Sample records for alignment analysis revealed
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kuo, Alan; Grigoriev, Igor
2009-06-12
22 percent ESTs do no align with scaffolds. EST Pipeleine assembles 17126 consensi from the noaligned ESTs. Annotation Pipeline predicts 8564 ORFS on the consensi. Domain analysis of ORFs reveals missing genes. Cluster analysis reveals missing genes. Expression analysis reveals potential strain specific genes.
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Attitude sensor alignment calibration for the solar maximum mission
NASA Technical Reports Server (NTRS)
Pitone, Daniel S.; Shuster, Malcolm D.
1990-01-01
An earlier heuristic study of the fine attitude sensors for the Solar Maximum Mission (SMM) revealed a temperature dependence of the alignment about the yaw axis of the pair of fixed-head star trackers relative to the fine pointing Sun sensor. Here, new sensor alignment algorithms which better quantify the dependence of the alignments on the temperature are developed and applied to the SMM data. Comparison with the results from the previous study reveals the limitations of the heuristic approach. In addition, some of the basic assumptions made in the prelaunch analysis of the alignments of the SMM are examined. The results of this work have important consequences for future missions with stringent attitude requirements and where misalignment variations due to variations in the temperature will be significant.
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Guo, Shaoyin; Hihath, Joshua; Díez-Pérez, Ismael; Tao, Nongjian
2011-11-30
We report on the measurement and statistical study of thousands of current-voltage characteristics and transition voltage spectra (TVS) of single-molecule junctions with different contact geometries that are rapidly acquired using a new break junction method at room temperature. This capability allows one to obtain current-voltage, conductance voltage, and transition voltage histograms, thus adding a new dimension to the previous conductance histogram analysis at a fixed low-bias voltage for single molecules. This method confirms the low-bias conductance values of alkanedithiols and biphenyldithiol reported in literature. However, at high biases the current shows large nonlinearity and asymmetry, and TVS allows for the determination of a critically important parameter, the tunneling barrier height or energy level alignment between the molecule and the electrodes of single-molecule junctions. The energy level alignment is found to depend on the molecule and also on the contact geometry, revealing the role of contact geometry in both the contact resistance and energy level alignment of a molecular junction. Detailed statistical analysis further reveals that, despite the dependence of the energy level alignment on contact geometry, the variation in single-molecule conductance is primarily due to contact resistance rather than variations in the energy level alignment.
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Statistical Significance of Optical Map Alignments
Sarkar, Deepayan; Goldstein, Steve; Schwartz, David C.
2012-01-01
Abstract The Optical Mapping System constructs ordered restriction maps spanning entire genomes through the assembly and analysis of large datasets comprising individually analyzed genomic DNA molecules. Such restriction maps uniquely reveal mammalian genome structure and variation, but also raise computational and statistical questions beyond those that have been solved in the analysis of smaller, microbial genomes. We address the problem of how to filter maps that align poorly to a reference genome. We obtain map-specific thresholds that control errors and improve iterative assembly. We also show how an optimal self-alignment score provides an accurate approximation to the probability of alignment, which is useful in applications seeking to identify structural genomic abnormalities. PMID:22506568
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Dong, Fulong; Tian, Yiqun; Yu, Shujuan; Wang, Shang; Yang, Shiping; Chen, Yanjun
2015-07-13
We investigate the polarization properties of below-threshold harmonics from aligned molecules in linearly polarized laser fields numerically and analytically. We focus on lower-order harmonics (LOHs). Our simulations show that the ellipticity of below-threshold LOHs depends strongly on the orientation angle and differs significantly for different harmonic orders. Our analysis reveals that this LOH ellipticity is closely associated with resonance effects and the axis symmetry of the molecule. These results shed light on the complex generation mechanism of below-threshold harmonics from aligned molecules.
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Photo-elastic stress analysis of initial alignment archwires.
Badran, Serene A; Orr, John F; Stevenson, Mike; Burden, Donald J
2003-04-01
Photo-elastic models replicating a lower arch with a moderate degree of lower incisor crowding and a palatally displaced maxillary canine were used to evaluate the stresses transmitted to the roots of the teeth by initial alignment archwires. Six initial alignment archwires were compared, two multi-strand stainless steel wires, two non-super-elastic (stabilized martensitic form) nickel titanium wires, and two stress-induced super-elastic (austenitic active) nickel titanium wires. Three specimens of each archwire type were tested. Analysis of the photo-elastic fringe patterns, in the medium supporting the teeth, revealed that the non-super-elastic nickel titanium archwires produced the highest shear stresses (P = 0.001). However, the shear stresses generated by the super-elastic alignment archwires and the multi-strand stainless steel archwires were very similar (P = 1.00). These results show that even in situations where large deflections of initial alignment archwires are required, super-elastic archwires do not appear to have any marked advantage over multi-strand stainless steel alignment archwires in terms of the stresses transferred to the roots of the teeth.
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Evaluation of Eight Methods for Aligning Orientation of Two Coordinate Systems.
Mecheri, Hakim; Robert-Lachaine, Xavier; Larue, Christian; Plamondon, André
2016-08-01
The aim of this study was to evaluate eight methods for aligning the orientation of two different local coordinate systems. Alignment is very important when combining two different systems of motion analysis. Two of the methods were developed specifically for biomechanical studies, and because there have been at least three decades of algorithm development in robotics, it was decided to include six methods from this field. To compare these methods, an Xsens sensor and two Optotrak clusters were attached to a Plexiglas plate. The first optical marker cluster was fixed on the sensor and 20 trials were recorded. The error of alignment was calculated for each trial, and the mean, the standard deviation, and the maximum values of this error over all trials were reported. One-way repeated measures analysis of variance revealed that the alignment error differed significantly across the eight methods. Post-hoc tests showed that the alignment error from the methods based on angular velocities was significantly lower than for the other methods. The method using angular velocities performed the best, with an average error of 0.17 ± 0.08 deg. We therefore recommend this method, which is easy to perform and provides accurate alignment.
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FitzPatrick, Beverly; Hawboldt, John; Doyle, Daniel; Genge, Terri
2015-02-17
To determine whether national educational outcomes, course objectives, and classroom assessments for 2 therapeutics courses were aligned for curricular content and cognitive processes, and if they included higher-order thinking. Document analysis and student focus groups were used. Outcomes, objectives, and assessment tasks were matched for specific therapeutics content and cognitive processes. Anderson and Krathwohl's Taxonomy was used to define higher-order thinking. Students discussed whether assessments tested objectives and described their thinking when responding to assessments. There were 7 outcomes, 31 objectives, and 412 assessment tasks. The alignment for content and cognitive processes was not satisfactory. Twelve students participated in the focus groups. Students thought more short-answer questions than multiple choice questions matched the objectives for content and required higher-order thinking. The alignment analysis provided data that could be used to reveal and strengthen the enacted curriculum and improve student learning.
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Local alignment vectors reveal cancer cell-induced ECM fiber remodeling dynamics
Lee, Byoungkoo; Konen, Jessica; Wilkinson, Scott; Marcus, Adam I.; Jiang, Yi
2017-01-01
Invasive cancer cells interact with the surrounding extracellular matrix (ECM), remodeling ECM fiber network structure by condensing, degrading, and aligning these fibers. We developed a novel local alignment vector analysis method to quantitatively measure collagen fiber alignment as a vector field using Circular Statistics. This method was applied to human non-small cell lung carcinoma (NSCLC) cell lines, embedded as spheroids in a collagen gel. Collagen remodeling was monitored using second harmonic generation imaging under normal conditions and when the LKB1-MARK1 pathway was disrupted through RNAi-based approaches. The results showed that inhibiting LKB1 or MARK1 in NSCLC increases the collagen fiber alignment and captures outward alignment vectors from the tumor spheroid, corresponding to high invasiveness of LKB1 mutant cancer cells. With time-lapse imaging of ECM micro-fiber morphology, the local alignment vector can measure the dynamic signature of invasive cancer cell activity and cell-migration-induced ECM and collagen remodeling and realigning dynamics. PMID:28045069
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Vu, Trung N; Valkenborg, Dirk; Smets, Koen; Verwaest, Kim A; Dommisse, Roger; Lemière, Filip; Verschoren, Alain; Goethals, Bart; Laukens, Kris
2011-10-20
Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline. We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear improvements in comparison to other methods, and the down-to-earth quantitative analysis works well for the CluPA-aligned spectra. The whole workflow is embedded into a modular and statistically sound framework that is implemented as an R package called "speaq" ("spectrum alignment and quantitation"), which is freely available from http://code.google.com/p/speaq/.
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Panwar, Priyankar; Verma, A K; Dubey, Ashutosh
2018-05-01
Barnyard ( Echinochloa frumentacea ) and finger ( Eleusine coracana ) millet growing at northwestern Himalaya were explored for the α-amylase inhibitor (α-AI). The mature seeds of barnyard millet variety PRJ1 had maximum α-AI activity which increases in different developmental stage. α-AI was purified up to 22.25-fold from barnyard millet variety PRJ1. Semi-quantitative PCR of different developmental stages of barnyard millet seeds showed increased levels of the transcript from 7 to 28 days. Sequence analysis revealed that it contained 315 bp nucleotide which encodes 104 amino acid sequence with molecular weight 10.72 kDa. The predicted 3D structure of α-AI was 86.73% similar to a bifunctional inhibitor of ragi. In silico analysis of 71 α-AI protein sequences were carried out for biochemical features, homology search, multiple sequence alignment, phylogenetic tree construction, motif, and superfamily distribution of protein sequences. Analysis of multiple sequence alignment revealed the existence of conserved regions NPLP[S/G]CRWYVV[S/Q][Q/R]TCG[V/I] throughout sequences. Superfam analysis revealed that α-AI protein sequences were distributed among seven different superfamilies.
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Erickson, Ariane E.; Edmondson, Dennis; Chang, Fei-Chien; Wood, Dave; Gong, Alex; Levengood, Sheeny Lan; Zhang, Miqin
2016-01-01
The inability to produce large quantities of nanofibers has been a primary obstacle in advancement and commercialization of electrospinning technologies, especially when aligned nanofibers are desired. Here, we present a high-throughput centrifugal electrospinning (HTP-CES) system capable of producing a large number of highly-aligned nanofiber samples with high-yield and tunable diameters. The versatility of the design was revealed when bead-less nanofibers were produced from copolymer chitosan/polycaprolactone (C-PCL) solutions despite variations in polymer blend composition or spinneret needle gauge. Compared to conventional electrospinning techniques, fibers spun with the HTP-CES not only exhibited superior alignment, but also better diameter uniformity. Nanofiber alignment was quantified using Fast Fourier Transform (FFT) analysis. In addition, a concave correlation between the needle diameter and resultant fiber diameter was identified. This system can be easily scaled up for industrial production of highly-aligned nanofibers with tunable diameters that can potentially meet the requirements for various engineering and biomedical applications. PMID:26428148
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Collagen organization in canine myxomatous mitral valve disease: an x-ray diffraction study.
Hadian, Mojtaba; Corcoran, Brendan M; Han, Richard I; Grossmann, J Günter; Bradshaw, Jeremy P
2007-10-01
Collagen fibrils, a major component of mitral valve leaflets, play an important role in defining shape and providing mechanical strength and flexibility. Histopathological studies show that collagen fibrils undergo dramatic changes in the course of myxomatous mitral valve disease in both dogs and humans. However, little is known about the detailed organization of collagen in this disease. This study was designed to analyze and compare collagen fibril organization in healthy and lesional areas of myxomatous mitral valves of dogs, using synchrotron small-angle x-ray diffraction. The orientation, density, and alignment of collagen fibrils were mapped across six different valves. The findings reveal a preferred collagen alignment in the main body of the leaflets between two commissures. Qualitative and quantitative analysis of the data showed significant differences between affected and lesion-free areas in terms of collagen content, fibril alignment, and total tissue volume. Regression analysis of the amount of collagen compared to the total tissue content at each point revealed a significant relationship between these two parameters in lesion-free but not in affected areas. This is the first time this technique has been used to map collagen fibrils in cardiac tissue; the findings have important applications to human cardiology.
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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.
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The Function of Neuroendocrine Cells in Prostate Cancer
2013-04-01
integration site. We then performed deep sequencing and aligned reads to the genome. Our analysis revealed that both histological phenotypes are derived from...lentiviral integration site analysis . (B) Laser capture microdissection was performed on individual glands containing both squamous and...lentiviral integration site analysis . LTR: long terminal repeat (viral DNA), PCR: polymerase chain reaction. (D) Venn diagrams depict shared lentiviral
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Grustam, Andrija S; Vrijhoef, Hubertus J M; Koymans, Ron; Hukal, Philipp; Severens, Johan L
2017-10-11
The purpose of this study is to assess the Business-to-Consumer (B2C) model for telemonitoring patients with Chronic Heart Failure (CHF) by analysing the value it creates, both for organizations or ventures that provide telemonitoring services based on it, and for society. The business model assessment was based on the following categories: caveats, venture type, six-factor alignment, strategic market assessment, financial viability, valuation analysis, sustainability, societal impact, and technology assessment. The venture valuation was performed for three jurisdictions (countries) - Singapore, the Netherlands and the United States - in order to show the opportunities in a small, medium-sized, and large country (i.e. population). The business model assessment revealed that B2C telemonitoring is viable and profitable in the Innovating in Healthcare Framework. Analysis of the ecosystem revealed an average-to-excellent fit with the six factors. The structure and financing fit was average, public policy and technology alignment was good, while consumer alignment and accountability fit was deemed excellent. The financial prognosis revealed that the venture is viable and profitable in Singapore and the Netherlands but not in the United States due to relatively high salary inputs. The B2C model in telemonitoring CHF potentially creates value for patients, shareholders of the service provider, and society. However, the validity of the results could be improved, for instance by using a peer-reviewed framework, a systematic literature search, case-based cost/efficiency inputs, and varied scenario inputs.
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Yang, J S; Malone, R E
2008-12-01
A key element of Philip Morris's (PM's) corporate social responsibility initiatives is "societal alignment", defined as "strategies and programs to meet society's expectations of a responsible tobacco company". This study explored the genesis and implementation of Philip Morris' (PM) societal alignment efforts. The study retrieved and analysed approximately 375 previously undisclosed PM documents now available electronically. Using an iterative process, the study categorised themes and prepared a case analysis. Beginning in 1999, PM sought to become "societally aligned" by identifying expectations of a responsible tobacco company through public opinion research and developing and publicising programs to meet those expectations. Societal alignment was undertaken within the US and globally to ensure an environment favourable to PM's business objectives. Despite PM's claims to be "changing", however, societal alignment in practice was highly selective. PM responded to public "expectations" largely by retooling existing positions and programs, while entirely ignoring other expectations that might have interfered with its business goals. It also appears that convincing employees of the value and authenticity of societal alignment was difficult. As implementation of the Framework Convention on Tobacco Control proceeds, tobacco control advocates should closely monitor development of such "alignment" initiatives and expose the motivations and contradictions they reveal.
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Ford, Robert C; Sivo, Stephen A; Fottler, Myron D; Dickson, Duncan; Bradley, Kenneth; Johnson, Lee
2006-01-01
In today's competitive health care environment, service excellence is rapidly becoming a major differentiating advantage between health care providers. Too often, senior executives talk about their commitment to a mission statement that extols the virtues of providing world class service to their patients only to undermine those statements with what they do, write, and say. This article presents an exploratory investigation into a new application of an internal mission alignment instrument that seeks to assess the extent to which an organization's internal processes are aligned with its service mission. This instrument was sent to 250 randomly selected employees from all clinical departments of a large southeastern hospital to explore the underlying alignment factors. A factor analysis of the data revealed eight factors that predicted beneficial employee outcomes such as organizational commitment and satisfaction with the job and organization.
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REPPER—repeats and their periodicities in fibrous proteins
Gruber, Markus; Söding, Johannes; Lupas, Andrei N.
2005-01-01
REPPER (REPeats and their PERiodicities) is an integrated server that detects and analyzes regions with short gapless repeats in protein sequences or alignments. It finds periodicities by Fourier Transform (FTwin) and internal similarity analysis (REPwin). FTwin assigns numerical values to amino acids that reflect certain properties, for instance hydrophobicity, and gives information on corresponding periodicities. REPwin uses self-alignments and displays repeats that reveal significant internal similarities. Both programs use a sliding window to ensure that different periodic regions within the same protein are detected independently. FTwin and REPwin are complemented by secondary structure prediction (PSIPRED) and coiled coil prediction (COILS), making the server a versatile analysis tool for sequences of fibrous proteins. REPPER is available at . PMID:15980460
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Diffeomorphic functional brain surface alignment: Functional demons.
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.
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Cellular self-organization by autocatalytic alignment feedback
Junkin, Michael; Leung, Siu Ling; Whitman, Samantha; Gregorio, Carol C.; Wong, Pak Kin
2011-01-01
Myoblasts aggregate, differentiate and fuse to form skeletal muscle during both embryogenesis and tissue regeneration. For proper muscle function, long-range self-organization of myoblasts is required to create organized muscle architecture globally aligned to neighboring tissue. However, how the cells process geometric information over distances considerably longer than individual cells to self-organize into well-ordered, aligned and multinucleated myofibers remains a central question in developmental biology and regenerative medicine. Using plasma lithography micropatterning to create spatial cues for cell guidance, we show a physical mechanism by which orientation information can propagate for a long distance from a geometric boundary to guide development of muscle tissue. This long-range alignment occurs only in differentiating myoblasts, but not in non-fusing myoblasts perturbed by microfluidic disturbances or other non-fusing cell types. Computational cellular automata analysis of the spatiotemporal evolution of the self-organization process reveals that myogenic fusion in conjunction with rotational inertia functions in a self-reinforcing manner to enhance long-range propagation of alignment information. With this autocatalytic alignment feedback, well-ordered alignment of muscle could reinforce existing orientations and help promote proper arrangement with neighboring tissue and overall organization. Such physical self-enhancement might represent a fundamental mechanism for long-range pattern formation during tissue morphogenesis. PMID:22193956
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rVISTA 2.0: Evolutionary Analysis of Transcription Factor Binding Sites
DOE Office of Scientific and Technical Information (OSTI.GOV)
Loots, G G; Ovcharenko, I
2004-01-28
Identifying and characterizing the patterns of DNA cis-regulatory modules represents a challenge that has the potential to reveal the regulatory language the genome uses to dictate transcriptional dynamics. Several studies have demonstrated that regulatory modules are under positive selection and therefore are often conserved between related species. Using this evolutionary principle we have created a comparative tool, rVISTA, for analyzing the regulatory potential of noncoding sequences. The rVISTA tool combines transcription factor binding site (TFBS) predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions that are highly conserved and present in a specific configuration within an alignment. Heremore » we present the newly developed version 2.0 of the rVISTA tool that can process alignments generated by both zPicture and PipMaker alignment programs or use pre-computed pairwise alignments of seven vertebrate genomes available from the ECR Browser. The rVISTA web server is closely interconnected with the TRANSFAC database, allowing users to either search for matrices present in the TRANSFAC library collection or search for user-defined consensus sequences. rVISTA tool is publicly available at http://rvista.dcode.org/.« less
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Okuda, Mitsuhiro; Ogawa, Nobuhiro; Takeguchi, Masaki; Hashimoto, Ayako; Tagaya, Motohiro; Chen, Song; Hanagata, Nobutaka; Ikoma, Toshiyuki
2011-10-01
The mineralized structure of aligned collagen fibrils in a tilapia fish scale was investigated using transmission electron microscopy (TEM) techniques after a thin sample was prepared using aqueous techniques. Electron diffraction and electron energy loss spectroscopy data indicated that a mineralized internal layer consisting of aligned collagen fibrils contains hydroxyapatite crystals. Bright-field imaging, dark-field imaging, and energy-filtered TEM showed that the hydroxyapatite was mainly distributed in the hole zones of the aligned collagen fibrils structure, while needle-like materials composed of calcium compounds including hydroxyapatite existed in the mineralized internal layer. Dark-field imaging and three-dimensional observation using electron tomography revealed that hydroxyapatite and needle-like materials were mainly found in the matrix between the collagen fibrils. It was observed that hydroxyapatite and needle-like materials were preferentially distributed on the surface of the hole zones in the aligned collagen fibrils structure and in the matrix between the collagen fibrils in the mineralized internal layer of the scale.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Sushko, M. L.; Rosso, K. M.
Atomic-to-mesoscale simulations were used to reveal the origin of oriented attachment between anatase TiO2 nanoparticles in aqueous HCl solutions. Analysis of the distance and pH dependence of interparticle interactions demonstrates that ion correlation forces are responsible for facet-specific attraction and rotation into lattice co-alignment at long-range. These forces give rise to a metastable solvent separated capture minimum on the disjoining pressure-distance curve, with the barrier to attachment largely due to steric hydration forces from structured intervening solvent.
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Temperature dependence of attitude sensor coalignments on the Solar Maximum Mission (SMM)
NASA Technical Reports Server (NTRS)
Pitone, D. S.; Eudell, A. H.; Patt, F. S.
1989-01-01
Results are presented on the temperature correlation of the relative coalignment between the fine pointing sun sensor (FPSS) and fixed head star trackers (FHSTs) on the Solar Maximum Mission (SMM). This correlation can be caused by spacecraft electronic and mechanical effects. Routine daily measurements reveal a time dependent sensor coalignment variation. The magnitude of the alignment variation is on the order of 120 arc seconds (arc sec), which greatly exceeds the prelaunch thermal structural analysis estimate of 15 acr sec. Differences between FPSS-only and FHST-only yaw solutions as a function of mission day are correlated with the relevant spacecraft temperature. If unaccounted for, the sensor misalignments due to thermal effects are a significant source of error in attitude determination accuracy. Prominent sources of temperature variation are identified and correlated with the temperature profile observed on the SMM. It was determined that even relatively small changes in spacecraft temperature can affect the coalignments between the attitude hardware on the SMM and the science instrument support plate and that frequent recalibration of sensor alignments is necessary to compensate for this effect. An alterntive to frequent recalibration is to model the variation of alignments as a function of temperature and use this to maintain accurate ground or onboard alignment estimates. These flight data analysis results may be important consierations for prelaunch analysis of future missions.
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Colour stabilities of three types of orthodontic clear aligners exposed to staining agents
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
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Colour stabilities of three types of orthodontic clear aligners exposed to staining agents.
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.
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Stronghill, P; Pathan, N; Ha, H; Supijono, E; Hasenkampf, C
2010-08-01
A cytological comparative analysis of male meiocytes was performed for Arabidopsis wild type and the ahp2 (hop2) mutant with emphasis on ahp2's largely uncharacterized prophase I. Leptotene progression appeared normal in ahp2 meiocytes; chromosomes exhibited regular axis formation and assumed a typical polarized nuclear organization. In contrast, 4',6'-diamidino-2-phenylindole-stained ahp2 pachytene chromosome spreads demonstrated a severe reduction in stabilized pairing. However, transmission electron microscopy (TEM) analysis of sections from meiocytes revealed that ahp2 chromosome axes underwent significant amounts of close alignment (44% of total axis). This apparent paradox strongly suggests that the Ahp2 protein is involved in the stabilization of homologous chromosome close alignment. Fluorescent in situ hybridization in combination with Zyp1 immunostaining revealed that ahp2 mutants undergo homologous synapsis of the nucleolus-organizer-region-bearing short arms of chromosomes 2 and 4, despite the otherwise "nucleus-wide" lack of stabilized pairing. The duration of ahp2 zygotene was significantly prolonged and is most likely due to difficulties in chromosome alignment stabilization and subsequent synaptonemal complex formation. Ahp2 and Mnd1 proteins have previously been shown, "in vitro," to form a heterodimer. Here we show, "in situ," that the Ahp2 and Mnd1 proteins are synchronous in their appearance and disappearance from meiotic chromosomes. Both the Ahp2 and Mnd1 proteins localize along the chromosomal axis. However, localization of the Ahp2 protein was entirely foci-based whereas Mnd1 protein exhibited an immunostaining pattern with some foci along the axis and a diffuse staining for the rest of the chromosome.
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Johnson, Jed; Nowicki, M. Oskar; Lee, Carol H.; Chiocca, E. Antonio; Viapiano, Mariano S.; Lawler, Sean E.
2009-01-01
Malignant gliomas are the most common tumors originating within the central nervous system and account for over 15,000 deaths annually in the United States. The median survival for glioblastoma, the most common and aggressive of these tumors, is only 14 months. Therapeutic strategies targeting glioma cells migrating away from the tumor core are currently hampered by the difficulty of reproducing migration in the neural parenchyma in vitro. We utilized a tissue engineering approach to develop a physiologically relevant model of glioma cell migration. This revealed that glioma cells display dramatic differences in migration when challenged by random versus aligned electrospun poly-ɛ-caprolactone nanofibers. Cells on aligned fibers migrated at an effective velocity of 4.2 ± 0.39 μm/h compared to 0.8 ± 0.08 μm/h on random fibers, closely matching in vivo models and prior observations of glioma spread in white versus gray matter. Cells on random fibers exhibited extension along multiple fiber axes that prevented net motion; aligned fibers promoted a fusiform morphology better suited to infiltration. Time-lapse microscopy revealed that the motion of individual cells was complex and was influenced by cell cycle and local topography. Glioma stem cell–containing neurospheres seeded on random fibers did not show cell detachment and retained their original shape; on aligned fibers, cells detached and migrated in the fiber direction over a distance sixfold greater than the perpendicular direction. This chemically and physically flexible model allows time-lapse analysis of glioma cell migration while recapitulating in vivo cell morphology, potentially allowing identification of physiological mediators and pharmacological inhibitors of invasion. PMID:19199562
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Korkosh, V S; Zhorov, B S; Tikhonov, D B
2016-05-01
The family of P-loop channels includes potassium, sodium, calcium, cyclic nucleotide-gated and TRPV channels, as well as ionotropic glutamate receptors. Despite vastly different physiological and pharmacological properties, the channels have structurally conserved folding of the pore domain. Furthermore, crystallographic data demonstrate surprisingly similar mutual disposition of transmembrane and membrane-diving helices. To understand determinants of this conservation, here we have compared available high-resolution structures of sodium, potassium, and TRPV1 channels. We found that some residues, which are in matching positions of the sequence alignment, occur in different positions in the 3D alignment. Surprisingly, we found 3D mismatches in well-packed P-helices. Analysis of energetics of individual residues in Monte Carlo minimized structures revealed cyclic patterns of energetically favorable inter- and intra-subunit contacts of P-helices with S6 helices. The inter-subunit contacts are rather conserved in all the channels, whereas the intra-subunit contacts are specific for particular types of the channels. Our results suggest that these residue-residue contacts contribute to the folding stabilization. Analysis of such contacts is important for structural and phylogenetic studies of homologous proteins.
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Wu, Jing Qin; Wang, Xi; Beveridge, Natalie J.; Tooney, Paul A.; Scott, Rodney J.; Carr, Vaughan J.; Cairns, Murray J.
2012-01-01
Background While hybridization based analysis of the cortical transcriptome has provided important insight into the neuropathology of schizophrenia, it represents a restricted view of disease-associated gene activity based on predetermined probes. By contrast, sequencing technology can provide un-biased analysis of transcription at nucleotide resolution. Here we use this approach to investigate schizophrenia-associated cortical gene expression. Methodology/Principal Findings The data was generated from 76 bp reads of RNA-Seq, aligned to the reference genome and assembled into transcripts for quantification of exons, splice variants and alternative promoters in postmortem superior temporal gyrus (STG/BA22) from 9 male subjects with schizophrenia and 9 matched non-psychiatric controls. Differentially expressed genes were then subjected to further sequence and functional group analysis. The output, amounting to more than 38 Gb of sequence, revealed significant alteration of gene expression including many previously shown to be associated with schizophrenia. Gene ontology enrichment analysis followed by functional map construction identified three functional clusters highly relevant to schizophrenia including neurotransmission related functions, synaptic vesicle trafficking, and neural development. Significantly, more than 2000 genes displayed schizophrenia-associated alternative promoter usage and more than 1000 genes showed differential splicing (FDR<0.05). Both types of transcriptional isoforms were exemplified by reads aligned to the neurodevelopmentally significant doublecortin-like kinase 1 (DCLK1) gene. Conclusions This study provided the first deep and un-biased analysis of schizophrenia-associated transcriptional diversity within the STG, and revealed variants with important implications for the complex pathophysiology of schizophrenia. PMID:22558445
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SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.
Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf
2015-08-01
RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of [Formula: see text]. Subsequently, numerous faster 'Sankoff-style' approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity ([Formula: see text] quartic time). Breaking this barrier, we introduce the novel Sankoff-style algorithm 'sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)', which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff's original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. © The Author 2015. Published by Oxford University Press.
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Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data.
da Silva Paiva, Thiago; do Nascimento Borges, Bárbara; da Silva-Neto, Inácio Domingos
2013-12-01
The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank database. Emphasis was placed on the use of two nucleotide alignment criteria that involved variation in the gap-opening and gap-extension parameters and the use of rRNA secondary structure to orientate multiple-alignment. A sensitivity analysis of 76 data sets was run to assess the effect of variations in indel parameters on tree topologies. Bayesian inference, maximum likelihood and maximum parsimony phylogenetic analyses were used to explore how different analytic frameworks influenced the resulting hypotheses. A sensitivity analysis revealed that the relationships among higher taxa of the Intramacronucleata were dependent upon how indels were determined during multiple-alignment of nucleotides. The phylogenetic analyses rejected the monophyly of the Armophorea most of the time and consistently indicated that the Metopidae and Nyctotheridae were related to the Litostomatea. There was no consensus on the placement of the Caenomorphidae, which could be a sister group of the Metopidae + Nyctorheridae, or could have diverged at the base of the Spirotrichea branch or the Intramacronucleata tree.
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Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data
da Silva Paiva, Thiago; do Nascimento Borges, Bárbara; da Silva-Neto, Inácio Domingos
2013-01-01
The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank database. Emphasis was placed on the use of two nucleotide alignment criteria that involved variation in the gap-opening and gap-extension parameters and the use of rRNA secondary structure to orientate multiple-alignment. A sensitivity analysis of 76 data sets was run to assess the effect of variations in indel parameters on tree topologies. Bayesian inference, maximum likelihood and maximum parsimony phylogenetic analyses were used to explore how different analytic frameworks influenced the resulting hypotheses. A sensitivity analysis revealed that the relationships among higher taxa of the Intramacronucleata were dependent upon how indels were determined during multiple-alignment of nucleotides. The phylogenetic analyses rejected the monophyly of the Armophorea most of the time and consistently indicated that the Metopidae and Nyctotheridae were related to the Litostomatea. There was no consensus on the placement of the Caenomorphidae, which could be a sister group of the Metopidae + Nyctorheridae, or could have diverged at the base of the Spirotrichea branch or the Intramacronucleata tree. PMID:24385862
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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.
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NASA Astrophysics Data System (ADS)
Azatov, Mikheil; Sun, Xiaoyu; Suberi, Alexandra; Fourkas, John T.; Upadhyaya, Arpita
2017-12-01
Cells can sense and adapt to mechanical properties of their environment. The local geometry of the extracellular matrix, such as its topography, has been shown to modulate cell morphology, migration, and proliferation. Here we investigate the effect of micro/nanotopography on the morphology and cytoskeletal dynamics of human pancreatic tumor-associated fibroblast cells (TAFs). We use arrays of parallel nanoridges with variable spacings on a subcellular scale to investigate the response of TAFs to the topography of their environment. We find that cell shape and stress fiber organization both align along the direction of the nanoridges. Our analysis reveals a strong bimodal relationship between the degree of alignment and the spacing of the nanoridges. Furthermore, focal adhesions align along ridges and form preferentially on top of the ridges. Tracking actin stress fiber movement reveals enhanced dynamics of stress fibers on topographically patterned surfaces. We find that components of the actin cytoskeleton move preferentially along the ridges with a significantly higher velocity along the ridges than on a flat surface. Our results suggest that a complex interplay between the actin cytoskeleton and focal adhesions coordinates the cellular response to micro/nanotopography.
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NASA Astrophysics Data System (ADS)
Gupta, Bipin Kumar; Kedawat, Garima; Gangwar, Amit Kumar; Nagpal, Kanika; Kashyap, Pradeep Kumar; Srivastava, Shubhda; Singh, Satbir; Kumar, Pawan; Suryawanshi, Sachin R.; Seo, Deok Min; Tripathi, Prashant; More, Mahendra A.; Srivastava, O. N.; Hahm, Myung Gwan; Late, Dattatray J.
2018-01-01
The vertical aligned carbon nanotubes (CNTs)-based pillar architectures were created on laminated silicon oxide/silicon (SiO2/Si) wafer substrate at 775 °C by using water-assisted chemical vapor deposition under low pressure process condition. The lamination was carried out by aluminum (Al, 10.0 nm thickness) as a barrier layer and iron (Fe, 1.5 nm thickness) as a catalyst precursor layer sequentially on a silicon wafer substrate. Scanning electron microscope (SEM) images show that synthesized CNTs are vertically aligned and uniformly distributed with a high density. The CNTs have approximately 2-30 walls with an inner diameter of 3-8 nm. Raman spectrum analysis shows G-band at 1580 cm-1 and D-band at 1340 cm-1. The G-band is higher than D-band, which indicates that CNTs are highly graphitized. The field emission analysis of the CNTs revealed high field emission current density (4mA/cm2 at 1.2V/μm), low turn-on field (0.6 V/μm) and field enhancement factor (6917) with better stability and longer lifetime. Emitter morphology resulting in improved promising field emission performances, which is a crucial factor for the fabrication of pillared shaped vertical aligned CNTs bundles as practical electron sources.
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Radotić, Viktorija; Braeken, Dries; Kovačić, Damir
2017-12-01
Many studies have shown that the topography of the substrate on which neurons are cultured can promote neuronal adhesion and guide neurite outgrowth in the same direction as the underlying topography. To investigate this effect, isotropic substrate-complementary metal-oxide-semiconductor (CMOS) chips were used as one example of microelectrode arrays (MEAs) for directing neurite growth of spiral ganglion neurons. Neurons were isolated from 5 to 7-day-old rat pups, cultured 1 day in vitro (DIV) and 4 DIV, and then fixed with 4% paraformaldehyde. For analysis of neurite alignment and orientation, fast Fourier transformation (FFT) was used. Results revealed that on the micro-patterned surface of a CMOS chip, neurons orient their neurites along three directional axes at 30, 90, and 150° and that neurites aligned in straight lines between adjacent pillars and mostly followed a single direction while occasionally branching perpendicularly. We conclude that the CMOS substrate guides neurites towards electrodes by means of their structured pillar organization and can produce electrical stimulation of aligned neurons as well as monitoring their neural activities once neurites are in the vicinity of electrodes. These findings are of particular interest for neural tissue engineering with the ultimate goal of developing a new generation of MEA essential for improved electrical stimulation of auditory neurons.
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Biomineralization of superhydrophilic vertically aligned carbon nanotubes.
Marsi, Teresa Cristina O; Santos, Tiago G; Pacheco-Soares, Cristina; Corat, Evaldo J; Marciano, Fernanda R; Lobo, Anderson O
2012-03-06
Vertically aligned carbon nanotubes (VACNT) promise a great role for the study of tissue regeneration. In this paper, we introduce a new biomimetic mineralization routine employing superhydrophilic VACNT films as highly stable template materials. The biomineralization was obtained after VACNT soaking in simulated body fluid solution. Detailed structural analysis reveals that the polycrystalline biological apatites formed due to the -COOH terminations attached to VACNT tips after oxygen plasma etching. Our approach not only provides a novel route for nanostructured materials, but also suggests that COOH termination sites can play a significant role in biomimetic mineralization. These new nanocomposites are very promising as nanobiomaterials due to the excellent human osteoblast adhesion.
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Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline.
Dowsey, Andrew W; Dunn, Michael J; Yang, Guang-Zhong
2008-04-01
The quest for high-throughput proteomics has revealed a number of challenges in recent years. Whilst substantial improvements in automated protein separation with liquid chromatography and mass spectrometry (LC/MS), aka 'shotgun' proteomics, have been achieved, large-scale open initiatives such as the Human Proteome Organization (HUPO) Brain Proteome Project have shown that maximal proteome coverage is only possible when LC/MS is complemented by 2D gel electrophoresis (2-DE) studies. Moreover, both separation methods require automated alignment and differential analysis to relieve the bioinformatics bottleneck and so make high-throughput protein biomarker discovery a reality. The purpose of this article is to describe a fully automatic image alignment framework for the integration of 2-DE into a high-throughput differential expression proteomics pipeline. The proposed method is based on robust automated image normalization (RAIN) to circumvent the drawbacks of traditional approaches. These use symbolic representation at the very early stages of the analysis, which introduces persistent errors due to inaccuracies in modelling and alignment. In RAIN, a third-order volume-invariant B-spline model is incorporated into a multi-resolution schema to correct for geometric and expression inhomogeneity at multiple scales. The normalized images can then be compared directly in the image domain for quantitative differential analysis. Through evaluation against an existing state-of-the-art method on real and synthetically warped 2D gels, the proposed analysis framework demonstrates substantial improvements in matching accuracy and differential sensitivity. High-throughput analysis is established through an accelerated GPGPU (general purpose computation on graphics cards) implementation. Supplementary material, software and images used in the validation are available at http://www.proteomegrid.org/rain/.
