and high-J attractors, analogous to RAT alignment by anisotropic radiation. We also show that the joint action of MATs and magnetic torques in grains with iron inclusions can lead to perfect MAT alignment. Our results point out the potential importance of MAT alignment for HIS grains predicted by the analytical model of Lazarian & Hoang, although more theoretical and observational studies are required due to uncertainty in the shape of interstellar grains. We outline astrophysical environments where MAT alignment is potentially important.

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

Optical Alignment of the JWST ISIM to the OTE Simulator (OSIM): Current Concept and Design Studies

NASA Technical Reports Server (NTRS)

Frey, Bradley J.; Davila, Pamela S.; Marsh, James M.; Ohl, Raymond G.; Sullivan, Joseph

2007-01-01

The James Webb Space Telescope's (JWST) Integrated Science Instrument Module (ISIM) is the scientific payload of the observatory and contai ns four science instruments. During alignment and test of the integrated ISIM (i.e. ISIM + science instruments) at NASA's Goddard Space Fli ght Center (GSFC), the Optical telescope element SIMulator (OSIM) wil l be used to optically stimulate the science instruments to verify their operation and performance. In this paper we present the design of two cryogenic alignment fixtures that will be used to determine and verify the proper alignment of OSIM to ISIM during testing at GSFC. The se fixtures, the Master Alignment Target Fixture (MATF) and the ISIM Alignment Target Fixture (IATF), will provide continuous, 6 degree of freedom feedback to OSIM during initial ambient alignment as well as during cryogenic vacuum testing.

Image Alignment for Multiple Camera High Dynamic Range Microscopy.

PubMed

Eastwood, Brian S; Childs, Elisabeth C

2012-01-09

This paper investigates the problem of image alignment for multiple camera high dynamic range (HDR) imaging. HDR imaging combines information from images taken with different exposure settings. Combining information from multiple cameras requires an alignment process that is robust to the intensity differences in the images. HDR applications that use a limited number of component images require an alignment technique that is robust to large exposure differences. We evaluate the suitability for HDR alignment of three exposure-robust techniques. We conclude that image alignment based on matching feature descriptors extracted from radiant power images from calibrated cameras yields the most accurate and robust solution. We demonstrate the use of this alignment technique in a high dynamic range video microscope that enables live specimen imaging with a greater level of detail than can be captured with a single camera.

Image Alignment for Multiple Camera High Dynamic Range Microscopy

PubMed Central

Eastwood, Brian S.; Childs, Elisabeth C.

2012-01-01

This paper investigates the problem of image alignment for multiple camera high dynamic range (HDR) imaging. HDR imaging combines information from images taken with different exposure settings. Combining information from multiple cameras requires an alignment process that is robust to the intensity differences in the images. HDR applications that use a limited number of component images require an alignment technique that is robust to large exposure differences. We evaluate the suitability for HDR alignment of three exposure-robust techniques. We conclude that image alignment based on matching feature descriptors extracted from radiant power images from calibrated cameras yields the most accurate and robust solution. We demonstrate the use of this alignment technique in a high dynamic range video microscope that enables live specimen imaging with a greater level of detail than can be captured with a single camera. PMID:22545028

Effect of alignment changes on socket reaction moments while walking in transtibial prostheses with energy storage and return feet

PubMed Central

Kobayashi, Toshiki; Arabian, Adam K.; Orendurff, Michael S.; Rosenbaum-Chou, Teri G.; Boone, David A.

2014-01-01

Background Energy storage and return feet are designed for active amputees. However, little is known about the socket reaction moments in transtibial prostheses with energy storage and return feet. The aim of this study was to investigate the effect of alignment changes on the socket reaction moments during gait while using the energy storage and return feet. Methods A Smart Pyramid™ was used to measure the socket reaction moments in 10 subjects with transtibial prostheses while walking under 25 alignment conditions, including a nominal alignment (as defined by conventional clinical methods), as well as angle malalignments of 2°, 4° and 6° (flexion, extension, abduction, and adduction) and translation malalignments of 5mm, 10mm and 15mm (anterior, posterior, lateral, and medial) referenced from the nominal alignment. The socket reaction moments of the nominal alignment were compared with each malalignment. Findings Both coronal and sagittal alignment changes demonstrated systematic effects on the socket reaction moments. In the sagittal plane, angle and translation alignment changes demonstrated significant differences (P<0.05) in the minimum moment, the moment at 45% of stance and the maximum moment for some comparisons. In the coronal plane, angle and translation alignment changes demonstrated significant differences (P<0.05) in the moment at 30% and 75% of stance for all comparisons. Interpretation The alignment may have systematic effects on the socket reaction moments in transtibial prostheses with energy storage and return feet. The socket reaction moments could potentially be a useful biomechanical parameter to evaluate the alignment of the transtibial prostheses. PMID:24315709

Effect of prosthetic alignment changes on socket reaction moment impulse during walking in transtibial amputees

PubMed Central

Kobayashi, Toshiki; Orendurff, Michael S.; Arabian, Adam K.; Rosenbaum-Chou, Teri G.; Boone, David A.

2014-01-01

The alignment of a lower limb prosthesis affects the way load is transferred to the residual limb through the socket, and this load is critically important for the comfort and function of the prosthesis. Both magnitude and duration of the moment are important factors that may affect the residual limb health. Moment impulse is a well-accepted measurement that incorporates both factors via moment–time integrals. The aim of this study was to investigate the effect of alignment changes on the socket reaction moment impulse in transtibial prostheses. Ten amputees with transtibial prostheses participated in this study. The socket reaction moment impulse was measured at a self-selected walking speed using a Smart Pyramid™ in 25 alignment conditions, including a nominal alignment (clinically aligned by a prosthetist), as well as angle malalignments of 2°, 4° and 6° (abduction, adduction, extension and flexion) and translation malalignments of 5 mm, 10 mm and 15 mm (lateral, medial, anterior and posterior). The socket reaction moment impulse of the nominal alignment was compared for each condition. The relationship between the alignment and the socket reaction moment impulse was clearly observed in the coronal angle, coronal translation and sagittal translation alignment changes. However, this relationship was not evident in the sagittal angle alignment changes. The results of this study suggested that the socket reaction moment impulse could potentially serve as a valuable parameter to assist the alignment tuning process for transtibial prostheses. Further study is needed to investigate the influence of the socket reaction moment impulse on the residual limb health. PMID:24612718

The Impact of Imaging Modality on the Measurement of Coronal Plane Alignment After Total Knee Arthroplasty.

PubMed

Nam, Denis; Vajapey, Sravya; Nunley, Ryan M; Barrack, Robert L

2016-10-01

The optimal coronal alignment after total knee arthroplasty (TKA) has become an area of increased debate. Sources of variability among investigations include the radiographic technique used for both preoperative surgical planning and postoperative alignment assessments. This study's purpose was to assess the impact of the imaging modality used on the measurement of coronal plane alignment after TKA. A consecutive series of patients undergoing TKA using the same cruciate-retaining prosthesis were included for analysis. Postoperatively, all patients received both a rotationally controlled, scout computed tomography scan and a hip-knee-ankle (HKA) image using the EOS Imaging system (EOS Inc., Paris, France). Two, independent observers measured the HKA angle, and femoral and tibial component alignment from each image. After classifying overall and component alignment as neutral, varus, or valgus, 40.6% (65 of 160) of knees had a discordant alignment classification for HKA, 28.1% (45 of 160) for femoral component alignment, and 26.9% (43 of 160) for tibial component alignment between their computed tomography and EOS images. Overall, 24.4% (39 of 160) of patients had a HKA difference of ≥3° between the 2 images, whereas 18.8% (30 of 160) and 20.0% (32 of 160) of patients had a femoral and tibial component alignment difference of ≥2°, respectively. Significant differences are present when comparing 2 measurement techniques of mechanical alignment after TKA. The impact of imaging modality on postoperative assessments must be accounted for and be consistent when comparing the results of different investigations. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

Transition of vertically aligned liquid crystal driven by fan-shaped electric field

NASA Astrophysics Data System (ADS)

Tsung, J. W.; Ting, T. L.; Chen, C. Y.; Liang, W. L.; Lai, C. W.; Lin, T. H.; Hsu, W. H.