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Modeling discrete and continuous entities with fractions and decimals.
Rapp, Monica; Bassok, Miriam; DeWolf, Melissa; Holyoak, Keith J
2015-03-01
When people use mathematics to model real-life situations, their use of mathematical expressions is often mediated by semantic alignment (Bassok, Chase, & Martin, 1998): The entities in a problem situation evoke semantic relations (e.g., tulips and vases evoke the functionally asymmetric "contain" relation), which people align with analogous mathematical relations (e.g., the noncommutative division operation, tulips/vases). Here we investigate the possibility that semantic alignment is also involved in the comprehension and use of rational numbers (fractions and decimals). A textbook analysis and results from two experiments revealed that both mathematic educators and college students tend to align the discreteness versus continuity of the entities in word problems (e.g., marbles vs. distance) with distinct symbolic representations of rational numbers--fractions versus decimals, respectively. In addition, fractions and decimals tend to be used with nonmetric units and metric units, respectively. We discuss the importance of the ontological distinction between continuous and discrete entities to mathematical cognition, the role of symbolic notations, and possible implications of our findings for the teaching of rational numbers. PsycINFO Database Record (c) 2015 APA, all rights reserved.
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Sequence Diversity Diagram for comparative analysis of multiple sequence alignments.
Sakai, Ryo; Aerts, Jan
2014-01-01
The sequence logo is a graphical representation of a set of aligned sequences, commonly used to depict conservation of amino acid or nucleotide sequences. Although it effectively communicates the amount of information present at every position, this visual representation falls short when the domain task is to compare between two or more sets of aligned sequences. We present a new visual presentation called a Sequence Diversity Diagram and validate our design choices with a case study. Our software was developed using the open-source program called Processing. It loads multiple sequence alignment FASTA files and a configuration file, which can be modified as needed to change the visualization. The redesigned figure improves on the visual comparison of two or more sets, and it additionally encodes information on sequential position conservation. In our case study of the adenylate kinase lid domain, the Sequence Diversity Diagram reveals unexpected patterns and new insights, for example the identification of subgroups within the protein subfamily. Our future work will integrate this visual encoding into interactive visualization tools to support higher level data exploration tasks.
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Permanent bending and alignment of ZnO nanowires.
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.
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NASA Astrophysics Data System (ADS)
Liu, Yifei; Manjubala, Inderchand; Roschger, Paul; Schell, Hanna; Duda, Georg N.; Fratzl, Peter
2010-10-01
Callus tissue formed during bone fracture healing is a mixture of different tissue types as revealed by histological analysis. But the structural characteristics of mineral crystals within the healing callus are not well known. Since two-dimensional (2D) scanning small-angle X-ray scattering (sSAXS) patterns showed that the size and orientation of callus crystals vary both spatially and temporally [1] and 2D electron microscopic analysis implies an anisotropic property of the callus morphology, the mineral crystals within the callus are also expected to vary in size and orientation in 3D. Three-dimensional small-angle X-ray scattering (3D SAXS), which combines 2D SAXS patterns collected at different angles of sample tilting, has been previously applied to investigate bone minerals in horse radius [2] and oim/oim mouse femur/tibia [3]. We implement a similar 3D SAXS method but with a different way of data analysis to gather information on the mineral alignment in fracture callus. With the proposed accurate yet fast assessment of 3D SAXS information, it was shown that the plate shaped mineral particles in the healing callus were aligned in groups with their predominant orientations occurring as a fiber texture.
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Bodin, Orjan; Crona, Beatrice; Thyresson, Matilda; Golz, Anna-Lea; Tengö, Maria
2014-10-01
How to create and adjust governing institutions so that they align (fit) with complex ecosystem processes and structures across scales is an issue of increasing concern in conservation. It is argued that lack of such social-ecological fit makes governance and conservation difficult, yet progress in explicitly defining and rigorously testing what constitutes a good fit has been limited. We used a novel modeling approach and data from case studies of fishery and forest conservation to empirically test presumed relationships between conservation outcomes and certain patterns of alignment of social-ecological interdependences. Our approach made it possible to analyze conservation outcome on a systems level while also providing information on how individual actors are positioned in the complex web of social-ecological interdependencies. We found that when actors who shared resources were also socially linked, conservation at the level of the whole social-ecological system was positively affected. When the scales at which individual actors used resources and the scale at which ecological resources were interconnected to other ecological resources were aligned through tightened feedback loops, conservation outcome was better than when they were not aligned. The analysis of individual actors' positions in the web of social-ecological interdependencies was helpful in understanding why a system has a certain level of social-ecological fit. Results of analysis of positions showed that different actors contributed in very different ways to achieve a certain fit and revealed some underlying difference between the actors, for example in terms of actors' varying rights to access and use different ecological resources. © 2014 Society for Conservation Biology.
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Subbotin, S A; Vierstraete, A; De Ley, P; Rowe, J; Waeyenberge, L; Moens, M; Vanfleteren, J R
2001-10-01
The ITS1, ITS2, and 5.8S gene sequences of nuclear ribosomal DNA from 40 taxa of the family Heteroderidae (including the genera Afenestrata, Cactodera, Heterodera, Globodera, Punctodera, Meloidodera, Cryphodera, and Thecavermiculatus) were sequenced and analyzed. The ITS regions displayed high levels of sequence divergence within Heteroderinae and compared to outgroup taxa. Unlike recent findings in root knot nematodes, ITS sequence polymorphism does not appear to complicate phylogenetic analysis of cyst nematodes. Phylogenetic analyses with maximum-parsimony, minimum-evolution, and maximum-likelihood methods were performed with a range of computer alignments, including elision and culled alignments. All multiple alignments and phylogenetic methods yielded similar basic structure for phylogenetic relationships of Heteroderidae. The cyst-forming nematodes are represented by six main clades corresponding to morphological characters and host specialization, with certain clades assuming different positions depending on alignment procedure and/or method of phylogenetic inference. Hypotheses of monophyly of Punctoderinae and Heteroderinae are, respectively, strongly and moderately supported by the ITS data across most alignments. Close relationships were revealed between the Avenae and the Sacchari groups and between the Humuli group and the species H. salixophila within Heteroderinae. The Goettingiana group occupies a basal position within this subfamily. The validity of the genera Afenestrata and Bidera was tested and is discussed based on molecular data. We conclude that ITS sequence data are appropriate for studies of relationships within the different species groups and less so for recovery of more ancient speciations within Heteroderidae. Copyright 2001 Academic Press.
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Yang, J S; Malone, R E
2009-01-01
Background A key element of Philip Morris's (PM's) corporate social responsibility initiatives is “societal alignment”, defined as “strategies and programs to meet society's expectations of a responsible tobacco company”. This study explored the genesis and implementation of Philip Morris' (PM) societal alignment efforts. Methods The study retrieved and analysed approximately 375 previously undisclosed PM documents now available electronically. Using an iterative process, the study categorised themes and prepared a case analysis. Results Beginning in 1999, PM sought to become “societally aligned” by identifying expectations of a responsible tobacco company through public opinion research and developing and publicising programs to meet those expectations. Societal alignment was undertaken within the US and globally to ensure an environment favourable to PM's business objectives. Despite PM's claims to be “changing”, however, societal alignment in practice was highly selective. PM responded to public “expectations” largely by retooling existing positions and programs, while entirely ignoring other expectations that might have interfered with its business goals. It also appears that convincing employees of the value and authenticity of societal alignment was difficult. Conclusions As implementation of the Framework Convention on Tobacco Control proceeds, tobacco control advocates should closely monitor development of such “alignment” initiatives and expose the motivations and contradictions they reveal. PMID:18845623
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Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring
2012-01-01
Background Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. Results The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Conclusions Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family. PMID:22793672
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Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.
Durston, Kirk K; Chiu, David Ky; Wong, Andrew Kc; Li, Gary Cl
2012-07-13
Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.
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Integrative network alignment reveals large regions of global network similarity in yeast and human.
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/.
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Recombination Proteins Mediate Meiotic Spatial Chromosome Organization and Pairing
Storlazzi, Aurora; Gargano, Silvana; Ruprich-Robert, Gwenael; Falque, Matthieu; David, Michelle; Kleckner, Nancy; Zickler, Denise
2010-01-01
SUMMARY Meiotic chromosome pairing involves not only recognition of homology but also juxtaposition of entire chromosomes in a topologically regular way. Analysis of filamentous fungus Sordaria macrospora reveals that recombination proteins Mer3, Msh4 and Mlh1 play direct roles in all of these aspects, in advance of their known roles in recombination. Absence of Mer3 helicase results in interwoven chromosomes, thereby revealing the existence of features that specifically ensure “entanglement avoidance”. Entanglements that remain at zygotene, i.e. “interlockings”, require Mlh1 for resolution, likely to eliminate constraining recombinational connections. Patterns of Mer3 and Msh4 foci along aligned chromosomes show that the double-strand breaks mediating homologous alignment have spatially separated ends, one localized to each partner axis, and that pairing involves interference among developing interhomolog interactions. We propose that Mer3, Msh4 and Mlh1 execute all of these roles during pairing by modulating the state of nascent double-strand break/partner DNA contacts within axis-associated recombination complexes. PMID:20371348
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Diversity of sharp-wave-ripple LFP signatures reveals differentiated brain-wide dynamical events.
Ramirez-Villegas, Juan F; Logothetis, Nikos K; Besserve, Michel
2015-11-17
Sharp-wave-ripple (SPW-R) complexes are believed to mediate memory reactivation, transfer, and consolidation. However, their underlying neuronal dynamics at multiple scales remains poorly understood. Using concurrent hippocampal local field potential (LFP) recordings and functional MRI (fMRI), we study local changes in neuronal activity during SPW-R episodes and their brain-wide correlates. Analysis of the temporal alignment between SPW and ripple components reveals well-differentiated SPW-R subtypes in the CA1 LFP. SPW-R-triggered fMRI maps show that ripples aligned to the positive peak of their SPWs have enhanced neocortical metabolic up-regulation. In contrast, ripples occurring at the trough of their SPWs relate to weaker neocortical up-regulation and absent subcortical down-regulation, indicating differentiated involvement of neuromodulatory pathways in the ripple phenomenon mediated by long-range interactions. To our knowledge, this study provides the first evidence for the existence of SPW-R subtypes with differentiated CA1 activity and metabolic correlates in related brain areas, possibly serving different memory functions.
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Diversity of sharp-wave–ripple LFP signatures reveals differentiated brain-wide dynamical events
Ramirez-Villegas, Juan F.; Logothetis, Nikos K.; Besserve, Michel
2015-01-01
Sharp-wave–ripple (SPW-R) complexes are believed to mediate memory reactivation, transfer, and consolidation. However, their underlying neuronal dynamics at multiple scales remains poorly understood. Using concurrent hippocampal local field potential (LFP) recordings and functional MRI (fMRI), we study local changes in neuronal activity during SPW-R episodes and their brain-wide correlates. Analysis of the temporal alignment between SPW and ripple components reveals well-differentiated SPW-R subtypes in the CA1 LFP. SPW-R–triggered fMRI maps show that ripples aligned to the positive peak of their SPWs have enhanced neocortical metabolic up-regulation. In contrast, ripples occurring at the trough of their SPWs relate to weaker neocortical up-regulation and absent subcortical down-regulation, indicating differentiated involvement of neuromodulatory pathways in the ripple phenomenon mediated by long-range interactions. To our knowledge, this study provides the first evidence for the existence of SPW-R subtypes with differentiated CA1 activity and metabolic correlates in related brain areas, possibly serving different memory functions. PMID:26540729
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Multi-spectrometer calibration transfer based on independent component analysis.
Liu, Yan; Xu, Hao; Xia, Zhenzhen; Gong, Zhiyong
2018-02-26
Calibration transfer is indispensable for practical applications of near infrared (NIR) spectroscopy due to the need for precise and consistent measurements across different spectrometers. In this work, a method for multi-spectrometer calibration transfer is described based on independent component analysis (ICA). A spectral matrix is first obtained by aligning the spectra measured on different spectrometers. Then, by using independent component analysis, the aligned spectral matrix is decomposed into the mixing matrix and the independent components of different spectrometers. These differing measurements between spectrometers can then be standardized by correcting the coefficients within the independent components. Two NIR datasets of corn and edible oil samples measured with three and four spectrometers, respectively, were used to test the reliability of this method. The results of both datasets reveal that spectra measurements across different spectrometers can be transferred simultaneously and that the partial least squares (PLS) models built with the measurements on one spectrometer can predict that the spectra can be transferred correctly on another.
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Zeng, Wenjin; Liu, Xingming; Guo, Xiangru; Niu, Qiaoli; Yi, Jianpeng; Xia, Ruidong; Min, Yong
2017-03-24
This review presents an overall discussion on the morphology analysis and optimization for perovskite (PVSK) solar cells. Surface morphology and energy alignment have been proven to play a dominant role in determining the device performance. The effect of the key parameters such as solution condition and preparation atmosphere on the crystallization of PVSK, the characterization of surface morphology and interface distribution in the perovskite layer is discussed in detail. Furthermore, the analysis of interface energy level alignment by using X-ray photoelectron spectroscopy and ultraviolet photoelectron spectroscopy is presented to reveals the correlation between morphology and charge generation and collection within the perovskite layer, and its influence on the device performance. The techniques including architecture modification, solvent annealing, etc. were reviewed as an efficient approach to improve the morphology of PVSK. It is expected that further progress will be achieved with more efforts devoted to the insight of the mechanism of surface engineering in the field of PVSK solar cells.
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Peters, Amanda; Vanstone, Meredith; Monteiro, Sandra; Norman, Geoff; Sherbino, Jonathan; Sibbald, Matthew
2017-05-01
According to the dual process model of reasoning, physicians make diagnostic decisions using two mental systems: System 1, which is rapid, unconscious, and intuitive, and System 2, which is slow, rational, and analytical. Currently, little is known about physicians' use of System 1 or intuitive reasoning in practice. In a qualitative study of clinical reasoning, physicians were asked to tell stories about times when they used intuitive reasoning while working up an acutely unwell patient, and we combine socio-narratology and rhetorical theory to analyze physicians' stories. Our analysis reveals that in describing their work, physicians draw on two competing narrative structures: one that is aligned with an evidence-based medicine approach valuing System 2 and one that is aligned with cooperative decision making involving others in the clinical environment valuing System 1. Our findings support an understanding of clinical reasoning as distributed, contextual, and influenced by professional culture.
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A Novel Framework for the Comparative Analysis of Biological Networks
Pache, Roland A.; Aloy, Patrick
2012-01-01
Genome sequencing projects provide nearly complete lists of the individual components present in an organism, but reveal little about how they work together. Follow-up initiatives have deciphered thousands of dynamic and context-dependent interrelationships between gene products that need to be analyzed with novel bioinformatics approaches able to capture their complex emerging properties. Here, we present a novel framework for the alignment and comparative analysis of biological networks of arbitrary topology. Our strategy includes the prediction of likely conserved interactions, based on evolutionary distances, to counter the high number of missing interactions in the current interactome networks, and a fast assessment of the statistical significance of individual alignment solutions, which vastly increases its performance with respect to existing tools. Finally, we illustrate the biological significance of the results through the identification of novel complex components and potential cases of cross-talk between pathways and alternative signaling routes. PMID:22363585
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SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics
Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf
2015-01-01
Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity (≥ quartic time). Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm ‘sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)’, which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff’s original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. Availability and implementation: SPARSE is freely available at http://www.bioinf.uni-freiburg.de/Software/SPARSE. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25838465
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Low, V L; Lim, P E; Chen, C D; Lim, Y A L; Tan, T K; Norma-Rashid, Y; Lee, H L; Sofian-Azirun, M
2014-06-01
The present study explored the intraspecific genetic diversity, dispersal patterns and phylogeographic relationships of Culex quinquefasciatus Say (Diptera: Culicidae) in Malaysia using reference data available in GenBank in order to reveal this species' phylogenetic relationships. A statistical parsimony network of 70 taxa aligned as 624 characters of the cytochrome c oxidase subunit I (COI) gene and 685 characters of the cytochrome c oxidase subunit II (COII) gene revealed three haplotypes (A1-A3) and four haplotypes (B1-B4), respectively. The concatenated sequences of both COI and COII genes with a total of 1309 characters revealed seven haplotypes (AB1-AB7). Analysis using tcs indicated that haplotype AB1 was the common ancestor and the most widespread haplotype in Malaysia. The genetic distance based on concatenated sequences of both COI and COII genes ranged from 0.00076 to 0.00229. Sequence alignment of Cx. quinquefasciatus from Malaysia and other countries revealed four haplotypes (AA1-AA4) by the COI gene and nine haplotypes (BB1-BB9) by the COII gene. Phylogenetic analyses demonstrated that Malaysian Cx. quinquefasciatus share the same genetic lineage as East African and Asian Cx. quinquefasciatus. This study has inferred the genetic lineages, dispersal patterns and hypothetical ancestral genotypes of Cx. quinquefasciatus. © 2013 The Royal Entomological Society.
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Passively aligned multichannel fiber-pigtailing of planar integrated optical waveguides
NASA Astrophysics Data System (ADS)
Kremmel, Johannes; Lamprecht, Tobias; Crameri, Nino; Michler, Markus
2017-02-01
A silicon device to simplify the coupling of multiple single-mode fibers to embedded single-mode waveguides has been developed. The silicon device features alignment structures that enable a passive alignment of fibers to integrated waveguides. For passive alignment, precisely machined V-grooves on a silicon device are used and the planar lightwave circuit board features high-precision structures acting as a mechanical stop. The approach has been tested for up to eight fiber-to-waveguide connections. The alignment approach, the design, and the fabrication of the silicon device as well as the assembly process are presented. The characterization of the fiber-to-waveguide link reveals total coupling losses of (0.45±0.20 dB) per coupling interface, which is significantly lower than the values reported in earlier works. Subsequent climate tests reveal that the coupling losses remain stable during thermal cycling but increases significantly during an 85°C/85 Rh-test. All applied fabrication and bonding steps have been performed using standard MOEMS fabrication and packaging processes.
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Ventura, Marco; Canchaya, Carlos; Meylan, Valèrie; Klaenhammer, Todd R.; Zink, Ralf
2003-01-01
We analyzed the tuf gene, encoding elongation factor Tu, from 33 strains representing 17 Lactobacillus species and 8 Bifidobacterium species. The tuf sequences were aligned and used to infer phylogenesis among species of lactobacilli and bifidobacteria. We demonstrated that the synonymous substitution affecting this gene renders elongation factor Tu a reliable molecular clock for investigating evolutionary distances of lactobacilli and bifidobacteria. In fact, the phylogeny generated by these tuf sequences is consistent with that derived from 16S rRNA analysis. The investigation of a multiple alignment of tuf sequences revealed regions conserved among strains belonging to the same species but distinct from those of other species. PCR primers complementary to these regions allowed species-specific identification of closely related species, such as Lactobacillus casei group members. These tuf gene-based assays developed in this study provide an alternative to present methods for the identification for lactic acid bacterial species. Since a variable number of tuf genes have been described for bacteria, the presence of multiple genes was examined. Southern analysis revealed one tuf gene in the genomes of lactobacilli and bifidobacteria, but the tuf gene was arranged differently in the genomes of these two taxa. Our results revealed that the tuf gene in bifidobacteria is flanked by the same gene constellation as the str operon, as originally reported for Escherichia coli. In contrast, bioinformatic and transcriptional analyses of the DNA region flanking the tuf gene in four Lactobacillus species indicated the same four-gene unit and suggested a novel tuf operon specific for the genus Lactobacillus. PMID:14602655
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StructAlign, a Program for Alignment of Structures of DNA-Protein Complexes.
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.
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Patterned growth of carbon nanotubes on Si substrates without predeposition of metal catalysts
NASA Astrophysics Data System (ADS)
Chen, Y.; Yu, J.
2005-07-01
Aligned carbon nanotubes (CNTs) can be readily synthesized on quartz or silicon-oxide-coated Si substrates using a chemical vapor deposition method, but it is difficult to grow them on pure Si substrates without predeposition of metal catalysts. We report that aligned CNTs were grown by pyrolysis of iron phthalocyanine at 1000°C on the templates created on Si substrates with simple mechanical scratching. Scanning electron microscopy and x-ray energy spectroscopy analysis revealed that the trenches and patterns created on the surface of Si substrates were preferred nucleation sites for nanotube growth due to a high surface energy, metastable surface structure, and possible capillarity effect. A two-step pyrolysis process maintained Fe as an active catalyst.
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GraphCrunch 2: Software tool for network modeling, alignment and clustering.
Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne; Pržulj, Nataša
2011-01-19
Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an algorithm for clustering nodes within a network based solely on their topological similarities. Using GraphCrunch 2, we demonstrate that eukaryotic and viral PPI networks may belong to different graph model families and show that topology-based clustering can reveal important functional similarities between proteins within yeast and human PPI networks. GraphCrunch 2 is a software tool that implements the latest research on biological network analysis. It parallelizes computationally intensive tasks to fully utilize the potential of modern multi-core CPUs. It is open-source and freely available for research use. It runs under the Windows and Linux platforms.
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Hresko, Michael T; Labelle, Hubert; Roussouly, Pierre; Berthonnaud, Eric
2007-09-15
Retrospective review of a radiographic database of high-grade spondylolisthesis patients in comparison with asymptomatic controls. To analyze the sagittal spinopelvic alignment in high-grade spondylolisthesis patients and identify subgroups that may require reduction to restore sagittal balance. High-grade spondylolisthesis is associated with an abnormally high pelvic incidence (PI); however, the spatial orientation of the pelvis, determined by sacral slope (SS) and pelvic tilt (PT), is not known. We hypothesized that sagittal spinal alignment would vary with the pelvic orientation. Digitized sagittal radiographs of 133 high-grade spondylolisthesis patients (mean age, 17 years) were measured to determined sagittal alignment. K-means cluster analysis identified 2 groups based on the PT and SS, which were compared by paired t test. Comparisons were made to asymptomatic controls matched for PI. High-grade spondylolisthesis patients had a mean PI of 78.9 degrees +/- 12.1 degrees . Cluster analysis identified a retroverted, unbalanced pelvis group with high PT (36.5 degrees +/- 8.0 degrees )/low SS (40.3 degrees +/- 9.0 degrees ) and a balanced pelvic group with low PT (mean 21.3 degrees +/- 8.2 degrees )/high SS (59.9 degrees +/- 11.2 degrees ). The retroverted pelvis group had significantly greater L5 incidence and lumbosacral angle with less thoracic kyphosis than the balanced pelvic group. A total of 83% of controls had a "balanced pelvis" based on the categorization by SS and PT. Analysis of sagittal alignment of high-grade spondylolisthesis patients revealed distinct groups termed "balanced" and "unbalanced" pelvis. The PT and SS were similar in controls and balanced pelvis patients. Unbalanced pelvis patients had a sagittal spinal alignment that differed from the balanced pelvis and control groups. Treatment strategies for high-grade spondylolisthesis should reflect the different mechanical strain on the spinopelvic junction in each group; reduction techniques might be considered in patients with an unbalanced pelvis high-grade spondylolisthesis.
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Evolutionary profiles from the QR factorization of multiple sequence alignments
Sethi, Anurag; O'Donoghue, Patrick; Luthey-Schulten, Zaida
2005-01-01
We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. We observe a general trend that these smaller, more evolutionarily balanced profiles have comparable and, in many cases, better performance in database searches than conventional profiles containing hundreds of sequences, constructed in an iterative and computationally intensive procedure. For more diverse families or superfamilies, with sequence identity <30%, structural alignments, based purely on the geometry of the protein structures, provide better alignments than pure sequence-based methods. Merging the structure and sequence information allows the construction of accurate profiles for distantly related groups. These structure-based profiles outperformed other sequence-based methods for finding distant homologs and were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. Phylogenetic analysis showed the putative class II CysRSs to be a monophyletic group and homology modeling revealed a constellation of active site residues similar to that in the known class I CysRS. PMID:15741270
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Díaz, David; Esteban, Francisco J.; Hernández, Pilar; Caballero, Juan Antonio; Guevara, Antonio
2014-01-01
We have developed the MC64-ClustalWP2 as a new implementation of the Clustal W algorithm, integrating a novel parallelization strategy and significantly increasing the performance when aligning long sequences in architectures with many cores. It must be stressed that in such a process, the detailed analysis of both the software and hardware features and peculiarities is of paramount importance to reveal key points to exploit and optimize the full potential of parallelism in many-core CPU systems. The new parallelization approach has focused into the most time-consuming stages of this algorithm. In particular, the so-called progressive alignment has drastically improved the performance, due to a fine-grained approach where the forward and backward loops were unrolled and parallelized. Another key approach has been the implementation of the new algorithm in a hybrid-computing system, integrating both an Intel Xeon multi-core CPU and a Tilera Tile64 many-core card. A comparison with other Clustal W implementations reveals the high-performance of the new algorithm and strategy in many-core CPU architectures, in a scenario where the sequences to align are relatively long (more than 10 kb) and, hence, a many-core GPU hardware cannot be used. Thus, the MC64-ClustalWP2 runs multiple alignments more than 18x than the original Clustal W algorithm, and more than 7x than the best x86 parallel implementation to date, being publicly available through a web service. Besides, these developments have been deployed in cost-effective personal computers and should be useful for life-science researchers, including the identification of identities and differences for mutation/polymorphism analyses, biodiversity and evolutionary studies and for the development of molecular markers for paternity testing, germplasm management and protection, to assist breeding, illegal traffic control, fraud prevention and for the protection of the intellectual property (identification/traceability), including the protected designation of origin, among other applications. PMID:24710354
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Shrestha, Nabeen K; Bui, Hoa Thi; Lee, Taegweon; Noh, Yong-Young
2018-04-17
The present work demonstrates the formation of self-aligned nanoporous architecture of gallium oxide by anodization of gallium metal film controlled at -15 °C in aqueous electrolyte consisting of phosphoric acid. SEM examination of the anodized film reveals that by adding ethylene glycol to the electrolyte and optimizing the ratio of phosphoric acid and water, chemical etching at the oxide/electrolyte interfaces can be controlled, leading to the formation of aligned nanotubular oxide structures with closed bottom. XPS analysis confirms the chemical composition of the oxide film as Ga 2 O 3 . Further, XRD and SAED examination reveals that the as-synthesized nanotubular structure is amorphous, and can be crystallized to β-Ga 2 O 3 phase by annealing the film at 600 °C. The nanotubular structured film, when used as photoanode for photoelectrochemical splitting of water, achieved a higher photocurrent of about two folds than that of the nanoporous film, demonstrating the rewarding effect of the nanotubular structure. In addition, the work also demonstrates the formation of highly organized nonporous Ga 2 O 3 structure on a nonconducting glass substrate coated with thin film of Ga-metal, highlighting that the current approach can be extended for the formation of self-organized nanoporous Ga 2 O 3 thin film even on nonconducting flexible substrates.
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Functional Alignment of Metabolic Networks.
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.
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Characterization and functional analyses of a novel chicken CD8a variant X1 (CD8a1)
USDA-ARS?s Scientific Manuscript database
We provide the first description of cloning, as well as structural and functional analysis of a novel variant in the chicken CD8alpha family, termed the CD8-alpha X1 (CD8alpha1) gene. Multiple alignment of CD8alpha1 with known CD8alpha and beta sequences of other species revealed relatively low con...
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Social perceptions versus meteorological observations of snow and winter along the Front Range
NASA Astrophysics Data System (ADS)
Milligan, William James, IV
This research aims to increase understanding of Front Range residents' perceptions of snow, winter and hydrologic events. This study also investigates how an individual's characteristics may shape perceptions of winter weather and climate. A survey was administered to determine if perceptions of previous winters align with observed meteorological data. The survey also investigated how individual characteristics influence perceptions of snow and winter weather. The survey was conducted primarily along the Front Range area of the state of Colorado in the United States of America. This is a highly populated semi-arid region that acts as an interface between the agricultural plains to the east that extend to the Mississippi River and the Rocky Mountains to the west. The climate is continental, and while many people recreate in the snowy areas of the mountains, most live where annual snowfall amounts are low. Precipitation, temperature, and wind speed datasets from selected weather stations were analyzed to determine correct survey responses. Survey analysis revealed that perceptions of previous winters do not necessarily align with observed meteorological data. The mean percentage of correct responses to all survey questions was 36.8%. Further analysis revealed that some individual characteristics (e.g. winter recreation, source of winter weather information) did influence correct responses to survey questions.
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van der Waals Heterostructures with High Accuracy Rotational Alignment.
Kim, Kyounghwan; Yankowitz, Matthew; Fallahazad, Babak; Kang, Sangwoo; Movva, Hema C P; Huang, Shengqiang; Larentis, Stefano; Corbet, Chris M; Taniguchi, Takashi; Watanabe, Kenji; Banerjee, Sanjay K; LeRoy, Brian J; Tutuc, Emanuel
2016-03-09
We describe the realization of van der Waals (vdW) heterostructures with accurate rotational alignment of individual layer crystal axes. We illustrate the approach by demonstrating a Bernal-stacked bilayer graphene formed using successive transfers of monolayer graphene flakes. The Raman spectra of this artificial bilayer graphene possess a wide 2D band, which is best fit by four Lorentzians, consistent with Bernal stacking. Scanning tunneling microscopy reveals no moiré pattern on the artificial bilayer graphene, and tunneling spectroscopy as a function of gate voltage reveals a constant density of states, also in agreement with Bernal stacking. In addition, electron transport probed in dual-gated samples reveals a band gap opening as a function of transverse electric field. To illustrate the applicability of this technique to realize vdW heterostructuctures in which the functionality is critically dependent on rotational alignment, we demonstrate resonant tunneling double bilayer graphene heterostructures separated by hexagonal boron-nitride dielectric.
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Walther, Stefanie; Tietze, Manfred; Czerny, Claus-Peter; König, Sven; Diesterbeck, Ulrike S
2016-01-01
We have developed a new bioinformatics framework for the analysis of rearranged bovine heavy chain immunoglobulin (Ig) variable regions by combining and refining widely used alignment algorithms. This bioinformatics framework allowed us to investigate alignments of heavy chain framework regions (FRHs) and the separate alignments of FRHs and heavy chain complementarity determining regions (CDRHs) to determine their germline origin in the four cattle breeds Aubrac, German Black Pied, German Simmental, and Holstein Friesian. Now it is also possible to specifically analyze Ig heavy chains possessing exceptionally long CDR3Hs. In order to gain more insight into breed specific differences in Ig combinatorial diversity, somatic hypermutations and putative gene conversions of IgG, we compared the dominantly transcribed variable (IGHV), diversity (IGHD), and joining (IGHJ) segments and their recombination in the four cattle breeds. The analysis revealed the use of 15 different IGHV segments, 21 IGHD segments, and two IGHJ segments with significant different transcription levels within the breeds. Furthermore, there are preferred rearrangements within the three groups of CDR3H lengths. In the sequences of group 2 (CDR3H lengths (L) of 11-47 amino acid residues (aa)) a higher number of recombination was observed than in sequences of group 1 (L≤10 aa) and 3 (L≥48 aa). The combinatorial diversity of germline IGHV, IGHD, and IGHJ-segments revealed 162 rearrangements that were significantly different. The few preferably rearranged gene segments within group 3 CDR3H regions may indicate specialized antibodies because this length is unique in cattle. The most important finding of this study, which was enabled by using the bioinformatics framework, is the discovery of strong evidence for gene conversion as a rare event using pseudogenes fulfilling all definitions for this particular diversification mechanism.
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Czerny, Claus-Peter; König, Sven; Diesterbeck, Ulrike S.
2016-01-01
We have developed a new bioinformatics framework for the analysis of rearranged bovine heavy chain immunoglobulin (Ig) variable regions by combining and refining widely used alignment algorithms. This bioinformatics framework allowed us to investigate alignments of heavy chain framework regions (FRHs) and the separate alignments of FRHs and heavy chain complementarity determining regions (CDRHs) to determine their germline origin in the four cattle breeds Aubrac, German Black Pied, German Simmental, and Holstein Friesian. Now it is also possible to specifically analyze Ig heavy chains possessing exceptionally long CDR3Hs. In order to gain more insight into breed specific differences in Ig combinatorial diversity, somatic hypermutations and putative gene conversions of IgG, we compared the dominantly transcribed variable (IGHV), diversity (IGHD), and joining (IGHJ) segments and their recombination in the four cattle breeds. The analysis revealed the use of 15 different IGHV segments, 21 IGHD segments, and two IGHJ segments with significant different transcription levels within the breeds. Furthermore, there are preferred rearrangements within the three groups of CDR3H lengths. In the sequences of group 2 (CDR3H lengths (L) of 11–47 amino acid residues (aa)) a higher number of recombination was observed than in sequences of group 1 (L≤10 aa) and 3 (L≥48 aa). The combinatorial diversity of germline IGHV, IGHD, and IGHJ-segments revealed 162 rearrangements that were significantly different. The few preferably rearranged gene segments within group 3 CDR3H regions may indicate specialized antibodies because this length is unique in cattle. The most important finding of this study, which was enabled by using the bioinformatics framework, is the discovery of strong evidence for gene conversion as a rare event using pseudogenes fulfilling all definitions for this particular diversification mechanism. PMID:27828971
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Dynamics and allostery of the ionotropic glutamate receptors and the ligand binding domain.
Tobi, Dror
2016-02-01
The dynamics of the ligand-binding domain (LBD) and the intact ionotropic glutamate receptor (iGluR) were studied using Gaussian Network Model (GNM) analysis. The dynamics of LBDs with various allosteric modulators is compared using a novel method of multiple alignment of GNM modes of motion. The analysis reveals that allosteric effectors change the dynamics of amino acids at the upper lobe interface of the LBD dimer as well as at the hinge region between the upper- and lower- lobes. For the intact glutamate receptor the analysis show that the clamshell-like movement of the LBD upper and lower lobes is coupled to the bending of the trans-membrane domain (TMD) helices which may open the channel pore. The results offer a new insight on the mechanism of action of allosteric modulators on the iGluR and support the notion of TMD helices bending as a possible mechanism for channel opening. In addition, the study validates the methodology of multiple GNM modes alignment as a useful tool to study allosteric effect and its relation to proteins dynamics. © 2015 Wiley Periodicals, Inc.
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Scalable synthesis of aligned carbon nanotubes bundles using green natural precursor: neem oil
NASA Astrophysics Data System (ADS)
Kumar, Rajesh; Tiwari, Radhey Shyam; Srivastava, Onkar Nath
2011-12-01
Practical application of aligned carbon nanotubes (ACNTs) would have to be determined by a matter of its economical and large-scale preparation. In this study, neem oil (also named Margoaa oil, extracted from the seeds of the neem-- Azadirachta indica) was used as carbon source to fabricate the bundles of ACNTs. ACNTs have been synthesized by spray pyrolysis of neem oil and ferrocene mixture at 825°C. The major components of neem oil are hydrocarbon with less amount of oxygen, which provided the precursor species in spray pyrolysis growth of CNTs. The bundles of ACNTs have been grown directly inside the quartz tube. The as-grown ACNTs have been characterized through Raman spectroscopy, scanning and transmission electron microscopic (SEM/TEM) techniques. SEM images reveal that the bundles of ACNTs are densely packed and are of several microns in length. High-resolution TEM analysis reveals these nanotubes to be multi-walled CNTs. These multi-walled CNTs were found to have inner diameter between 15 and 30 nm. It was found that present technique gives high yield with high density of bundles of ACNTs.
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Scalable synthesis of aligned carbon nanotubes bundles using green natural precursor: neem oil.
Kumar, Rajesh; Tiwari, Radhey Shyam; Srivastava, Onkar Nath
2011-01-18
Practical application of aligned carbon nanotubes (ACNTs) would have to be determined by a matter of its economical and large-scale preparation. In this study, neem oil (also named Margoaa oil, extracted from the seeds of the neem--Azadirachta indica) was used as carbon source to fabricate the bundles of ACNTs. ACNTs have been synthesized by spray pyrolysis of neem oil and ferrocene mixture at 825°C. The major components of neem oil are hydrocarbon with less amount of oxygen, which provided the precursor species in spray pyrolysis growth of CNTs. The bundles of ACNTs have been grown directly inside the quartz tube. The as-grown ACNTs have been characterized through Raman spectroscopy, scanning and transmission electron microscopic (SEM/TEM) techniques. SEM images reveal that the bundles of ACNTs are densely packed and are of several microns in length. High-resolution TEM analysis reveals these nanotubes to be multi-walled CNTs. These multi-walled CNTs were found to have inner diameter between 15 and 30 nm. It was found that present technique gives high yield with high density of bundles of ACNTs.
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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.
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Quantification of facial and smile esthetics.
Koidou, Vasiliki P; Chatzopoulos, Georgios S; Rosenstiel, Stephen F
2018-02-01
Whether deviations in alignment discrepancy, width-to-length ratio, application of the golden proportion, or number of teeth revealed in smile affect attractiveness is yet unknown. The purpose of this analytical study was to quantify dental and facial esthetics to determine whether individuals identified as having superior smiles display differences in alignment discrepancies (angulation between interpupillary and commissure line); width-to-length ratios of maxillary anterior teeth; application of the golden proportion (approximately 1.618:1); and number of teeth revealed in an animated smile when compared with an average population. An Internet search for "best smile" and "celebrity" identified 108 celebrities. Photographs showing smiles within 10 degrees of a frontal view were collected, while photographs of dental students were used for the control group. Alignment discrepancies, widths and lengths of the anterior teeth, and number of teeth revealed in an animated smile were measured with photo-editing software, and ratios were calculated. The groups were compared with repeated-measures ANOVA, the Mann-Whitney U test, and the Wilcoxon signed-rank test (α=.05). Usable photographs were obtained for 90 celebrities (58 women, 32 men) and compared with photographs of 97 dental students (54 women, 43 men). Statistically significant differences were found for alignment discrepancies (celebrities 0.97, students 1.25, P=.034) and for the number of teeth displayed (P=.049); 22.2% of the celebrities revealed 12 teeth, versus 6.2% of the students. In both groups, significant differences from the golden ratio (1.618:1) for the width of the central incisor/lateral incisor right and left and for the width of the lateral incisor/canine right and left were observed through 95% confidence intervals. Sex and left-right were nonsignificant factors. Celebrities identified as having a best smile had smaller mean alignment discrepancies and revealed a greater number of teeth in an animated smile than dental students. Copyright © 2017 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.
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Fauzi, M B; Lokanathan, Y; Aminuddin, B S; Ruszymah, B H I; Chowdhury, S R
2016-11-01
Collagen is the most abundant extracellular matrix (ECM) protein in the human body, thus widely used in tissue engineering and subsequent clinical applications. This study aimed to extract collagen from ovine (Ovis aries) Achilles tendon (OTC), and to evaluate its physicochemical properties and its potential to fabricate thin film with collagen fibrils in a random or aligned orientation. Acid-solubilized protein was extracted from ovine Achilles tendon using 0.35M acetic acid, and 80% of extracted protein was measured as collagen. SDS-PAGE and mass spectrometry analysis revealed the presence of alpha 1 and alpha 2 chain of collagen type I (col I). Further analysis with Fourier transform infrared spectrometry (FTIR), X-ray diffraction (XRD) and energy dispersive X-ray spectroscopy (EDS) confirms the presence of triple helix structure of col I, similar to commercially available rat tail col I. Drying the OTC solution at 37°C resulted in formation of a thin film with randomly orientated collagen fibrils (random collagen film; RCF). Introduction of unidirectional mechanical intervention using a platform rocker prior to drying facilitated the fabrication of a film with aligned orientation of collagen fibril (aligned collagen film; ACF). It was shown that both RCF and ACF significantly enhanced human dermal fibroblast (HDF) attachment and proliferation than that on plastic surface. Moreover, cells were distributed randomly on RCF, but aligned with the direction of mechanical intervention on ACF. In conclusion, ovine tendon could be an alternative source of col I to fabricate scaffold for tissue engineering applications. Copyright © 2016 Elsevier B.V. All rights reserved.
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Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.
Kaczor-Urbanowicz, Karolina Elzbieta; Kim, Yong; Li, Feng; Galeev, Timur; Kitchen, Rob R; Gerstein, Mark; Koyano, Kikuye; Jeong, Sung-Hee; Wang, Xiaoyan; Elashoff, David; Kang, So Young; Kim, Su Mi; Kim, Kyoung; Kim, Sung; Chia, David; Xiao, Xinshu; Rozowsky, Joel; Wong, David T W
2018-01-01
Analysis of RNA sequencing (RNA-Seq) data in human saliva is challenging. Lack of standardization and unification of the bioinformatic procedures undermines saliva's diagnostic potential. Thus, it motivated us to perform this study. We applied principal pipelines for bioinformatic analysis of small RNA-Seq data of saliva of 98 healthy Korean volunteers including either direct or indirect mapping of the reads to the human genome using Bowtie1. Analysis of alignments to exogenous genomes by another pipeline revealed that almost all of the reads map to bacterial genomes. Thus, salivary exRNA has fundamental properties that warrant the design of unique additional steps while performing the bioinformatic analysis. Our pipelines can serve as potential guidelines for processing of RNA-Seq data of human saliva. Processing and analysis results of the experimental data generated by the exceRpt (v4.6.3) small RNA-seq pipeline (github.gersteinlab.org/exceRpt) are available from exRNA atlas (exrna-atlas.org). Alignment to exogenous genomes and their quantification results were used in this paper for the analyses of small RNAs of exogenous origin. dtww@ucla.edu. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
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Development of a group work assessment pedagogy using constructive alignment theory.
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.
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Direction-specific interaction forces underlying zinc oxide crystal growth by oriented attachment
Zhang, X.; Shen, Z.; Liu, J.; ...
2017-10-10
Here, crystallization by particle attachment is impacting our understanding of natural mineralization processes and holds promise for novel materials design. When particles assemble in crystallographic registry, expulsion of the intervening solvent and particle coalescence is enabled by near-perfect co-alignment via interparticle forces that remain poorly quantified. Here we report measurement and simulation of these nanoscale aligning forces for the ZnO(0001)-ZnO(000¯1) system in aqueous solution. Dynamic force spectroscopy using nanoengineered single crystal probes reveals an attractive force with 60o rotational periodicity. Calculated distance and orientation-dependent potentials of mean force show several attractive free energy wells distinguished by numbers of intervening watermore » layers, which reach a minimum when aligned. The calculated activation energy to separate the attractively bound solvated interfaces perfectly reproduces the measured 60o periodicity, revealing the key role of intervening water structuring as a basis to generate the interparticle torque that completes alignment and enables coalescence.« less
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Direction-specific interaction forces underlying zinc oxide crystal growth by oriented attachment
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhang, X.; Shen, Z.; Liu, J.
Here, crystallization by particle attachment is impacting our understanding of natural mineralization processes and holds promise for novel materials design. When particles assemble in crystallographic registry, expulsion of the intervening solvent and particle coalescence is enabled by near-perfect co-alignment via interparticle forces that remain poorly quantified. Here we report measurement and simulation of these nanoscale aligning forces for the ZnO(0001)-ZnO(000¯1) system in aqueous solution. Dynamic force spectroscopy using nanoengineered single crystal probes reveals an attractive force with 60o rotational periodicity. Calculated distance and orientation-dependent potentials of mean force show several attractive free energy wells distinguished by numbers of intervening watermore » layers, which reach a minimum when aligned. The calculated activation energy to separate the attractively bound solvated interfaces perfectly reproduces the measured 60o periodicity, revealing the key role of intervening water structuring as a basis to generate the interparticle torque that completes alignment and enables coalescence.« less
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Ultralight anisotropic foams from layered aligned carbon nanotube sheets
NASA Astrophysics Data System (ADS)
Faraji, Shaghayegh; L. Stano, Kelly; Yildiz, Ozkan; Li, Ang; Zhu, Yuntian; Bradford, Philip D.
2015-10-01
In this work, we present large scale, ultralight aligned carbon nanotube (CNT) structures which have densities an order of magnitude lower than CNT arrays, have tunable properties and exhibit resiliency after compression. By stacking aligned sheets of carbon nanotubes and then infiltrating with a pyrolytic carbon (PyC), resilient foam-like materials were produced that exhibited complete recovery from 90% compressive strain. With density as low as 3.8 mg cm-3, the foam structure is over 500 times less dense than bulk graphite. Microscopy revealed that PyC coated the junctions among CNTs, and also increased CNT surface roughness. These changes in the morphology explain the transition from inelastic behavior to foam-like recovery of the layered CNT sheet structure. Mechanical and thermal properties of the foams were tuned for different applications through variation of PyC deposition duration while dynamic mechanical analysis showed no change in mechanical properties over a large temperature range. Observation of a large and linear electrical resistance change during compression of the aligned CNT/carbon (ACNT/C) foams makes strain/pressure sensors a relevant application. The foams have high oil absorption capacities, up to 275 times their own weight, which suggests they may be useful in water treatment and oil spill cleanup. Finally, the ACNT/C foam's high porosity, surface area and stability allow for demonstration of the foams as catalyst support structures.In this work, we present large scale, ultralight aligned carbon nanotube (CNT) structures which have densities an order of magnitude lower than CNT arrays, have tunable properties and exhibit resiliency after compression. By stacking aligned sheets of carbon nanotubes and then infiltrating with a pyrolytic carbon (PyC), resilient foam-like materials were produced that exhibited complete recovery from 90% compressive strain. With density as low as 3.8 mg cm-3, the foam structure is over 500 times less dense than bulk graphite. Microscopy revealed that PyC coated the junctions among CNTs, and also increased CNT surface roughness. These changes in the morphology explain the transition from inelastic behavior to foam-like recovery of the layered CNT sheet structure. Mechanical and thermal properties of the foams were tuned for different applications through variation of PyC deposition duration while dynamic mechanical analysis showed no change in mechanical properties over a large temperature range. Observation of a large and linear electrical resistance change during compression of the aligned CNT/carbon (ACNT/C) foams makes strain/pressure sensors a relevant application. The foams have high oil absorption capacities, up to 275 times their own weight, which suggests they may be useful in water treatment and oil spill cleanup. Finally, the ACNT/C foam's high porosity, surface area and stability allow for demonstration of the foams as catalyst support structures. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03899e
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7TMRmine: a Web server for hierarchical mining of 7TMR proteins
Lu, Guoqing; Wang, Zhifang; Jones, Alan M; Moriyama, Etsuko N
2009-01-01
Background Seven-transmembrane region-containing receptors (7TMRs) play central roles in eukaryotic signal transduction. Due to their biomedical importance, thorough mining of 7TMRs from diverse genomes has been an active target of bioinformatics and pharmacogenomics research. The need for new and accurate 7TMR/GPCR prediction tools is paramount with the accelerated rate of acquisition of diverse sequence information. Currently available and often used protein classification methods (e.g., profile hidden Markov Models) are highly accurate for identifying their membership information among already known 7TMR subfamilies. However, these alignment-based methods are less effective for identifying remote similarities, e.g., identifying proteins from highly divergent or possibly new 7TMR families. In this regard, more sensitive (e.g., alignment-free) methods are needed to complement the existing protein classification methods. A better strategy would be to combine different classifiers, from more specific to more sensitive methods, to identify a broader spectrum of 7TMR protein candidates. Description We developed a Web server, 7TMRmine, by integrating alignment-free and alignment-based classifiers specifically trained to identify candidate 7TMR proteins as well as transmembrane (TM) prediction methods. This new tool enables researchers to easily assess the distribution of GPCR functionality in diverse genomes or individual newly-discovered proteins. 7TMRmine is easily customized and facilitates exploratory analysis of diverse genomes. Users can integrate various alignment-based, alignment-free, and TM-prediction methods in any combination and in any hierarchical order. Sixteen classifiers (including two TM-prediction methods) are available on the 7TMRmine Web server. Not only can the 7TMRmine tool be used for 7TMR mining, but also for general TM-protein analysis. Users can submit protein sequences for analysis, or explore pre-analyzed results for multiple genomes. The server currently includes prediction results and the summary statistics for 68 genomes. Conclusion 7TMRmine facilitates the discovery of 7TMR proteins. By combining prediction results from different classifiers in a multi-level filtering process, prioritized sets of 7TMR candidates can be obtained for further investigation. 7TMRmine can be also used as a general TM-protein classifier. Comparisons of TM and 7TMR protein distributions among 68 genomes revealed interesting differences in evolution of these protein families among major eukaryotic phyla. PMID:19538753
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Collaboration leads to enhanced curriculum.
Valerius, J; Mohan, V; Doctor, D; Hersh, W
2015-01-01
In 2007, we initiated a health information management (HIM) track of our biomedical informatics graduate program, and subsequent ongoing program assessment revealed a confluence of topics and courses within HIM and clinical informatics (CI) tracks. We completed a thorough comparative analysis of competencies derived from AMIA, AHIMA, and CAHIIM. Coupled with the need to streamline course offerings, the process, described in this paper allowed new opportunities for faculty collaboration, resulted in the creation of a model assessment for best practice in courses, and led to new avenues of growth within the program. The objective of the case study is to provide others in the informatics educational community with a model for analysis of curriculum in order to improve quality of student learning. We describe a case study where an academic informatics program realigned its course offerings to better reflect the HIM of today, and prepare for challenges of the future. Visionary leadership, intra-departmental self-analysis and alignment of the curriculum through defined mapping process reduced overlap within the CI and HIM tracks. Teaching within courses was optimized through the work of core faculty collaboration. The analysis of curriculum resulted in reduction of overlap within course curriculum. This allowed for additional and new course content to be added to existing courses. Leadership fostered an environment where top-down as well as bottom-up collaborative assessment activities resulted in a model to consolidate learning and reduce unnecessary duplication within courses. A focus on curriculum integration, emphasis on course alignment and strategic consolidation of course content raised the quality of informatics education provided to students. Faculty synergy was an essential component of this redesign process. Continuous quality improvement strategy included an ongoing alignment of curriculum and competencies through a comparative analysis approach. Through these efforts, new innovation was possible.
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Rebelling for a Reason: Protein Structural “Outliers”
Arumugam, Gandhimathi; Nair, Anu G.; Hariharaputran, Sridhar; Ramanathan, Sowdhamini
2013-01-01
Analysis of structural variation in domain superfamilies can reveal constraints in protein evolution which aids protein structure prediction and classification. Structure-based sequence alignment of distantly related proteins, organized in PASS2 database, provides clues about structurally conserved regions among different functional families. Some superfamily members show large structural differences which are functionally relevant. This paper analyses the impact of structural divergence on function for multi-member superfamilies, selected from the PASS2 superfamily alignment database. Functional annotations within superfamilies, with structural outliers or ‘rebels’, are discussed in the context of structural variations. Overall, these data reinforce the idea that functional similarities cannot be extrapolated from mere structural conservation. The implication for fold-function prediction is that the functional annotations can only be inherited with very careful consideration, especially at low sequence identities. PMID:24073209
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SUSTAINABLE ENERGY SYSTEMS DESIGN FOR A TRIBAL VILLAGE IN INDIA
Lab testing and limited field testing revealed the effectiveness of the following products designed in this study:The role of 3D microenvironmental organization in MCF-7 epithelial–mesenchymal transition after 7 culture daysDOE Office of Scientific and Technical Information (OSTI.GOV)
Foroni, Laura; Vasuri, Francesco, E-mail: vasurifrancesco@libero.it; Chair of Vascular Surgery, Department of Specialistic Surgery and Anaesthesiological Sciences, S. Orsola-Malpighi Hospital, Bologna University
2013-06-10
We present a multi-technique study on in vitro epithelial–mesenchymal transition (EMT) in human MCF-7 cells cultured on electrospun scaffolds of poly(L-lactic acid) (PLA), with random and aligned fiber orientations. Our aim is to investigate the morphological and genetic characteristics induced by extracellular matrix in tumor cells cultured in different 3D environments, and at different time points. Cell vitality was assessed with AlamarBlue at days 1, 3, 5 and 7. Scanning electron microscopy was performed at culture days 3 and 7. Immunohistochemistry (for E-cadherin, β-catenin, cytokeratins, nucleophosmin, tubulin, Ki-67 and vimentin), immunofluorescence (for F-actin) western blot (for E-cadherin, β-catenin and vimentin)more » and transmission electron microscopy were carried out at day 7. An EMT gene array followed by PCR analysis confirmed the regulation of selected genes. At day 7, scanning electron microscopy on aligned-PLA revealed spindle-shaped cells gathered in buds and ribbon-like structures, with a higher nucleolar/nuclear ratio and a loss in E-cadherin and β-catenin at immunohistochemistry and western blot. An up-regulation of SMAD2, TGF-β2, TFPI2 and SOX10 was found in aligned-PLA compared to random-PLA cultured cells. The topography of the extracellular matrix has a role in tumor EMT, and a more aggressive phenotype characterizes MCF-7 cells cultured on aligned-PLA scaffold. -- Highlights: • After 7 culture days an aligned-PLA scaffold induces a spindle shape to MCF-7 cells. • Despite these changes, the aligned MCF-7 cells keep an epithelial phenotype. • The extracellular environment alone influences the E-cadherin/β-catenin axis. • The extracellular environment can promote the epithelial–mesenchymal transition.« less
XUV ionization of aligned molecules
NASA Astrophysics Data System (ADS)
Kelkensberg, F.; Rouzée, A.; Siu, W.; Gademann, G.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.; Vrakking, M. J. J.
2011-11-01
New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO2 molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.
NASA Astrophysics Data System (ADS)
Shougaijam, B.; Swain, R.; Ngangbam, C.; Lenka, T. R.
2017-06-01
The effect of annealing on vertically aligned TiO2 NWs deposited by glancing angle deposition (GLAD) method on Si substrate using pressed and sintered TiO2 pellets as source material is studied. The FE-SEM images reveal the retention of vertically aligned NWs on Si substrate after annealing process. The EDS analysis of TiO2 NWs sample annealed at 600 °C in air for 1 h shows the higher weight percentage ratio of ˜2.6 (i.e., 72.27% oxygen and 27.73% titanium). The XRD pattern reveals that the polycrystalline nature of anatase TiO2 dominates the annealed NWs sample. The electrical characteristics of Al/TiO2-NWs/TiO2-TF/p-Si (NW device) and Al/TiO2-TF/p-Si (TF device) based on annealed samples are compared. It is riveting to observe a lower leakage current of ˜1.32 × 10-7 A/cm2 at +1 V with interface trap density of ˜6.71 × 1011 eV-1 cm-2 in NW device compared to ˜2.23 × 10-7 A/cm2 in TF device. The dominant leakage mechanism is investigated to be generally Schottky emission; however Poole-Frenkel emission also takes place during high reverse bias beyond 4 V for NWs and 3 V for TF device.
Deak, Zsuszsanna; Krtakovska, Aina; Ruschi, Francesco; Kammer, Nora; Wirth, Stefan; Reiser, Maximilian; Geyer, Lucas
2016-01-01
Objective: To evaluate whether straightening of the cervical spine (C-spine) alignment after trauma can be considered a significant multidetector CT (MDCT) finding. Methods: 160 consecutive patients after C-spine trauma admitted to a Level 1 trauma centre received MDCT according to Canadian Cervical Spine Rule and National Emergency X-Radiography Utilization Study indication rule; subgroups with and without cervical collar immobilization (CCI +/−) were compared with a control group (n = 20) of non-traumatized patients. Two independent readers evaluated retrospectively the alignment, determined the absolute rotational angle of the posterior surface of C2 and C7 (ARA C2–7) and grouped the results for lordosis (<−13°), straight (−13 to +6°) and kyphosis (>+6°). Results: In the two CCI−/CCI+ study groups, the straight or kyphotic alignment significantly (p = 0.001) predominated over lordosis. The number of patients with straight C-spine alignment was higher in the CCI+ group (CCI+ 69% vs CCI− 49%, p = 0.05). A comparison of the CCI+ group vs the CCI− group revealed a slightly smaller number of kyphotic (10% vs 18%, p = 0.34) and lordotic (21% vs 33%, p = 0.33) alignments. Statistically, however, the differences were of no significance. The control group revealed no significant differences. Conclusion: Straightening of the C-spine alone is not a definitive sign of injury but is a biomechanical variation due to CCI and neck positioning during MDCT or active patient control. Advances in knowledge: Straightening of the C-spine alignment in MDCT alone is not a definitive sign of injury. Straightening of the C-spine alignment is related to neck positioning and active patient control. CCI has a straightening effect on the cervical alignment. PMID:26764283
Block 3. Central view of Block 3 observed from the ...
Block 3. Central view of Block 3 observed from the west to the east. This photograph reveals the alignment of trees within the central path of the park. In addition, this photograph exposes broken bricks aligning tree beds - Skyline Park, 1500-1800 Arapaho Street, Denver, Denver County, CO
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.
Baumler, David J.; Banta, Lois M.; Hung, Kai F.; Schwarz, Jodi A.; Cabot, Eric L.; Glasner, Jeremy D.; Perna, Nicole T.
2012-01-01
Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of Genomes database. In the second module, students use an alignment of five Yersinia pestis genomes to analyze single-nucleotide polymorphisms of three genes to classify strains into biovar groups. Students are then given sequences of bacterial DNA amplified from the teeth of corpses from the first and second pandemics of the bubonic plague and asked to classify these new samples. Learning-assessment results reveal student improvement in self-efficacy and content knowledge, as well as students' ability to use BLAST to identify genomic islands and conduct analyses of virulence factors from E. coli O157:H7 or Y. pestis. Each of these educational modules offers educators new ready-to-implement resources for integrating comparative genomic topics into their curricula. PMID:22383620
2011-01-01
Background Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome. Methods We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays. Results Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%. We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the SLC45A3-ELK4 e4-e2 TIC to ERG-negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer cell lines. Conclusions Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues. Prostate and reference samples exhibit a wide range of TIC events, involving more genes than estimated previously using ESTs. Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as MSMB-NCOA4, may play functional roles in cancer. PMID:21261984
CAFE: aCcelerated Alignment-FrEe sequence analysis.
Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A; Waterman, Michael S; Sun, Fengzhu
2017-07-03
Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Mathematical modelling of anisotropy of illite-rich shale
Chesnokov, E.M.; Tiwary, D.K.; Bayuk, I.O.; Sparkman, M.A.; Brown, R.L.
2009-01-01
The estimation of illite-rich shale anisotropy to account for the alignment of clays and gas- or brine-filled cracks is presented via mathematical modelling. Such estimation requires analysis to interpret the dominance of one effect over another. This knowledge can help to evaluate the permeability in the unconventional reservoir, stress orientation, and the seal capacity for the conventional reservoir. Effective media modelling is used to predict the elastic properties of the illite-rich shale and to identify the dominant contributions to the shale anisotropy. We consider two principal reasons of the shale anisotropy: orientation of clay platelets and orientation of fluid-filled cracks. In reality, both of these two factors affect the shale anisotropy. The goal of this study is, first, to separately analyse the effect of these two factors to reveal the specific features in P- and S-wave velocity behaviour typical of each of the factors, and, then, consider a combined effect of the factors when the cracks are horizontally or vertically aligned. To do this, we construct four models of shale. The behaviour of P- and S-wave velocities is analysed when gas- and water-filled cracks embedded in a host matrix are randomly oriented, or horizontally or vertically aligned. The host matrix can be either isotropic or anisotropic (of VTI symmetry). In such a modelling, we use published data on mineralogy and clay platelet alignment along with other micromechanical measurements. In the model, where the host matrix is isotropic, the presence of a singularity point (when the difference VS1 - VS2 changes its sign) in shear wave velocities is an indicator of brine-filled aligned cracks. In the model with the VTI host matrix and horizontally aligned cracks filled with gas, an increase in their volume concentration leads to that the azimuth at which the singularity is observed moves toward the symmetry axis. In this case, if the clay content is small (around 20 per cent), the singularity point may even vanish. The Thomsen parameters are helpful in fluid type indication in shale. An indicator of gas-filled aligned cracks is ?? > ??. If aligned cracks in illite-rich shale are brine-filled, ?? < ??. Negative value of ?? indicates brine-filled cracks in illite-rich shale. A shale with brine-filled cracks exhibits higher Vp/Vs ratio in the vertical direction as compared to the gas-filled shale. A disorientation of clay platelets and brine-filled cracks may lead to that the singularity point is absent for brine-saturated shale as well. In this case one can also observe ?? > ?? and decreased values of Vp/Vs in the vertical direction as in the case of gas-filled cracks. In the presence of vertically aligned cracks, shales exhibit distinctly revealed features of orthorhombic symmetry. The results have important applications where seismic measurements are applied to predict the maturity state of the shale. ?? 2009 The Authors Journal compilation ?? 2009 RAS.
Revealing Conceptual Understanding of International Business
ERIC Educational Resources Information Center
Ashley, Sue; Schaap, Harmen; de Bruijn, Elly
2017-01-01
This study aims to identify an adequate approach for revealing conceptual understanding in higher professional education. Revealing students' conceptual understanding is an important step towards developing effective curricula, assessment and aligned teaching strategies to enhance conceptual understanding in higher education. Essays and concept…
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XUV ionization of aligned molecules
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kelkensberg, F.; Siu, W.; Gademann, G.
2011-11-15
New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.
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Fast switchable ferroelectric liquid crystal gratings with two electro-optical modes
DOE Office of Scientific and Technical Information (OSTI.GOV)
Ma, Ying; Srivastava, A. K., E-mail: abhishek-srivastava-lu@yahoo.co.in; Chigrinov, V. G.
In this article, we reveal a theoretical and experimental illustration of the Ferroelectric liquid crystal (FLC) grating fabricated by mean of patterned alignment based on photo-alignment. The complexity related to the mismatching of the predefined alignment domains on the top and bottom substrate has been avoided by incorporating only one side photo aligned substrate while the other substrate does not have any alignment layer. Depending on the easy axis in the said alignment domains and the azimuth plane of the impinging polarized light, the diffracting element can be tuned in two modes i.e. DIFF/OFF switchable and DIFF/TRANS switchable modes, whichmore » can be applied to different applications. The diffraction profile has been illustrated theoretically that fits well with the experimental finding and thus the proposed diffraction elements with fast response time and high diffraction efficiency could find application in many modern devices.« less
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Herawati, Elisa; Kanoh, Hatsuho
2016-01-01
Multiciliated cells (MCCs) promote fluid flow through coordinated ciliary beating, which requires properly organized basal bodies (BBs). Airway MCCs have large numbers of BBs, which are uniformly oriented and, as we show here, align linearly. The mechanism for BB alignment is unexplored. To study this mechanism, we developed a long-term and high-resolution live-imaging system and used it to observe green fluorescent protein–centrin2–labeled BBs in cultured mouse tracheal MCCs. During MCC differentiation, the BB array adopted four stereotypical patterns, from a clustering “floret” pattern to the linear “alignment.” This alignment process was correlated with BB orientations, revealed by double immunostaining for BBs and their asymmetrically associated basal feet (BF). The BB alignment was disrupted by disturbing apical microtubules with nocodazole and by a BF-depleting Odf2 mutation. We constructed a theoretical model, which indicated that the apical cytoskeleton, acting like a viscoelastic fluid, provides a self-organizing mechanism in tracheal MCCs to align BBs linearly for mucociliary transport. PMID:27573463
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Ultralight anisotropic foams from layered aligned carbon nanotube sheets.
Faraji, Shaghayegh; Stano, Kelly L; Yildiz, Ozkan; Li, Ang; Zhu, Yuntian; Bradford, Philip D
2015-10-28
In this work, we present large scale, ultralight aligned carbon nanotube (CNT) structures which have densities an order of magnitude lower than CNT arrays, have tunable properties and exhibit resiliency after compression. By stacking aligned sheets of carbon nanotubes and then infiltrating with a pyrolytic carbon (PyC), resilient foam-like materials were produced that exhibited complete recovery from 90% compressive strain. With density as low as 3.8 mg cm(-3), the foam structure is over 500 times less dense than bulk graphite. Microscopy revealed that PyC coated the junctions among CNTs, and also increased CNT surface roughness. These changes in the morphology explain the transition from inelastic behavior to foam-like recovery of the layered CNT sheet structure. Mechanical and thermal properties of the foams were tuned for different applications through variation of PyC deposition duration while dynamic mechanical analysis showed no change in mechanical properties over a large temperature range. Observation of a large and linear electrical resistance change during compression of the aligned CNT/carbon (ACNT/C) foams makes strain/pressure sensors a relevant application. The foams have high oil absorption capacities, up to 275 times their own weight, which suggests they may be useful in water treatment and oil spill cleanup. Finally, the ACNT/C foam's high porosity, surface area and stability allow for demonstration of the foams as catalyst support structures.
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Cell-cell interactions mediate cytoskeleton organization and collective endothelial cell chemotaxis.
Shamloo, Amir
2014-09-01
This study investigates the role of cell-cell and cell-ligand interactions in cytoskeleton organization of endothelial cells (ECs) and their directional migration within a microfluidic device. The migration of ECs in response to a biochemical factor was studied. Mathematical analysis of the cell migration pathways and cellular cytoskeleton revealed that directional migration, migration persistence length, migration speed, and cytoskeletal stress fiber alignment can be mediated by the level of cell contacts as well as the presence or absence of a biochemical polarizing factor. It was shown that in the presence of a biochemical polarizing factor, higher cell density and more frequent cell contacts has a reinforcing effect on collective cell chemotaxis. In contrast, in the absence of a polarizing factor, high cell density can decrease or suppress the ability of the cells to migrate. Also, the correlation of actin stress fiber organization and alignment with directional migration of ECs was investigated. It was shown that in the presence of a biochemical polarizing factor, stress fibers within the cytoskeleton of ECs can be significantly aligned parallel to the gradient direction when the cells have higher level of contacts. The results also show that the organization and alignment of actin stress fibers is mediated by cell adhesion junctions during collective cell migration and introduce cell-cell interactions as a key factor during collective cell chemotaxis. © 2014 Wiley Periodicals, Inc.
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Osteogenesis imperfecta type III/Ehlers-Danlos overlap syndrome in a Chinese man.
Lu, Yanqin; Wang, Yanzhou; Rauch, Frank; Li, Hu; Zhang, Yao; Zhai, Naixiang; Zhang, Jian; Ren, Xiuzhi; Han, Jinxiang
2018-02-01
Osteogenesis imperfecta (OI) and Ehlers-Danlos syndrome (EDS) are rare genetic disorders that are typically inherited in an autosomal dominant manner. Few cases of OI/EDS overlap syndrome have been documented. Described here is a 30-year-old Chinese male with OI type III and EDS. Sequencing of genomic DNA revealed a heterozygous COL1A1 mutation (c.671G>A, p.Gly224Asp) that affected the N-anchor domain of the alpha 1 chain of collagen type I. Ultrastructural analysis of a skin biopsy specimen revealed thin collagen fibers with irregular alignment of collagen fibers. These findings have expanded the genotypic spectrum of the OI/EDS overlap syndrome.
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Beginning Learners' Development of Interactional Competence: Alignment Activity
ERIC Educational Resources Information Center
Tecedor, Marta
2016-01-01
This study examined the development of interactional competence (Hall, 1993; He & Young, 1998) by beginning learners of Spanish as indexed by their use of alignment moves. Discourse analysis techniques and quantitative data analysis were used to explore how 52 learners expressed alignment and changes in participation patterns in two sets of…
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Liu, Xueqing; Peng, Sha; Gao, Shuyu; Cao, Yuancheng; You, Qingliang; Zhou, Liyong; Jin, Yongcheng; Liu, Zhihong; Liu, Jiyan
2018-05-09
It is of great significance to seek high-performance solid electrolytes via a facile chemistry and simple process for meeting the requirements of solid batteries. Previous reports revealed that ion conducting pathways within ceramic-polymer composite electrolytes mainly occur at ceramic particles and the ceramic-polymer interface. Herein, one facile strategy toward ceramic particles' alignment and assembly induced by an external alternating-current (AC) electric field is presented. It was manifested by an in situ optical microscope that Li 1.3 Al 0.3 Ti 1.7 (PO 4 ) 3 particles and poly(ethylene glycol) diacrylate in poly(dimethylsiloxane) (LATP@PEGDA@PDMS) assembled into three-dimensional connected networks on applying an external AC electric field. Scanning electron microscopy revealed that the ceramic LATP particles aligned into a necklacelike assembly. Electrochemical impedance spectroscopy confirmed that the ionic conductivity of this necklacelike alignment was significantly enhanced compared to that of the random one. It was demonstrated that this facile strategy of applying an AC electric field can be a very effective approach for architecting three-dimensional lithium-ion conductive networks within solid composite electrolyte.
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Dzikowski, R; Levy, M G; Poore, M F; Flowers, J R; Paperna, I
2003-12-29
Metacercariae of Bolbophorus species are serious pathogens of farmed fish. Molecular diagnostic tools, capable of identifying and differentiating these parasites, may assist in the development of rationale control strategies. The rDNA 18S (small sub-unit: SSU) genes of adult B. confusus and B. levantinus obtained from a pelican, Pelecanus onocrotalus, and a night heron, Nycticorax nycticorax, respectively, were amplified, sequenced, and aligned. Based on this alignment, we developed a genetic differentiation assay between B. confusus and B. levantinus. These 2 species were compared genetically with the North American species B. damnificus and Bolbophorus sp. ('Type 2'). The relationship between species is outlined and discussed. In addition to the molecular study, specimens of B. confusus and B. levantinus were compared morphologically, using scanning electron microscopy. Morphologic analysis revealed interspecific differences in details of the holdfast organ and the position of the acetabulum.
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PhAST: pharmacophore alignment search tool.
Hähnke, Volker; Hofmann, Bettina; Grgat, Tomislav; Proschak, Ewgenij; Steinhilber, Dieter; Schneider, Gisbert
2009-04-15
We present a ligand-based virtual screening technique (PhAST) for rapid hit and lead structure searching in large compound databases. Molecules are represented as strings encoding the distribution of pharmacophoric features on the molecular graph. In contrast to other text-based methods using SMILES strings, we introduce a new form of text representation that describes the pharmacophore of molecules. This string representation opens the opportunity for revealing functional similarity between molecules by sequence alignment techniques in analogy to homology searching in protein or nucleic acid sequence databases. We favorably compared PhAST with other current ligand-based virtual screening methods in a retrospective analysis using the BEDROC metric. In a prospective application, PhAST identified two novel inhibitors of 5-lipoxygenase product formation with minimal experimental effort. This outcome demonstrates the applicability of PhAST to drug discovery projects and provides an innovative concept of sequence-based compound screening with substantial scaffold hopping potential. 2008 Wiley Periodicals, Inc.
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Local relative density modulates failure and strength in vertically aligned carbon nanotubes.
Pathak, Siddhartha; Mohan, Nisha; Decolvenaere, Elizabeth; Needleman, Alan; Bedewy, Mostafa; Hart, A John; Greer, Julia R
2013-10-22
Micromechanical experiments, image analysis, and theoretical modeling revealed that local failure events and compressive stresses of vertically aligned carbon nanotubes (VACNTs) were uniquely linked to relative density gradients. Edge detection analysis of systematically obtained scanning electron micrographs was used to quantify a microstructural figure-of-merit related to relative local density along VACNT heights. Sequential bottom-to-top buckling and hardening in stress-strain response were observed in samples with smaller relative density at the bottom. When density gradient was insubstantial or reversed, bottom regions always buckled last, and a flat stress plateau was obtained. These findings were consistent with predictions of a 2D material model based on a viscoplastic solid with plastic non-normality and a hardening-softening-hardening plastic flow relation. The hardening slope in compression generated by the model was directly related to the stiffness gradient along the sample height, and hence to the local relative density. These results demonstrate that a microstructural figure-of-merit, the effective relative density, can be used to quantify and predict the mechanical response.