2017-09-01

Interdigital electrodes are implemented in many commercial and novel liquid crystal devices to align molecules. Although many empirical principles and patents apply to electrode design, only a few numerical simulations of alignment have been conducted. Why and how the molecules align in an ordered manner has never been adequately explained. Hence, this investigation addresses the Fréedericksz transition of vertically aligned liquid crystal that is driven by fishbone electrodes, and thereafter identifies the mechanism of liquid crystal alignment. Theoretical calculations suggest that the periodic deformation that is caused by the fan-shaped fringe field minimizes the free energy in the liquid crystal cell, and the optimal alignment can be obtained when the cell parameters satisfy the relation p /2 d =√{k11/k33 } , where p is the spatial period of the strips of the electrode; d denotes the cell gap; and k11 and k33 are the splay and bend elastic constants of the liquid crystal, respectively. Polymer-stabilized vertical alignment test cells with various p values and spacings between the electrodes were fabricated, and the process of liquid crystal alignment was observed under an optical microscope. The degree of alignment was evaluated by measuring the transmittance of the test cell. The experimental results were consistent with the theoretical predictions. The principle of design, p /2 d =√{k11/k33 } , greatly improves the uniformity and stability of the aligned liquid crystal. The methods that are presented here can be further applied to cholesteric liquid crystal and other self-assembled soft materials.

An Alignment/Transfer Experiment with Low Socioeconomic Level Students.

ERIC Educational Resources Information Center

Elia, June Isaacs

1994-01-01

This study examined the amount of variance explained by alignment of testing to instruction among low socioeconomic level fourth graders, proposing two instructional alignment hypotheses. Results indicated that alignment had an unusually high effect. Low performing low socioeconomic level students achieved high success levels when conditions of…

Vertically aligned nanostructure scanning probe microscope tips

DOEpatents

Guillorn, Michael A.; Ilic, Bojan; Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Simpson, Michael L.

2006-12-19

Methods and apparatus are described for cantilever structures that include a vertically aligned nanostructure, especially vertically aligned carbon nanofiber scanning probe microscope tips. An apparatus includes a cantilever structure including a substrate including a cantilever body, that optionally includes a doped layer, and a vertically aligned nanostructure coupled to the cantilever body.

Temporal Effects of Alignment in Text-Based, Task-Oriented Discourse

ERIC Educational Resources Information Center

Foltz, Anouschka; Gaspers, Judith; Meyer, Carolin; Thiele, Kristina; Cimiano, Philipp; Stenneken, Prisca

2015-01-01

Communicative alignment refers to adaptation to one's communication partner. Temporal aspects of such alignment have been little explored. This article examines temporal aspects of lexical and syntactic alignment (i.e., tendencies to use the interlocutor's lexical items and syntactic structures) in task-oriented discourse. In particular, we…

Opportunities to Align California's PreK-3 Education System

ERIC Educational Resources Information Center

Policy Analysis for California Education, PACE, 2016

2016-01-01

"PreK-3 Alignment in California's Education System: Obstacles and Opportunities" by Rachel Valentino and Deborah J. Stipek reviews the opportunities and challenges that must be addressed to better align PreK-3 education in California. The report describes policies and practices that districts have implemented to strengthen alignment, and…

Alignment of Iron Nanoparticles in a Magnetic Field Due to Shape Anisotropy

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

Radhakrishnan, Balasubramaniam; Nicholson, Don M; Eisenbach, Markus

2015-07-09

During high magnetic field processing there is evidence for alignment of non-spherical metallic particles above the Curie temperature in alloys with negligible magneto-crystalline anisotropy. The main driving force for alignment is the magnetic shape anisotropy. Current understanding of the phenomenon is not adequate to quantify the effect of particle size, aspect ratio, temperature and the magnetic field on particle alignment. We demonstrate a Monte Carlo approach coupled with size scaling to show the conditions under which alignment is possible.

Permanent bending and alignment of ZnO nanowires.

PubMed

Borschel, Christian; Spindler, Susann; Lerose, Damiana; Bochmann, Arne; Christiansen, Silke H; Nietzsche, Sandor; Oertel, Michael; Ronning, Carsten

2011-05-06

Ion beams can be used to permanently bend and re-align nanowires after growth. We have irradiated ZnO nanowires with energetic ions, achieving bending and alignment in different directions. Not only the bending of single nanowires is studied in detail, but also the simultaneous alignment of large ensembles of ZnO nanowires. Computer simulations reveal how the bending is initiated by ion beam induced damage. Detailed structural characterization identifies dislocations to relax stresses and make the bending and alignment permanent, even surviving annealing procedures.

A facile method to align carbon nanotubes on polymeric membrane substrate

PubMed Central

Zhao, Haiyang; Zhou, Zhijun; Dong, Hang; Zhang, Lin; Chen, Huanlin; Hou, Lian

2013-01-01

The alignment of carbon nanotubes (CNT) is the fundamental requirement to ensure their excellent functions but seems to be desolated in recent years. A facile method, hot-press combined with peel-off (HPPO), is introduced here, through which CNT can be successfully vertically aligned on the polymeric membrane substrate. Shear force and mechanical stretch are proposed to be the main forces to align the tubes perpendicular to the substrate surface during the peel-off process. The alignment of CNT keeps its orientation in a thin hybrid membrane by dip-coating cellulose acetate dope solution. It is expected that the stable alignment of CNT by HPPO would contribute to the realization of its potential applications. PMID:24326297

Chromaligner: a web server for chromatogram alignment.

PubMed

Wang, San-Yuan; Ho, Tsung-Jung; Kuo, Ching-Hua; Tseng, Yufeng J

2010-09-15

Chromaligner is a tool for chromatogram alignment to align retention time for chromatographic methods coupled to spectrophotometers such as high performance liquid chromatography and capillary electrophoresis for metabolomics works. Chromaligner resolves peak shifts by a constrained chromatogram alignment. For a collection of chromatograms and a set of defined peaks, Chromaligner aligns the chromatograms on defined peaks using correlation warping (COW). Chromaligner is faster than the original COW algorithm by k(2) times, where k is the number of defined peaks in a chromatogram. It also provides alignments based on known component peaks to reach the best results for further chemometric analysis. Chromaligner is freely accessible at http://cmdd.csie.ntu.edu.tw/~chromaligner.

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

PubMed Central

Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong

2015-01-01

Abstract We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate—slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory. PMID:25549288

In-flight alignment using H ∞ filter for strapdown INS on aircraft.

PubMed

Pei, Fu-Jun; Liu, Xuan; Zhu, Li

2014-01-01

In-flight alignment is an effective way to improve the accuracy and speed of initial alignment for strapdown inertial navigation system (INS). During the aircraft flight, strapdown INS alignment was disturbed by lineal and angular movements of the aircraft. To deal with the disturbances in dynamic initial alignment, a novel alignment method for SINS is investigated in this paper. In this method, an initial alignment error model of SINS in the inertial frame is established. The observability of the system is discussed by piece-wise constant system (PWCS) theory and observable degree is computed by the singular value decomposition (SVD) theory. It is demonstrated that the system is completely observable, and all the system state parameters can be estimated by optimal filter. Then a H ∞ filter was designed to resolve the uncertainty of measurement noise. The simulation results demonstrate that the proposed algorithm can reach a better accuracy under the dynamic disturbance condition.

A Method for the Alignment of Heterogeneous Macromolecules from Electron Microscopy

PubMed Central

Shatsky, Maxim; Hall, Richard J.; Brenner, Steven E.; Glaeser, Robert M.

2009-01-01

We propose a feature-based image alignment method for single-particle electron microscopy that is able to accommodate various similarity scoring functions while efficiently sampling the two-dimensional transformational space. We use this image alignment method to evaluate the performance of a scoring function that is based on the Mutual Information (MI) of two images rather than one that is based on the cross-correlation function. We show that alignment using MI for the scoring function has far less model-dependent bias than is found with cross-correlation based alignment. We also demonstrate that MI improves the alignment of some types of heterogeneous data, provided that the signal to noise ratio is relatively high. These results indicate, therefore, that use of MI as the scoring function is well suited for the alignment of class-averages computed from single particle images. Our method is tested on data from three model structures and one real dataset. PMID:19166941

Multiple nodes transfer alignment for airborne missiles based on inertial sensor network

NASA Astrophysics Data System (ADS)

Si, Fan; Zhao, Yan

2017-09-01

Transfer alignment is an important initialization method for airborne missiles because the alignment accuracy largely determines the performance of the missile. However, traditional alignment methods are limited by complicated and unknown flexure angle, and cannot meet the actual requirement when wing flexure deformation occurs. To address this problem, we propose a new method that uses the relative navigation parameters between the weapons and fighter to achieve transfer alignment. First, in the relative inertial navigation algorithm, the relative attitudes and positions are constantly computed in wing flexure deformation situations. Secondly, the alignment results of each weapon are processed using a data fusion algorithm to improve the overall performance. Finally, the feasibility and performance of the proposed method were evaluated under two typical types of deformation, and the simulation results demonstrated that the new transfer alignment method is practical and has high-precision.

Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.

PubMed

Bauer, Markus; Klau, Gunnar W; Reinert, Knut

2007-07-27

The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP). We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

Automated interferometric alignment system for paraboloidal mirrors

DOEpatents

Maxey, L.C.

1993-09-28

A method is described for a systematic method of interpreting interference fringes obtained by using a corner cube retroreflector as an alignment aid when aligning a paraboloid to a spherical wavefront. This is applicable to any general case where such alignment is required, but is specifically applicable in the case of aligning an autocollimating test using a diverging beam wavefront. In addition, the method provides information which can be systematically interpreted such that independent information about pitch, yaw and focus errors can be obtained. Thus, the system lends itself readily to automation. Finally, although the method is developed specifically for paraboloids, it can be seen to be applicable to a variety of other aspheric optics when applied in combination with a wavefront corrector that produces a wavefront which, when reflected from the correctly aligned aspheric surface will produce a collimated wavefront like that obtained from the paraboloid when it is correctly aligned to a spherical wavefront. 14 figures.

Development of a group work assessment pedagogy using constructive alignment theory.

PubMed

Croy, Suzanne R

2018-02-01

The purpose of this paper is to explore group work assessment underpinned by constructive alignment theory to develop a new assessment pedagogy. A review was undertaken of an existing module 'Mental Health Nursing 1', with student nurses participating in the BSc (Hons) Nursing Programme. Constructive alignment theory requires teachers to adopt a deep approach to learning where module learning outcomes are aligned with the teaching environment and modes of assessment. As the module progressed, reviewing the Mental Health Nursing 1 module became an excellent opportunity to begin to understand how constructive alignment theory can inform a group work assessment pedagogy. Working using a constructively aligned assessment process became a valuable learning experience for the module leader whilst at the same time revealed a gap in the research around the impact of constructively aligned teaching and group work assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Alignment Test System for AXAF-I's High Resolution Mirror Assembly

NASA Technical Reports Server (NTRS)

Waldman, Mark

1995-01-01

The AXAF-1 High Resolution Mirror Assembly (HRMA) consists of four nested mirror pairs of Wolter Type-1 grazing incidence optics. The HRMA assembly and alignment will take place in a vibration-isolated, cleanliness class 100, 18 meter high tower at an Eastman Kodak Company facility in Rochester, NY. Each mirror pair must be aligned such that its image is coma-free, and the four pairs must be aligned such that their images are coincident. In addition, both the HRMA optical axis and focal point must be precisely known with respect to physical references on the HRMA. The alignment of the HRMA mirrors is measured by the HRMA Alignment Test System (HATS), which is an integral part of the tower facility. The HATS is configured as a double-pass, autocollimating Hartmann test where each mirror aperture is scanned to determine the state of alignment. This paper will describe the design and operation of the HATS.

Simple chained guide trees give high-quality protein multiple sequence alignments

PubMed Central

Boyce, Kieran; Sievers, Fabian; Higgins, Desmond G.

2014-01-01

Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence alignment heuristic. These guide trees are often the limiting factor in making large alignments, and considerable effort has been expended over the years in making these quickly or accurately. In this article we show that, at least for protein families with large numbers of sequences that can be benchmarked with known structures, simple chained guide trees give the most accurate alignments. These also happen to be the fastest and simplest guide trees to construct, computationally. Such guide trees have a striking effect on the accuracy of alignments produced by some of the most widely used alignment packages. There is a marked increase in accuracy and a marked decrease in computational time, once the number of sequences goes much above a few hundred. This is true, even if the order of sequences in the guide tree is random. PMID:25002495

Effect of mat pilates exercise on postural alignment and body composition of middle-aged women.

PubMed

Lee, Hyo Taek; Oh, Hyun Ok; Han, Hui Seung; Jin, Kwang Youn; Roh, Hyo Lyun

2016-06-01

[Purpose] This study attempted to examine whether Pilates is an effective exercise for improving the postural alignment and health of middle-aged women. [Subjects and Methods] The participants in this study were 36 middle-aged women (20 in the experimental group, 16 in the control group). The experimental group participated in Pilates exercise sessions three times a week for 12 weeks. Body alignment and composition measurements before and after applying the Pilates exercise program were performed with a body composition analyzer and a three-dimensional scanner. [Results] Postural alignment in the sagittal and horizontal planes was enhanced in the Pilates exercise group. Trunk alignment showed correlations with body fat and muscle mass. [Conclusion] The Pilates exercises are performed symmetrically and strengthen the deep muscles. Moreover, the results showed that muscle mass was correlated with trunk postural alignment and that the proper amount of muscle is critical in maintaining trunk postural alignment.

Qualitative Variation in Constructive Alignment in Curriculum Design

ERIC Educational Resources Information Center

Trigwell, Keith; Prosser, Michael

2014-01-01

Constructive alignment has emerged as a powerful curriculum design idea, but little is known of the extent to which the effectiveness of this idea is a function of qualitative variation. This article introduces a model of qualitative variation in constructive alignment, and uses the results from known alignment studies to test the model. The…

Tests of Alignment among Assessment, Standards, and Instruction Using Generalized Linear Model Regression

ERIC Educational Resources Information Center

Fulmer, Gavin W.; Polikoff, Morgan S.

2014-01-01

An essential component in school accountability efforts is for assessments to be well-aligned with the standards or curriculum they are intended to measure. However, relatively little prior research has explored methods to determine statistical significance of alignment or misalignment. This study explores analyses of alignment as a special case…

21 CFR 872.1820 - Dental x-ray exposure alignment device.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Dental x-ray exposure alignment device. 872.1820... (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Diagnostic Devices § 872.1820 Dental x-ray exposure alignment device. (a) Identification. A dental x-ray exposure alignment device is a device intended to position x...

21 CFR 872.1820 - Dental x-ray exposure alignment device.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Dental x-ray exposure alignment device. 872.1820... (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Diagnostic Devices § 872.1820 Dental x-ray exposure alignment device. (a) Identification. A dental x-ray exposure alignment device is a device intended to position x...

21 CFR 872.1820 - Dental x-ray exposure alignment device.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Dental x-ray exposure alignment device. 872.1820... (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Diagnostic Devices § 872.1820 Dental x-ray exposure alignment device. (a) Identification. A dental x-ray exposure alignment device is a device intended to position x...

21 CFR 872.1820 - Dental x-ray exposure alignment device.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Dental x-ray exposure alignment device. 872.1820... (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Diagnostic Devices § 872.1820 Dental x-ray exposure alignment device. (a) Identification. A dental x-ray exposure alignment device is a device intended to position x...

21 CFR 872.1820 - Dental x-ray exposure alignment device.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Dental x-ray exposure alignment device. 872.1820... (CONTINUED) MEDICAL DEVICES DENTAL DEVICES Diagnostic Devices § 872.1820 Dental x-ray exposure alignment device. (a) Identification. A dental x-ray exposure alignment device is a device intended to position x...

Sensitive Technique For Detecting Alignment Of Seed Laser

NASA Technical Reports Server (NTRS)

Barnes, Norman P.

1994-01-01

Frequency response near resonance measured. Improved technique for detection and quantification of alignment of injection-seeding laser with associated power-oscillator laser proposed. Particularly useful in indicating alignment at spectral purity greater than 98 percent because it becomes more sensitive as perfect alignment approached. In addition, implemented relatively easily, without turning on power-oscillator laser.