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Shin, Yong Cheol; Kim, Chuntae; Song, Su-Jin; Jun, Seungwon; Kim, Chang-Seok; Hong, Suck Won; Hyon, Suong-Hyu; Han, Dong-Wook; Oh, Jin-Woo
2018-01-01
Recently, there have been tremendous efforts to develop the biofunctional scaffolds by incorporating various biochemical factors. In the present study, we fabricated poly(lactic-co-glycolic acid) (PLGA) nanofiber sheets decorated with graphene oxide (GO) and RGD peptide. The decoration of GO and RGD peptide was readily achieved by using RGD peptide-displaying M13 bacteriophage (RGD-M13 phage) and electrospinning. Furthermore, the aligned GO-decorated PLGA/RGD peptide (GO-PLGA/RGD) ternary nanofiber sheets were prepared by magnetic field-assisted electrospinning, and their potentials as bifunctional scaffolds for facilitating myogenesis were explored. We characterized the physicochemical and mechanical properties of the sheets by scanning electron microscopy, Raman spectroscopy, contact angle measurement, and tensile test. In addition, the C2C12 skeletal myoblasts were cultured on the aligned GO-PLGA/RGD nanofiber sheets, and their cellular behaviors, including initial attachment, proliferation and myogenic differentiation, were evaluated. Our results revealed that the GO-PLGA/RGD nanofiber sheets had suitable physicochemical and mechanical properties for supporting cell growth, and could significantly promote the spontaneous myogenic differentiation of C2C12 skeletal myoblasts. Moreover, it was revealed that the myogenic differentiation was further accelerated on the aligned GO-PLGA/RGD nanofiber sheets due to the synergistic effects of RGD peptide, GO and aligned nanofiber structure. Therefore, , it is suggested that the aligned GO-PLGA/RGD ternary nanofiber sheets are one of the most promising approaches for facilitating myogenesis and promoting skeletal tissue regeneration. PMID:29577018
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Shin, Yong Cheol; Kim, Chuntae; Song, Su-Jin; Jun, Seungwon; Kim, Chang-Seok; Hong, Suck Won; Hyon, Suong-Hyu; Han, Dong-Wook; Oh, Jin-Woo
2018-01-01
Recently, there have been tremendous efforts to develop the biofunctional scaffolds by incorporating various biochemical factors. In the present study, we fabricated poly(lactic- co -glycolic acid) (PLGA) nanofiber sheets decorated with graphene oxide (GO) and RGD peptide. The decoration of GO and RGD peptide was readily achieved by using RGD peptide-displaying M13 bacteriophage (RGD-M13 phage) and electrospinning. Furthermore, the aligned GO-decorated PLGA/RGD peptide (GO-PLGA/RGD) ternary nanofiber sheets were prepared by magnetic field-assisted electrospinning, and their potentials as bifunctional scaffolds for facilitating myogenesis were explored. We characterized the physicochemical and mechanical properties of the sheets by scanning electron microscopy, Raman spectroscopy, contact angle measurement, and tensile test. In addition, the C2C12 skeletal myoblasts were cultured on the aligned GO-PLGA/RGD nanofiber sheets, and their cellular behaviors, including initial attachment, proliferation and myogenic differentiation, were evaluated. Our results revealed that the GO-PLGA/RGD nanofiber sheets had suitable physicochemical and mechanical properties for supporting cell growth, and could significantly promote the spontaneous myogenic differentiation of C2C12 skeletal myoblasts. Moreover, it was revealed that the myogenic differentiation was further accelerated on the aligned GO-PLGA/RGD nanofiber sheets due to the synergistic effects of RGD peptide, GO and aligned nanofiber structure. Therefore, , it is suggested that the aligned GO-PLGA/RGD ternary nanofiber sheets are one of the most promising approaches for facilitating myogenesis and promoting skeletal tissue regeneration.
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Das, Pranab J; McCarthy, Fiona; Vishnoi, Monika; Paria, Nandina; Gresham, Cathy; Li, Gang; Kachroo, Priyanka; Sudderth, A Kendrick; Teague, Sheila; Love, Charles C; Varner, Dickson D; Chowdhary, Bhanu P; Raudsepp, Terje
2013-01-01
Mature mammalian sperm contain a complex population of RNAs some of which might regulate spermatogenesis while others probably play a role in fertilization and early development. Due to this limited knowledge, the biological functions of sperm RNAs remain enigmatic. Here we report the first characterization of the global transcriptome of the sperm of fertile stallions. The findings improved understanding of the biological significance of sperm RNAs which in turn will allow the discovery of sperm-based biomarkers for stallion fertility. The stallion sperm transcriptome was interrogated by analyzing sperm and testes RNA on a 21,000-element equine whole-genome oligoarray and by RNA-seq. Microarray analysis revealed 6,761 transcripts in the sperm, of which 165 were sperm-enriched, and 155 were differentially expressed between the sperm and testes. Next, 70 million raw reads were generated by RNA-seq of which 50% could be aligned with the horse reference genome. A total of 19,257 sequence tags were mapped to all horse chromosomes and the mitochondrial genome. The highest density of mapped transcripts was in gene-rich ECA11, 12 and 13, and the lowest in gene-poor ECA9 and X; 7 gene transcripts originated from ECAY. Structural annotation aligned sperm transcripts with 4,504 known horse and/or human genes, rRNAs and 82 miRNAs, whereas 13,354 sequence tags remained anonymous. The data were aligned with selected equine gene models to identify additional exons and splice variants. Gene Ontology annotations showed that sperm transcripts were associated with molecular processes (chemoattractant-activated signal transduction, ion transport) and cellular components (membranes and vesicles) related to known sperm functions at fertilization, while some messenger and micro RNAs might be critical for early development. The findings suggest that the rich repertoire of coding and non-coding RNAs in stallion sperm is not a random remnant from spermatogenesis in testes but a selectively retained and functionally coherent collection of RNAs.
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Das, Pranab J.; McCarthy, Fiona; Vishnoi, Monika; Paria, Nandina; Gresham, Cathy; Li, Gang; Kachroo, Priyanka; Sudderth, A. Kendrick; Teague, Sheila; Love, Charles C.; Varner, Dickson D.; Chowdhary, Bhanu P.; Raudsepp, Terje
2013-01-01
Mature mammalian sperm contain a complex population of RNAs some of which might regulate spermatogenesis while others probably play a role in fertilization and early development. Due to this limited knowledge, the biological functions of sperm RNAs remain enigmatic. Here we report the first characterization of the global transcriptome of the sperm of fertile stallions. The findings improved understanding of the biological significance of sperm RNAs which in turn will allow the discovery of sperm-based biomarkers for stallion fertility. The stallion sperm transcriptome was interrogated by analyzing sperm and testes RNA on a 21,000-element equine whole-genome oligoarray and by RNA-seq. Microarray analysis revealed 6,761 transcripts in the sperm, of which 165 were sperm-enriched, and 155 were differentially expressed between the sperm and testes. Next, 70 million raw reads were generated by RNA-seq of which 50% could be aligned with the horse reference genome. A total of 19,257 sequence tags were mapped to all horse chromosomes and the mitochondrial genome. The highest density of mapped transcripts was in gene-rich ECA11, 12 and 13, and the lowest in gene-poor ECA9 and X; 7 gene transcripts originated from ECAY. Structural annotation aligned sperm transcripts with 4,504 known horse and/or human genes, rRNAs and 82 miRNAs, whereas 13,354 sequence tags remained anonymous. The data were aligned with selected equine gene models to identify additional exons and splice variants. Gene Ontology annotations showed that sperm transcripts were associated with molecular processes (chemoattractant-activated signal transduction, ion transport) and cellular components (membranes and vesicles) related to known sperm functions at fertilization, while some messenger and micro RNAs might be critical for early development. The findings suggest that the rich repertoire of coding and non-coding RNAs in stallion sperm is not a random remnant from spermatogenesis in testes but a selectively retained and functionally coherent collection of RNAs. PMID:23409192
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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.
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Wang, Wei; Itoh, Soichiro; Konno, Katsumi; Kikkawa, Takeshi; Ichinose, Shizuko; Sakai, Katsuyoshi; Ohkuma, Tsuneo; Watabe, Kazuhiko
2009-12-15
We have constructed a chitosan nonwoven nanofiber mesh tube consisting of oriented fibers by the electrospinning method. The efficacy of oriented nanofibers on Schwann cell alignment and positive effect of this tube on peripheral nerve regeneration were confirmed. The physical properties of the chitosan nanofiber mesh sheets prepared by electrospinning with or without fiber orientation were characterized. Then, immortalized Schwann cells were cultured on these sheets. Furthermore, the chitosan nanofiber mesh tubes with or without orientation, and bilayered chitosan mesh tube with an inner layer of oriented nanofibers and an outer layer of randomized nanofibers were bridgegrafted into rat sciatic nerve defect. As a result of fiber orientation, the tensile strength along the axis of the sheet increased. Because Schwann cells aligned along the nanofibers, oriented fibrous sheets could exhibit a Schwann cell column. Functional recovery and electrophysiological recovery occurred in time in the oriented group as well as in the bilayered group, and approximately matched those in the isograft. Furthermore, histological analysis revealed that the sprouting of myelinated axons occurred vigorously followed by axonal maturation in the isograft, oriented, and bilayered group in the order. The oriented chitosan nanofiber mesh tube may be a promising substitute for autogenous nerve graft.
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Template-Based Modeling of Protein-RNA Interactions.
Zheng, Jinfang; Kundrotas, Petras J; Vakser, Ilya A; Liu, Shiyong
2016-09-01
Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes.
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Chen, Z H; Yeung, S Y; Li, H; Qian, J C; Zhang, W J; Li, Y Y; Bello, I
2012-05-21
ZnO/Zn(1-x)Pb(x)Se core-shell nanowires (NWs) have been synthesized by a solution based surface ion transfer method at various temperatures. The energy dispersive spectroscopic (EDS) mapping of single NWs suggests that the Zn, Pb and Se atoms are uniformly distributed in their shell layers. The ternary Zn(1-x)Pb(x)Se layers with tunable bandgaps extend the band-edge of optical absorption from 450 nm to 700 nm contrasting with the binary ZnSe layers. The ultraviolet photoelectron spectroscopic (UPS) analysis reveals a transition from the type I to type II band alignment when the x fraction decreases from 0.66 to the value of 0.36 in the nanoshell layers. This quantitative investigation of electronic energy levels at ZnO and Zn(1-x)Pb(x)Se interfaces indicates that the proper type II band alignment is well suited for photovoltaic energy conversion. The photovoltaic cells comprising a ZnO/Zn(1-x)Pb(x)Se nano-heterojunction with the optimized Pb content are expected to be more efficient than the devices sensitized by binary ZnSe or PbSe.
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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.
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Energy level alignment at the methylammonium lead iodide/copper phthalocyanine interface
DOE Office of Scientific and Technical Information (OSTI.GOV)
Chen, Shi; Goh, Teck Wee; Sum, Tze Chien, E-mail: Alfred@ntu.edu.sg, E-mail: Tzechien@ntu.edu.sg
2014-08-01
The energy level alignment at the CH{sub 3}NH{sub 3}PbI{sub 3}/copper phthalocyanine (CuPc) interface is investigated by X-ray photoelectron spectroscopy (XPS) and ultraviolet photoelectron spectroscopy (UPS). XPS reveal a 0.3 eV downward band bending in the CuPc film. UPS validate this finding and further reveal negligible interfacial dipole formation – verifying the viability of vacuum level alignment. The highest occupied molecular orbital of CuPc is found to be closer to the Fermi level than the valance band maximum of CH{sub 3}NH{sub 3}PbI{sub 3}, facilitating hole transfer from CH{sub 3}NH{sub 3}PbI{sub 3} to CuPc. However, subsequent hole extraction from CuPc may bemore » impeded by the downward band bending in the CuPc layer.« less
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Facile fabrication and electrical investigations of nanostructured p-Si/n-TiO2 hetero-junction diode
NASA Astrophysics Data System (ADS)
Kumar, Arvind; Mondal, Sandip; Rao, K. S. R. Koteswara
2018-05-01
In this work, we have fabricated the nanostructured p-Si/n-TiO2 hetero-junction diode by using a facile spin-coating method. The XRD analysis suggests the presence of well crystalline anatase TiO2 film on Si with small grain size (˜16 nm). We have drawn the band alignment using Anderson model to understand the electrical transport across the junction. The current-voltage (J-V) characteristics analysis reveals the good rectification ratio (103 at ± 3 V) and slightly higher ideality factor (4.7) of our device. The interface states are responsible for the large ideality factor as Si/TiO2 form a dissimilar interface and possess a large number of dangling bonds. The study reveals the promises to be used Si/TiO2 diode as an alternative to the traditional p-n homo-junction diode, which typically require high budget.
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2013-01-01
Peak alignment is a critical procedure in mass spectrometry-based biomarker discovery in metabolomics. One of peak alignment approaches to comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) data is peak matching-based alignment. A key to the peak matching-based alignment is the calculation of mass spectral similarity scores. Various mass spectral similarity measures have been developed mainly for compound identification, but the effect of these spectral similarity measures on the performance of peak matching-based alignment still remains unknown. Therefore, we selected five mass spectral similarity measures, cosine correlation, Pearson's correlation, Spearman's correlation, partial correlation, and part correlation, and examined their effects on peak alignment using two sets of experimental GC×GC-MS data. The results show that the spectral similarity measure does not affect the alignment accuracy significantly in analysis of data from less complex samples, while the partial correlation performs much better than other spectral similarity measures when analyzing experimental data acquired from complex biological samples. PMID:24151524
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García-Arias, Francy L; Osorio-Guarín, Jaime A; Núñez Zarantes, Victor M
2018-01-01
Association mapping has been proposed as an efficient approach to assist plant breeding programs to investigate the genetic basis of agronomic traits. In this study, we evaluated 18 traits related to yield, (FWP, NF, FWI, and FWII), fruit size-shape (FP, FA, MW, WMH, MH, HMW, DI, FSI, FSII, OVO, OBO), and fruit quality (FIR, CF, and SST), in a diverse collection of 100 accessions of Physalis peruviana including wild, landraces, and anther culture derived lines. We identified seven accessions with suitable traits: fruit weight per plant (FWP) > 7,000 g/plant and cracked fruits (CF) < 4%, to be used as parents in cape gooseberry breeding program. In addition, the accessions were also characterized using Genotyping By Sequencing (GBS). We discovered 27,982 and 36,142 informative SNP markers based on the alignment against the two cape gooseberry references transcriptomes. Besides, 30,344 SNPs were identified based on alignment to the tomato reference genome. Genetic structure analysis showed that the population could be divided into two or three sub-groups, corresponding to landraces-anther culture and wild accessions for K = 2 and wild, landraces, and anther culture plants for K = 3. Association analysis was carried out using a Mixed Linear Model (MLM) and 34 SNP markers were significantly associated. These results reveal the basis of the genetic control of important agronomic traits and may facilitate marker-based breeding in P. peruviana .
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García-Arias, Francy L.; Osorio-Guarín, Jaime A.; Núñez Zarantes, Victor M.
2018-01-01
Association mapping has been proposed as an efficient approach to assist plant breeding programs to investigate the genetic basis of agronomic traits. In this study, we evaluated 18 traits related to yield, (FWP, NF, FWI, and FWII), fruit size-shape (FP, FA, MW, WMH, MH, HMW, DI, FSI, FSII, OVO, OBO), and fruit quality (FIR, CF, and SST), in a diverse collection of 100 accessions of Physalis peruviana including wild, landraces, and anther culture derived lines. We identified seven accessions with suitable traits: fruit weight per plant (FWP) > 7,000 g/plant and cracked fruits (CF) < 4%, to be used as parents in cape gooseberry breeding program. In addition, the accessions were also characterized using Genotyping By Sequencing (GBS). We discovered 27,982 and 36,142 informative SNP markers based on the alignment against the two cape gooseberry references transcriptomes. Besides, 30,344 SNPs were identified based on alignment to the tomato reference genome. Genetic structure analysis showed that the population could be divided into two or three sub-groups, corresponding to landraces-anther culture and wild accessions for K = 2 and wild, landraces, and anther culture plants for K = 3. Association analysis was carried out using a Mixed Linear Model (MLM) and 34 SNP markers were significantly associated. These results reveal the basis of the genetic control of important agronomic traits and may facilitate marker-based breeding in P. peruviana. PMID:29616069
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Marques, Ana Rita; Coutinho, Pedro M; Videira, Paula; Fialho, Arsénio M; Sá-Correia, Isabel
2003-01-01
The Sphingomonas paucimobilis beta-glucosidase Bgl1 is encoded by the bgl1 gene, associated with an 1308 bp open reading frame. The deduced protein has a potential signal peptide of 24 amino acids in the N-terminal region, and experimental evidence is consistent with the processing and export of the Bgl1 protein through the inner membrane to the periplasmic space. A His(6)-tagged 44.3 kDa protein was over-produced in the cytosol of Escherichia coli from a recombinant plasmid, which contained the S. paucimobilis bgl1 gene lacking the region encoding the putative signal peptide. Mature beta-glucosidase Bgl1 is specific for aryl-beta-glucosides and has no apparent activity with oligosaccharides derived from cellulose hydrolysis and other saccharides. A structure-based alignment established structural relations between S. paucimobilis Bgl1 and other members of the glycoside hydrolase (GH) family 1 enzymes. At subsite -1, the conserved residues required for catalysis by GH1 enzymes are present in Bgl1 with only minor differences. Major differences are found at subsite +1, the aglycone binding site. This alignment seeded a sequence-based phylogenetic analysis of GH1 enzymes, revealing an absence of horizontal transfer between phyla. Bootstrap analysis supported the definition of subfamilies and revealed that Bgl1, the first characterized beta-glucosidase from the genus Sphingomonas, represents a very divergent bacterial subfamily, closer to archaeal subfamilies than to others of bacterial origin. PMID:12444924
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Node fingerprinting: an efficient heuristic for aligning biological networks.
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.
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Optical Analysis And Alignment Applications Using The Infrared Smartt Interferometer
NASA Astrophysics Data System (ADS)
Viswanathan, V. K.; Bolen, P. D.; Liberman, I.; Seery, B. D.
1981-12-01
The possiblility of using the infrared Smartt interferometer for optical analysis and alignment of infrared laser systems has been discussed previously. In this paper, optical analysis of the Gigawatt Test Facility at Los Alamos, as well as a deformable mirror manufactured by Rocketdyne, are discussed as examples of the technique. The possibility of optically characterizing, as well as aligning, pulsed high energy laser systems like Helios and Antares is discussed in some detail.
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Optical analysis and alignment applications using the infrared Smartt interferometer
NASA Astrophysics Data System (ADS)
Viswanathan, V. K.; Bolen, P. D.; Liberman, I.; Seery, B. D.
The possibility of using the infrared Smartt interferometer for optical analysis and alignment of infrared laser systems has been discussed previously. In this paper, optical analysis of the Gigawatt Test Facility at Los Alamos, as well as a deformable mirror manufactured by Rocketdyne, are discussed as examples of the technique. The possibility of optically characterizing, as well as aligning, pulsed high energy laser systems like Helios and Antares is discussed in some detail.
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NASA Astrophysics Data System (ADS)
Koumoulos, Elias P.; Charitidis, C. A.
2017-02-01
Carbon nanotube (CNT) based architectures have increased the scientific interest owning to their exceptional performance rendering them promising candidates for advanced industrial applications in the nanotechnology field. Despite individual CNTs being considered as one of the most known strong materials, much less is known about other CNT forms, such as CNT arrays, in terms of their mechanical performance (integrity). In this work, thermal chemical vapor deposition (CVD) method is employed to produce vertically aligned multiwall (VA-MW) CNT carpets. Their structural properties were studied by means of scanning electron microscopy (SEM), X-Ray diffraction (XRD) and Raman spectroscopy, while their hydrophobic behavior was investigated via contact angle measurements. The resistance to indentation deformation of VA-MWCNT carpets was investigated through nanoindentation technique. The synthesized VA-MWCNTs carpets consisted of well-aligned MWCNTs. Static contact angle measurements were performed with water and glycerol, revealing a rather super-hydrophobic behavior. The structural analysis, hydrophobic behavior and indentation response of VA-MWCNTs carpets synthesized via CVD method are clearly demonstrated. Additionally, cycle indentation load-depth curve was applied and hysteresis loops were observed in the indenter loading-unloading cycle due to the local stress distribution. Hardness (as resistance to applied load) and modulus mapping, at 200 nm of displacement for a grid of 70 μm2 is presented. Through trajection, the resistance is clearly divided in 2 regions, namely the MWCNT probing and the in-between area MWCNT - MWCNT interface.
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Pair aligning improved motility of Quincke rollers.
Lu, Shi Qing; Zhang, Bing Yue; Zhang, Zhi Chao; Shi, Yan; Zhang, Tian Hui
2018-06-06
Density-dependent speed is studied in a two-dimensional active colloid in which the colloidal particles are propelled by an external electric field via a Quincke rotation. Above the critcal electric field, dense dynamic clusters form spotaneously, in which the particles are highly aligned in velocity and move much faster than isolated units. Detailed observations on pair collision reveal that the alignment of velocity is induced by the long-ranged hydrodynamic interactions and the improvement of speed in the clusters arises from pair aligning in which two particles are closely paired and rotate synchronically. In the aligning state, the short-range in-plane dipole-dipole attraction enhances the rotation torque and gives rises to a larger rolling speed. The pair aligning becomes difficult and unstable at high electric field where the normal dipole-dipole repulsion becomes dominant. As a consequence, the dependence of speed on density becomes weak increasingly upon the increase of the electric field. This result offers an interpretation for the discrepancy between our and previous observations on Quincke rollers.
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Johnson, Kevin J; Wright, Bob W; Jarman, Kristin H; Synovec, Robert E
2003-05-09
A rapid retention time alignment algorithm was developed as a preprocessing utility to be used prior to chemometric analysis of large datasets of diesel fuel profiles obtained using gas chromatography (GC). Retention time variation from chromatogram-to-chromatogram has been a significant impediment against the use of chemometric techniques in the analysis of chromatographic data due to the inability of current chemometric techniques to correctly model information that shifts from variable to variable within a dataset. The alignment algorithm developed is shown to increase the efficacy of pattern recognition methods applied to diesel fuel chromatograms by retaining chemical selectivity while reducing chromatogram-to-chromatogram retention time variations and to do so on a time scale that makes analysis of large sets of chromatographic data practical. Two sets of diesel fuel gas chromatograms were studied using the novel alignment algorithm followed by principal component analysis (PCA). In the first study, retention times for corresponding chromatographic peaks in 60 chromatograms varied by as much as 300 ms between chromatograms before alignment. In the second study of 42 chromatograms, the retention time shifting exhibited was on the order of 10 s between corresponding chromatographic peaks, and required a coarse retention time correction prior to alignment with the algorithm. In both cases, an increase in retention time precision afforded by the algorithm was clearly visible in plots of overlaid chromatograms before and then after applying the retention time alignment algorithm. Using the alignment algorithm, the standard deviation for corresponding peak retention times following alignment was 17 ms throughout a given chromatogram, corresponding to a relative standard deviation of 0.003% at an average retention time of 8 min. This level of retention time precision is a 5-fold improvement over the retention time precision initially provided by a state-of-the-art GC instrument equipped with electronic pressure control and was critical to the performance of the chemometric analysis. This increase in retention time precision does not come at the expense of chemical selectivity, since the PCA results suggest that essentially all of the chemical selectivity is preserved. Cluster resolution between dissimilar groups of diesel fuel chromatograms in a two-dimensional scores space generated with PCA is shown to substantially increase after alignment. The alignment method is robust against missing or extra peaks relative to a target chromatogram used in the alignment, and operates at high speed, requiring roughly 1 s of computation time per GC chromatogram.
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Guardiola, Mathilde; Bertrand, Roxane
2013-01-01
This paper investigates how and when interactional convergence is established by participants in conversation. We analyze sequences of storytelling using an original method that combines Conversation Analysis and a corpus-based approach. In storytelling, the participant in the position of "listener" is expected to produce either generic or specific responses adapted to the storyteller's narrative. The listener's behavior produced within the current activity is a cue of his/her interactional alignment. We show here that the listener can produce a specific type of (aligned) response, which we term a reported speech utterance in echo. The participant who is not telling the story is nonetheless able to animate the characters, while reversing the usual asymmetric roles of storyteller and listener. The use of this device is a way for the listener to display his/her stance toward the events told by the storyteller. If the listener's stance is congruent with that of the storyteller, this reveals a high degree of affiliation between the participants. We present seventeen excerpts from a collection of 94 instances of Echo Reported Speech (ERS) which we examined using the concepts of alignment and affiliation in order to show how different kinds of convergent sequences are constructed. We demonstrate that this phenomenon is mainly used by the listener to align and affiliate with the storyteller by means of reformulative, enumerative, or overbidding ERS. We also show that in affiliative sequences, reported speech can be used by the listener in a humorous way in order to temporarily disalign. This disalignment constitutes a potential starting point for an oblique sequence, which, if accepted and continued by the storyteller, gives rise to a highly convergent sequence.
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Guardiola, Mathilde; Bertrand, Roxane
2013-01-01
This paper investigates how and when interactional convergence is established by participants in conversation. We analyze sequences of storytelling using an original method that combines Conversation Analysis and a corpus-based approach. In storytelling, the participant in the position of “listener” is expected to produce either generic or specific responses adapted to the storyteller's narrative. The listener's behavior produced within the current activity is a cue of his/her interactional alignment. We show here that the listener can produce a specific type of (aligned) response, which we term a reported speech utterance in echo. The participant who is not telling the story is nonetheless able to animate the characters, while reversing the usual asymmetric roles of storyteller and listener. The use of this device is a way for the listener to display his/her stance toward the events told by the storyteller. If the listener's stance is congruent with that of the storyteller, this reveals a high degree of affiliation between the participants. We present seventeen excerpts from a collection of 94 instances of Echo Reported Speech (ERS) which we examined using the concepts of alignment and affiliation in order to show how different kinds of convergent sequences are constructed. We demonstrate that this phenomenon is mainly used by the listener to align and affiliate with the storyteller by means of reformulative, enumerative, or overbidding ERS. We also show that in affiliative sequences, reported speech can be used by the listener in a humorous way in order to temporarily disalign. This disalignment constitutes a potential starting point for an oblique sequence, which, if accepted and continued by the storyteller, gives rise to a highly convergent sequence. PMID:24115939
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Kocabas, Coskun; Hur, Seung-Hyun; Gaur, Anshu; Meitl, Matthew A; Shim, Moonsub; Rogers, John A
2005-11-01
A convenient process for generating large-scale, horizontally aligned arrays of pristine, single-walled carbon nanotubes (SWNTs) is described. The approach uses guided growth, by chemical vapor deposition (CVD), of SWNTs on miscut single-crystal quartz substrates. Studies of the growth reveal important relationships between the density and alignment of the tubes, the CVD conditions, and the morphology of the quartz. Electrodes and dielectrics patterned on top of these arrays yield thin-film transistors that use the SWNTs as effective thin-film semiconductors. The ability to build high-performance devices of this type suggests significant promise for large-scale aligned arrays of SWNTs in electronics, sensors, and other applications.
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CAFE: aCcelerated Alignment-FrEe sequence analysis
Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A.; Waterman, Michael S.
2017-01-01
Abstract Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$d_2^*$\\end{document} and \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$d_2^S$\\end{document} are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. PMID:28472388
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Chan, Jeremy Y; Williams, Benjamin R; Nair, Pallavi; Young, Elizabeth; Sofka, Carolyn; Deland, Jonathan T; Ellis, Scott J
2013-02-01
Successful correction of hindfoot alignment in adult acquired flatfoot deformity (AAFD) is likely influenced by the degree of medializing calcaneal osteotomy (MCO) performed, but it is not known if other reconstruction procedures significantly contribute as well. The purpose of this study was to evaluate the correlation between common preoperative and postoperative variables and hindfoot alignment. Thirty patients with stage II AAFD undergoing flatfoot reconstruction were followed prospectively. Preoperative and postoperative radiographs were reviewed to assess for correction in hindfoot alignment as measured by the change in hindfoot moment arm. Nineteen variables were analyzed, including age, gender, height, weight, body mass index (BMI), medial cuneiform-fifth metatarsal height, anteroposterior (AP) talonavicular coverage, AP talus-first metatarsal, lateral talus-first metatarsal and calcaneal pitch angles as well as intraoperative use of the MCO, lateral column lengthening (LCL), Cotton osteotomy, first tarsometatarsal fusion, flexor digitorum longus transfer, spring ligament reconstruction, and gastrocnemius recession or Achilles lengthening. Mean age was 57.3 years (range, 22-77). Final radiographs were obtained at a mean of 47 weeks (range, 25-78) postoperatively. Seven variables were found to significantly affect hindfoot moment arm. These were gender (P < .05), the amount of MCO performed (P < .001), LCL (P < .01), first tarsometatarsal fusion (P < .01), spring ligament reconstruction (P < .01), medial cuneiform-fifth metatarsal height (P < .001), and calcaneal pitch angle (P < .05). Multivariate regression analysis revealed that MCO was the only significant predictor of hindfoot moment arm. The final regression model for MCO showed a good fit (R(2) = .93, P < .001). Correction of hindfoot valgus alignment obtained in flatfoot reconstruction is primarily determined by the MCO procedure and can be modeled linearly. We believe that the hindfoot alignment view can serve as a valuable preoperative measurement to help surgeons adjust the proper amount of correction intraoperatively. Level IV, prospective case series.
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Thermal Conductivity of Polyimide/Carbon Nanofiller Blends
NASA Technical Reports Server (NTRS)
Delozier, D. M.; Watson, K. A.; Ghose, S.; Working, D. C.; Connell, J. W.; Smith, J. G.; Sun, Y. P.; Lin, Y.
2006-01-01
Ultem(TM) was mixed with three different carbon-based nanofillers in efforts to increase the thermal conductivity of the polymer. After initial mixing, the nanocomposites were extruded or processed via the Laboratory Mixing Molder (LMM) process. High resolution scanning electron microscopy (HRSEM) revealed significant alignment of the nanofillers in the extruded samples. Thermal conductivity measurements were made both in the direction and perpendicular to the direction of alignment of nanofillers as well as for unaligned samples. It was found that the largest improvement in thermal conductivity was achieved in the case of aligned samples when the measurement was performed in the direction of alignment. Unaligned samples also showed a significant improvement in thermal conductivity and may be useful in applications when it is not possible to align the nanofiller. However the improvements in thermal conductivity did not approach those expected based on a rule of mixtures. This is likely due to poor phonon transfer through the matrix.
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Murphy, Gail Tomblin; Birch, Stephen; MacKenzie, Adrian; Rigby, Janet; Purkis, Mary Ellen
2017-01-01
Clarifying the healthcare innovation agenda is critical in order to advance the impact of system innovations. As part of this agenda-setting it is important to address the four conditions within which innovations can enhance system sustainability: 1) the innovation agenda reflects and is aligned with healthcare objectives and policy; 2) planning methodologies for services, workforce and funding are aligned with healthcare objectives and policy; 3) innovations in services are accommodated in systems through innovations in policy, planning and funding; and 4) innovations are systematically monitored and evaluated. In order to illustrate these conditions, the authors present a case study of an evaluation of one Canadian Health Authority's efforts to transform healthcare delivery. This case study reveals that aligning innovations in policy, planning, funding and health services is critical to transforming health systems and that, in the absence of such alignment, sustainable health systems are difficult to achieve.
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Methods for Room Acoustic Analysis and Synthesis using a Monopole-Dipole Microphone Array
NASA Technical Reports Server (NTRS)
Abel, J. S.; Begault, Durand R.; Null, Cynthia H. (Technical Monitor)
1998-01-01
In recent work, a microphone array consisting of an omnidirectional microphone and colocated dipole microphones having orthogonally aligned dipole axes was used to examine the directional nature of a room impulse response. The arrival of significant reflections was indicated by peaks in the power of the omnidirectional microphone response; reflection direction of arrival was revealed by comparing zero-lag crosscorrelations between the omnidirectional response and the dipole responses to the omnidirectional response power to estimate arrival direction cosines with respect to the dipole axes.
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A nucleolar protein RRS1 contributes to chromosome congression.
Gambe, Arni E; Matsunaga, Sachihiro; Takata, Hideaki; Ono-Maniwa, Rika; Baba, Akiko; Uchiyama, Susumu; Fukui, Kiichi
2009-06-18
We report here the functional analysis of human Regulator of Ribosome Synthesis 1 (RRS1) protein during mitosis. We demonstrate that RRS1 localizes in the nucleolus during interphase and is distributed at the chromosome periphery during mitosis. RNA interference experiments revealed that RRS1-depleted cells show abnormalities in chromosome alignment and spindle organization, which result in mitotic delay. RRS1 knockdown also perturbs the centromeric localization of Shugoshin 1 and results in premature separation of sister chromatids. Our results suggest that a nucleolar protein RRS1 contributes to chromosome congression.
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A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.
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.
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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…
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Lucero, Mary E.; Unc, Adrian; Cooke, Peter; Dowd, Scot; Sun, Shulei
2011-01-01
Microbial diversity associated with micropropagated Atriplex species was assessed using microscopy, isolate culturing, and sequencing. Light, electron, and confocal microscopy revealed microbial cells in aseptically regenerated leaves and roots. Clone libraries and tag-encoded FLX amplicon pyrosequencing (TEFAP) analysis amplified sequences from callus homologous to diverse fungal and bacterial taxa. Culturing isolated some seed borne endophyte taxa which could be readily propagated apart from the host. Microbial cells were observed within biofilm-like residues associated with plant cell surfaces and intercellular spaces. Various universal primers amplified both plant and microbial sequences, with different primers revealing different patterns of fungal diversity. Bacterial and fungal TEFAP followed by alignment with sequences from curated databases revealed 7 bacterial and 17 ascomycete taxa in A. canescens, and 5 bacterial taxa in A. torreyi. Additional diversity was observed among isolates and clone libraries. Micropropagated Atriplex retains a complex, intimately associated microbiome which includes diverse strains well poised to interact in manners that influence host physiology. Microbiome analysis was facilitated by high throughput sequencing methods, but primer biases continue to limit recovery of diverse sequences from even moderately complex communities. PMID:21437280
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Joint Multi-Leaf Segmentation, Alignment, and Tracking for Fluorescence Plant Videos.
Yin, Xi; Liu, Xiaoming; Chen, Jin; Kramer, David M
2018-06-01
This paper proposes a novel framework for fluorescence plant video processing. The plant research community is interested in the leaf-level photosynthetic analysis within a plant. A prerequisite for such analysis is to segment all leaves, estimate their structures, and track them over time. We identify this as a joint multi-leaf segmentation, alignment, and tracking problem. First, leaf segmentation and alignment are applied on the last frame of a plant video to find a number of well-aligned leaf candidates. Second, leaf tracking is applied on the remaining frames with leaf candidate transformation from the previous frame. We form two optimization problems with shared terms in their objective functions for leaf alignment and tracking respectively. A quantitative evaluation framework is formulated to evaluate the performance of our algorithm with four metrics. Two models are learned to predict the alignment accuracy and detect tracking failure respectively in order to provide guidance for subsequent plant biology analysis. The limitation of our algorithm is also studied. Experimental results show the effectiveness, efficiency, and robustness of the proposed method.
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Genomic characterization and taxonomic position of a rhabdovirus from a hybrid snakehead.
Zeng, Weiwei; Wang, Qing; Wang, Yingying; Liu, Cun; Liang, Hongru; Fang, Xiang; Wu, Shuqin
2014-09-01
A new rhabdovirus, tentatively designated as hybrid snakehead rhabdovirus C1207 (HSHRV-C1207), was first isolated from a moribund hybrid snakehead (Channa maculata×Channa argus) in China. We present the complete genome sequence of HSHRV-C1207 and a comprehensive sequence comparison between HSHRV-C1207 and other rhabdoviruses. Sequence alignment and phylogenetic analysis revealed that HSHRV-C1207 shared the highest degree of homology with Monopterus albus rhabdovirus and Siniperca chuatsi rhabdovirus. All three viruses clustered into a single group that was distinct from the recognized genera in the family Rhabdoviridae. Our analysis suggests that HSHRV-C1207, as well as MARV and SCRV, should be assigned to a new rhabdovirus genus.
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Thermal characterization of magnetically aligned carbonyl iron/agar composites.
Diaz-Bleis, D; Vales-Pinzón, C; Freile-Pelegrín, Y; Alvarado-Gil, J J
2014-01-01
Composites of magnetic particles into polymeric matrices have received increasing research interest due to their capacity to respond to external magnetic or electromagnetic fields. In this study, agar from Gelidium robustum has been chosen as natural biocompatible polymer to build the matrix of the magnetic carbonyl iron particles (CIP) for their uses in biomedical fields. Heat transfer behavior of the CIP-agar composites containing different concentrations (5, 10, 15, 20, 25 and 30% w/w) of magnetically aligned and non-aligned CIP in the agar matrix was studied using photothermal radiometry (PTR) in the back-propagation emission configuration. The morphology of the CIP-agar composites with aligned and non-aligned CIP under magnetic field was also evaluated by scanning electron microscopy (SEM). The results revealed a dominant effect of CIP concentration over the alignment patterns induced by the magnetic field, which agrees with the behavior of the thermal diffusivity and thermal conductivity. Agar served as a perfect matrix to be used with CIP, and CIP-agar composites magnetically aligned at 20% CIP concentration can be considered as promising 'smart' material for hyperthermia treatments in the biomedical field. Copyright © 2013 Elsevier Ltd. All rights reserved.
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Sugimoto, K; Williamson, R E; Wasteneys, G O
2000-12-01
This article explores root epidermal cell elongation and its dependence on two structural elements of cells, cortical microtubules and cellulose microfibrils. The recent identification of Arabidopsis morphology mutants with putative cell wall or cytoskeletal defects demands a procedure for examining and comparing wall architecture and microtubule organization patterns in this species. We developed methods to examine cellulose microfibrils by field emission scanning electron microscopy and microtubules by immunofluorescence in essentially intact roots. We were able to compare cellulose microfibril and microtubule alignment patterns at equivalent stages of cell expansion. Field emission scanning electron microscopy revealed that Arabidopsis root epidermal cells have typical dicot primary cell wall structure with prominent transverse cellulose microfibrils embedded in pectic substances. Our analysis showed that microtubules and microfibrils have similar orientation only during the initial phase of elongation growth. Microtubule patterns deviate from a predominantly transverse orientation while cells are still expanding, whereas cellulose microfibrils remain transverse until well after expansion finishes. We also observed microtubule-microfibril alignment discord before cells enter their elongation phase. This study and the new technology it presents provide a starting point for further investigations on the physical properties of cell walls and their mechanisms of assembly.
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Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families
Salinas, Natalia; Tennessen, Jacob A.; Zurn, Jason D.; Sargent, Daniel James; Hancock, James; Bassil, Nahla V.
2017-01-01
Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria × ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. × ananassa chromosomal regions derived from diploid ancestor F. vesca. PMID:28875078
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Template-Based Modeling of Protein-RNA Interactions
Zheng, Jinfang; Kundrotas, Petras J.; Vakser, Ilya A.
2016-01-01
Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes. PMID:27662342
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ERIC Educational Resources Information Center
Edwards, Nazeem
2010-01-01
I report on an analysis of the alignment between the South African Grade 12 Physical Sciences core curriculum content and the exemplar papers of 2008, and the final examination papers of 2008 and 2009. A two-dimensional table was used for both the curriculum and the examination in order to calculate the Porter alignment index, which indicates the…
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Okada, Eijiro; Ichihara, Daisuke; Chiba, Kazuhiro; Toyama, Yoshiaki; Fujiwara, Hirokazu; Momoshima, Suketaka; Nishiwaki, Yuji; Hashimoto, Takeshi; Ogawa, Jun; Watanabe, Masahiko; Takahata, Takeshi
2009-01-01
There have been few studies that investigated and clarified the relationships between progression of degenerative changes and sagittal alignment of the cervical spine. The objective of the study was to longitudinally evaluate the relationships among progression of degenerative changes of the cervical spine with age, the development of clinical symptoms and sagittal alignment of the cervical spine in healthy subjects. Out of 497 symptom-free volunteers who underwent MRI and plain radiography of the cervical spine between 1994 and 1996, 113 subjects (45 males and 68 females) who responded to our contacts were enrolled. All subjects underwent another MRI at an average of 11.3 years after the initial study. Their mean age at the time of the initial imaging was 36.6 ± 14.5 years (11–65 years). The items evaluated on MRI were (1) decrease in signal intensity of the intervertebral disks, (2) posterior disk protrusion, and (3) disk space narrowing. Each item was evaluated using a numerical grading system. The subjects were divided into four groups according to the age and sagittal alignment of the cervical spine, i.e., subjects under or over the age of 40 years, and subjects with the lordosis or non-lordosis type of sagittal alignment of the cervical spine. During the 10-year period, progression of decrease in signal intensity of the disk, posterior disk protrusion, and disk space narrowing were recognized in 64.6, 65.5, and 28.3% of the subjects, respectively. Progression of posterior disk protrusion was significantly more frequent in subjects over 40 years of age with non-lordosis type of sagittal alignment. Logistic regression analysis revealed that stiff shoulder was closely correlated with females (P = 0.001), and that numbness of the upper extremity was closely correlated with age (P = 0.030) and male (P = 0.038). However, no significant correlation between the sagittal alignment of the cervical spine and clinical symptoms was detected. Sagittal alignment of the cervical spine had some impact on the progression of degenerative changes of the cervical spine with aging; however, it had no correlation with the occurrence of future clinical symptoms. PMID:19609784
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Raveendran, Rajkumar Nallour; Babu, Raiju J; Hess, Robert F; Bobier, William R
2014-03-01
To test the hypothesis that fixational stability of the amblyopic eye in strabismics will improve when viewing provides both bifoveal fixation and reduced inter-ocular suppression by reducing the contrast to the fellow eye. Seven strabismic amblyopes (Age: 29.2 ± 9 years; five esotropes and two exotropes) showing clinical characteristics of central suppression were recruited. Interocular suppression was measured by a global motion task. For each participant, a balance point was determined which defined contrast levels for each eye where binocular combination was optimal (interocular suppression minimal). When the balance point could not be determined, this participant was excluded. Bifoveal fixation was established by ocular alignment using a haploscope. Participants dichoptically viewed similar targets (a cross of 2.3° surrounded by a square of 11.3°) at 40 cm. Target contrasts presented to each eye were either high contrast (100% to both eyes) or balanced contrast (attenuated contrast in the fellow fixing eye). Fixation stability was measured over a 5 min period and quantified using bivariate contour ellipse areas in four different binocular conditions; unaligned/high contrast, unaligned/balance point, aligned/high contrast and aligned/balance point. Fixation stability was also measured in six control subjects (Age: 25.3 ± 4 years). Bifoveal fixation in the strabismics was transient (58.15 ± 15.7 s). Accordingly, fixational stability was analysed over the first 30 s using repeated measures anova. Post hoc analysis revealed that for the amblyopic subjects, the fixational stability of the amblyopic eye was significantly improved in aligned/high contrast (p = 0.01) and aligned/balance point (p < 0.01) conditions. Fixational stability of the fellow fixing eye was not different statistically across conditions. Bivariate contour ellipse areas of the amblyopic and fellow fixing eyes were therefore averaged for each amblyope in the four conditions and compared with normals. This averaged bivariate contour ellipse area was significantly greater (reduced fixational stability, p = 0.04) in amblyopes compared to controls except in the case of aligned and balanced contrast (aligned/balance point, p = 0.19). Fixation stability in the amblyopic eye appears to improve with bifoveal fixation and reduced interocular suppression. However, once initiated, bifoveal fixation is transient with the strabismic eye drifting away from foveal alignment, thereby increasing the angle of strabismus. © 2014 The Authors Ophthalmic & Physiological Optics © 2014 The College of Optometrists.
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NASA Technical Reports Server (NTRS)
Clauer, C. R.; Banks, P. M.
1986-01-01
The electrical coupling between the solar wind, magnetosphere, and ionosphere is studied. The coupling is analyzed using observations of high-latitude ion convection measured by the Sondre Stromfjord radar in Greenland and a computer simulation. The computer simulation calculates the ionospheric electric potential distribution for a given configuration of field-aligned currents and conductivity distribution. The technique for measuring F-region in velocities at high time resolution over a large range of latitudes is described. Variations in the currents on ionospheric plasma convection are examined using a model of field-aligned currents linking the solar wind with the dayside, high-latitude ionosphere. The data reveal that high-latitude ionospheric convection patterns, electric fields, and field-aligned currents are dependent on IMF orientation; it is observed that the electric field, which drives the F-region plasma curve, responds within about 14 minutes to IMF variations in the magnetopause. Comparisons of the simulated plasma convection with the ion velocity measurements reveal good correlation between the data.
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Modifying the morphology and properties of aligned CNT foams through secondary CNT growth.
Faraji, Shaghayegh; Stano, Kelly; Akyildiz, Halil; Yildiz, Ozkan; Jur, Jesse S; Bradford, Philip D
2018-07-20
In this work, we report for the first time, growth of secondary carbon nanotubes (CNTs) throughout a three-dimensional assembly of CNTs. The assembly of nanotubes was in the form of aligned CNT/carbon (ACNT/C) foams. These low-density CNT foams were conformally coated with an alumina buffer layer using atomic layer deposition. Chemical vapor deposition was further used to grow new CNTs. The CNT foam's extremely high porosity allowed for growth of secondary CNTs inside the bulk of the foams. Due to the heavy growth of new nanotubes, density of the foams increased more than 2.5 times. Secondary nanotubes had the same graphitic quality as the primary CNTs. Microscopy and chemical analysis revealed that the thickness of the buffer layer affected the diameter, nucleation density as well as growth uniformity across the thickness of the foams. The effects of secondary nanotubes on the compressive mechanical properties of the foams was also investigated.
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Dynamic switching mechanisms of a CC chemokine, CCL5 (RANTES). A simulation study
NASA Astrophysics Data System (ADS)
Peter, Emanuel; Pivkin, Igor
CCL5 (RANTES) belongs to the class of pro-inflammatory chemokines which are part of the human immune-response. It is known to activate leukocytes through its associated chemokine receptor 5 (CCR5) and plays a key role in several malignancies, including HIV-1 infections and cancer. In this talk, we present our results from enhanced sampling simulations of the CCL5 (RANTES) monomer. We find that this protein can adopt 2 different conformations : a globular form, with an orthogonal alignment of the N-terminal part, and a 'cis' form, in which the N-terminus is aligned parallel to the β-strand interface. A detailed analysis of the structure reveals that each of these states is stabilized by salt-bridges along the sequence, and corresponds to a defined dihedral-geometry of the 2 disulfide bridges Cys10-34 and Cys11-50. We derive a uniform distribution of transitions from the globular form of CCL5 (RANTES), and find that each of the main conformers adopts different electrostatic patterns.
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Modifying the morphology and properties of aligned CNT foams through secondary CNT growth
NASA Astrophysics Data System (ADS)
Faraji, Shaghayegh; Stano, Kelly; Akyildiz, Halil; Yildiz, Ozkan; Jur, Jesse S.; Bradford, Philip D.
2018-07-01
In this work, we report for the first time, growth of secondary carbon nanotubes (CNTs) throughout a three-dimensional assembly of CNTs. The assembly of nanotubes was in the form of aligned CNT/carbon (ACNT/C) foams. These low-density CNT foams were conformally coated with an alumina buffer layer using atomic layer deposition. Chemical vapor deposition was further used to grow new CNTs. The CNT foam’s extremely high porosity allowed for growth of secondary CNTs inside the bulk of the foams. Due to the heavy growth of new nanotubes, density of the foams increased more than 2.5 times. Secondary nanotubes had the same graphitic quality as the primary CNTs. Microscopy and chemical analysis revealed that the thickness of the buffer layer affected the diameter, nucleation density as well as growth uniformity across the thickness of the foams. The effects of secondary nanotubes on the compressive mechanical properties of the foams was also investigated.
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McCormick, Ashlee; Fisher, Karen; Brierley, Gary
2015-04-15
Promoting community support in rehabilitation efforts through incorporation of aesthetic considerations is an important component of environmental management. This research utilised a small-scale survey methodology to explore relationships among the ecological and morphological goals of scientists and the aesthetic goals of the public using the Twin Streams Catchment, Auckland, New Zealand, as a case study. Analyses using a linear model and a generalised linear mixed model showed statistically significant relationships between perceived naturalness of landscapes and their aesthetic ratings, and among ratings of perceived naturalness and ecological integrity and morphological condition. Expert measures of health and the aesthetic evaluations of the public were well aligned, indicating public preferences for landscapes of high ecological integrity with good morphological condition. Further analysis revealed participants used 'cues to care' to rate naturalness. This suggests that environmental education endeavours could further align values with these cues in efforts to enhance approaches to landscape sustainability. Copyright © 2014 Elsevier Ltd. All rights reserved.
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NASA Technical Reports Server (NTRS)
He, Maosheng; Vogt, Joachim; Luehr, Hermann; Sorbalo, Eugen; Blagau, Adrian; Le, Guan; Lu, Gang
2012-01-01
Ten years of CHAMP magnetic field measurements are integrated into MFACE, a model of field-aligned currents (FACs) using empirical orthogonal functions (EOFs). EOF1 gives the basic Region-1/Region-2 pattern varying mainly with the interplanetary magnetic field Bz component. EOF2 captures separately the cusp current signature and By-related variability. Compared to existing models, MFACE yields significantly better spatial resolution, reproduces typically observed FAC thickness and intensity, improves on the magnetic local time (MLT) distribution, and gives the seasonal dependence of FAC latitudes and the NBZ current signature. MFACE further reveals systematic dependences on By, including 1) Region-1/Region-2 topology modifications around noon; 2) imbalance between upward and downward maximum current density; 3) MLT location of the Harang discontinuity. Furthermore, our procedure allows quantifying response times of FACs to solar wind driving at the bow shock nose: we obtain 20 minutes and 35-40 minutes lags for the FAC density and latitude, respectively.
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B-MIC: An Ultrafast Three-Level Parallel Sequence Aligner Using MIC.
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.
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ZHENG, ZHENZHEN; CHOU, CHING-SHAN; YI, TAU-MU; NIE, QING
2013-01-01
Cell polarization, in which substances previously uniformly distributed become asymmetric due to external or/and internal stimulation, is a fundamental process underlying cell mobility, cell division, and other polarized functions. The yeast cell S. cerevisiae has been a model system to study cell polarization. During mating, yeast cells sense shallow external spatial gradients and respond by creating steeper internal gradients of protein aligned with the external cue. The complex spatial dynamics during yeast mating polarization consists of positive feedback, degradation, global negative feedback control, and cooperative effects in protein synthesis. Understanding such complex regulations and interactions is critical to studying many important characteristics in cell polarization including signal amplification, tracking dynamic signals, and potential trade-off between achieving both objectives in a robust fashion. In this paper, we study some of these questions by analyzing several models with different spatial complexity: two compartments, three compartments, and continuum in space. The step-wise approach allows detailed characterization of properties of the steady state of the system, providing more insights for biological regulations during cell polarization. For cases without membrane diffusion, our study reveals that increasing the number of spatial compartments results in an increase in the number of steady-state solutions, in particular, the number of stable steady-state solutions, with the continuum models possessing infinitely many steady-state solutions. Through both analysis and simulations, we find that stronger positive feedback, reduced diffusion, and a shallower ligand gradient all result in more steady-state solutions, although most of these are not optimally aligned with the gradient. We explore in the different settings the relationship between the number of steady-state solutions and the extent and accuracy of the polarization. Taken together these results furnish a detailed description of the factors that influence the tradeoff between a single correctly aligned but poorly polarized stable steady-state solution versus multiple more highly polarized stable steady-state solutions that may be incorrectly aligned with the external gradient. PMID:21936604
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Lombardo, Luca; Arreghini, Angela; Maccarrone, Roberta; Bianchi, Anna; Scalia, Santo; Siciliani, Giuseppe
2015-01-01
The aim was to assess and compare absorbance and transmittance values of three types of clear orthodontic aligners before and after two cycles of in vitro aging. Nine samples of orthodontic aligners from three different manufacturers (Invisalign, Align Technology, Santa Clara, CA, USA; All-In, Micerium, Avegno, GE, Italy; F22 Aligner, Sweden & Martina, Due Carrare, PD, Italy) were selected, and each sample was subjected to spectrophotometry analysis of both its transmittance and absorbance a total of 27 times. Samples were subsequently aged in vitro at a constant temperature in artificial saliva supplemented with food colouring for two cycles of 14 days each. The spectrophotometry protocol was then repeated, and the resulting data were analysed and compared by means of ANOVA (p < 0.05). All types of aligners tested yielded lower transmittance and higher absorbance values after aging, but the difference was not significant in any case. That being said, the F22 aligners were found to be most transparent, both before and after aging, followed by Invisalign and All-In, and these differences were statistically significant. Commercial aligners possess significantly different optical, and therefore aesthetic, properties, both as delivered and following aging.
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Strain-induced alignment and phase behavior of blue phase liquid crystals confined to thin films.
Bukusoglu, Emre; Martinez-Gonzalez, Jose A; Wang, Xiaoguang; Zhou, Ye; de Pablo, Juan J; Abbott, Nicholas L
2017-12-06
We report on the influence of surface confinement on the phase behavior and strain-induced alignment of thin films of blue phase liquid crystals (BPs). Confining surfaces comprised of bare glass, dimethyloctadecyl [3-(trimethoxysilyl)propyl] ammonium chloride (DMOAP)-functionalized glass, or polyvinyl alcohol (PVA)-coated glass were used with or without mechanically rubbing to influence the azimuthal anchoring of the BPs. These experiments reveal that confinement can change the phase behavior of the BP films. For example, in experiments performed with rubbed-PVA surfaces, we measured the elastic strain of the BPs to change the isotropic-BPII phase boundary, suppressing formation of BPII for film thicknesses incommensurate with the BPII lattice. In addition, we observed strain-induced alignment of the BPs to exhibit a complex dependence on both the surface chemistry and azimuthal alignment of the BPs. For example, when using bare glass surfaces causing azimuthally degenerate and planar anchoring, BPI oriented with (110) planes of the unit cell parallel to the contacting surfaces for thicknesses below 3 μm but transitioned to an orientation with (200) planes aligned parallel to the contacting surfaces for thicknesses above 4 μm. In contrast, BPI aligned with (110) planes parallel to confining surfaces for all other thicknesses and surface treatments, including bare glass with uniform azimuthal alignment. Complementary simulations based on minimization of the total free energy (Landau-de Gennes formalism) confirmed a thickness-dependent reorientation due to strain of BPI unit cells within a window of surface anchoring energies and in the absence of uniform azimuthal alignment. In contrast to BPI, BPII did not exhibit thickness-dependent orientations but did exhibit orientations that were dependent on the surface chemistry, a result that was also captured in simulations by varying the anchoring energies. Overall, the results in this paper reveal that the orientations assumed by BPs in thin films reflect a complex interplay of surface interactions and elastic energies associated with strain of the BP lattice. The results also provide new principles and methods to control the structure and properties of BP thin films, which may find use in BP-templated material synthesis, and BP-based optical and electronic devices.
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Sex differences in knee joint loading: Cross-sectional study in geriatric population.
Ro, Du Hyun; Lee, Dong Yeon; Moon, Giho; Lee, Sahnghoon; Seo, Sang Gyo; Kim, Seong Hwan; Park, In Woong; Lee, Myung Chul
2017-06-01
This study investigated sex differences in knee biomechanics and investigated determinants for difference in a geriatric population. Age-matched healthy volunteers (42 males and 42 females, average age 65 years) without knee OA were included in the study. Subjects underwent physical examination on their knee and standing full-limb radiography for anthropometric measurements. Linear, kinetic, and kinematic parameters were compared using a three-dimensional, 12-camera motion capture system. Gait parameters were evaluated and determinants for sex difference were evaluated with multiple regression analysis. Females had a higher peak knee adduction moment (KAM) during gait (p = 0.004). Females had relatively wider pelvis and narrower step width (both p < 0.001). However, coronal knee alignment was not significantly different between the sexes. Multiple regression analysis revealed that coronal alignment (b = 0.014, p < 0.001), step width (b = -0.010, p = 0.011), and pelvic width/height ratio (b = 1.703, p = 0.046) were significant determinants of peak KAM. Because coronal alignment was not different between the sexes, narrow step width and high pelvic width/height ratio of female were the main contributors to higher peak KAM in females. Sex differences in knee biomechanics were present in the geriatric population. Increased mechanical loading on the female knee, which was associated with narrow step width and wide pelvis, may play an important role in future development and progression of OA. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:1283-1289, 2017. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.
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Barroca, Nathalie; Marote, Ana; Vieira, Sandra I; Almeida, Abílio; Fernandes, Maria H V; Vilarinho, Paula M; da Cruz E Silva, Odete A B
2018-07-01
Tissue engineering is evolving towards the production of smart platforms exhibiting stimulatory cues to guide tissue regeneration. This work explores the benefits of electrical polarization to produce more efficient neural tissue engineering platforms. Poly (l-lactic) acid (PLLA)-based scaffolds were prepared as solvent cast films and electrospun aligned nanofibers, and electrically polarized by an in-lab built corona poling device. The characterization of the platforms by thermally stimulated depolarization currents reveals a polarization of 60 × 10 -10 C cm -2 that is stable on poled electrospun nanofibers for up to 6 months. Further in vitro studies using neuroblastoma cells reveals that platforms' polarization potentiates Retinoic Acid-induced neuronal differentiation. Additionally, in differentiating embryonic cortical neurons, poled aligned nanofibers further increased neurite outgrowth by 30% (+70 μm) over non-poled aligned nanofibers, and by 50% (+100 μm) over control conditions. Therefore, the synergy of topographical cues and electrical polarization of poled aligned nanofibers places them as promising biocompatible and bioactive platforms for neural tissue regeneration. Given their long lasting induced polarization, these PLLA poled nanofibrous scaffolds can be envisaged as therapeutic devices of long shelf life for neural repair applications. Copyright © 2018 Elsevier B.V. All rights reserved.
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The influence of atomic alignment on absorption and emission spectroscopy
NASA Astrophysics Data System (ADS)
Zhang, Heshou; Yan, Huirong; Richter, Philipp
2018-06-01
Spectroscopic observations play essential roles in astrophysics. They are crucial for determining physical parameters in the universe, providing information about the chemistry of various astronomical environments. The proper execution of the spectroscopic analysis requires accounting for all the physical effects that are compatible to the signal-to-noise ratio. We find in this paper the influence on spectroscopy from the atomic/ground state alignment owing to anisotropic radiation and modulated by interstellar magnetic field, has significant impact on the study of interstellar gas. In different observational scenarios, we comprehensively demonstrate how atomic alignment influences the spectral analysis and provide the expressions for correcting the effect. The variations are even more pronounced for multiplets and line ratios. We show the variation of the deduced physical parameters caused by the atomic alignment effect, including alpha-to-iron ratio ([X/Fe]) and ionisation fraction. Synthetic observations are performed to illustrate the visibility of such effect with current facilities. A study of PDRs in ρ Ophiuchi cloud is presented to demonstrate how to account for atomic alignment in practice. Our work has shown that due to its potential impact, atomic alignment has to be included in an accurate spectroscopic analysis of the interstellar gas with current observational capability.
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Ogilvie, Lesley A.; Caplin, Jonathan; Dedi, Cinzia; Diston, David; Cheek, Elizabeth; Bowler, Lucas; Taylor, Huw; Ebdon, James; Jones, Brian V.
2012-01-01
Bacteriophage associated with the human gut microbiome are likely to have an important impact on community structure and function, and provide a wealth of biotechnological opportunities. Despite this, knowledge of the ecology and composition of bacteriophage in the gut bacterial community remains poor, with few well characterized gut-associated phage genomes currently available. Here we describe the identification and in-depth (meta)genomic, proteomic, and ecological analysis of a human gut-specific bacteriophage (designated φB124-14). In doing so we illuminate a fraction of the biological dark matter extant in this ecosystem and its surrounding eco-genomic landscape, identifying a novel and uncharted bacteriophage gene-space in this community. φB124-14 infects only a subset of closely related gut-associated Bacteroides fragilis strains, and the circular genome encodes functions previously found to be rare in viral genomes and human gut viral metagenome sequences, including those which potentially confer advantages upon phage and/or host bacteria. Comparative genomic analyses revealed φB124-14 is most closely related to φB40-8, the only other publically available Bacteroides sp. phage genome, whilst comparative metagenomic analysis of both phage failed to identify any homologous sequences in 136 non-human gut metagenomic datasets searched, supporting the human gut-specific nature of this phage. Moreover, a potential geographic variation in the carriage of these and related phage was revealed by analysis of their distribution and prevalence within 151 human gut microbiomes and viromes from Europe, America and Japan. Finally, ecological profiling of φB124-14 and φB40-8, using both gene-centric alignment-driven phylogenetic analyses, as well as alignment-free gene-independent approaches was undertaken. This not only verified the human gut-specific nature of both phage, but also indicated that these phage populate a distinct and unexplored ecological landscape within the human gut microbiome. PMID:22558115
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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
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Decoster, Laura C; Burns, Matthew F; Swartz, Erik E; Murthi, Dinakar S; Hernandez, Adam E; Vailas, James C; Isham, Linda L
2012-04-15
Descriptive laboratory study. To determine whether the placement of padding beneath the occiput after helmet removal is an effective intervention to maintain neutral sagittal cervical spine alignment in a position comparable with the helmeted condition. Current on-field recommendations for managing football athletes with suspected cervical spine injuries call for face mask removal, rather than helmet removal, because the combination of helmet and shoulder pads has been shown to maintain neutral cervical alignment. Therefore, in cases when helmet removal is required, recommendations also call for shoulder pad removal. Because removal of equipment causes motion, any technique that postpones the need to remove the shoulder pads would reduce prehospital motion. Four lateral radiographs of 20 male participants were obtained (age = 23.6 ± 2.7 years). Radiographs of participants wearing shoulder pads and helmet were first obtained. The helmet was removed and radiographs of participants with occipital padding were obtained immediately and 20 minutes later and finally without occipital padding. Cobb angle measurements for C2-C6 vertebral segments were determined by an orthopedic spine surgeon blinded to the study's purpose. Intraobserver reliability was determined using intraclass coefficient analysis. Measurements were analyzed using a 1×4 repeated-measures analysis of variance and post hoc pairwise comparisons with Bonferroni correction. Intraobserver analysis showed excellent reliability (intraclass correlation = 1.0; 95% confidence interval [CI], 0.999-1.0). Repeated-measures analysis of variance detected significant differences (F(3,17) = 13.34; P < 0.001). Pairwise comparisons revealed no differences in cervical alignment (all measurements reported reflect lordosis) when comparing the baseline helmeted condition (10.1° ± 8.7°; 95% CI, 6.0-14.1) with the padded conditions. Measurements taken after removal of occipital padding (14.4° ± 8.1°; 95% CI, 10.6-18.2) demonstrated a significant increase in cervical lordosis compared with the immediate padded measurement (9.5° ± 6.9°; 95% CI, 6.3-12.7; P = 0.011) and the 20-minute padded measurement (6.5° ± 6.8°; 95% CI, 3.4-9.7; P < 0.001). Although face mask removal remains the standard, if it becomes necessary to remove the football helmet in the field, occipital padding (along with full body/head immobilization techniques) may be used to limit cervical lordosis, allowing safe delay of shoulder pad removal.
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Onorbit IMU alignment error budget
NASA Technical Reports Server (NTRS)
Corson, R. W.
1980-01-01
The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.
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Tobi, Dror
2017-08-01
A new algorithm for comparison of protein dynamics is presented. Compared protein structures are superposed and their modes of motions are calculated using the anisotropic network model. The obtained modes are aligned using the dynamic programming algorithm of Needleman and Wunsch, commonly used for sequence alignment. Dynamical comparison of hemoglobin in the T and R2 states reveals that the dynamics of the allosteric effector 2,3-bisphosphoglycerate binding site is different in the two states. These differences can contribute to the selectivity of the effector to the T state. Similar comparison of the ionotropic glutamate receptor in the kainate+(R,R)-2b and ZK bound states reveals that the kainate+(R,R)-2b bound states slow modes describe upward motions of ligand binding domain and the transmembrane domain regions. Such motions may lead to the opening of the receptor. The upper lobes of the LBDs of the ZK bound state have a smaller interface with the amino terminal domains above them and have a better ability to move together. The present study exemplifies the use of dynamics comparison as a tool to study protein function. Proteins 2017; 85:1507-1517. © 2014 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
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Boone, David A; Kobayashi, Toshiki; Chou, Teri G; Arabian, Adam K; Coleman, Kim L; Orendurff, Michael S; Zhang, Ming
2013-04-01
Alignment - the process and measured orientation of the prosthetic socket relative to the foot - is important for proper function of a transtibial prosthesis. Prosthetic alignment is performed by prosthetists using visual gait observation and amputees' feedback. The aim of this study was to investigate the effect of transtibial prosthesis malalignment on the moments measured at the base of the socket: the socket reaction moments. Eleven subjects with transtibial amputation were recruited from the community. An instrumented prosthesis alignment component was used to measure socket reaction moments during ambulation under 17 alignment conditions, including nominally aligned using conventional clinical methods, and angle perturbations of 3° and 6° (flexion, extension, abduction, and adduction) and translation perturbations of 5mm and 10mm (anterior, posterior, lateral, and medial) referenced from the nominal alignment. Coronal alignment perturbations caused systematic changes in the coronal socket reaction moments. All angle and translation perturbations revealed statistically significant differences on coronal socket reaction moments compared to the nominal alignment at 30% and 75% of stance phase (P<0.05). The effect of sagittal alignment perturbations on sagittal socket reaction moments was not as responsive as that of the coronal perturbations. The sagittal angle and translation perturbations of the socket led to statistically significant changes in minimum moment, maximum moment, and moments at 45% of stance phase in the sagittal plane. Therefore, malalignment affected the socket reaction moments in amputees with transtibial prostheses. Copyright © 2012 Elsevier B.V. All rights reserved.
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Tan, Yen Hock; Huang, He; Kihara, Daisuke
2006-08-15
Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more experimentally solved structures are available as templates for protein structure modeling. Toward this end, recent structure prediction methods employ profile-profile alignments, and various ways of aligning two profiles have been developed. More fundamentally, a better amino acid similarity matrix can improve a profile itself; thereby resulting in more accurate profile-profile alignments. Here we have developed novel amino acid similarity matrices from knowledge-based amino acid contact potentials. Contact potentials are used because the contact propensity to the other amino acids would be one of the most conserved features of each position of a protein structure. The derived amino acid similarity matrices are tested on benchmark alignments at three different levels, namely, the family, the superfamily, and the fold level. Compared to BLOSUM45 and the other existing matrices, the contact potential-based matrices perform comparably in the family level alignments, but clearly outperform in the fold level alignments. The contact potential-based matrices perform even better when suboptimal alignments are considered. Comparing the matrices themselves with each other revealed that the contact potential-based matrices are very different from BLOSUM45 and the other matrices, indicating that they are located in a different basin in the amino acid similarity matrix space.
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Johnson, Jessica L; Chauvin, Sheila
2016-12-25
Objective. To examine the extent to which reflective essays written by graduating pharmacy students revealed professional identity formation and self-authorship development. Design. Following a six-week advanced pharmacy practice experience (APPE) grounded in Baxter-Magolda's Learning Partnerships Model of self-authorship development, students completed a culminating reflective essay on their rotation experiences and professional identity formation. Assessment. Thematic and categorical analysis of 41 de-identified essays revealed nine themes and evidence of all Baxter-Magolda's domains and phases of self-authorship. Analysis also suggested relationships between self-authorship and pharmacist professional identity formation. Conclusion. Results suggest that purposeful structuring of learning experiences can facilitate professional identity formation. Further, Baxter-Magolda's framework for self-authorship and use of the Learning Partnership Model seem to align well with pharmacist professional identify formation. Results of this study could be used by pharmacy faculty members when considering how to fill gaps in professional identity formation in future course and curriculum development.
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Chauvin, Sheila
2016-01-01
Objective. To examine the extent to which reflective essays written by graduating pharmacy students revealed professional identity formation and self-authorship development. Design. Following a six-week advanced pharmacy practice experience (APPE) grounded in Baxter-Magolda’s Learning Partnerships Model of self-authorship development, students completed a culminating reflective essay on their rotation experiences and professional identity formation. Assessment. Thematic and categorical analysis of 41 de-identified essays revealed nine themes and evidence of all Baxter-Magolda’s domains and phases of self-authorship. Analysis also suggested relationships between self-authorship and pharmacist professional identity formation. Conclusion. Results suggest that purposeful structuring of learning experiences can facilitate professional identity formation. Further, Baxter-Magolda’s framework for self-authorship and use of the Learning Partnership Model seem to align well with pharmacist professional identify formation. Results of this study could be used by pharmacy faculty members when considering how to fill gaps in professional identity formation in future course and curriculum development. PMID:28179721
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Pourabed, Ehsan; Ghane Golmohamadi, Farzan; Soleymani Monfared, Peyman; Razavi, Seyed Morteza; Shobbar, Zahra-Sadat
2015-01-01
The basic leucine zipper (bZIP) family is one of the largest and most diverse transcription factors in eukaryotes participating in many essential plant processes. We identified 141 bZIP proteins encoded by 89 genes from the Hordeum vulgare genome. HvbZIPs were classified into 11 groups based on their DNA-binding motif. Amino acid sequence alignment of the HvbZIPs basic-hinge regions revealed some highly conserved residues within each group. The leucine zipper heptads were analyzed predicting their dimerization properties. 34 conserved motifs were identified outside the bZIP domain. Phylogenetic analysis indicated that major diversification within the bZIP family predated the monocot/dicot divergence, although intra-species duplication and parallel evolution seems to be occurred afterward. Localization of HvbZIPs on the barley chromosomes revealed that different groups have been distributed on seven chromosomes of barley. Six types of intron pattern were detected within the basic-hinge regions. Most of the detected cis-elements in the promoter and UTR sequences were involved in seed development or abiotic stress response. Microarray data analysis revealed differential expression pattern of HvbZIPs in response to ABA treatment, drought, and cold stresses and during barley grain development and germination. This information would be helpful for functional characterization of bZIP transcription factors in barley.
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Local-global alignment for finding 3D similarities in protein structures
Zemla, Adam T [Brentwood, CA
2011-09-20
A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.
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SSAW: A new sequence similarity analysis method based on the stationary discrete wavelet transform.
Lin, Jie; Wei, Jing; Adjeroh, Donald; Jiang, Bing-Hua; Jiang, Yue
2018-05-02
Alignment-free sequence similarity analysis methods often lead to significant savings in computational time over alignment-based counterparts. A new alignment-free sequence similarity analysis method, called SSAW is proposed. SSAW stands for Sequence Similarity Analysis using the Stationary Discrete Wavelet Transform (SDWT). It extracts k-mers from a sequence, then maps each k-mer to a complex number field. Then, the series of complex numbers formed are transformed into feature vectors using the stationary discrete wavelet transform. After these steps, the original sequence is turned into a feature vector with numeric values, which can then be used for clustering and/or classification. Using two different types of applications, namely, clustering and classification, we compared SSAW against the the-state-of-the-art alignment free sequence analysis methods. SSAW demonstrates competitive or superior performance in terms of standard indicators, such as accuracy, F-score, precision, and recall. The running time was significantly better in most cases. These make SSAW a suitable method for sequence analysis, especially, given the rapidly increasing volumes of sequence data required by most modern applications.
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Attenuation-emission alignment in cardiac PET∕CT based on consistency conditions
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
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kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences
2017-01-01
Abstract Motifs of only 1–4 letters can play important roles when present at key locations within macromolecules. Because existing motif-discovery tools typically miss these position-specific short motifs, we developed kpLogo, a probability-based logo tool for integrated detection and visualization of position-specific ultra-short motifs from a set of aligned sequences. kpLogo also overcomes the limitations of conventional motif-visualization tools in handling positional interdependencies and utilizing ranked or weighted sequences increasingly available from high-throughput assays. kpLogo can be found at http://kplogo.wi.mit.edu/. PMID:28460012
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DNA Translator and Aligner: HyperCard utilities to aid phylogenetic analysis of molecules.
Eernisse, D J
1992-04-01
DNA Translator and Aligner are molecular phylogenetics HyperCard stacks for Macintosh computers. They manipulate sequence data to provide graphical gene mapping, conversions, translations and manual multiple-sequence alignment editing. DNA Translator is able to convert documented GenBank or EMBL documented sequences into linearized, rescalable gene maps whose gene sequences are extractable by clicking on the corresponding map button or by selection from a scrolling list. Provided gene maps, complete with extractable sequences, consist of nine metazoan, one yeast, and one ciliate mitochondrial DNAs and three green plant chloroplast DNAs. Single or multiple sequences can be manipulated to aid in phylogenetic analysis. Sequences can be translated between nucleic acids and proteins in either direction with flexible support of alternate genetic codes and ambiguous nucleotide symbols. Multiple aligned sequence output from diverse sources can be converted to Nexus, Hennig86 or PHYLIP format for subsequent phylogenetic analysis. Input or output alignments can be examined with Aligner, a convenient accessory stack included in the DNA Translator package. Aligner is an editor for the manual alignment of up to 100 sequences that toggles between display of matched characters and normal unmatched sequences. DNA Translator also generates graphic displays of amino acid coding and codon usage frequency relative to all other, or only synonymous, codons for approximately 70 select organism-organelle combinations. Codon usage data is compatible with spreadsheet or UWGCG formats for incorporation of additional molecules of interest. The complete package is available via anonymous ftp and is free for non-commercial uses.
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Alignment control study for the solar optical telescope
NASA Technical Reports Server (NTRS)
1976-01-01
Analysis of the alignment and focus errors than can be tolerated, methods of sensing such errors, and mechanisms to make the necessary corrections were addressed. Alternate approaches and their relative merits were considered. The results of this study indicate that adequate alignment control can be achieved.