Forced Alignment for Understudied Language Varieties: Testing Prosodylab-Aligner with Tongan Data

ERIC Educational Resources Information Center

Johnson, Lisa M.; Di Paolo, Marianna; Bell, Adrian

2018-01-01

Automated alignment of transcriptions to audio files expedites the process of preparing data for acoustic analysis. Unfortunately, the benefits of auto-alignment have generally been available only to researchers studying majority languages, for which large corpora exist and for which acoustic models have been created by large-scale research…

Estimating Critical Values for Strength of Alignment among Curriculum, Assessments, and Instruction

ERIC Educational Resources Information Center

Fulmer, Gavin W.

2010-01-01

School accountability decisions based on standardized tests hinge on the degree of alignment of the test with a state's standards. Yet no established criteria were available for judging strength of alignment. Previous studies of alignment among tests, standards, and teachers' instruction have yielded mixed results that are difficult to interpret…

Estimating Critical Values for Strength of Alignment among Curriculum, Assessments, and Instruction

ERIC Educational Resources Information Center

Fulmer, Gavin W.

2011-01-01

School accountability decisions based on standardized tests hinge on the degree of alignment of the test with the state's standards documents. Yet, there exist no established criteria for judging strength of alignment. Previous measures of alignment among tests, standards, and teachers' instruction have yielded mixed results that are difficult to…

DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors.

PubMed

Schmollinger, Martin; Nieselt, Kay; Kaufmann, Michael; Morgenstern, Burkhard

2004-09-09

Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics. Herein, a parallel version of the multi-alignment program DIALIGN is introduced. We propose two ways of dividing the program into independent sub-routines that can be run on different processors: (a) pair-wise sequence alignments that are used as a first step to multiple alignment account for most of the CPU time in DIALIGN. Since alignments of different sequence pairs are completely independent of each other, they can be distributed to multiple processors without any effect on the resulting output alignments. (b) For alignments of large genomic sequences, we use a heuristics by splitting up sequences into sub-sequences based on a previously introduced anchored alignment procedure. For our test sequences, this combined approach reduces the program running time of DIALIGN by up to 97%. By distributing sub-routines to multiple processors, the running time of DIALIGN can be crucially improved. With these improvements, it is possible to apply the program in large-scale genomics and proteomics projects that were previously beyond its scope.

A distributed system for fast alignment of next-generation sequencing data.

PubMed

Srimani, Jaydeep K; Wu, Po-Yen; Phan, John H; Wang, May D

2010-12-01

We developed a scalable distributed computing system using the Berkeley Open Interface for Network Computing (BOINC) to align next-generation sequencing (NGS) data quickly and accurately. NGS technology is emerging as a promising platform for gene expression analysis due to its high sensitivity compared to traditional genomic microarray technology. However, despite the benefits, NGS datasets can be prohibitively large, requiring significant computing resources to obtain sequence alignment results. Moreover, as the data and alignment algorithms become more prevalent, it will become necessary to examine the effect of the multitude of alignment parameters on various NGS systems. We validate the distributed software system by (1) computing simple timing results to show the speed-up gained by using multiple computers, (2) optimizing alignment parameters using simulated NGS data, and (3) computing NGS expression levels for a single biological sample using optimal parameters and comparing these expression levels to that of a microarray sample. Results indicate that the distributed alignment system achieves approximately a linear speed-up and correctly distributes sequence data to and gathers alignment results from multiple compute clients.

An Accurate Scalable Template-based Alignment Algorithm

PubMed Central

Gardner, David P.; Xu, Weijia; Miranker, Daniel P.; Ozer, Stuart; Cannone, Jamie J.; Gutell, Robin R.

2013-01-01

The rapid determination of nucleic acid sequences is increasing the number of sequences that are available. Inherent in a template or seed alignment is the culmination of structural and functional constraints that are selecting those mutations that are viable during the evolution of the RNA. While we might not understand these structural and functional, template-based alignment programs utilize the patterns of sequence conservation to encapsulate the characteristics of viable RNA sequences that are aligned properly. We have developed a program that utilizes the different dimensions of information in rCAD, a large RNA informatics resource, to establish a profile for each position in an alignment. The most significant include sequence identity and column composition in different phylogenetic taxa. We have compared our methods with a maximum of eight alternative alignment methods on different sets of 16S and 23S rRNA sequences with sequence percent identities ranging from 50% to 100%. The results showed that CRWAlign outperformed the other alignment methods in both speed and accuracy. A web-based alignment server is available at http://www.rna.ccbb.utexas.edu/SAE/2F/CRWAlign. PMID:24772376

SVM-dependent pairwise HMM: an application to protein pairwise alignments.

PubMed

Orlando, Gabriele; Raimondi, Daniele; Khan, Taushif; Lenaerts, Tom; Vranken, Wim F

2017-12-15

Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well-known benchmark datasets when aligning highly divergent sequences. A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. wim.vranken@vub.be. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

The Alignment effect of brightest cluster galaxies in the SDSS

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

Kim, R. S. J.; Annis, J.; Strauss, M. A.

2001-10-01

One of the most vital observational clues for unraveling the origin of Brightest Cluster Galaxies (BCG) is the observed alignment of the BCGs with their host cluster and its surroundings. We have examined the BCG-cluster alignment effect, using clusters of galaxies detected from the Sloan Digital Sky Survey (SDSS). We find that the BCGs are preferentially aligned with the principal axis of their hosts, to a much higher redshift (z >~ 0.3) than probed by previous studies (z <~ 0.1). The alignment effect strongly depends on the magnitude difference of the BCG and the second and third brightest cluster members:more » we find a strong alignment effect for the dominant BCGs, while less dominant BCGs do not show any departure from random alignment with respect to the cluster. We therefore claim that the alignment process originates from the same process that makes the BCG grow dominant, be it direct mergers in the early stage of cluster formation, or a later process that resembles the galactic cannibalism scenario. We do not find strong evidence for (or against) redshift evolution between 0« less

System alignment using the Talbot effect

NASA Astrophysics Data System (ADS)

Chevallier, Raymond; Le Falher, Eric; Heggarty, Kevin

1990-08-01

The Talbot effect is utilized to correct an alignment problem related to a neural network used for image recognition, which required the alignment of a spatial light modulator (SLM) with the input module. A mathematical model which employs the Fresnel diffraction theory is presented to describe the method. The calculation of the diffracted amplitude describes the wavefront sphericity and the original object transmittance function in order to qualify the lateral shift of the Talbot image. Another explanation is set forth in terms of plane-wave illumination in the neural network. Using a Fourier series and by describing planes where all the harmonics are in phase, the reconstruction of Talbot images is explained. The alignment is effective when the lenslet array is aligned on the even Talbot images of the SLM pixels and the incident wave is a plane wave. The alignment is evaluated in terms of source and periodicity errors, tilt of the incident plane waves, and finite object dimensions. The effects of the error sources are concluded to be negligible, the lenslet array is shown to be successfully aligned with the SLM, and other alignment applications are shown to be possible.

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos

PubMed Central

2014-01-01

Background The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. Results The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. Conclusions The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org. PMID:25237393

Statistical inference of protein structural alignments using information and compression.

PubMed

Collier, James H; Allison, Lloyd; Lesk, Arthur M; Stuckey, Peter J; Garcia de la Banda, Maria; Konagurthu, Arun S

2017-04-01

Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML). The quality of any alignment is measured by its explanatory power-the amount of lossless compression achieved to explain the protein coordinates using that alignment. We have implemented this approach in MMLigner , the first program able to infer statistically significant structural alignments. We also demonstrate the reliability of MMLigner 's alignment results when compared with the state of the art. Importantly, MMLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes. Source code, binaries and an interactive web version are available at http://lcb.infotech.monash.edu.au/mmligner . arun.konagurthu@monash.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Radiographic assessment of knee-ankle alignment after total knee arthroplasty for varus and valgus knee osteoarthritis.

PubMed

Gao, Fuqiang; Ma, Jinhui; Sun, Wei; Guo, Wanshou; Li, Zirong; Wang, Weiguo

2017-01-01

There are unanswered questions about knee-ankle alignment after total knee arthroplasty (TKA) for varus and valgus osteoarthritis (OA) of the knee. The aim of this retrospective study was to assess knee-ankle alignment after TKA. The study consisted of 149 patients who had undergone TKA due to varus and valgus knee OA. The alignment and angles in the selected knees and ankles were measured on full-length standing anteroposterior radiographs, both pre-operatively and post-operatively. The paired t-test and Pearson's correlation tests were used for statistical analysis. The results showed that ankle alignment correlated with knee alignment both pre-operatively and postoperatively (P<0.05). The pre-operative malalignment of the knee was corrected (P<0.05), and the ankle tilt angle was accordingly improved in the operative side after TKA (P<0.05). In addition, TKA had little effect on knee-ankle alignment on the non-operative side (P>0.05). These findings indicated that routine TKA could correct the varus or valgus deformity of a knee, and improve the tilt of the ankle. Ankle alignment correlated with knee alignment both pre-operatively and postoperatively. Both pre-operative knee and ankle malalignment can be simultaneously corrected following TKA. Level III. Copyright © 2016 Elsevier B.V. All rights reserved.

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Alignment-Annotator web server: rendering and annotating sequence alignments

PubMed Central

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-01-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

MEMS Integrated Submount Alignment for Optoelectronics

NASA Astrophysics Data System (ADS)

Shakespeare, W. Jeffrey; Pearson, Raymond A.; Grenestedt, Joachim L.; Hutapea, Parsaoran; Gupta, Vikas

2005-02-01

One of the most expensive and time-consuming production processes for single-mode fiber-optic components is the alignment of the photonic chip or waveguide to the fiber. The alignment equipment is capital intensive and usually requires trained technicians to achieve desired results. Current technology requires active alignment since tolerances are only ~0.2 μ m or less for a typical laser diode. This is accomplished using piezoelectric actuated stages and active optical feedback. Joining technologies such as soldering, epoxy bonding, or laser welding may contribute significant postbond shift, and final coupling efficiencies are often less than 80%. This paper presents a method of adaptive optical alignment to freeze in place directly on an optical submount using a microelectromechanical system (MEMS) shape memory alloy (SMA) actuation technology. Postbond shift is eliminated since the phase change is the alignment actuation. This technology is not limited to optical alignment but can be applied to a variety of MEMS actuations, including nano-actuation and nano-alignment for biomedical applications. Experimental proof-of-concept results are discussed, and a simple analytical model is proposed to predict the stress strain behavior of the optical submount. Optical coupling efficiencies and alignment times are compared with traditional processes. The feasibility of this technique in high-volume production is discussed.

Nanofiber Alignment Regulates NIH3T3 Cell Orientation and Cytoskeletal Gene Expression on Electrospun PCL+Gelatin Nanofibers.

PubMed

Fee, Timothy; Surianarayanan, Swetha; Downs, Crawford; Zhou, Yong; Berry, Joel

2016-01-01

To examine the influence of substrate topology on the behavior of fibroblasts, tissue engineering scaffolds were electrospun from polycaprolactone (PCL) and a blend of PCL and gelatin (PCL+Gel) to produce matrices with both random and aligned nanofibrous orientations. The addition of gelatin to the scaffold was shown to increase the hydrophilicity of the PCL matrix and to increase the proliferation of NIH3T3 cells compared to scaffolds of PCL alone. The orientation of nanofibers within the matrix did not have an effect on the proliferation of adherent cells, but cells on aligned substrates were shown to elongate and align parallel to the direction of substrate fiber alignment. A microarray of cyotoskeleton regulators was probed to examine differences in gene expression between cells grown on an aligned and randomly oriented substrates. It was found that transcriptional expression of eight genes was statistically different between the two conditions, with all of them being upregulated in the aligned condition. The proteins encoded by these genes are linked to production and polymerization of actin microfilaments, as well as focal adhesion assembly. Taken together, the data indicates NIH3T3 fibroblasts on aligned substrates align themselves parallel with their substrate and increase production of actin and focal adhesion related genes.

Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

PubMed Central

Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

2013-01-01

Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/. PMID:24116042

Current distribution and ac susceptibility response of a thin superconducting disc in an axial field: a theoretical approach

NASA Astrophysics Data System (ADS)

Aruna, S. A.; Zhang, P.; Lin, F. Y.; Ding, S. Y.; Yao, X. X.

2000-04-01

Within the framework of the thermally activated process of the flux line or flux line bundles, and by time integration of the 1D equation of motion of the circulating current density icons/Journals/Common/vecJ" ALT="vecJ" ALIGN="TOP"/> (icons/Journals/Common/rho" ALT="rho" ALIGN="TOP"/> ,t ), which is suitable for thin superconducting films (R >>d ,icons/Journals/Common/le" ALT="le" ALIGN="TOP"/> icons/Journals/Common/lambda" ALT="lambda" ALIGN="TOP"/> ), we present numerical calculations of the current profiles, magnetization hysteresis loops and ac susceptibility icons/Journals/Common/chi" ALT="chi" ALIGN="TOP"/> n = icons/Journals/Common/chi" ALT="chi" ALIGN="TOP"/> ´n +iicons/Journals/Common/chi" ALT="chi" ALIGN="TOP"/> ´´n for n = 1, 3 and 5 of a thin disc immersed in an axial time-dependent external magnetic field Ba (t ) = Bdc +Bac cos(2icons/Journals/Common/pi" ALT="pi" ALIGN="TOP"/> icons/Journals/Common/nu" ALT="nu" ALIGN="TOP"/> t ). Our calculated results are compared with those of the critical state model (CSM) and found to prove the approximate validity of the CSM below the irreversibility field. The differences between our computed results and those of the CSM are also discussed.

Formation of precessing jets by tilted black hole discs in 3D general relativistic MHD simulations

NASA Astrophysics Data System (ADS)

Liska, M.; Hesp, C.; Tchekhovskoy, A.; Ingram, A.; van der Klis, M.; Markoff, S.

2018-02-01

Gas falling into a black hole (BH) from large distances is unaware of BH spin direction, and misalignment between the accretion disc and BH spin is expected to be common. However, the physics of tilted discs (e.g. angular momentum transport and jet formation) is poorly understood. Using our new GPU-accelerated code H-AMR, we performed 3D general relativistic magnetohydrodynamic simulations of tilted thick accretion discs around rapidly spinning BHs, at the highest resolution to date. We explored the limit where disc thermal pressure dominates magnetic pressure, and showed for the first time that, for different magnetic field strengths on the BH, these flows launch magnetized relativistic jets propagating along the rotation axis of the tilted disc (rather than of the BH). If strong large-scale magnetic flux reaches the BH, it bends the inner few gravitational radii of the disc and jets into partial alignment with the BH spin. On longer time-scales, the simulated disc-jet system as a whole undergoes Lense-Thirring precession and approaches alignment, demonstrating for the first time that jets can be used as probes of disc precession. When the disc turbulence is well resolved, our isolated discs spread out, causing both the alignment and precession to slow down.

Spontaneous magnetic alignment behaviour in free-living lizards.

PubMed

Diego-Rasilla, Francisco J; Pérez-Mellado, Valentín; Pérez-Cembranos, Ana

2017-04-01

Several species of vertebrates exhibit spontaneous longitudinal body axis alignment relative to the Earth's magnetic field (i.e., magnetic alignment) while they are performing different behavioural tasks. Since magnetoreception is still not fully understood, studying magnetic alignment provides evidence for magnetoreception and broadens current knowledge of magnetic sense in animals. Furthermore, magnetic alignment widens the roles of magnetic sensitivity in animals and may contribute to shed new light on magnetoreception. In this context, spontaneous alignment in two species of lacertid lizards (Podarcis muralis and Podarcis lilfordi) during basking periods was monitored. Alignments in 255 P. muralis and 456 P. lilfordi were measured over a 5-year period. The possible influence of the sun's position (i.e., altitude and azimuth) and geomagnetic field values corresponding to the moment in which a particular lizard was observed on lizards' body axis orientation was evaluated. Both species exhibited a highly significant bimodal orientation along the north-northeast and south-southwest magnetic axis. The evidence from this study suggests that free-living lacertid lizards exhibit magnetic alignment behaviour, since their body alignments cannot be explained by an effect of the sun's position. On the contrary, lizard orientations were significantly correlated with geomagnetic field values at the time of each observation. We suggest that this behaviour might provide lizards with a constant directional reference while they are sun basking. This directional reference might improve their mental map of space to accomplish efficient escape behaviour. This study is the first to provide spontaneous magnetic alignment behaviour in free-living reptiles.