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DiCanio, Christian; Nam, Hosung; Whalen, Douglas H.; Timothy Bunnell, H.; Amith, Jonathan D.; García, Rey Castillo
2013-01-01
While efforts to document endangered languages have steadily increased, the phonetic analysis of endangered language data remains a challenge. The transcription of large documentation corpora is, by itself, a tremendous feat. Yet, the process of segmentation remains a bottleneck for research with data of this kind. This paper examines whether a speech processing tool, forced alignment, can facilitate the segmentation task for small data sets, even when the target language differs from the training language. The authors also examined whether a phone set with contextualization outperforms a more general one. The accuracy of two forced aligners trained on English (hmalign and p2fa) was assessed using corpus data from Yoloxóchitl Mixtec. Overall, agreement performance was relatively good, with accuracy at 70.9% within 30 ms for hmalign and 65.7% within 30 ms for p2fa. Segmental and tonal categories influenced accuracy as well. For instance, additional stop allophones in hmalign's phone set aided alignment accuracy. Agreement differences between aligners also corresponded closely with the types of data on which the aligners were trained. Overall, using existing alignment systems was found to have potential for making phonetic analysis of small corpora more efficient, with more allophonic phone sets providing better agreement than general ones. PMID:23967953
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DiCanio, Christian; Nam, Hosung; Whalen, Douglas H; Bunnell, H Timothy; Amith, Jonathan D; García, Rey Castillo
2013-09-01
While efforts to document endangered languages have steadily increased, the phonetic analysis of endangered language data remains a challenge. The transcription of large documentation corpora is, by itself, a tremendous feat. Yet, the process of segmentation remains a bottleneck for research with data of this kind. This paper examines whether a speech processing tool, forced alignment, can facilitate the segmentation task for small data sets, even when the target language differs from the training language. The authors also examined whether a phone set with contextualization outperforms a more general one. The accuracy of two forced aligners trained on English (hmalign and p2fa) was assessed using corpus data from Yoloxóchitl Mixtec. Overall, agreement performance was relatively good, with accuracy at 70.9% within 30 ms for hmalign and 65.7% within 30 ms for p2fa. Segmental and tonal categories influenced accuracy as well. For instance, additional stop allophones in hmalign's phone set aided alignment accuracy. Agreement differences between aligners also corresponded closely with the types of data on which the aligners were trained. Overall, using existing alignment systems was found to have potential for making phonetic analysis of small corpora more efficient, with more allophonic phone sets providing better agreement than general ones.
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Kemeny, Steven Frank; Clyne, Alisa Morss
2011-04-01
Fiber alignment plays a critical role in the structure and function of cells and tissues. While fiber alignment quantification is important to experimental analysis and several different methods for quantifying fiber alignment exist, many studies focus on qualitative rather than quantitative analysis perhaps due to the complexity of current fiber alignment methods. Speed and sensitivity were compared in edge detection and fast Fourier transform (FFT) for measuring actin fiber alignment in cells exposed to shear stress. While edge detection using matrix multiplication was consistently more sensitive than FFT, image processing time was significantly longer. However, when MATLAB functions were used to implement edge detection, MATLAB's efficient element-by-element calculations and fast filtering techniques reduced computation cost 100 times compared to the matrix multiplication edge detection method. The new computation time was comparable to the FFT method, and MATLAB edge detection produced well-distributed fiber angle distributions that statistically distinguished aligned and unaligned fibers in half as many sample images. When the FFT sensitivity was improved by dividing images into smaller subsections, processing time grew larger than the time required for MATLAB edge detection. Implementation of edge detection in MATLAB is simpler, faster, and more sensitive than FFT for fiber alignment quantification.
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BAYESIAN PROTEIN STRUCTURE ALIGNMENT.
Rodriguez, Abel; Schmidler, Scott C
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.
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Zhang, Qi; Zeng, Xin; Younkin, Sam; Kawli, Trupti; Snyder, Michael P; Keleş, Sündüz
2016-02-24
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments revolutionized genome-wide profiling of transcription factors and histone modifications. Although maturing sequencing technologies allow these experiments to be carried out with short (36-50 bps), long (75-100 bps), single-end, or paired-end reads, the impact of these read parameters on the downstream data analysis are not well understood. In this paper, we evaluate the effects of different read parameters on genome sequence alignment, coverage of different classes of genomic features, peak identification, and allele-specific binding detection. We generated 101 bps paired-end ChIP-seq data for many transcription factors from human GM12878 and MCF7 cell lines. Systematic evaluations using in silico variations of these data as well as fully simulated data, revealed complex interplay between the sequencing parameters and analysis tools, and indicated clear advantages of paired-end designs in several aspects such as alignment accuracy, peak resolution, and most notably, allele-specific binding detection. Our work elucidates the effect of design on the downstream analysis and provides insights to investigators in deciding sequencing parameters in ChIP-seq experiments. We present the first systematic evaluation of the impact of ChIP-seq designs on allele-specific binding detection and highlights the power of pair-end designs in such studies.
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2007-03-01
information dominance , Joint Network Operations (NETOPS) organizations need to be strategically aligned. As result, to enhance the capabilities-based effects of NETOPS and reduce our NETOP infrastructures susceptibility to compromise. Once the key organizations were identified, their strategic plans were analyzed using a structured content analysis framework. The results illustrated that the strategic plans were aligned with the community of interests tasking to conduct NETOPS. Further research is required into the strategic alignment beyond the strategic
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Hot spot dynamics in carbon nanotube array devices.
Engel, Michael; Steiner, Mathias; Seo, Jung-Woo T; Hersam, Mark C; Avouris, Phaedon
2015-03-11
We report on the dynamics of spatial temperature distributions in aligned semiconducting carbon nanotube array devices with submicrometer channel lengths. By using high-resolution optical microscopy in combination with electrical transport measurements, we observe under steady state bias conditions the emergence of time-variable, local temperature maxima with dimensions below 300 nm, and temperatures above 400 K. On the basis of time domain cross-correlation analysis, we investigate how the intensity fluctuations of the thermal radiation patterns are correlated with the overall device current. The analysis reveals the interdependence of electrical current fluctuations and time-variable hot spot formation that limits the overall device performance and, ultimately, may cause device degradation. The findings have implications for the future development of carbon nanotube-based technologies.
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[Hydrophidae identification through analysis on Cyt b gene barcode].
Liao, Li-xi; Zeng, Ke-wu; Tu, Peng-fei
2015-08-01
Hydrophidae, one of the precious traditional Chinese medicines, is generally drily preserved to prevent corruption, but it is hard to identify the species of Hydrophidae through the appearance because of the change due to the drying process. The identification through analysis on gene barcode, a new technique in species identification, can avoid the problem. The gene barcodes of the 6 species of Hydrophidae like Lapemis hardwickii were aquired through DNA extraction and gene sequencing. These barcodes were then in sequence alignment and test the identification efficency by BLAST. Our results revealed that the barcode sequences performed high identification efficiency, and had obvious difference between intra- and inter-species. These all indicated that Cyt b DNA barcoding can confirm the Hydrophidae identification.
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History of Science in the Physics Curriculum: A Directed Content Analysis of Historical Sources
NASA Astrophysics Data System (ADS)
Seker, Hayati; Guney, Burcu G.
2012-05-01
Although history of science is a potential resource for instructional materials, teachers do not have a tendency to use historical materials in their lessons. Studies showed that instructional materials should be adaptable and consistent with curriculum. This study purports to examine the alignment between history of science and the curriculum in the light of the facilitator model on the use of history of science in science teaching, and to expose possible difficulties in preparing historical materials. For this purpose, qualitative content analysis method was employed. Codes and themes were defined beforehand, with respect to levels and their sublevels of the model. The analysis revealed several problems with the alignment of historical sources for the physics curriculum: limited information about scientists' personal lives, the difficulty of linking with content knowledge, the lack of emphasis on scientific process in the physics curriculum, differences between chronology and sequence of topics, the lack of information about scientists' reasoning. Based on the findings of the analysis, it would be difficult to use original historical sources; educators were needed to simplify historical knowledge within a pedagogical perspective. There is a need for historical sources, like Harvard Case Histories in Experimental Science, since appropriate historical information to the curriculum objectives can only be obtained by simplifying complex information at the origin. The curriculum should leave opportunities for educators interested in history of science, even historical sources provides legitimate amount of information for every concepts in the curriculum.
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NASA Astrophysics Data System (ADS)
Akande, Amos A.; Rammutla, Koena E.; Moyo, Thomas; Osman, Nadir S. E.; Nkosi, Steven S.; Jafta, Charl J.; Mwakikunga, Bonex W.
2015-02-01
We report on the magnetic property of 0.67-WO3+0.33-VOx mixture film deposit on the corning glass substrate using the chemical sol-gel and atmospheric pressure chemical vapor deposition (APCVD) methods. The XRD and Raman spectroscopy confirm species of both materials, and the morphological studies with FIB-SEM and TEM reveal segregation of W and V atoms. XPS reveals that V4+ from VO2 forms only 11% of the film; V3+ in the form of V2O3 form 1% of the film, 21% is V5+ from V2O5 and 67% is given to W6+ from WO3. The analysis of the ESR data shows some sharp changes in the magnetism near the metal-to-insulator (MIT), which could be theoretically interpreted as the ordering or alignment of electron spins from net moment nature to parallel alignment of magnetic moment. The derivatives of magnetic susceptibility established the thermally induced magnetic property: two distinct transitions of 339 K for heating data and 338 K for cooling data for 151.2 mT field were obtained. Similar results were also obtained for 308.7 mT field, 336 K for heating data and 335 K for cooling data. VSM results confirm a paramagnetic phase with a small amount of magnetically ordered phase.
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Zhou, Yixuan; E, Yiwen; Xu, Xinlong; Li, Weilong; Wang, Huan; Zhu, Lipeng; Bai, Jintao; Ren, Zhaoyu; Wang, Li
2016-12-14
Spatial dispersion effect of aligned carbon nanotubes (CNTs) in the terahertz (THz) region has significance for both theoretical and applied consideration due to the unique intrinsically anisotropic physical properties of CNTs. Herein, we report the angular dependent reflection of p-polarized THz wave from vertically aligned multi-walled CNT arrays in both experiment and theory. The spectra indicate that the reflection depends on the film thickness of vertically aligned CNTs, the incident angle, and the frequency. The calculation model is based on the spatial dispersion effect of aligned CNTs and performed with effective impedance method and the Maxwell-Garnett approximation. The results fit well with the experiment when the thickness of CNT film is thin, which reveals a coherent superposition mechanism of the CNT surface reflection and CNTs/Si interface reflection. For thick CNT films, the CNTs/Si interface response determines the reflection at small incident angles, while the CNTs surface effect dominates at large incident angles. This work investigates the spatial dispersion effect of vertically aligned CNT arrays in the THz region, and paves a way for potential anisotropic THz applications based on CNTs with oblique incidence requirements.
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NASA Astrophysics Data System (ADS)
Zhou, Yixuan; Yiwen, E.; Xu, Xinlong; Li, Weilong; Wang, Huan; Zhu, Lipeng; Bai, Jintao; Ren, Zhaoyu; Wang, Li
2016-12-01
Spatial dispersion effect of aligned carbon nanotubes (CNTs) in the terahertz (THz) region has significance for both theoretical and applied consideration due to the unique intrinsically anisotropic physical properties of CNTs. Herein, we report the angular dependent reflection of p-polarized THz wave from vertically aligned multi-walled CNT arrays in both experiment and theory. The spectra indicate that the reflection depends on the film thickness of vertically aligned CNTs, the incident angle, and the frequency. The calculation model is based on the spatial dispersion effect of aligned CNTs and performed with effective impedance method and the Maxwell-Garnett approximation. The results fit well with the experiment when the thickness of CNT film is thin, which reveals a coherent superposition mechanism of the CNT surface reflection and CNTs/Si interface reflection. For thick CNT films, the CNTs/Si interface response determines the reflection at small incident angles, while the CNTs surface effect dominates at large incident angles. This work investigates the spatial dispersion effect of vertically aligned CNT arrays in the THz region, and paves a way for potential anisotropic THz applications based on CNTs with oblique incidence requirements.
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Comparative Analysis of the Measurement of Total Instructional Alignment
ERIC Educational Resources Information Center
Kick, Laura C.
2013-01-01
In 2007, Lisa Carter created the Total Instructional Alignment system--a process that aligns standards, curriculum, assessment, and instruction. Employed in several hundred school systems, the TIA process is a successful professional development program. The researcher developed an instrument to measure the success of the TIA process with the…
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AlignMe—a membrane protein sequence alignment web server
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
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A Kalman Filter for SINS Self-Alignment Based on Vector Observation.
Xu, Xiang; Xu, Xiaosu; Zhang, Tao; Li, Yao; Tong, Jinwu
2017-01-29
In this paper, a self-alignment method for strapdown inertial navigation systems based on the q -method is studied. In addition, an improved method based on integrating gravitational apparent motion to form apparent velocity is designed, which can reduce the random noises of the observation vectors. For further analysis, a novel self-alignment method using a Kalman filter based on adaptive filter technology is proposed, which transforms the self-alignment procedure into an attitude estimation using the observation vectors. In the proposed method, a linear psuedo-measurement equation is adopted by employing the transfer method between the quaternion and the observation vectors. Analysis and simulation indicate that the accuracy of the self-alignment is improved. Meanwhile, to improve the convergence rate of the proposed method, a new method based on parameter recognition and a reconstruction algorithm for apparent gravitation is devised, which can reduce the influence of the random noises of the observation vectors. Simulations and turntable tests are carried out, and the results indicate that the proposed method can acquire sound alignment results with lower standard variances, and can obtain higher alignment accuracy and a faster convergence rate.
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A Kalman Filter for SINS Self-Alignment Based on Vector Observation
Xu, Xiang; Xu, Xiaosu; Zhang, Tao; Li, Yao; Tong, Jinwu
2017-01-01
In this paper, a self-alignment method for strapdown inertial navigation systems based on the q-method is studied. In addition, an improved method based on integrating gravitational apparent motion to form apparent velocity is designed, which can reduce the random noises of the observation vectors. For further analysis, a novel self-alignment method using a Kalman filter based on adaptive filter technology is proposed, which transforms the self-alignment procedure into an attitude estimation using the observation vectors. In the proposed method, a linear psuedo-measurement equation is adopted by employing the transfer method between the quaternion and the observation vectors. Analysis and simulation indicate that the accuracy of the self-alignment is improved. Meanwhile, to improve the convergence rate of the proposed method, a new method based on parameter recognition and a reconstruction algorithm for apparent gravitation is devised, which can reduce the influence of the random noises of the observation vectors. Simulations and turntable tests are carried out, and the results indicate that the proposed method can acquire sound alignment results with lower standard variances, and can obtain higher alignment accuracy and a faster convergence rate. PMID:28146059
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Ajawatanawong, Pravech; Atkinson, Gemma C; Watson-Haigh, Nathan S; Mackenzie, Bryony; Baldauf, Sandra L
2012-07-01
Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.
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Ho, Kai-Yu; Epstein, Ryan; Garcia, Ron; Riley, Nicole; Lee, Szu-Ping
2017-02-01
Study Design Controlled laboratory study. Background Although it has been theorized that patellofemoral joint (PFJ) taping can correct patellar malalignment, the effects of PFJ taping techniques on patellar alignment and contact area have not yet been studied during weight bearing. Objective To examine the effects of 2 taping approaches (Kinesio and McConnell) on PFJ alignment and contact area. Methods Fourteen female subjects with patellofemoral pain and PFJ malalignment participated. Each subject underwent a pretaping magnetic resonance imaging (MRI) scan session and 2 MRI scan sessions after the application of the 2 taping techniques, which aimed to correct lateral patellar displacement. Subjects were asked to report their pain level prior to each scan session. During MRI assessment, subjects were loaded with 25% of body weight on their involved/more symptomatic leg at 0°, 20°, and 40° of knee flexion. The outcome measures included patellar lateral displacement (bisect-offset [BSO] index), mediolateral patellar tilt angle, patellar height (Insall-Salvati ratio), contact area, and pain. Patellofemoral joint alignment and contact area were compared among the 3 conditions (no tape, Kinesio, and McConnell) at 3 knee angles using a 2-factor, repeated-measures analysis of variance. Pain was compared among the 3 conditions using the Friedman test and post hoc Wilcoxon signed-rank tests. Results Our data did not reveal any significant effects of either McConnell or Kinesio taping on the BSO index, patellar tilt angle, Insall-Salvati ratio, or contact area across the 3 knee angles, whereas knee angle had a significant effect on the BSO index and contact area. A reduction in pain was observed after the application of the Kinesio taping technique. Conclusion In a weight-bearing condition, this preliminary study did not support the use of PFJ taping as a medial correction technique to alter the PFJ contact area or alignment of the patella. J Orthop Sports Phys Ther 2017;47(2):115-123. doi:10.2519/jospt.2017.6936.
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Highly aligned arrays of high aspect ratio barium titanate nanowires via hydrothermal synthesis
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bowland, Christopher C.; Zhou, Zhi; Malakooti, Mohammad H.
2015-06-01
We report on the development of a hydrothermal synthesis procedure that results in the growth of highly aligned arrays of high aspect ratio barium titanate nanowires. Using a multiple step, scalable hydrothermal reaction, a textured titanium dioxide film is deposited on titanium foil upon which highly aligned nanowires are grown via homoepitaxy and converted to barium titanate. Scanning electron microscope images clearly illustrate the effect the textured film has on the degree of orientation of the nanowires. The alignment of nanowires is quantified by calculating the Herman's Orientation Factor, which reveals a 58% improvement in orientation as compared to growthmore » in the absence of the textured film. The ferroelectric properties of barium titanate combined with the development of this scalable growth procedure provide a powerful route towards increasing the efficiency and performance of nanowire-based devices in future real-world applications such as sensing and power harvesting.« less
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NASA Astrophysics Data System (ADS)
Fukuma, Takeshi; Mostaert, Anika S.; Serpell, Louise C.; Jarvis, Suzanne P.
2008-09-01
We have investigated the surface structure of islet amyloid polypeptide (IAPP) fibrils and α-synuclein protofibrils in liquid by means of frequency modulation atomic force microscopy (FM-AFM). Ångström-resolution FM-AFM imaging of isolated macromolecules in liquid is demonstrated for the first time. Individual β-strands aligned perpendicular to the fibril axis with a spacing of 0.5 nm are resolved in FM-AFM images, which confirms cross-β structure of IAPP fibrils in real space. FM-AFM images also reveal the existence of 4 nm periodic domains along the axis of IAPP fibrils. Stripe features with 0.5 nm spacing are also found in images of α-synuclein protofibrils. However, in contrast to the case for IAPP fibrils, the stripes are oriented 30° from the axis, suggesting the possibility of β-strand alignment in protofibrils different from that in mature fibrils or the regular arrangement of thioflavin T molecules present during the fibril preparation aligned at the surface of the protofibrils.
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PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments.
Caffrey, Daniel R; Dana, Paul H; Mathur, Vidhya; Ocano, Marco; Hong, Eun-Jong; Wang, Yaoyu E; Somaroo, Shyamal; Caffrey, Brian E; Potluri, Shobha; Huang, Enoch S
2007-10-11
By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. Here we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple annotations is a key component of this release as it provides a framework for most of the new functionalities. The sequence annotations are accessible from the alignment and tree, where they are typically used to label sequences or hyperlink them to related databases. Sequence annotations can be created manually or extracted automatically from UniProt entries. Once a multiple sequence alignment is populated with sequence annotations, sequences can be easily selected and sorted through a sophisticated search dialog. The selected sequences can be further analyzed using statistical methods that explicitly model relationships between the sequence annotations and residue properties. Residue annotations are accessible from the alignment viewer and are typically used to designate binding sites or properties for a particular residue. Residue annotations are also searchable, and allow one to quickly select alignment columns for further sequence analysis, e.g. computing percent identities. Other features include: novel algorithms to compute sequence conservation, mapping conservation scores to a 3D structure in Jmol, displaying secondary structure elements, and sorting sequences by residue composition. PFAAT provides a framework whereby end-users can specify knowledge for a protein family in the form of annotation. The annotations can be combined with sophisticated analysis to test hypothesis that relate to sequence, structure and function.
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High Strength and Ductility of Additively Manufactured 316L Stainless Steel Explained
NASA Astrophysics Data System (ADS)
Shamsujjoha, Md.; Agnew, Sean R.; Fitz-Gerald, James M.; Moore, William R.; Newman, Tabitha A.
2018-04-01
Structure-property relationships of an additively manufactured 316L stainless steel were explored. A scanning electron microscope and electron backscattered diffraction (EBSD) analysis revealed a fine cellular-dendritic (0.5 to 2 μm) substructure inside large irregularly shaped grains ( 100 μm). The cellular structure grows along the <100> crystallographic directions. However, texture analysis revealed that the main <100> texture component is inclined by 15 deg from the building direction. X-ray diffraction line profile analysis indicated a high dislocation density of 1 × 1015 m-2 in the as-built material, which correlates well with the observed EBSD microstructure and high-yield strength, via the traditional Taylor hardening equation. Significant variations in strain hardening behavior and ductility were observed for the horizontal (HB) and vertical (VB) built samples. Ductility of HB and VB samples measured 49 and 77 pct, respectively. The initial growth texture and subsequent texture evolution during tensile deformation are held responsible for the observed anisotropy. Notably, EBSD analysis of deformed samples showed deformation twins, which predominately form in the grains with <111> aligned parallel to the loading direction. The VB samples showed higher twinning activity, higher strain hardening rates at high strain, and therefore, higher ductility. Analysis of annealed samples revealed that the observed microstructures and properties are thermally stable, with only a moderate decrease in strength and very similar levels of ductility and anisotropy, compared with the as-built condition.
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High Strength and Ductility of Additively Manufactured 316L Stainless Steel Explained
NASA Astrophysics Data System (ADS)
Shamsujjoha, Md.; Agnew, Sean R.; Fitz-Gerald, James M.; Moore, William R.; Newman, Tabitha A.
2018-07-01
Structure-property relationships of an additively manufactured 316L stainless steel were explored. A scanning electron microscope and electron backscattered diffraction (EBSD) analysis revealed a fine cellular-dendritic (0.5 to 2 μm) substructure inside large irregularly shaped grains ( 100 μm). The cellular structure grows along the <100> crystallographic directions. However, texture analysis revealed that the main <100> texture component is inclined by 15 deg from the building direction. X-ray diffraction line profile analysis indicated a high dislocation density of 1 × 1015 m-2 in the as-built material, which correlates well with the observed EBSD microstructure and high-yield strength, via the traditional Taylor hardening equation. Significant variations in strain hardening behavior and ductility were observed for the horizontal (HB) and vertical (VB) built samples. Ductility of HB and VB samples measured 49 and 77 pct, respectively. The initial growth texture and subsequent texture evolution during tensile deformation are held responsible for the observed anisotropy. Notably, EBSD analysis of deformed samples showed deformation twins, which predominately form in the grains with <111> aligned parallel to the loading direction. The VB samples showed higher twinning activity, higher strain hardening rates at high strain, and therefore, higher ductility. Analysis of annealed samples revealed that the observed microstructures and properties are thermally stable, with only a moderate decrease in strength and very similar levels of ductility and anisotropy, compared with the as-built condition.
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Comparative quantitative trait loci for silique length and seed weight in Brassica napus.
Fu, Ying; Wei, Dayong; Dong, Hongli; He, Yajun; Cui, Yixin; Mei, Jiaqin; Wan, Huafang; Li, Jiana; Snowdon, Rod; Friedt, Wolfgang; Li, Xiaorong; Qian, Wei
2015-09-23
Silique length (SL) and seed weight (SW) are important yield-associated traits in rapeseed (Brassica napus). Although many quantitative trait loci (QTL) for SL and SW have been identified in B. napus, comparative analysis for those QTL is seldom performed. In the present study, 20 and 21 QTL for SL and SW were identified in doubled haploid (DH) and DH-derived reconstructed F2 populations in rapeseed, explaining 55.1-74.3% and 24.4-62.9% of the phenotypic variation across three years, respectively. Of which, 17 QTL with partially or completely overlapped confidence interval on chromosome A09, were homologous with two overlapped QTL on chromosome C08 by aligning QTL confidence intervals with the reference genomes of Brassica crops. By high density selective genotyping of DH lines with extreme phenotypes, using a Brassica single-nucleotide polymorphism (SNP) array, the QTL on chromosome A09 was narrowed, and aligned into 1.14-Mb region from 30.84 to 31.98 Mb on chromosome R09 of B. rapa and 1.05-Mb region from 27.21 to 28.26 Mb on chromosome A09 of B. napus. The alignment of QTL with Brassica reference genomes revealed homologous QTL on A09 and C08 for SL. The narrowed QTL region provides clues for gene cloning and breeding cultivars by marker-assisted selection.
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Structural interpretations based on ERTS-1 imagery, Bighorn Region, Wyoming-Montana
NASA Technical Reports Server (NTRS)
Hoppin, R. A.
1973-01-01
Structural analysis is being carried out on bands MSS 5 and 7 of scene 1085-17294. Geologic strucutre is primarily revealed in the topographic relief and drainage. Topographic linears are particularly well developed in the bighorn uplift. Many of these occur along known faults and shear zones in the Precambrian core; several have not been previously mapped. These linears, however, do not continue into the younger rocks of the flanks or do so in a much less marked manner than in the core. Linears are far less abundant in the basin or are manifested only in very subtle tonal contrasts and somewhat straight drainage segments. Some of the linears are aligned along trends previously postulated on the basis of surface mapping to be lineaments. The imagery reveals little or no evidence of strike-slip displacements along these lineaments.
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2010-01-01
Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size. PMID:20565983
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Kiryu, Hisanori; Kin, Taishin; Asai, Kiyoshi
2007-02-15
Recent transcriptomic studies have revealed the existence of a considerable number of non-protein-coding RNA transcripts in higher eukaryotic cells. To investigate the functional roles of these transcripts, it is of great interest to find conserved secondary structures from multiple alignments on a genomic scale. Since multiple alignments are often created using alignment programs that neglect the special conservation patterns of RNA secondary structures for computational efficiency, alignment failures can cause potential risks of overlooking conserved stem structures. We investigated the dependence of the accuracy of secondary structure prediction on the quality of alignments. We compared three algorithms that maximize the expected accuracy of secondary structures as well as other frequently used algorithms. We found that one of our algorithms, called McCaskill-MEA, was more robust against alignment failures than others. The McCaskill-MEA method first computes the base pairing probability matrices for all the sequences in the alignment and then obtains the base pairing probability matrix of the alignment by averaging over these matrices. The consensus secondary structure is predicted from this matrix such that the expected accuracy of the prediction is maximized. We show that the McCaskill-MEA method performs better than other methods, particularly when the alignment quality is low and when the alignment consists of many sequences. Our model has a parameter that controls the sensitivity and specificity of predictions. We discussed the uses of that parameter for multi-step screening procedures to search for conserved secondary structures and for assigning confidence values to the predicted base pairs. The C++ source code that implements the McCaskill-MEA algorithm and the test dataset used in this paper are available at http://www.ncrna.org/papers/McCaskillMEA/. Supplementary data are available at Bioinformatics online.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Nutzman, Philip A.; Fabrycky, Daniel C.; Fortney, Jonathan J., E-mail: pnutzman@ucolick.org
Spectroscopic follow-up of dozens of transiting planets has revealed the degree of alignment between the equators of stars and the orbits of the planets they host. Here we determine a method, applicable to spotted stars, that can reveal the same information from the photometric discovery data, with no need for follow-up. A spot model fit to the global light curve, parameterized by the spin orientation of the star, predicts when the planet will transit the spots. Observing several spot crossings during different transits then leads to constraints on the spin-orbit alignment. In cases where stellar spots are small, the stellarmore » inclination, i{sub s} , and hence the true alignment, rather than just the sky projection, can be obtained. This method has become possible with the advent of space telescopes such as CoRoT and Kepler, which photometrically monitor transiting planets over a nearly continuous, long time baseline. We apply our method to CoRoT-2 and find the projected spin-orbit alignment angle, {lambda} = 4.{sup 0}7 {+-} 12.{sup 0}3, in excellent agreement with a previous determination that employed the Rossiter-McLaughlin effect. The large spots of the parent star, CoRoT-2, limit our precision on i{sub s} : 84{sup 0} {+-} 36{sup 0}, where i{sub s} < 90{sup 0}(> 90{sup 0}) indicates that the rotation axis is tilted toward (away from) the line of sight.« less
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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Margulies, Elliott H.; Cooper, Gregory M.; Asimenos, George; Thomas, Daryl J.; Dewey, Colin N.; Siepel, Adam; Birney, Ewan; Keefe, Damian; Schwartz, Ariel S.; Hou, Minmei; Taylor, James; Nikolaev, Sergey; Montoya-Burgos, Juan I.; Löytynoja, Ari; Whelan, Simon; Pardi, Fabio; Massingham, Tim; Brown, James B.; Bickel, Peter; Holmes, Ian; Mullikin, James C.; Ureta-Vidal, Abel; Paten, Benedict; Stone, Eric A.; Rosenbloom, Kate R.; Kent, W. James; Bouffard, Gerard G.; Guan, Xiaobin; Hansen, Nancy F.; Idol, Jacquelyn R.; Maduro, Valerie V.B.; Maskeri, Baishali; McDowell, Jennifer C.; Park, Morgan; Thomas, Pamela J.; Young, Alice C.; Blakesley, Robert W.; Muzny, Donna M.; Sodergren, Erica; Wheeler, David A.; Worley, Kim C.; Jiang, Huaiyang; Weinstock, George M.; Gibbs, Richard A.; Graves, Tina; Fulton, Robert; Mardis, Elaine R.; Wilson, Richard K.; Clamp, Michele; Cuff, James; Gnerre, Sante; Jaffe, David B.; Chang, Jean L.; Lindblad-Toh, Kerstin; Lander, Eric S.; Hinrichs, Angie; Trumbower, Heather; Clawson, Hiram; Zweig, Ann; Kuhn, Robert M.; Barber, Galt; Harte, Rachel; Karolchik, Donna; Field, Matthew A.; Moore, Richard A.; Matthewson, Carrie A.; Schein, Jacqueline E.; Marra, Marco A.; Antonarakis, Stylianos E.; Batzoglou, Serafim; Goldman, Nick; Hardison, Ross; Haussler, David; Miller, Webb; Pachter, Lior; Green, Eric D.; Sidow, Arend
2007-01-01
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization. PMID:17567995
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Della, Lindsay J.; DeJoy, David M.; Goetzel, Ron Z.; Ozminkowski, Ronald J.; Wilson, Mark G.
2009-01-01
Objective This paper describes the development of the Leading by Example (LBE) instrument. Methods Exploratory factor analysis was used to obtain an initial factor structure. Factor validity was evaluated using confirmatory factor analysis methods. Cronbach’s alpha and item-total correlations provided information on the reliability of the factor subscales. Results Four subscales were identified: business alignment with health promotion objectives; awareness of the health-productivity link; worksite support for health promotion; leadership support for health promotion. Factor by group comparisons revealed that the initial factor structure is effective in detecting differences in organizational support for health promotion across different employee groups Conclusions Management support for health promotion can be assessed using the LBE, a brief, self-report questionnaire. Researchers can use the LBE to diagnose, track, and evaluate worksite health promotion programs. PMID:18517097
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NASA Astrophysics Data System (ADS)
Müller, Oliver; Schmiedel, Theresa; Gorbacheva, Elena; vom Brocke, Jan
2016-01-01
While researchers have analysed the organisational competences that are required for successful Business Process Management (BPM) initiatives, individual BPM competences have not yet been studied in detail. In this study, latent semantic analysis is used to examine a collection of 1507 BPM-related job advertisements in order to develop a typology of BPM professionals. This empirical analysis reveals distinct ideal types and profiles of BPM professionals on several levels of abstraction. A closer look at these ideal types and profiles confirms that BPM is a boundary-spanning field that requires interdisciplinary sets of competence that range from technical competences to business and systems competences. Based on the study's findings, it is posited that individual and organisational alignment with the identified ideal types and profiles is likely to result in high employability and organisational BPM success.
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NASA Technical Reports Server (NTRS)
Kneifel, A. A.; Guerrero, C.
2003-01-01
In this web site usability case study, two methods of participative inquiry are used to align a development team's objectives with their users' needs and to promote the team awareness of the benefit of qualitative usability analysis.
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Ancient DNA sequence revealed by error-correcting codes.
Brandão, Marcelo M; Spoladore, Larissa; Faria, Luzinete C B; Rocha, Andréa S L; Silva-Filho, Marcio C; Palazzo, Reginaldo
2015-07-10
A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code.
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Ancient DNA sequence revealed by error-correcting codes
Brandão, Marcelo M.; Spoladore, Larissa; Faria, Luzinete C. B.; Rocha, Andréa S. L.; Silva-Filho, Marcio C.; Palazzo, Reginaldo
2015-01-01
A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code. PMID:26159228
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Silk Fibroin Degradation Related to Rheological and Mechanical Properties.
Partlow, Benjamin P; Tabatabai, A Pasha; Leisk, Gary G; Cebe, Peggy; Blair, Daniel L; Kaplan, David L
2016-05-01
Regenerated silk fibroin has been proposed as a material substrate for biomedical, optical, and electronic applications. Preparation of the silk fibroin solution requires extraction (degumming) to remove contaminants, but results in the degradation of the fibroin protein. Here, a mechanism of fibroin degradation is proposed and the molecular weight and polydispersity is characterized as a function of extraction time. Rheological analysis reveals significant changes in the viscosity of samples while mechanical characterization of cast and drawn films shows increased moduli, extensibility, and strength upon drawing. Fifteen minutes extraction time results in degraded fibroin that generates the strongest films. Structural analysis by wide angle X-ray scattering (WAXS) and Fourier transform infrared spectroscopy (FTIR) indicates molecular alignment in the drawn films and shows that the drawing process converts amorphous films into the crystalline, β-sheet, secondary structure. Most interesting, by using selected extraction times, films with near-native crystallinity, alignment, and molecular weight can be achieved; yet maximal mechanical properties for the films from regenerated silk fibroin solutions are found with solutions subjected to some degree of degradation. These results suggest that the regenerated solutions and the film casting and drawing processes introduce more complexity than native spinning processes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Flores Fernández, José Miguel; Barragán Álvarez, Carla Patricia; Sánchez Hernández, Carla Vanessa; Padilla Camberos, Eduardo; González Castillo, Celia; Ortuño Sahagún, Daniel; Martínez Velázquez, Moisés
2016-11-01
The cattle tick Rhipicephalus (Boophilus) microplus is a hematophagous ectoparasite of major importance for the livestock industry. It shows a remarkable ability to survive over long periods without feeding. However, the mechanisms used to endure long-term starvation are poorly understood. It is believed that autophagy, a process of intracellular protein degradation, may play a significant role to confront adverse environmental conditions. To advance our understanding of autophagy in R. microplus, in the present study we report the molecular characterization of three autophagy-related (ATG) genes, namely, RmATG3, RmATG4 and RmATG6, as well as their expression profiles in different developmental stages and organs of the parasite. The deduced amino acid sequences derived from the characterized gene sequences were subjected to Basic Local Alignment Search Tool analysis. The testing produced significant alignments with respective ATG proteins from Haemaphysalis longicornis and Ixodes scapularis ticks. Real-time polymerase chain reaction assays revealed that RmATG4 and RmATG6 transcripts were elevated in egg and ovary tissue, when compared with larva and midgut samples, while RmATG3 expression in midgut was 2-fold higher than in egg, larva and ovary samples.
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Røge, Rasmus; Riber-Hansen, Rikke; Nielsen, Søren; Vyberg, Mogens
2016-07-01
Manual estimation of Ki67 Proliferation Index (PI) in breast carcinoma classification is labor intensive and prone to intra- and interobserver variation. Standard Digital Image Analysis (DIA) has limitations due to issues with tumor cell identification. Recently, a computer algorithm, DIA based on Virtual Double Staining (VDS), segmenting Ki67-positive and -negative tumor cells using digitally fused parallel cytokeratin (CK) and Ki67-stained slides has been introduced. In this study, we compare VDS with manual stereological counting of Ki67-positive and -negative cells and examine the impact of the physical distance of the parallel slides on the alignment of slides. TMAs, containing 140 cores of consecutively obtained breast carcinomas, were stained for CK and Ki67 using optimized staining protocols. By means of stereological principles, Ki67-positive and -negative cell profiles were counted in sampled areas and used for the estimation of PIs of the whole tissue core. The VDS principle was applied to both the same sampled areas and the whole tissue core. Additionally, five neighboring slides were stained for CK in order to examine the alignment algorithm. Correlation between manual counting and VDS in both sampled areas and whole core was almost perfect (correlation coefficients above 0.97). Bland-Altman plots did not reveal any skewness in any data ranges. There was a good agreement in alignment (>85 %) in neighboring slides, whereas agreement decreased in non-neighboring slides. VDS gave similar results compared with manual counting using stereological principles. Introduction of this method in clinical and research practice may improve accuracy and reproducibility of Ki67 PI.