Tidal alignment of galaxies

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

Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact ofmore » smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used "nonlinear alignment model," finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the "GI" term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.« less

Tidal alignment of galaxies

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

Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš, E-mail: blazek@berkeley.edu, E-mail: zvlah@stanford.edu, E-mail: useljak@berkeley.edu

We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact ofmore » smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used 'nonlinear alignment model,' finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the 'GI' term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.« less

Individual responses to alignment perturbations in socket reaction moments while walking in transtibial prostheses.

PubMed

Kobayashi, Toshiki; Orendurff, Michael S; Zhang, Ming; Boone, David A

2014-05-01

The alignment of transtibial prostheses has a systematic effect on the mean socket reaction moments in amputees. However, understanding their individual differences in response to alignment perturbations is also important for prosthetists to fully utilize the socket reaction moments for dynamic alignment in each unique patient. The aim of this study was to investigate individual responses to alignment perturbations in transtibial prostheses with solid-ankle-cushion-heel feet. A custom instrumented prosthesis alignment component was used to measure the socket reaction moments while walking in 11 amputees with transtibial prostheses under 17 alignment conditions, including 3° and 6° of flexion, extension, abduction, and adduction of the socket, 5mm and 10mm of anterior, posterior, lateral, and medial translation of the socket, and an initial baseline alignment. Coronal moments at 30% of stance and maximum sagittal moments were extracted for comparisons from each amputee. In the coronal plane, varus moment at 30% of stance was generally reduced by adduction or medial translation of the socket in all the amputees. In the sagittal plane, extension moment was generally increased by posterior translation or flexion of the socket; however, this was not necessarily the case for all the amputees. Individual responses to alignment perturbations are not always consistent, and prosthetists would need to be aware of this variance when addressing individual socket reaction moments during dynamic alignment in clinical setting. Copyright © 2014 Elsevier Ltd. All rights reserved.

Diffeomorphic functional brain surface alignment: Functional demons.

PubMed

Nenning, Karl-Heinz; Liu, Hesheng; Ghosh, Satrajit S; Sabuncu, Mert R; Schwartz, Ernst; Langs, Georg

2017-08-01

Aligning brain structures across individuals is a central prerequisite for comparative neuroimaging studies. Typically, registration approaches assume a strong association between the features used for alignment, such as macro-anatomy, and the variable observed, such as functional activation or connectivity. Here, we propose to use the structure of intrinsic resting state fMRI signal correlation patterns as a basis for alignment of the cortex in functional studies. Rather than assuming the spatial correspondence of functional structures between subjects, we have identified locations with similar connectivity profiles across subjects. We mapped functional connectivity relationships within the brain into an embedding space, and aligned the resulting maps of multiple subjects. We then performed a diffeomorphic alignment of the cortical surfaces, driven by the corresponding features in the joint embedding space. Results show that functional alignment based on resting state fMRI identifies functionally homologous regions across individuals with higher accuracy than alignment based on the spatial correspondence of anatomy. Further, functional alignment enables measurement of the strength of the anatomo-functional link across the cortex, and reveals the uneven distribution of this link. Stronger anatomo-functional dissociation was found in higher association areas compared to primary sensory- and motor areas. Functional alignment based on resting state features improves group analysis of task based functional MRI data, increasing statistical power and improving the delineation of task-specific core regions. Finally, a comparison of the anatomo-functional dissociation between cohorts is demonstrated with a group of left and right handed subjects. Copyright © 2017 Elsevier Inc. All rights reserved.

Flexible and Lightweight Pressure Sensor Based on Carbon Nanotube/Thermoplastic Polyurethane-Aligned Conductive Foam with Superior Compressibility and Stability.

PubMed

Huang, Wenju; Dai, Kun; Zhai, Yue; Liu, Hu; Zhan, Pengfei; Gao, Jiachen; Zheng, Guoqiang; Liu, Chuntai; Shen, Changyu

2017-12-06

Flexible and lightweight carbon nanotube (CNT)/thermoplastic polyurethane (TPU) conductive foam with a novel aligned porous structure was fabricated. The density of the aligned porous material was as low as 0.123 g·cm -3 . Homogeneous dispersion of CNTs was achieved through the skeleton of the foam, and an ultralow percolation threshold of 0.0023 vol % was obtained. Compared with the disordered foam, mechanical properties of the aligned foam were enhanced and the piezoresistive stability of the flexible foam was improved significantly. The compression strength of the aligned TPU foam increases by 30.7% at the strain of 50%, and the stress of the aligned foam is 22 times that of the disordered foam at the strain of 90%. Importantly, the resistance variation of the aligned foam shows a fascinating linear characteristic under the applied strain until 77%, which would benefit the application of the foam as a desired pressure sensor. During multiple cyclic compression-release measurements, the aligned conductive CNT/TPU foam represents excellent reversibility and reproducibility in terms of resistance. This nice capability benefits from the aligned porous structure composed of ladderlike cells along the orientation direction. Simultaneously, the human motion detections, such as walk, jump, squat, etc. were demonstrated by using our flexible pressure sensor. Because of the lightweight, flexibility, high compressibility, excellent reversibility, and reproducibility of the conductive aligned foam, the present study is capable of providing new insights into the fabrication of a high-performance pressure sensor.

Alignment Test Results of the JWST Pathfinder Telescope Mirrors in the Cryogenic Environment

NASA Technical Reports Server (NTRS)

Whitman, Tony L.; Wells, Conrad; Hadaway, James; Knight, J. Scott; Lunt, Sharon

2016-01-01

After integration of the Optical Telescope Element (OTE) to the Integrated Science Instrument Module (ISIM) to become the OTIS, the James Webb Space Telescope OTIS is tested at NASAs Johnson Space Center (JSC) in the cryogenic vacuum Chamber A for alignment and optical performance. The alignment of the mirrors comprises a sequence of steps as follows: The mirrors are coarsely aligned using photogrammetry cameras with reflective targets attached to the sides of the mirrors. Then a multi-wavelength interferometer is aligned to the 18-segment primary mirror using cameras at the center of curvature to align reflected light from the segments and using fiducials at the edge of the primary mirror. Once the interferometer is aligned, the 18 primary mirror segments are then adjusted to optimize wavefront error of the aggregate mirror. This process phases the piston and tilt positions of all the mirror segments. An optical fiber placed at the Cassegrain focus of the telescope then emits light towards the secondary mirror to create a collimated beam emitting from the primary mirror. Portions of the collimated beam are retro-reflected from flat mirrors at the top of the chamber to pass through the telescope to the SI detector. The image on the detector is used for fine alignment of the secondary mirror and a check of the primary mirror alignment using many of the same analysis techniques used in the on-orbit alignment. The entire process was practiced and evaluated in 2015 at cryogenic temperature with the Pathfinder telescope.

DNAAlignEditor: DNA alignment editor tool

PubMed Central

Sanchez-Villeda, Hector; Schroeder, Steven; Flint-Garcia, Sherry; Guill, Katherine E; Yamasaki, Masanori; McMullen, Michael D

2008-01-01

Background With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor. Results We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected. Conclusion We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism. PMID:18366684

Spontaneous magnetic alignment behaviour in free-living lizards

NASA Astrophysics Data System (ADS)

Diego-Rasilla, Francisco J.; Pérez-Mellado, Valentín; Pérez-Cembranos, Ana

2017-04-01

Several species of vertebrates exhibit spontaneous longitudinal body axis alignment relative to the Earth's magnetic field (i.e., magnetic alignment) while they are performing different behavioural tasks. Since magnetoreception is still not fully understood, studying magnetic alignment provides evidence for magnetoreception and broadens current knowledge of magnetic sense in animals. Furthermore, magnetic alignment widens the roles of magnetic sensitivity in animals and may contribute to shed new light on magnetoreception. In this context, spontaneous alignment in two species of lacertid lizards ( Podarcis muralis and Podarcis lilfordi) during basking periods was monitored. Alignments in 255 P. muralis and 456 P. lilfordi were measured over a 5-year period. The possible influence of the sun's position (i.e., altitude and azimuth) and geomagnetic field values corresponding to the moment in which a particular lizard was observed on lizards' body axis orientation was evaluated. Both species exhibited a highly significant bimodal orientation along the north-northeast and south-southwest magnetic axis. The evidence from this study suggests that free-living lacertid lizards exhibit magnetic alignment behaviour, since their body alignments cannot be explained by an effect of the sun's position. On the contrary, lizard orientations were significantly correlated with geomagnetic field values at the time of each observation. We suggest that this behaviour might provide lizards with a constant directional reference while they are sun basking. This directional reference might improve their mental map of space to accomplish efficient escape behaviour. This study is the first to provide spontaneous magnetic alignment behaviour in free-living reptiles.