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Chromaligner: a web server for chromatogram alignment.
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.
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Sahu, Indra D; Mayo, Daniel J; Subbaraman, Nidhi; Inbaraj, Johnson J; McCarrick, Robert M; Lorigan, Gary A
2017-08-01
Characterizing membrane protein structure and dynamics in the lipid bilayer membrane is very important but experimentally challenging. EPR spectroscopy offers a unique set of techniques to investigate a membrane protein structure, dynamics, topology, and distance constraints in lipid bilayers. Previously our lab demonstrated the use of magnetically aligned phospholipid bilayers (bicelles) for probing topology and dynamics of the membrane peptide M2δ of the acetyl choline receptor (AchR) as a proof of concept. In this study, magnetically aligned phospholipid bilayers and rigid spin labels were further utilized to provide improved dynamic information and topology of M2δ peptide. Seven TOAC-labeled AchR M2δ peptides were synthesized to demonstrate the utility of a multi-labeling amino acid substitution alignment strategy. Our data revealed the helical tilts to be 11°, 17°, 9°, 17°, 16°, 11°, 9°±4° for residues I7TOAC, Q13TOAC, A14TOAC, V15TOAC, C16TOAC, L17TOAC, and L18TOAC, respectively. The average helical tilt of the M2δ peptide was determined to be ∼13°. This study also revealed that the TOAC labels were attached to the M2δ peptide with different dynamics suggesting that the sites towards the C-terminal end are more rigid when compared to the sites towards the N-terminus. The dynamics of the TOAC labeled sites were more resolved in the aligned samples when compared to the randomly disordered samples. This study highlights the use of magnetically aligned lipid bilayer EPR technique to determine a more accurate helical tilt and more resolved local dynamics of AchR M2δ peptide. Copyright © 2017 Elsevier B.V. All rights reserved.
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MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer
Gauthier, Nicholas Paul; Reznik, Ed; Gao, Jianjiong; Sumer, Selcuk Onur; Schultz, Nikolaus; Sander, Chris; Miller, Martin L.
2016-01-01
The MutationAligner web resource, available at http://www.mutationaligner.org, enables discovery and exploration of somatic mutation hotspots identified in protein domains in currently (mid-2015) more than 5000 cancer patient samples across 22 different tumor types. Using multiple sequence alignments of protein domains in the human genome, we extend the principle of recurrence analysis by aggregating mutations in homologous positions across sets of paralogous genes. Protein domain analysis enhances the statistical power to detect cancer-relevant mutations and links mutations to the specific biological functions encoded in domains. We illustrate how the MutationAligner database and interactive web tool can be used to explore, visualize and analyze mutation hotspots in protein domains across genes and tumor types. We believe that MutationAligner will be an important resource for the cancer research community by providing detailed clues for the functional importance of particular mutations, as well as for the design of functional genomics experiments and for decision support in precision medicine. MutationAligner is slated to be periodically updated to incorporate additional analyses and new data from cancer genomics projects. PMID:26590264
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Munger, Steven C.; Raghupathy, Narayanan; Choi, Kwangbom; Simons, Allen K.; Gatti, Daniel M.; Hinerfeld, Douglas A.; Svenson, Karen L.; Keller, Mark P.; Attie, Alan D.; Hibbs, Matthew A.; Graber, Joel H.; Chesler, Elissa J.; Churchill, Gary A.
2014-01-01
Massively parallel RNA sequencing (RNA-seq) has yielded a wealth of new insights into transcriptional regulation. A first step in the analysis of RNA-seq data is the alignment of short sequence reads to a common reference genome or transcriptome. Genetic variants that distinguish individual genomes from the reference sequence can cause reads to be misaligned, resulting in biased estimates of transcript abundance. Fine-tuning of read alignment algorithms does not correct this problem. We have developed Seqnature software to construct individualized diploid genomes and transcriptomes for multiparent populations and have implemented a complete analysis pipeline that incorporates other existing software tools. We demonstrate in simulated and real data sets that alignment to individualized transcriptomes increases read mapping accuracy, improves estimation of transcript abundance, and enables the direct estimation of allele-specific expression. Moreover, when applied to expression QTL mapping we find that our individualized alignment strategy corrects false-positive linkage signals and unmasks hidden associations. We recommend the use of individualized diploid genomes over reference sequence alignment for all applications of high-throughput sequencing technology in genetically diverse populations. PMID:25236449
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Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis
Steele, Joe; Bastola, Dhundy
2014-01-01
Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing to their inherent computational expense when processing large amounts of sequence data. These methods are prone to giving misleading information because of genetic recombination, genetic shuffling and other inherent biological events. New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming. These new methods are often preferred, as their algorithms are simpler and are not affected by synteny-related problems. In this review, we provide a detailed discussion of computational tools, which stem from alignment-free methods based on statistical analysis from word frequencies. We provide several clear examples to demonstrate applications and the interpretations over several different areas of alignment-free analysis such as base–base correlations, feature frequency profiles, compositional vectors, an improved string composition and the D2 statistic metric. Additionally, we provide detailed discussion and an example of analysis by Lempel–Ziv techniques from data compression. PMID:23904502
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Roettger, Mayo; Martin, William; Dagan, Tal
2009-09-01
Among the methods currently used in phylogenomic practice to detect the presence of lateral gene transfer (LGT), one of the most frequently employed is the comparison of gene tree topologies for different genes. In cases where the phylogenies for different genes are incompatible, or discordant, for well-supported branches there are three simple interpretations for the result: 1) gene duplications (paralogy) followed by many independent gene losses have occurred, 2) LGT has occurred, or 3) the phylogeny is well supported but for reasons unknown is nonetheless incorrect. Here, we focus on the third possibility by examining the properties of 22,437 published multiple sequence alignments, the Bayesian maximum likelihood trees for which either do or do not suggest the occurrence of LGT by the criterion of discordant branches. The alignments that produce discordant phylogenies differ significantly in several salient alignment properties from those that do not. Using a support vector machine, we were able to predict the inference of discordant tree topologies with up to 80% accuracy from alignment properties alone.
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Mills, Kathryn; Hunt, Michael A; Leigh, Ryan; Ferber, Reed
2013-08-01
Neuromuscular alterations are increasingly reported in individuals with knee osteoarthritis (KOA) during level walking. We aimed to determine which neuromuscular alterations are consistent in KOA individuals and how these may be influenced by osteoarthritis severity, varus alignment and/or joint laxity. Electronic databases were searched up to July 2012. Cross-sectional observational studies comparing lower-limb neuromuscular activity in individuals with KOA, healthy controls or with different KOA cohorts were included. Two reviewers assessed methodological quality. Effect sizes were used to quantify the magnitude of observed differences. Where studies were homogenous, effect sizes were pooled using a fixed-effects model. Fourteen studies examining neuromuscular alterations in indices of co-contraction, muscle amplitude and muscle activity duration were included. Data pooling revealed that moderate KOA individuals exhibit increased co-contraction of lateral knee muscles (ES 0.64 [0.3 to 0.97]) and moderately increased rectus femoris (ES 0.73 [0.23 to 1.22]), vastus lateralis (ES 0.77 [0.27 to 1.27]) and biceps femoris (ES 1.18 [0.67 to 1.7]) mean amplitude. Non-pooled data indicated prolonged activity of these muscles. Increased medial knee neuromuscular activity was prevalent for those exhibiting varus alignment and medial knee joint laxity. Interpretation Individuals with KOA exhibited increased co-contraction, amplitude and duration of lateral knee muscles regardless of disease severity, limb alignment or medial joint laxity. Individuals with severe disease, varus alignment and medial joint laxity demonstrate up-regulation of medial knee muscles. Future research investigating the efficacy of neuromuscular rehabilitation programs should consider the effect of simultaneous up-regulation of medial and lateral knee muscles on disease progression. © 2013.
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DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data.
Gaspar, John M; Hart, Ronald P
2017-11-29
DNA methylation is an epigenetic modification that is studied at a single-base resolution with bisulfite treatment followed by high-throughput sequencing. After alignment of the sequence reads to a reference genome, methylation counts are analyzed to determine genomic regions that are differentially methylated between two or more biological conditions. Even though a variety of software packages is available for different aspects of the bioinformatics analysis, they often produce results that are biased or require excessive computational requirements. DMRfinder is a novel computational pipeline that identifies differentially methylated regions efficiently. Following alignment, DMRfinder extracts methylation counts and performs a modified single-linkage clustering of methylation sites into genomic regions. It then compares methylation levels using beta-binomial hierarchical modeling and Wald tests. Among its innovative attributes are the analyses of novel methylation sites and methylation linkage, as well as the simultaneous statistical analysis of multiple sample groups. To demonstrate its efficiency, DMRfinder is benchmarked against other computational approaches using a large published dataset. Contrasting two replicates of the same sample yielded minimal genomic regions with DMRfinder, whereas two alternative software packages reported a substantial number of false positives. Further analyses of biological samples revealed fundamental differences between DMRfinder and another software package, despite the fact that they utilize the same underlying statistical basis. For each step, DMRfinder completed the analysis in a fraction of the time required by other software. Among the computational approaches for identifying differentially methylated regions from high-throughput bisulfite sequencing datasets, DMRfinder is the first that integrates all the post-alignment steps in a single package. Compared to other software, DMRfinder is extremely efficient and unbiased in this process. DMRfinder is free and open-source software, available on GitHub ( github.com/jsh58/DMRfinder ); it is written in Python and R, and is supported on Linux.
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Growth of high-aspect ratio horizontally-aligned ZnO nanowire arrays.
Soman, Pranav; Darnell, Max; Feldman, Marc D; Chen, Shaochen
2011-08-01
A method of fabricating horizontally-aligned zinc-oxide (ZnO) nanowire (NW) arrays with full control over the width and length is demonstrated. SEM images reveal the hexagonal structure typical of zinc oxide NWs. Arrays of high-aspect ratio horizontal ZnO NWs are fabricated by making use of the lateral overgrowth from dot patterns created by electron beam lithography (EBL). An array of patterned wires are lifted off and transferred to a flexible PDMS substrate with possible applications in several key nanotechnology areas.
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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.
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Anisotropic thermal property of magnetically oriented carbon nanotube polymer composites
NASA Astrophysics Data System (ADS)
Li, Bin; Dong, Shuai; Wang, Caiping; Wang, Xiaojie; Fang, Jun
2016-04-01
This paper proposes a method for preparing multi-walled carbon nanotubea/polydimethylsiloxane (MWCNTs/PDMS) composites with enhanced thermal properties by using a high magnetic field (up to 10T). The MWCNT are oriented magnetically inside a silicone by in-situ polymerization method. The anisotropic structure would be expected to produce directional thermal conductivity. This study will provide a new approach to the development of anisotropic thermal-conductive polymer composites. Systematic studies with the preparation of silicone/graphene composites corresponding to their thermal and mechanical properties are carried out under various conditions: intensity of magnetic field, time, temperature, fillings. The effect of MWCNT/graphene content and preparation procedures on thermal conductivity of composites is investigated. Dynamic mechanical analysis (DMA) is used to reveal the mechanical properties of the composites in terms of the filling contents and magnetic field strength. The scanning electron microscope (SEM) is used to observe the micro-structure of the MWCNT composites. The alignment of MWCNTs in PDMS matrix is also studied by Raman spectroscopy. The thermal conductivity measurements show that the magnetically aligned CNT-composites feature high anisotropy in thermal conductivity.
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Kuchel, Philip W; Shishmarev, Dmitry; Puckeridge, Max; Levitt, Malcolm H; Naumann, Christoph; Chapman, Bogdan E
2015-12-01
(133)Cs nuclear magnetic resonance (NMR) spectroscopy was conducted on (133)Cs(+) in gelatin hydrogels that were either relaxed or stretched. Stretching generated a septet from this spin-7/2 nucleus, and its nuclear magnetic relaxation was studied via z-spectra, and two-dimensional nuclear Overhauser (NOESY) spectroscopy. Various spectral features were well simulated by using Mathematica and the software package SpinDynamica. Spectra of CsCl in suspensions of human erythrocytes embedded in gelatin gel showed separation of the resonances from the cation inside and outside the cells. Upon stretching the sample, the extracellular (133)Cs(+) signal split into a septet, while the intracellular peak was unchanged, revealing different alignment/ordering properties of the environment inside and around the cells. Differential interference contrast light microscopy confirmed that the cells were stretched when the overall sample was elongated. Analysis of the various spectral features of (133)Cs(+) reported here opens up applications of this K(+) congener for studies of cation-handling by metabolically-active cells and tissues in aligned states. Copyright © 2015 Elsevier Inc. All rights reserved.
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Ewell, Patrick J; Guadagno, Rosanna E; Jones, Matthew; Dunn, Robert Andrew
2016-07-01
Popular video games often provide people with the option to play characters that are good or evil in nature, and yet, little is known about how individual differences in personality relate to the moral and ethical alignments people chose in their digital representations. We examined whether participants' pre-existing levels of moral disengagement and Big 5 scores predicted the alignments they selected for their avatar in video game play. Results revealed that men, relative to women, were more likely to play "bad guys" and that moral disengagement predicted this finding. Agreeableness and conscientiousness mediated the relationship between moral disengagement and alignment such that those higher in these two traits were more likely to play good characters.
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String-fluid transition in systems with aligned anisotropic interactions.
Brandt, P C; Ivlev, A V; Morfill, G E
2010-06-21
Systems with aligned anisotropic interactions between particles exhibit numerous phase transitions. A remarkable example of the fluid phase transition occurring in such systems is the formation of particle strings--the so-called "string" or "chain" fluids. We employ an approach based on the Ornstein-Zernike (OZ) equation, which allows us to calculate structural properties of fluids with aligned anisotropic interactions. We show that the string-fluid transition can be associated with the bifurcation of the "isotropic" correlation length into two distinct scales which characterize the longitudinal and transverse order in string fluids and, hence, may be used as a fingerprint of this transition. The comparison of the proposed OZ theory with the Monte Carlo simulations reveals fairly good agreement.
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NASA Astrophysics Data System (ADS)
Ma, Biao; Zhou, Xiao; Bao, Hua; Li, Xingwei; Wang, Gengchao
2012-10-01
Hierarchical composites of sulfonated graphene-supported vertically aligned polyaniline nanorods (sGNS/PANI) are successfully synthesized via interfacial polymerization of aniline monomers in the presence of sulfonated graphene nanosheets (sGNS). The FE-SEM images indicate that the morphologies of sGNS/PANI composites can be controlled by adjusting the concentration of aniline monomers. FTIR and Raman spectra reveal that aligned PANI nanorod arrays for sGNS/PANI exhibit higher degree of conjugation compared with pristine PANI nanorods. The hierarchical composite based on the two-electrode cell possesses higher specific capacitance (497 F g-1 at 0.2 A g-1), better rate capability and cycling stability (5.7% capacitance loss after 2000 cycles) than those of pristine PANI nanorods.
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Cryo-EM image alignment based on nonuniform fast Fourier transform.
Yang, Zhengfan; Penczek, Pawel A
2008-08-01
In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.
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Levrini, Luca; Mangano, Alessandro; Margherini, Silvia; Tenconi, Camilla; Vigetti, Davide; Muollo, Raffaele; Marco Abbate, Gian
2016-01-01
Purpose. The aim was to quantify the bacteria concentration on the surface of orthodontic clear aligners using three different cleaning methods. Furthermore the objective was to validate the efficacy of the bioluminometer in assessing the bacteria concentration. Materials and Methods. Twenty subjects (six males and fourteen females) undergoing orthodontic therapy with clear aligners (Invisalign® Align Technology, Santa Clara, California) were enrolled in this study. The observation time was of six weeks. The patients were instructed to use different cleaning methods (water, brushing with toothpaste, and brushing with toothpaste and use of sodium carbonate and sulphate tablet). At the end of each phase a microbiological analysis was performed using the bioluminometer. Results. The highest bacteria concentration was found on aligners cleaned using only water (583 relative light units); a value of 189 relative light units was found on aligners cleaned with brushing and toothpaste. The lowest bacteria concentration was recorded on aligners cleaned with brushing and toothpaste and the use of sodium carbonate and sulfate tablet. Conclusions. The mechanical removal of the bacterial biofilm proved to be effective with brushing and toothpaste. The best results in terms of bacteria concentration were achieved adding the use of sodium carbonate and sulfate tablet. PMID:27242901
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Pitch contour matching and interactional alignment across turns: an acoustic investigation.
Gorisch, Jan; Wells, Bill; Brown, Guy J
2012-03-01
In order to explore the influence of context on the phonetic design of talk-in-interaction, we investigated the pitch characteristics of short turns (insertions) that are produced by one speaker between turns from another speaker. We investigated the hypothesis that the speaker of the insertion designs her turn as a pitch match to the prior turn in order to align with the previous speaker's agenda, whereas non-matching displays that the speaker of the insertion is non-aligning, for example to initiate a new action. Data were taken from the AMI meeting corpus, focusing on the spontaneous talk of first-language English participants. Using sequential analysis, 177 insertions were classified as either aligning or non-aligning in accordance with definitions of these terms in the Conversation Analysis literature. The degree of similarity between the pitch contour of the insertion and that of the prior speaker's turn was measured, using a new technique that integrates normalized F0 and intensity information. The results showed that aligning insertions were significantly more similar to the immediately preceding turn, in terms of pitch contour, than were non-aligning insertions. This supports the view that choice of pitch contour is managed locally, rather than by reference to an intonational lexicon.
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Cryo-EM Image Alignment Based on Nonuniform Fast Fourier Transform
Yang, Zhengfan; Penczek, Pawel A.
2008-01-01
In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform Fast Fourier Transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis. PMID:18499351
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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.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kumar, Rishi, E-mail: kkraina@gmail.com; Sood, Srishti, E-mail: kkraina@gmail.com; Raina, K. K., E-mail: kkraina@gmail.com
2014-04-24
We have developed azo dye doped nematic liquid crystal complex for advanced photonic liquid crystal display technology aspects. Disperse orange azo dye self introduced planer alignment in the nematic liquid crystal without any surface anchoring treatment. Planer alignment was characterized by optical polarizing microscopy. The electro-optical switching response of dye disperse planer aligned nematic cell was investigated as a function of applied voltage with the help of photoluminescence spectrophotometer for the tuning of photoluminescence contrast.
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An Analysis of Strategies for Teaching Standards-Based Lesson Plan Alignment to Preservice Teachers
ERIC Educational Resources Information Center
Drost, Bryan R.; Levine, Anita C.
2015-01-01
Research consistently shows that well-aligned lesson plans lead to better student learning outcomes. The development of these plans challenges both preservice teachers and the teacher educators who instruct them. This exploratory study examined strategies for teaching lesson plan alignment utilized by 87 teacher educators in the United States.…
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Grade-Aligned Math Instruction for Secondary Students with Moderate Intellectual Disability
ERIC Educational Resources Information Center
Browder, Diane M.; Jimenez, Bree A.; Trela, Katherine
2012-01-01
The purpose of this study was to examine the effects of grade-aligned math instruction on math skill acquisition of four middle schools with moderate intellectual disability. Teachers were trained to follow a task analysis to teach grade-aligned math to middle school students using adapted math problem stories and graphic organizers. The teacher…
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Is multiple-sequence alignment required for accurate inference of phylogeny?
Höhl, Michael; Ragan, Mark A
2007-04-01
The process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple alignment of these sequences but can also be based on methods that do not involve multiple sequence alignment. Very little is known about the accuracy with which such alignment-free methods recover the correct phylogeny or about the potential for increasing their accuracy. We conducted a large-scale comparison of ten alignment-free methods, among them one new approach that does not calculate distances and a faster variant of our pattern-based approach; all distance-based alignment-free methods are freely available from http://www.bioinformatics.org.au (as Python package decaf+py). We show that most methods exhibit a higher overall reconstruction accuracy in the presence of high among-site rate variation. Under all conditions that we considered, variants of the pattern-based approach were significantly better than the other alignment-free methods. The new pattern-based variant achieved a speed-up of an order of magnitude in the distance calculation step, accompanied by a small loss of tree reconstruction accuracy. A method of Bayesian inference from k-mers did not improve on classical alignment-free (and distance-based) methods but may still offer other advantages due to its Bayesian nature. We found the optimal word length k of word-based methods to be stable across various data sets, and we provide parameter ranges for two different alphabets. The influence of these alphabets was analyzed to reveal a trade-off in reconstruction accuracy between long and short branches. We have mapped the phylogenetic accuracy for many alignment-free methods, among them several recently introduced ones, and increased our understanding of their behavior in response to biologically important parameters. In all experiments, the pattern-based approach emerged as superior, at the expense of higher resource consumption. Nonetheless, no alignment-free method that we examined recovers the correct phylogeny as accurately as does an approach based on maximum-likelihood distance estimates of multiply aligned sequences.
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Zhang, Kuihua; Huang, Dianwu; Yan, Zhiyong; Wang, Chunyang
2017-07-01
Biomimicing topological structure of natural nerve tissue to direct axon growth and controlling sustained release of moderate neurotrophic factors are extremely propitious to the functional recovery of damaged nervous systems. In this study, the heparin/collagen encapsulating nerve growth factor (NGF) multilayers were coated onto the aligned poly-L-lactide (PLLA) nanofibrous scaffolds via a layer-by-layer (LbL) self-assembly technique to combine biomolecular signals, and physical guidance cues for peripheral nerve regeneration. Scanning electronic microscopy (SEM) revealed that the surface of aligned PLLA nanofibrous scaffolds coated with heparin/collagen multilayers became rougher and appeared some net-like filaments and protuberances in comparison with PLLA nanofibrous scaffolds. The heparin/collagen multilayers did not destroy the alignment of nanofibers. X-ray photoelectron spectroscopy and water contact angles displayed that heparin and collagen were successfully coated onto the aligned PLLA nanofibrous scaffolds and improved its hydrophilicity. Three-dimensional (3 D) confocal microscopy images further demonstrated that collagen, heparin, and NGF were not only coated onto the surface of aligned PLLA nanofibrous scaffolds but also permeated into the inner of scaffolds. Moreover, NGF presented a sustained release for 2 weeks from aligned nanofibrous scaffolds coated with 5.5 bilayers or above and remained good bioactivity. The heparin/collagen encapsulating NGF multilayers coated aligned nanofibrous scaffolds, in particular 5.5 bilayers or above, was more beneficial to Schwann cells (SCs) proliferation and PC12 cells differentiation as well as the SC cytoskeleton and neurite growth along the direction of nanofibrous alignment compared to the aligned PLLA nanofibrous scaffolds. This novel scaffolds combining sustained release of bioactive NGF and aligned nanofibrous topography presented an excellent potential in peripheral nerve regeneration. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1900-1910, 2017. © 2017 Wiley Periodicals, Inc.
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Feature Based Retention Time Alignment for Improved HDX MS Analysis
NASA Astrophysics Data System (ADS)
Venable, John D.; Scuba, William; Brock, Ansgar
2013-04-01
An algorithm for retention time alignment of mass shifted hydrogen-deuterium exchange (HDX) data based on an iterative distance minimization procedure is described. The algorithm performs pairwise comparisons in an iterative fashion between a list of features from a reference file and a file to be time aligned to calculate a retention time mapping function. Features are characterized by their charge, retention time and mass of the monoisotopic peak. The algorithm is able to align datasets with mass shifted features, which is a prerequisite for aligning hydrogen-deuterium exchange mass spectrometry datasets. Confidence assignments from the fully automated processing of a commercial HDX software package are shown to benefit significantly from retention time alignment prior to extraction of deuterium incorporation values.
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Tran-Ba, Khanh-Hoa; Higgins, Daniel A; Ito, Takashi
2014-09-25
Flow-based approaches are promising routes to preparation of aligned block copolymer microdomains within confined spaces. An in-depth characterization of such nanoscale morphologies within macroscopically nonuniform materials under ambient conditions is, however, often challenging. In this study, single-molecule tracking (SMT) methods were employed to probe the flow-induced alignment of cylindrical microdomains (ca. 22 nm in diameter) in polystyrene-poly(ethylene oxide) diblock copolymer (PS-b-PEO) films. Films of micrometer-scale thicknesses were prepared by overlaying a benzene solution droplet on a glass coverslip with a rectangular glass plate, followed by solvent evaporation under a nitrogen atmosphere. The microdomain alignment was quantitatively assessed from SMT data exhibiting the diffusional motions of individual sulforhodamine B fluorescent probes that preferentially partitioned into cylindrical PEO microdomains. Better overall microdomain orientation along the flow direction was observed near the substrate interface in films prepared at a higher flow rate, suggesting that the microdomain alignment was primarily induced by shear flow. The SMT data also revealed the presence of micrometer-scale grains consisting of highly ordered microdomains with coherent orientation. The results of this study provide insights into shear-based preparation of aligned cylindrical microdomains in block copolymer films from solutions within confined spaces.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Park, Hong-Gyu; Lee, Yun-Gun; Jang, Sang Bok
2015-11-15
Hafnium yttrium gallium oxide (HfYGaO) films were applied to liquid crystal displays (LCDs) as liquid crystal (LC) alignment layers, replacing conventional polyimide (PI) layers. The HfYGaO alignment layers were prepared by fabricating solution-processed HfYGaO films, annealing them, and treating them with ion-beam (IB) irradiation. The authors studied the effects of annealing temperature and IB irradiation of the solution-derived HfYGaO films on the orientation of LC molecules. The LC molecules on the solution-derived HfYGaO films were homogeneously and uniformly aligned by IB irradiation, irrespective of the annealing temperature. Atomic force microscopy analyses revealed that the surface reformation of the HfYGaO filmsmore » induced by IB irradiation strengthened the van der Waals force between the LC molecules and the HfYGaO films, leading to uniform LC alignment. Enhanced electro-optical characteristics were observed in the twisted-nematic (TN) LCDs based on IB-irradiated HfYGaO films compared with those of TN-LCDs based on PI layers, demonstrating the high application potential of the proposed solution-derived HfYGaO films as LC alignment layers.« less
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Ibupoto, Zafar Hussain; Khun, Kimleang; Eriksson, Martin; AlSalhi, Mohammad; Atif, Muhammad; Ansari, Anees; Willander, Magnus
2013-08-19
Well aligned ZnO nanorods have been prepared by a low temperature aqueous chemical growth method, using a biocomposite seed layer of ZnO nanoparticles prepared in starch and cellulose bio polymers. The effect of different concentrations of biocomposite seed layer on the alignment of ZnO nanorods has been investigated. ZnO nanorods grown on a gold-coated glass substrate have been characterized by X-ray diffraction (XRD) and field emission scanning electron microscopy (FESEM) techniques. These techniques have shown that the ZnO nanorods are well aligned and perpendicular to the substrate, and grown with a high density and uniformity on the substrate. Moreover, ZnO nanorods can be grown with an orientation along the c -axis of the substrate and exhibit a wurtzite crystal structure with a dominant (002) peak in an XRD spectrum and possessed a high crystal quality. A photoluminescence (PL) spectroscopy study of the ZnO nanorods has revealed a conventional near band edge ultraviolet emission, along with emission in the visible part of the electromagnetic spectrum due to defect emission. This study provides an alternative method for the fabrication of well aligned ZnO nanorods. This method can be helpful in improving the performance of devices where alignment plays a significant role.
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Ibupoto, Zafar Hussain; Khun, Kimleang; Eriksson, Martin; AlSalhi, Mohammad; Atif, Muhammad; Ansari, Anees; Willander, Magnus
2013-01-01
Well aligned ZnO nanorods have been prepared by a low temperature aqueous chemical growth method, using a biocomposite seed layer of ZnO nanoparticles prepared in starch and cellulose bio polymers. The effect of different concentrations of biocomposite seed layer on the alignment of ZnO nanorods has been investigated. ZnO nanorods grown on a gold-coated glass substrate have been characterized by X-ray diffraction (XRD) and field emission scanning electron microscopy (FESEM) techniques. These techniques have shown that the ZnO nanorods are well aligned and perpendicular to the substrate, and grown with a high density and uniformity on the substrate. Moreover, ZnO nanorods can be grown with an orientation along the c-axis of the substrate and exhibit a wurtzite crystal structure with a dominant (002) peak in an XRD spectrum and possessed a high crystal quality. A photoluminescence (PL) spectroscopy study of the ZnO nanorods has revealed a conventional near band edge ultraviolet emission, along with emission in the visible part of the electromagnetic spectrum due to defect emission. This study provides an alternative method for the fabrication of well aligned ZnO nanorods. This method can be helpful in improving the performance of devices where alignment plays a significant role. PMID:28811454
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NASA Technical Reports Server (NTRS)
Brink, Jeffrey S.
2005-01-01
The space shuttle Aft Propulsion System (APS) pod requires precision alignment to be installed onto the orbiter deck. The Ground Support Equipment (GSE) used to perform this task cannot be manipulated along a single Cartesian axis without causing motion along the other Cartesian axes. As a result, manipulations required to achieve a desired motion are not intuitive. My study calculated the joint angles required to align the APS pod, using reverse kinematic analysis techniques. Knowledge of these joint angles will allow the ground support team to align the APS pod more safely and efficiently. An uncertainty analysis was also performed to estimate the accuracy associated with this approach and to determine whether any inexpensive modifications can be made to further improve accuracy.
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Science Learning Outcomes in Alignment with Learning Environment Preferences
NASA Astrophysics Data System (ADS)
Chang, Chun-Yen; Hsiao, Chien-Hua; Chang, Yueh-Hsia
2011-04-01
This study investigated students' learning environment preferences and compared the relative effectiveness of instructional approaches on students' learning outcomes in achievement and attitude among 10th grade earth science classes in Taiwan. Data collection instruments include the Earth Science Classroom Learning Environment Inventory and Earth Science Learning Outcomes Inventory. The results showed that most students preferred learning in a classroom environment where student-centered and teacher-centered instructional approaches coexisted over a teacher-centered learning environment. A multivariate analysis of covariance also revealed that the STBIM students' cognitive achievement and attitude toward earth science were enhanced when the learning environment was congruent with their learning environment preference.
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Gibau, Gina Sanchez
2015-01-01
Qualitative studies that examine the experiences of underrepresented minority students in science, technology, engineering, and mathematics fields are comparatively few. This study explores the self-reported experiences of underrepresented graduate students in the biomedical sciences of a large, midwestern, urban university. Document analysis of interview transcripts from program evaluations capture firsthand accounts of student experiences and reveal the need for a critical examination of current intervention programs designed to reverse the trend of underrepresentation in the biomedical sciences. Findings point to themes aligned around the benefits and challenges of program components, issues of social adjustment, the utility of supportive relationships, and environmental impacts. PMID:26163562
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Imaging the in-plane distribution of helium precipitates at a Cu/V interface
Chen, Di; Li, Nan; Yuryev, Dina; ...
2017-02-15
Here, we describe a transmission electron microscopy investigation of the distribution of helium precipitates within the plane of an interface between Cu and V. Statistical analysis of precipitate locations reveals a weak tendency for interfacial precipitates to align alongmore » $$\\langle$$110$$\\rangle$$-type crystallographic directions within the Cu layer. Comparison of these findings with helium-free Cu/V interfaces suggests that the precipitates may be aggregating preferentially along atomic-size steps in the interface created by threading dislocations in the Cu layer. Our observations also suggest that some precipitates may be aggregating along intersections between interfacial misfit dislocations.« less
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Oliffe, John L; Grewal, Suki; Bottorff, Joan L; Luke, Haida; Toor, Harshbir
2007-01-01
The experiences of elderly South Asian (SA) men who have immigrated to Canada provide unique insights to men's health and illness behaviors and beliefs. In this article, we describe the connections between masculinity, culture, and health among a cohort of 14 SA immigrant men. The findings indicated that participants' health behaviors were closely aligned to those of western men. However, a fine-grained analysis revealed how complex cultural connections informed and influenced many men's health behaviors and beliefs. Based on the study findings, recommendations for the future design of healthcare services targeted to SA men are made.
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NASA Technical Reports Server (NTRS)
Fuelberg, Henry E.; Schudalla, Ronald L.
1989-01-01
The study presented utilized special mesoscale Cooperative Huntsville Meteorological Experiment (COHMEX) data to understand the evolution of the preconvective environment on June 17, 1986. Using the special mesoscale COHMEX data, several mechanisms for triggering the convection are investigated. Afternoon heating probably was a major factor as observed noontime temperatures were near the sounding-derived convection temperatures. The special surface network revealed a quasi-stationary area of convergence not aligned with the front that may be associated with the orography of the area. This study demonstrates that rapid, small scale atmospheric variations preceded convective development on June 17, 1986.
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Atomistic cluster alignment method for local order mining in liquids and glasses
NASA Astrophysics Data System (ADS)
Fang, X. W.; Wang, C. Z.; Yao, Y. X.; Ding, Z. J.; Ho, K. M.
2010-11-01
An atomistic cluster alignment method is developed to identify and characterize the local atomic structural order in liquids and glasses. With the “order mining” idea for structurally disordered systems, the method can detect the presence of any type of local order in the system and can quantify the structural similarity between a given set of templates and the aligned clusters in a systematic and unbiased manner. Moreover, population analysis can also be carried out for various types of clusters in the system. The advantages of the method in comparison with other previously developed analysis methods are illustrated by performing the structural analysis for four prototype systems (i.e., pure Al, pure Zr, Zr35Cu65 , and Zr36Ni64 ). The results show that the cluster alignment method can identify various types of short-range orders (SROs) in these systems correctly while some of these SROs are difficult to capture by most of the currently available analysis methods (e.g., Voronoi tessellation method). Such a full three-dimensional atomistic analysis method is generic and can be applied to describe the magnitude and nature of noncrystalline ordering in many disordered systems.
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Han, Ying-Li; Hou, Cong-Cong; Du, Chen; Zhu, Jun-Quan
2017-01-01
Heat shock proteins 70 (HSP70s) are molecular chaperones that aid in protection against environmental stress. In this study, we cloned and characterized five members of the HSP70 family (designated as HSPa1a, HSC70-1, HSC70-2, HSPa4 and HSPa14) from Lateolabrax maculatus using rapid amplification cDNA ends (RACE). Multiple sequence alignment and structural analysis revealed that all members of the HSP70 family had a conserved domain architecture, with some distinguishing features unique to each HSP70. Quantitative real-time (qPCR) analysis revealed that all members of the HSP70 family were ubiquitously and differentially expressed in all major types of tissues, including testicular tissue. This indicated that HSP70s have vital and conserved biological functions, and may also function in the development of germinal cells. The expression of mRNA of the five HSP70 family members mRNA expression was significantly increased in the head kidney, intestine and gill after Vibrio harveyi challenge, suggesting that HSP70s play an important role in the immune response. Copyright © 2016 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Amiroch, S.; Pradana, M. S.; Irawan, M. I.; Mukhlash, I.
2017-09-01
Multiple Alignment (MA) is a particularly important tool for studying the viral genome and determine the evolutionary process of the specific virus. Application of MA in the case of the spread of the Severe acute respiratory syndrome (SARS) epidemic is an interesting thing because this virus epidemic a few years ago spread so quickly that medical attention in many countries. Although there has been a lot of software to process multiple sequences, but the use of pairwise alignment to process MA is very important to consider. In previous research, the alignment between the sequences to process MA algorithm, Super Pairwise Alignment, but in this study used a dynamic programming algorithm Needleman wunchs simulated in Matlab. From the analysis of MA obtained and stable region and unstable which indicates the position where the mutation occurs, the system network topology that produced the phylogenetic tree of the SARS epidemic distance method, and system area networks mutation.
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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.
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Novel Models of Visual Topographic Map Alignment in the Superior Colliculus
El-Ghazawi, Tarek A.; Triplett, Jason W.