Effect of prosthetic alignment changes on socket reaction moment impulse during walking in transtibial amputees.

PubMed

Kobayashi, Toshiki; Orendurff, Michael S; Arabian, Adam K; Rosenbaum-Chou, Teri G; Boone, David A

2014-04-11

The alignment of a lower limb prosthesis affects the way load is transferred to the residual limb through the socket, and this load is critically important for the comfort and function of the prosthesis. Both magnitude and duration of the moment are important factors that may affect the residual limb health. Moment impulse is a well-accepted measurement that incorporates both factors via moment-time integrals. The aim of this study was to investigate the effect of alignment changes on the socket reaction moment impulse in transtibial prostheses. Ten amputees with transtibial prostheses participated in this study. The socket reaction moment impulse was measured at a self-selected walking speed using a Smart Pyramid in 25 alignment conditions, including a nominal alignment (clinically aligned by a prosthetist), as well as angle malalignments of 2°, 4° and 6° (abduction, adduction, extension and flexion) and translation malalignments of 5 mm, 10 mm and 15 mm (lateral, medial, anterior and posterior). The socket reaction moment impulse of the nominal alignment was compared for each condition. The relationship between the alignment and the socket reaction moment impulse was clearly observed in the coronal angle, coronal translation and sagittal translation alignment changes. However, this relationship was not evident in the sagittal angle alignment changes. The results of this study suggested that the socket reaction moment impulse could potentially serve as a valuable parameter to assist the alignment tuning process for transtibial prostheses. Further study is needed to investigate the influence of the socket reaction moment impulse on the residual limb health. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effect of alignment changes on socket reaction moments while walking in transtibial prostheses with energy storage and return feet.

PubMed

Kobayashi, Toshiki; Arabian, Adam K; Orendurff, Michael S; Rosenbaum-Chou, Teri G; Boone, David A

2014-01-01

Energy storage and return feet are designed for active amputees. However, little is known about the socket reaction moments in transtibial prostheses with energy storage and return feet. The aim of this study was to investigate the effect of alignment changes on the socket reaction moments during gait while using the energy storage and return feet. A Smart Pyramid™ was used to measure the socket reaction moments in 10 subjects with transtibial prostheses while walking under 25 alignment conditions, including a nominal alignment (as defined by conventional clinical methods), as well as angle malalignments of 2°, 4° and 6° (flexion, extension, abduction, and adduction) and translation malalignments of 5mm, 10mm and 15mm (anterior, posterior, lateral, and medial) referenced from the nominal alignment. The socket reaction moments of the nominal alignment were compared with each malalignment. Both coronal and sagittal alignment changes demonstrated systematic effects on the socket reaction moments. In the sagittal plane, angle and translation alignment changes demonstrated significant differences (P<0.05) in the minimum moment, the moment at 45% of stance and the maximum moment for some comparisons. In the coronal plane, angle and translation alignment changes demonstrated significant differences (P<0.05) in the moment at 30% and 75% of stance for all comparisons. The alignment may have systematic effects on the socket reaction moments in transtibial prostheses with energy storage and return feet. The socket reaction moments could potentially be a useful biomechanical parameter to evaluate the alignment of the transtibial prostheses. Copyright © 2013 Elsevier Ltd. All rights reserved.

Computational design and engineering of polymeric orthodontic aligners.

PubMed

Barone, S; Paoli, A; Razionale, A V; Savignano, R

2016-10-05

Transparent and removable aligners represent an effective solution to correct various orthodontic malocclusions through minimally invasive procedures. An aligner-based treatment requires patients to sequentially wear dentition-mating shells obtained by thermoforming polymeric disks on reference dental models. An aligner is shaped introducing a geometrical mismatch with respect to the actual tooth positions to induce a loading system, which moves the target teeth toward the correct positions. The common practice is based on selecting the aligner features (material, thickness, and auxiliary elements) by only considering clinician's subjective assessments. In this article, a computational design and engineering methodology has been developed to reconstruct anatomical tissues, to model parametric aligner shapes, to simulate orthodontic movements, and to enhance the aligner design. The proposed approach integrates computer-aided technologies, from tomographic imaging to optical scanning, from parametric modeling to finite element analyses, within a 3-dimensional digital framework. The anatomical modeling provides anatomies, including teeth (roots and crowns), jaw bones, and periodontal ligaments, which are the references for the down streaming parametric aligner shaping. The biomechanical interactions between anatomical models and aligner geometries are virtually reproduced using a finite element analysis software. The methodology allows numerical simulations of patient-specific conditions and the comparative analyses of different aligner configurations. In this article, the digital framework has been used to study the influence of various auxiliary elements on the loading system delivered to a maxillary and a mandibular central incisor during an orthodontic tipping movement. Numerical simulations have shown a high dependency of the orthodontic tooth movement on the auxiliary element configuration, which should then be accurately selected to maximize the aligner's effectiveness. Copyright © 2016 John Wiley & Sons, Ltd.

No condylar lift-off occurs because of excessive lateral soft tissue laxity in neutrally aligned total knee arthroplasty: a computer simulation study.

PubMed

Kuriyama, Shinichi; Ishikawa, Masahiro; Nakamura, Shinichiro; Furu, Moritoshi; Ito, Hiromu; Matsuda, Shuichi

2016-08-01

Condylar lift-off can induce excessive polyethylene wear after total knee arthroplasty (TKA). A computer simulation was used to evaluate the influence of femoral varus alignment and lateral collateral ligament (LCL) laxity on lift-off after single-design TKA. It was hypothesised that proper ligament balancing and coronal alignment would prevent lift-off. The computer model in this study is a dynamic musculoskeletal program that simulates gait up to 60° of knee flexion. The lift-off phenomenon was defined as positive with an intercomponent distance of >2 mm. In neutrally aligned components in the coronal plane, the femoral and tibial components were set perpendicular to the femoral and tibial mechanical axis, respectively. The femoral coronal alignment was changed from neutral to 5° varus in 1° increments. Simultaneously, the LCL length was elongated from 0 to 5 mm in 1-mm increments to provide a model of pathological slack. Within 2° of femoral varus alignment, lift-off did not occur even if the LCL was elongated by up to 5 mm. However, lift-off occurred easily in the stance phase in femoral varus alignments of >3° with slight LCL slack. The contact forces of the tibiofemoral joint were influenced more by femoral varus alignment than by LCL laxity. Aiming for neutral alignment in severely varus knees makes it difficult to achieve appropriate ligament balance. Our study suggests that no lift-off occurs with excessive LCL laxity alone in a neutrally aligned TKA and therefore that varus alignment should be avoided to decrease lift-off after TKA. Case series, Level IV.

Heuristics for multiobjective multiple sequence alignment.

PubMed

Abbasi, Maryam; Paquete, Luís; Pereira, Francisco B

2016-07-15

Aligning multiple sequences arises in many tasks in Bioinformatics. However, the alignments produced by the current software packages are highly dependent on the parameters setting, such as the relative importance of opening gaps with respect to the increase of similarity. Choosing only one parameter setting may provide an undesirable bias in further steps of the analysis and give too simplistic interpretations. In this work, we reformulate multiple sequence alignment from a multiobjective point of view. The goal is to generate several sequence alignments that represent a trade-off between maximizing the substitution score and minimizing the number of indels/gaps in the sum-of-pairs score function. This trade-off gives to the practitioner further information about the similarity of the sequences, from which she could analyse and choose the most plausible alignment. We introduce several heuristic approaches, based on local search procedures, that compute a set of sequence alignments, which are representative of the trade-off between the two objectives (substitution score and indels). Several algorithm design options are discussed and analysed, with particular emphasis on the influence of the starting alignment and neighborhood search definitions on the overall performance. A perturbation technique is proposed to improve the local search, which provides a wide range of high-quality alignments. The proposed approach is tested experimentally on a wide range of instances. We performed several experiments with sequences obtained from the benchmark database BAliBASE 3.0. To evaluate the quality of the results, we calculate the hypervolume indicator of the set of score vectors returned by the algorithms. The results obtained allow us to identify reasonably good choices of parameters for our approach. Further, we compared our method in terms of correctly aligned pairs ratio and columns correctly aligned ratio with respect to reference alignments. Experimental results show that our approaches can obtain better results than TCoffee and Clustal Omega in terms of the first ratio.

Alignment of galaxies relative to their local environment in SDSS-DR8

NASA Astrophysics Data System (ADS)

Hirv, A.; Pelt, J.; Saar, E.; Tago, E.; Tamm, A.; Tempel, E.; Einasto, M.

2017-03-01

Aims: We study the alignment of galaxies relative to their local environment in SDSS-DR8 and, using these data, we discuss evolution scenarios for different types of galaxies. Methods: We defined a vector field of the direction of anisotropy of the local environment of galaxies. We summed the unit direction vectors of all close neighbours of a given galaxy in a particular way to estimate this field. We found the alignment angles between the spin axes of disc galaxies, or the minor axes of elliptical galaxies, and the direction of anisotropy. The distributions of cosines of these angles are compared to the random distributions to analyse the alignment of galaxies. Results: Sab galaxies show perpendicular alignment relative to the direction of anisotropy in a sparse environment, for single galaxies and galaxies of low luminosity. Most of the parallel alignment of Scd galaxies comes from dense regions, from 2...3 member groups and from galaxies with low luminosity. The perpendicular alignment of S0 galaxies does not depend strongly on environmental density nor luminosity; it is detected for single and 2...3 member group galaxies, and for main galaxies of 4...10 member groups. The perpendicular alignment of elliptical galaxies is clearly detected for single galaxies and for members of ≤10 member groups; the alignment increases with environmental density and luminosity. Conclusions: We confirm the existence of fossil tidally induced alignment of Sab galaxies at low z. The alignment of Scd galaxies can be explained via the infall of matter to filaments. S0 galaxies may have encountered relatively massive mergers along the direction of anisotropy. Major mergers along this direction can explain the alignment of elliptical galaxies. Less massive, but repeated mergers are possibly responsible for the formation of elliptical galaxies in sparser areas and for less luminous elliptical galaxies.

BRIGHTEST SATELLITE GALAXY ALIGNMENT OF SLOAN DIGITAL SKY SURVEY GALAXY GROUPS

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

Li Zhigang; Wang Yougang; Chen Xuelei

2013-05-01

We study the alignment signal between the distribution of the brightest satellite galaxies (BSGs) and the major axes of their host groups using the Sloan Digital Sky Survey group catalog constructed by Yang et al. After correcting for the effect of group ellipticity, a statistically significant ({approx}5{sigma}) major-axis alignment is detected and the alignment angle is found to be 43. Degree-Sign 0 {+-} 0. Degree-Sign 4. More massive and richer groups show a stronger BSG alignment. The BSG alignment around blue brightest central galaxies (BCGs) is slightly stronger than that around red BCGs. Red BSGs have a much stronger major-axismore » alignment than blue BSGs. Unlike BSGs, other satellites do not show very significant alignment with their group's major axis. We further explore BSG alignment using the semi-analytic model (SAM) constructed by Guo et al. In general, we found good agreement of the model with observations: BSGs in the SAM show a strong major-axis alignment that depends on group mass and richness in the same way as in observations and none of the other satellites exhibit prominent alignment. However, a discrepancy also exists in that the SAM shows a BSG color dependence opposite of that in observations, which is most probably induced by a missing large-scale environment ingredient in the SAM. The combination of two popular scenarios can explain the BSG alignment we detected. First, satellites merged into the group along the surrounding filaments, which are strongly aligned with the major axis of the group. Second, BSGs entered their host group more recently than other satellites, so they have preserved more information about their assembling history and major-axis alignment. In the SAM, we found positive evidence for the second scenario in the fact that BSGs merged into groups statistically more recently than other satellites. We also found that most of the BSGs (80%) were BCGs before they merged into groups and earlier merging BSGs tend to be closer to their BCGs than other BSGs. On the other hand, although the BSG color dependence in observations is the opposite of that in the SAM, it might also indicate that the first scenario is a good explanation.« less

A Comprehensive Two-Dimensional Retention Time Alignment Algorithm To Enhance Chemometric Analysis of Comprehensive Two-Dimensional Separation Data

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

Pierce, Karisa M.; Wood, Lianna F.; Wright, Bob W.

2005-12-01

A comprehensive two-dimensional (2D) retention time alignment algorithm was developed using a novel indexing scheme. The algorithm is termed comprehensive because it functions to correct the entire chromatogram in both dimensions and it preserves the separation information in both dimensions. Although the algorithm is demonstrated by correcting comprehensive two-dimensional gas chromatography (GC x GC) data, the algorithm is designed to correct shifting in all forms of 2D separations, such as LC x LC, LC x CE, CE x CE, and LC x GC. This 2D alignment algorithm was applied to three different data sets composed of replicate GC x GCmore » separations of (1) three 22-component control mixtures, (2) three gasoline samples, and (3) three diesel samples. The three data sets were collected using slightly different temperature or pressure programs to engender significant retention time shifting in the raw data and then demonstrate subsequent corrections of that shifting upon comprehensive 2D alignment of the data sets. Thirty 12-min GC x GC separations from three 22-component control mixtures were used to evaluate the 2D alignment performance (10 runs/mixture). The average standard deviation of the first column retention time improved 5-fold from 0.020 min (before alignment) to 0.004 min (after alignment). Concurrently, the average standard deviation of second column retention time improved 4-fold from 3.5 ms (before alignment) to 0.8 ms (after alignment). Alignment of the 30 control mixture chromatograms took 20 min. The quantitative integrity of the GC x GC data following 2D alignment was also investigated. The mean integrated signal was determined for all components in the three 22-component mixtures for all 30 replicates. The average percent difference in the integrated signal for each component before and after alignment was 2.6%. Singular value decomposition (SVD) was applied to the 22-component control mixture data before and after alignment to show the restoration of trilinearity to the data, since trilinearity benefits chemometric analysis. By applying comprehensive 2D retention time alignment to all three data sets (control mixtures, gasoline samples, and diesel samples), classification by principal component analysis (PCA) substantially improved, resulting in 100% accurate scores clustering.« less

Extraction of the Wichita Fusion Nail after Knee Arthrodesis.

PubMed

Neuts, Ann-Sophie; Lammens, Johan; Stuyck, Jose

2016-01-01

To avoid a new exposition and partial damage of a knee arthrodesis site due to the removal of the Wichita fusion nail (WFN), a new extraction technique was developed, using a femoral osteotomy at the proximal end of the nail. Fixing the osteotomy with an Ilizarov frame offered the possibility to perform an additional correction of length and/or alignment if necessary.

[Fiber-reinforced composite in fixed prosthodontics].

PubMed

Pilo, R; Abu Rass, Z; Shmidt, A

2010-07-01

Fiber reinforced composite (FRC) is composed of resin matrix and fibers filler. Common types of fibers: polyethylene, carbon and glass. Fibers can be continuous and aligned, discontinuous and aligned, discontinuous and randomly oriented. The architecture of the fibers is unidirectional, woven or braided. The two main types are: dry fibers or impregnated. Inclusion of fibers to resin composite increased its average flexural strength in 100-200 MPa. FRC can be utilized by the dentist in direct approach (splinting, temporary winged bridge) or indirect approach (laboratory made fixed partial denture). Laboratory fixed partial denture (FPD) is made from FRC substructure and Hybrid/Microfill particulate composite veneer. Main indications: interim temporary FPD or FPD in cases of questionable abutment teeth, in aesthetic cases where All Ceram FPD is not feasible. Retention is attained by adhesive cementation to minimally prepared teeth or to conventionally prepared teeth; other options are inlay-onlay bridges or hybrid bridges. Contraindications are: poor hygiene, inability to control humidity, parafunction habits, and more than two pontics. Survival rate of FRC FPD over 5 years is 75%, lower compared to porcelain fused to metal FPD which is 95%. Main reasons for failure are: fracture of framework and delamination of the veneer. Part of the failures is repairable.

Optical Wireless Communications

NASA Astrophysics Data System (ADS)

Arnon, Shlomi; Britz, David M.; Boucouvalas, Anthony C.; Kavehrad, Mohsen

2005-01-01