2016-01-01
The establishment of precise neuronal connectivity during development is critical for sensing the external environment and informing appropriate behavioral responses. In the visual system, many connections are organized topographically, which preserves the spatial order of the visual scene. The superior colliculus (SC) is a midbrain nucleus that integrates visual inputs from the retina and primary visual cortex (V1) to regulate goal-directed eye movements. In the SC, topographically organized inputs from the retina and V1 must be aligned to facilitate integration. Previously, we showed that retinal input instructs the alignment of V1 inputs in the SC in a manner dependent on spontaneous neuronal activity; however, the mechanism of activity-dependent instruction remains unclear. To begin to address this gap, we developed two novel computational models of visual map alignment in the SC that incorporate distinct activity-dependent components. First, a Correlational Model assumes that V1 inputs achieve alignment with established retinal inputs through simple correlative firing mechanisms. A second Integrational Model assumes that V1 inputs contribute to the firing of SC neurons during alignment. Both models accurately replicate in vivo findings in wild type, transgenic and combination mutant mouse models, suggesting either activity-dependent mechanism is plausible. In silico experiments reveal distinct behaviors in response to weakening retinal drive, providing insight into the nature of the system governing map alignment depending on the activity-dependent strategy utilized. Overall, we describe novel computational frameworks of visual map alignment that accurately model many aspects of the in vivo process and propose experiments to test them. PMID:28027309
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Tsai, Tsung-Heng; Tadesse, Mahlet G.; Di Poto, Cristina; Pannell, Lewis K.; Mechref, Yehia; Wang, Yue; Ressom, Habtom W.
2013-01-01
Motivation: Liquid chromatography-mass spectrometry (LC-MS) has been widely used for profiling expression levels of biomolecules in various ‘-omic’ studies including proteomics, metabolomics and glycomics. Appropriate LC-MS data preprocessing steps are needed to detect true differences between biological groups. Retention time (RT) alignment, which is required to ensure that ion intensity measurements among multiple LC-MS runs are comparable, is one of the most important yet challenging preprocessing steps. Current alignment approaches estimate RT variability using either single chromatograms or detected peaks, but do not simultaneously take into account the complementary information embedded in the entire LC-MS data. Results: We propose a Bayesian alignment model for LC-MS data analysis. The alignment model provides estimates of the RT variability along with uncertainty measures. The model enables integration of multiple sources of information including internal standards and clustered chromatograms in a mathematically rigorous framework. We apply the model to LC-MS metabolomic, proteomic and glycomic data. The performance of the model is evaluated based on ground-truth data, by measuring correlation of variation, RT difference across runs and peak-matching performance. We demonstrate that Bayesian alignment model improves significantly the RT alignment performance through appropriate integration of relevant information. Availability and implementation: MATLAB code, raw and preprocessed LC-MS data are available at http://omics.georgetown.edu/alignLCMS.html Contact: hwr@georgetown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24013927
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Röst, Hannes L; Liu, Yansheng; D'Agostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben C; Gillet, Ludovic; Testa, Giuseppe; Malmström, Lars; Aebersold, Ruedi
2016-09-01
Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography-tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we developed TRIC (http://proteomics.ethz.ch/tric/), a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics. TRIC reduced the identification error compared to a state-of-the-art SWATH-MS analysis without alignment by more than threefold at constant recall while correcting for highly nonlinear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups. Thus, TRIC fills a gap in the pipeline for automated analysis of massively parallel targeted proteomics data sets.
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Alignment of an acoustic manipulation device with cepstral analysis of electronic impedance data.
Hughes, D A; Qiu, Y; Démoré, C; Weijer, C J; Cochran, S
2015-02-01
Acoustic particle manipulation is an emerging technology that uses ultrasonic standing waves to position objects with pressure gradients and acoustic radiation forces. To produce strong standing waves, the transducer and the reflector must be aligned properly such that they are parallel to each other. This can be a difficult process due to the need to visualise the ultrasound waves and as higher frequencies are introduced, this alignment requires higher accuracy. In this paper, we present a method for aligning acoustic resonators with cepstral analysis. This is a simple signal processing technique that requires only the electrical impedance measurement data of the resonator, which is usually recorded during the fabrication process of the device. We first introduce the mathematical basis of cepstral analysis and then demonstrate and validate it using a computer simulation of an acoustic resonator. Finally, the technique is demonstrated experimentally to create many parallel linear traps for 10 μm fluorescent beads inside an acoustic resonator. Copyright © 2014 Elsevier B.V. All rights reserved.
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A basic analysis toolkit for biological sequences
Giancarlo, Raffaele; Siragusa, Alessandro; Siragusa, Enrico; Utro, Filippo
2007-01-01
This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at under the GNU GPL. PMID:17877802
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A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching.
Romero, José R; Carballido, Jessica A; Garbus, Ingrid; Echenique, Viviana C; Ponzoni, Ignacio
2016-01-01
The identification of nested motifs in genomic sequences is a complex computational problem. The detection of these patterns is important to allow the discovery of transposable element (TE) insertions, incomplete reverse transcripts, deletions, and/or mutations. In this study, a de novo strategy for detecting patterns that represent nested motifs was designed based on exhaustive searches for pairs of motifs and combinatorial pattern analysis. These patterns can be grouped into three categories, motifs within other motifs, motifs flanked by other motifs, and motifs of large size. The methodology used in this study, applied to genomic sequences from the plant species Aegilops tauschii and Oryza sativa , revealed that it is possible to identify putative nested TEs by detecting these three types of patterns. The results were validated through BLAST alignments, which revealed the efficacy and usefulness of the new method, which is called Mamushka.
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Changes in structure and geometric properties of human hair by aging.
Nagase, Shinobu; Kajiura, Yoshio; Mamada, Akira; Abe, Hiroko; Shibuichi, Satoshi; Satoh, Naoki; Itou, Takashi; Shinohara, Yuya; Amemiya, Yoshiyuki
2009-01-01
To clarify hair changes by aging, the effect of age on hair properties was investigated from macro- to microscopic view points. Sensory hair luster tests were performed on 230 Japanese females from 10 to 70 years of age, revealing that hair luster decreases with age. The age dependence of the hair diameter and the ellipticity of the hair cross section could not explain luster reduction by aging. It has been determined that an irregular increase in fiber curvature occurs with age and is a cause of luster reduction with aging. A detailed structural analysis by synchrotron radiation microbeam X-ray diffraction revealed that the inhomogeneity in the lateral distribution of the hair microstructure increased with age and relates to the irregular increase in curvature. Such an increase in curvature is one of the important factors that leads to a poor alignment of hairs and luster reduction, and is related to the appearance of aging hair.
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Single-cell proteomics: potential implications for cancer diagnostics.
Gavasso, Sonia; Gullaksen, Stein-Erik; Skavland, Jørn; Gjertsen, Bjørn T
2016-01-01
Single-cell proteomics in cancer is evolving and promises to provide more accurate diagnoses based on detailed molecular features of cells within tumors. This review focuses on technologies that allow for collection of complex data from single cells, but also highlights methods that are adaptable to routine cancer diagnostics. Current diagnostics rely on histopathological analysis, complemented by mutational detection and clinical imaging. Though crucial, the information gained is often not directly transferable to defined therapeutic strategies, and predicting therapy response in a patient is difficult. In cancer, cellular states revealed through perturbed intracellular signaling pathways can identify functional mutations recurrent in cancer subsets. Single-cell proteomics remains to be validated in clinical trials where serial samples before and during treatment can reveal excessive clonal evolution and therapy failure; its use in clinical trials is anticipated to ignite a diagnostic revolution that will better align diagnostics with the current biological understanding of cancer.
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MaxAlign: maximizing usable data in an alignment.
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.
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Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis.
Bonham-Carter, Oliver; Steele, Joe; Bastola, Dhundy
2014-11-01
Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing to their inherent computational expense when processing large amounts of sequence data. These methods are prone to giving misleading information because of genetic recombination, genetic shuffling and other inherent biological events. New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming. These new methods are often preferred, as their algorithms are simpler and are not affected by synteny-related problems. In this review, we provide a detailed discussion of computational tools, which stem from alignment-free methods based on statistical analysis from word frequencies. We provide several clear examples to demonstrate applications and the interpretations over several different areas of alignment-free analysis such as base-base correlations, feature frequency profiles, compositional vectors, an improved string composition and the D2 statistic metric. Additionally, we provide detailed discussion and an example of analysis by Lempel-Ziv techniques from data compression. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.
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Phylogenetic inference under varying proportions of indel-induced alignment gaps
Dwivedi, Bhakti; Gadagkar, Sudhindra R
2009-01-01
Background The effect of alignment gaps on phylogenetic accuracy has been the subject of numerous studies. In this study, we investigated the relationship between the total number of gapped sites and phylogenetic accuracy, when the gaps were introduced (by means of computer simulation) to reflect indel (insertion/deletion) events during the evolution of DNA sequences. The resulting (true) alignments were subjected to commonly used gap treatment and phylogenetic inference methods. Results (1) In general, there was a strong – almost deterministic – relationship between the amount of gap in the data and the level of phylogenetic accuracy when the alignments were very "gappy", (2) gaps resulting from deletions (as opposed to insertions) contributed more to the inaccuracy of phylogenetic inference, (3) the probabilistic methods (Bayesian, PhyML & "MLε, " a method implemented in DNAML in PHYLIP) performed better at most levels of gap percentage when compared to parsimony (MP) and distance (NJ) methods, with Bayesian analysis being clearly the best, (4) methods that treat gapped sites as missing data yielded less accurate trees when compared to those that attribute phylogenetic signal to the gapped sites (by coding them as binary character data – presence/absence, or as in the MLε method), and (5) in general, the accuracy of phylogenetic inference depended upon the amount of available data when the gaps resulted from mainly deletion events, and the amount of missing data when insertion events were equally likely to have caused the alignment gaps. Conclusion When gaps in an alignment are a consequence of indel events in the evolution of the sequences, the accuracy of phylogenetic analysis is likely to improve if: (1) alignment gaps are categorized as arising from insertion events or deletion events and then treated separately in the analysis, (2) the evolutionary signal provided by indels is harnessed in the phylogenetic analysis, and (3) methods that utilize the phylogenetic signal in indels are developed for distance methods too. When the true homology is known and the amount of gaps is 20 percent of the alignment length or less, the methods used in this study are likely to yield trees with 90–100 percent accuracy. PMID:19698168
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Raimann, Jochen G; Ficociello, Linda H; Usvyat, Len A; Zhang, Hanjie; Pacelli, Lisa; Moore, Sandi; Sheppard, Penny; Xiao, Qingqing; Wang, Yuedong; Mullon, Claudy; Balter, Paul; Sullivan, Terry; Kotanko, Peter
2018-04-02
Evidence indicates favorable effects of dialysate (DNa + ) to serum sodium concentration (SNa + ) alignment, however, results from larger sample populations are needed. For this reason, we conducted a retrospective propensity score-matched cohort study from a quality improvement project to investigate the effects of alignment on population of maintenance hemodialysis patients. At 4 participating hemodialysis (HD) clinics, patients with SNa + lower than the standard DNa + of 137 mEq/L who received HD with DNa + aligned to the average of the last 4 SNa + measurements were evaluated (clinicaltrials.gov # NCT01825590 ). In this retrospective data analysis, an intention-to-treat (primary) and an as-treated "intervention" (secondary) cohort were created. "Aligned" patients from both cohorts (N = 163 for the primary and N = 137 for the secondary) were then propensity-score matched in a 1:1 fashion to "unaligned" patients from the Renal Research Institute database. The propensity score was generated based on age, gender, white race, Hispanic ethnicity, absence or presence of diabetes, hemodialysis vintage, interdialytic weight gain (IDWG; as a percentage of postdialysis body weight), catheter as primary dialysis access, predialysis systolic blood pressure, serum sodium concentration, hospitalization count during baseline. T-Test was employed for group comparisons of changes to the primary (volume-related and hemodynamic parameters) and tertiary outcomes. All-cause and fluid overload-related hospitalization admission rates were compared using Wilcoxon Rank Sum test and Cox regression analysis for repeated events. In the primary analysis, aligned and unaligned subjects showed comparable demographics at baseline. Treatment effects were significant for IDWG [-0.12 (95% CI -0.24 to 0) L] and showed decreasing non-significant trends for pre-dialysis hemodynamic parameters. Count comparison and Cox regression analysis showed no clear advantage of alignment in terms of all-cause and fluid overload-related hospitalization. Results from the largest sodium alignment program to date suggest positive treatment effects on volume-related and hemodynamic parameters, but no clear effect on risk of hospitalization. Well-matched control patients minimized confounding effects. Small effects and lack of significant differences may be explained by a low baseline DNa + limiting the interventional change.
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MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer.
Gauthier, Nicholas Paul; Reznik, Ed; Gao, Jianjiong; Sumer, Selcuk Onur; Schultz, Nikolaus; Sander, Chris; Miller, Martin L
2016-01-04
The MutationAligner web resource, available at http://www.mutationaligner.org, enables discovery and exploration of somatic mutation hotspots identified in protein domains in currently (mid-2015) more than 5000 cancer patient samples across 22 different tumor types. Using multiple sequence alignments of protein domains in the human genome, we extend the principle of recurrence analysis by aggregating mutations in homologous positions across sets of paralogous genes. Protein domain analysis enhances the statistical power to detect cancer-relevant mutations and links mutations to the specific biological functions encoded in domains. We illustrate how the MutationAligner database and interactive web tool can be used to explore, visualize and analyze mutation hotspots in protein domains across genes and tumor types. We believe that MutationAligner will be an important resource for the cancer research community by providing detailed clues for the functional importance of particular mutations, as well as for the design of functional genomics experiments and for decision support in precision medicine. MutationAligner is slated to be periodically updated to incorporate additional analyses and new data from cancer genomics projects. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Functional characterization of the turkey macrophage migration inhibitory factor.
Park, Myeongseon; Kim, Sungwon; Fetterer, Raymond H; Dalloul, Rami A
2016-08-01
Macrophage migration inhibitory factor (MIF) is a soluble protein that inhibits the random migration of macrophages and plays a pivotal immunoregulatory function in innate and adaptive immunity. The aim of this study was to clone the turkey MIF (TkMIF) gene, express the active protein, and characterize its basic function. The full-length TkMIF gene was amplified from total RNA extracted from turkey spleen, followed by cloning into a prokaryotic (pET11a) expression vector. Sequence analysis revealed that TkMIF consists of 115 amino acids with 12.5 kDa molecular weight. Multiple sequence alignment revealed 100%, 65%, 95% and 92% identity with chicken, duck, eagle and zebra finch MIFs, respectively. Recombinant TkMIF (rTkMIF) was expressed in Escherichia coli and purified through HPLC and endotoxin removal. SDS-PAGE analysis revealed an approximately 13.5 kDa of rTkMIF monomer containing T7 tag in soluble form. Western blot analysis showed that anti-chicken MIF (ChMIF) polyclonal antisera detected a monomer form of TkMIF at approximately 13.5 kDa size. Further functional analysis revealed that rTkMIF inhibits migration of both mononuclear cells and splenocytes in a dose-dependent manner, but was abolished by the addition of anti-ChMIF polyclonal antisera. qRT-PCR analysis revealed elevated transcripts of pro-inflammatory cytokines by rTkMIF in LPS-stimulated monocytes. rTkMIF also led to increased levels of IFN-γ and IL-17F transcripts in Con A-activated splenocytes, while IL-10 and IL-13 transcripts were decreased. Overall, the sequences of both the turkey and chicken MIF have high similarity and comparable biological functions with respect to migration inhibitory activities of macrophages and enhancement of pro-inflammatory cytokine expression, suggesting that turkey and chicken MIFs would be biologically cross-reactive. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Controllability analysis and decentralized control of a wet limestone flue gas desulfurization plant
DOE Office of Scientific and Technical Information (OSTI.GOV)
Perales, A.L.V.; Ortiz, F.J.G.; Ollero, P.
2008-12-15
Presently, decentralized feedback control is the only control strategy used in wet limestone flue gas desulfurization (WLFGD) plants. Proper tuning of this control strategy is becoming an important issue in WLFGD plants because more stringent SO{sub 2} regulations have come into force recently. Controllability analysis is a highly valuable tool for proper design of control systems, but it has not been applied to WLFGD plants so far. In this paper a decentralized control strategy is designed and applied to a WLFGD pilot plant taking into account the conclusions of a controllability analysis. The results reveal that good SO{sub 2} controlmore » in WLFGD plants can be achieved mainly because the main disturbance of the process is well-aligned with the plant and interactions between control loops are beneficial to SO{sub 2} control.« less
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PDBFlex: exploring flexibility in protein structures
Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya; Rotkiewicz, Piotr; Jaroszewski, Lukasz; Godzik, Adam
2016-01-01
The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software. PMID:26615193
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Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.
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.
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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.
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Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-yu; Zhang, Xiao-mei; Song, Da-feng; Zhang, Chen
2016-01-01
Objective: In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods: The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). Results: We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Conclusions: Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate. PMID:27487802
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Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-Yu; Zhang, Xiao-Mei; Song, Da-Feng; Zhang, Chen
2016-08-01
In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate.
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Vedhanarayanan, Balaraman; Nair, Vishnu S; Nair, Vijayakumar C; Ajayaghosh, Ayyappanpillai
2016-08-22
In an attempt to gather experimental evidence for the influence of carbon allotropes on supramolecular chirality, we found that carbon nanotubes (CNTs) facilitate amplification of the molecular chirality of a π-gelator (MC-OPV) to supramolecular helicity at a concentration much lower than that required for intermolecular interaction. For example, at a concentration 1.8×10(-4) m, MC-OPV did not exhibit a CD signal; however, the addition of 0-0.6 mg of SWNTs resulted in amplified chirality as evident from the CD spectrum. Surprisingly, AFM analysis revealed the formation of thick helical fibers with a width of more than 100 nm. High-resolution TEM analysis and solid-state UV/Vis/NIR spectroscopy revealed that the thick helical fibers were cylindrical cables composed of individually wrapped and coaxially aligned SWNTs. Such an impressive effect of CNTs on supramolecular chirality and cylindrical-cable formation has not been reported previously. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Identification of a serotype-independent linear epitope of foot-and-mouth disease virus.
Yang, Baolin; Wang, Mingxia; Liu, Wenming; Xu, Zhiqiang; Wang, Haiwei; Yang, Decheng; Ma, Wenge; Zhou, Guohui; Yu, Li
2017-12-01
Foot-and-mouth disease (FMD), caused by foot-and-mouth disease virus (FMDV), is a highly contagious infectious disease that affects domestic and wild cloven-hoofed animals worldwide. VP2 is a structural protein of FMDV. In this study, an FMDV serotype-independent monoclonal antibody (MAb), 10B10, against the viral capsid protein VP2 was generated, and a series of GST fusion proteins expressing a truncated peptide of VP2 was subjected to Western blot analysis using MAb 10B10. Their results indicated that the peptide 8 TLLEDRILT 16 of VP2 is the minimal requirement of the epitope recognized by MAb 10B10. Importantly, this linear epitope was highly conserved among all seven serotypes of FMDV in a sequence alignment analysis. Subsequent alanine-scanning mutagenesis analysis revealed that the residues Thr 8 and Asp 12 of the epitope were crucial for MAb-10B10 binding. Furthermore, Western blot analysis also revealed that the MAb 10B10-directed epitope could be recognized by positive sera from FMDV-infected cattle. The discovery that MAb 10B10 recognizes a serotype-independent linear epitope of FMDV suggests potential applications for this MAb in the development of serotype-independent tests for FMDV.
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Molecular characterization of the vitamin D receptor (VDR) gene in Holstein cows.
Ali, Mayar O; El-Adl, Mohamed A; Ibrahim, Hussam M M; Elseedy, Youssef Y; Rizk, Mohamed A; El-Khodery, Sabry A
2018-06-01
Vitamin D plays a vital role in calcium homeostasis, growth, and immunoregulation. Because little is known about the vitamin D receptor (VDR) gene in cattle, the aim of the present investigation was to present the molecular characterization of exons 5 and 6 of the VDR gene in Holstein cows. DNA extraction, genomic sequencing, phylogenetic analysis, synteny mapping and single nucleotide gene polymorphism analysis of the VDR gene were performed to assess blood samples collected from 50 clinically healthy Holstein cows. The results revealed the presence of a 450-base pair (bp) nucleotide sequence that resembled exons 5 and 6 with intron 5 enclosed between these exons. Sequence alignment and phylogenetic analysis revealed a close relationship between the sequenced VDR region and that found in Hereford cattle. A close association between this region and the corresponding region in small ruminants was also documented. Moreover, a single nucleotide polymorphism (SNP) that caused the replacement of a glutamate with an arginine in the deduced amino acid sequence was detected at position 7 of exon 5. In conclusion, Holstein and Hereford cattle differ with respect to exon 5 of the VDR gene. Phylogenetic analysis of the VDR gene based on nucleotide sequence produced different results from prior analyses based on amino acid sequence. Copyright © 2018 Elsevier Ltd. All rights reserved.
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Continuous high-yield production of vertically aligned carbon nanotubes on 2D and 3D substrates.
Guzmán de Villoria, Roberto; Hart, A John; Wardle, Brian L
2011-06-28
Vertically aligned carbon nanotubes (VACNTs) have certain advantages over bulk CNT powders and randomly oriented CNT mats for applications in flexible electronic devices, filtration membranes, biosensors and multifunctional aerospace materials. Here, a machine and a process to synthesize VACNTs in a continuous manner are presented showing uniform growth on 2D and 3D substrates, including alumina fibers, silicon wafer pieces, and stainless steel foils. Aligned multiwalled carbon nanotubes (MWNT) are synthesized at substrate feed rates of up to 6.8 cm/min, and the CNTs reach up to 60 μm in length depending on residence time in the reactor. In addition to the aligned morphology indicative of high yield growth, transmission electron microscopy and Raman spectroscopy reveal that the CNTs are of comparable quality to CNTs grown via a similar batch process. A significant reduction in time, reaction products, gases, and energy is demonstrated relative to batch processing, paving the way for industrial production of VACNTs.
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Desorption Kinetics of Methanol, Ethanol, and Water from Graphene
DOE Office of Scientific and Technical Information (OSTI.GOV)
Smith, R. Scott; Matthiesen, Jesper; Kay, Bruce D.
2014-09-18
The desorption kinetics of methanol, ethanol, and water from graphene covered Pt(111) are investigated. The temperature programmed desorption (TPD) spectra for both methanol and ethanol have well-resolved first, second, third, and multilayer layer desorption peaks. The alignment of the leading edges is consistent with zero-order desorption kinetics from all layers. In contrast, for water the first and second layers are not resolved. At low water coverages (< 1 ML) the initial desorption leading edges are aligned but then fall out of alignment at higher temperatures. For thicker water layers (10 to 100 ML), the desorption leading edges are in alignmentmore » throughout the desorption of the film. The coverage dependence of the desorption behavoir suggests that at low water coverages the non-alignment of the desorption leading edges is due to water dewetting from the graphene substrate. Kinetic simulations reveal that the experimental results are consistent with zero-order desorption. The simulations also show that fractional order desorption kinetics would be readily apparent in the experimental TPD spectra.« less
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Desorption kinetics of methanol, ethanol, and water from graphene.
Smith, R Scott; Matthiesen, Jesper; Kay, Bruce D
2014-09-18
The desorption kinetics of methanol, ethanol, and water from graphene covered Pt(111) are investigated. The temperature programmed desorption (TPD) spectra for both methanol and ethanol have well-resolved first, second, third, and multilayer layer desorption peaks. The alignment of the leading edges is consistent with zero-order desorption kinetics from all layers. In contrast, for water, the first and second layers are not resolved. At low water coverages (<1 monolayer (ML)) the initial desorption leading edges are aligned but then fall out of alignment at higher temperatures. For thicker water layers (10-100 ML), the desorption leading edges are in alignment throughout the desorption of the film. The coverage dependence of the desorption behavoir suggests that at low water coverages the nonalignment of the desorption leading edges is due to water dewetting from the graphene substrate. Kinetic simulations reveal that the experimental results are consistent with zero-order desorption. The simulations also show that fractional order desorption kinetics would be readily apparent in the experimental TPD spectra.
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A statistical physics perspective on alignment-independent protein sequence comparison.
Chattopadhyay, Amit K; Nasiev, Diar; Flower, Darren R
2015-08-01
Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative success of modern-day sequence alignment algorithms, so-called alignment-free approaches offer a complementary means of determining and expressing similarity, with potential benefits in certain key applications, such as regression analysis of protein structure-function studies, where alignment-base similarity has performed poorly. Here, we offer a fresh, statistical physics-based perspective focusing on the question of alignment-free comparison, in the process adapting results from 'first passage probability distribution' to summarize statistics of ensemble averaged amino acid propensity values. In this article, we introduce and elaborate this approach. © The Author 2015. Published by Oxford University Press.
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Spatio-temporal alignment of pedobarographic image sequences.
Oliveira, Francisco P M; Sousa, Andreia; Santos, Rubim; Tavares, João Manuel R S
2011-07-01
This article presents a methodology to align plantar pressure image sequences simultaneously in time and space. The spatial position and orientation of a foot in a sequence are changed to match the foot represented in a second sequence. Simultaneously with the spatial alignment, the temporal scale of the first sequence is transformed with the aim of synchronizing the two input footsteps. Consequently, the spatial correspondence of the foot regions along the sequences as well as the temporal synchronizing is automatically attained, making the study easier and more straightforward. In terms of spatial alignment, the methodology can use one of four possible geometric transformation models: rigid, similarity, affine, or projective. In the temporal alignment, a polynomial transformation up to the 4th degree can be adopted in order to model linear and curved time behaviors. Suitable geometric and temporal transformations are found by minimizing the mean squared error (MSE) between the input sequences. The methodology was tested on a set of real image sequences acquired from a common pedobarographic device. When used in experimental cases generated by applying geometric and temporal control transformations, the methodology revealed high accuracy. In addition, the intra-subject alignment tests from real plantar pressure image sequences showed that the curved temporal models produced better MSE results (P < 0.001) than the linear temporal model. This article represents an important step forward in the alignment of pedobarographic image data, since previous methods can only be applied on static images.
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ERIC Educational Resources Information Center
Vanfretti, L.; Milano, F.
2012-01-01
This paper describes how the use of free and open-source software (FOSS) can facilitate the application of constructive alignment theory in power systems engineering education by enabling the deep learning approach in power system analysis courses. With this aim, this paper describes the authors' approach in using the Power System Analysis Toolbox…
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Performance Reports: Mirror alignment system performance prediction comparison between SAO and EKC
NASA Technical Reports Server (NTRS)
Tananbaum, H. D.; Zhang, J. P.
1994-01-01
The objective of this study is to perform an independent analysis of the residual high resolution mirror assembly (HRMA) mirror distortions caused by force and moment errors in the mirror alignment system (MAS) to statistically predict the HRMA performance. These performance predictions are then compared with those performed by Kodak to verify their analysis results.
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Methodological Choices in the Content Analysis of Textbooks for Measuring Alignment with Standards
ERIC Educational Resources Information Center
Polikoff, Morgan S.; Zhou, Nan; Campbell, Shauna E.
2015-01-01
With the recent adoption of the Common Core standards in many states, there is a need for quality information about textbook alignment to standards. While there are many existing content analysis procedures, these generally have little, if any, validity or reliability evidence. One exception is the Surveys of Enacted Curriculum (SEC), which has…
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Bullock, Alison; Tseng, Hsu-Min; Wells, Stephanie E
2017-01-01
Objectives To examine how burnout across medical student to junior doctor transition relates to: measures of professional identity, team understanding, anxiety, gender, age and workplace learning (assistantship) alignment to first post. Design A longitudinal 1-year cohort design. Two groups of final-year medical students: (1) those undertaking end-of-year assistantships aligned in location and specialty with their first post and (2) those undertaking assistantships non-aligned. An online questionnaire included: Professional Identity Scale, Team Understanding Scale, modified Hamilton Anxiety Rating Scale and modified Copenhagen Burnout Inventory. Data were collected on four occasions: (T1) prior to graduation; (T2) 1 month post-transition; (T3) 6 months post-transition and (T4) 10 months post-transition. Questionnaires were analysed individually and using linear mixed-effect models. Setting Medical schools and postgraduate training in one UK country. Participants All aligned assistantship (n=182) and non-aligned assistantship students (n=319) were contacted; n=281 (56%) responded: 68% (n=183) females, 73% (n=206) 22–30 years, 46% aligned (n=129). Completion rates: aligned 72% (93/129) and non-aligned 64% (98/152). Results Analyses of individual scales revealed that self-reported anxiety, professional identity and patient-related burnout were stable, while team understanding, personal and work-related burnout increased, all irrespective of alignment. Three linear mixed-effect models (personal, patient-related and work-related burnout as outcome measures; age and gender as confounding variables) found that males self-reported significantly lower personal, but higher patient-related burnout, than females. Age and team understanding had no effect. Anxiety was significantly positively related and professional identity was significantly negatively related to burnout. Participants experiencing non-aligned assistantships reported higher personal and work-related burnout over time. Conclusions Implications for practice include medical schools’ consideration of an end-of-year workplace alignment with first-post before graduation or an extended shadowing period immediately postgraduation. How best to support undergraduate students’ early professional identity development should be examined. Support systems should be in place across the transition for individuals with a predisposition for anxiety. PMID:29284717
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Freund, D; Ding, X; Zhang, J
Purpose: In prostate proton radiotherapy, three fiducial markers are used for patient daily alignment. However fiducial alignment can change beamline heterogeneity in proton therapy. The purpose of this study is to determine the difference in fiducial and boney anatomy alignment for patient treatment. Methods and materials: Prostate cancer patients who received proton treatment were included in this study. 3 fiducial markers were implanted before the initial CT. All the patients were re-CT’d every 2 weeks to check the fiducial marker position reproducibility as well as dosimetric consistence of target coverage. In geometry study, re-CT were fused to the initial CTmore » base on the boney anatomy and the average fiducial marker displacement was measured the centers of the fiducials. Dosimetrically, the initial plan was recalculated directly to re-CT image set based on the boney alignment and fiducial alignment to determine the difference from daily treatment. Prostate coverage and hotspots were evaluated using the dose to 98% of the CTV (D98) and dose to 2% (D2), respectively. Results: The shift from the initial 6 patient CT image sets resulted in an average change in the fiducial location of 5.70 +/− 3 mm. Dosimetric comparison from a single patient revealed that differences from the planned dose resulted from both boney and fiducial alignment. Planned clinical treatment volume coverage resulted in a D98 of 70.44Gy and D2 of 70.84Gy compared to a D98 of 70.13Gy and D2 70.94Gy for boney alignment and a D98 of 70.08Gy and D2 71.18Gy for fiducial alignment respectively. Conclusion: This study demonstrates that with boney anatomy alignment there is little change to CTV coverage and only slightly worse CTV coverage and hotspot production with fiducial alignment. An increase patient cohort and further investigation is necessary to determine the whether boney alignment can help better control dose heterogeneity.« less
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FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies.
Kim, Jiwoong; Kim, Min Soo; Koh, Andrew Y; Xie, Yang; Zhan, Xiaowei
2016-10-10
Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging. The available functional analysis pipelines lack several key features: (i) an integrated alignment tool, (ii) operon-level analysis, and (iii) the ability to process large datasets. Here we introduce our open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data, FMAP (Functional Mapping and Analysis Pipeline). FMAP performs alignment, gene family abundance calculations, and statistical analysis (three levels of analyses are provided: differentially-abundant genes, operons and pathways). The resulting output can be easily visualized with heatmaps and functional pathway diagrams. FMAP functional predictions are consistent with currently available functional analysis pipelines. FMAP is a comprehensive tool for providing functional analysis of metagenomic/metatranscriptomic sequencing data. With the added features of integrated alignment, operon-level analysis, and the ability to process large datasets, FMAP will be a valuable addition to the currently available functional analysis toolbox. We believe that this software will be of great value to the wider biology and bioinformatics communities.
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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).
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Simulation-based comprehensive benchmarking of RNA-seq aligners
Baruzzo, Giacomo; Hayer, Katharina E; Kim, Eun Ji; Di Camillo, Barbara; FitzGerald, Garret A; Grant, Gregory R
2018-01-01
Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. We performed a comprehensive benchmarking of 14 common splice-aware aligners for base, read, and exon junction-level accuracy and compared default with optimized parameters. We found that performance varied by genome complexity, and accuracy and popularity were poorly correlated. The most widely cited tool underperforms for most metrics, particularly when using default settings. PMID:27941783
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Gate-tunable resonant tunneling in double bilayer graphene heterostructures.
Fallahazad, Babak; Lee, Kayoung; Kang, Sangwoo; Xue, Jiamin; Larentis, Stefano; Corbet, Christopher; Kim, Kyounghwan; Movva, Hema C P; Taniguchi, Takashi; Watanabe, Kenji; Register, Leonard F; Banerjee, Sanjay K; Tutuc, Emanuel
2015-01-14
We demonstrate gate-tunable resonant tunneling and negative differential resistance in the interlayer current-voltage characteristics of rotationally aligned double bilayer graphene heterostructures separated by hexagonal boron nitride (hBN) dielectric. An analysis of the heterostructure band alignment using individual layer densities, along with experimentally determined layer chemical potentials indicates that the resonance occurs when the energy bands of the two bilayer graphene are aligned. We discuss the tunneling resistance dependence on the interlayer hBN thickness, as well as the resonance width dependence on mobility and rotational alignment.
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Reddy, M K; Nair, S; Singh, B N; Mudgil, Y; Tewari, K K; Sopory, S K
2001-01-24
We report the cloning and sequencing of both cDNA and genomic DNA of a 33 kDa chloroplast ribonucleoprotein (33RNP) from pea. The analysis of the predicted amino acid sequence of the cDNA clone revealed that the encoded protein contains two RNA binding domains, including the conserved consensus ribonucleoprotein sequences CS-RNP1 and CS-RNP2, on the C-terminus half and the presence of a putative transit peptide sequence in the N-terminus region. The phylogenetic and multiple sequence alignment analysis of pea chloroplast RNP along with RNPs reported from the other plant sources revealed that the pea 33RNP is very closely related to Nicotiana sylvestris 31RNP and 28RNP and also to 31RNP and 28RNP of Arabidopsis and spinach, respectively. The pea 33RNP was expressed in Escherichia coli and purified to homogeneity. The in vitro import of precursor protein into chloroplasts confirmed that the N-terminus putative transit peptide is a bona fide transit peptide and 33RNP is localized in the chloroplast. The nucleic acid-binding properties of the recombinant protein, as revealed by South-Western analysis, showed that 33RNP has higher binding affinity for poly (U) and oligo dT than for ssDNA and dsDNA. The steady state transcript level was higher in leaves than in roots and the expression of this gene is light stimulated. Sequence analysis of the genomic clone revealed that the gene contains four exons and three introns. We have also isolated and analyzed the 5' flanking region of the pea 33RNP gene.
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Coan, Heather B.; Youker, Robert T.
2017-01-01
Understanding how proteins mutate is critical to solving a host of biological problems. Mutations occur when an amino acid is substituted for another in a protein sequence. The set of likelihoods for amino acid substitutions is stored in a matrix and input to alignment algorithms. The quality of the resulting alignment is used to assess the similarity of two or more sequences and can vary according to assumptions modeled by the substitution matrix. Substitution strategies with minor parameter variations are often grouped together in families. For example, the BLOSUM and PAM matrix families are commonly used because they provide a standard, predefined way of modeling substitutions. However, researchers often do not know if a given matrix family or any individual matrix within a family is the most suitable. Furthermore, predefined matrix families may inaccurately reflect a particular hypothesis that a researcher wishes to model or otherwise result in unsatisfactory alignments. In these cases, the ability to compare the effects of one or more custom matrices may be needed. This laborious process is often performed manually because the ability to simultaneously load multiple matrices and then compare their effects on alignments is not readily available in current software tools. This paper presents SubVis, an interactive R package for loading and applying multiple substitution matrices to pairwise alignments. Users can simultaneously explore alignments resulting from multiple predefined and custom substitution matrices. SubVis utilizes several of the alignment functions found in R, a common language among protein scientists. Functions are tied together with the Shiny platform which allows the modification of input parameters. Information regarding alignment quality and individual amino acid substitutions is displayed with the JavaScript language which provides interactive visualizations for revealing both high-level and low-level alignment information. PMID:28674656
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Biclustering as a method for RNA local multiple sequence alignment.
Wang, Shu; Gutell, Robin R; Miranker, Daniel P
2007-12-15
Biclustering is a clustering method that simultaneously clusters both the domain and range of a relation. A challenge in multiple sequence alignment (MSA) is that the alignment of sequences is often intended to reveal groups of conserved functional subsequences. Simultaneously, the grouping of the sequences can impact the alignment; precisely the kind of dual situation biclustering is intended to address. We define a representation of the MSA problem enabling the application of biclustering algorithms. We develop a computer program for local MSA, BlockMSA, that combines biclustering with divide-and-conquer. BlockMSA simultaneously finds groups of similar sequences and locally aligns subsequences within them. Further alignment is accomplished by dividing both the set of sequences and their contents. The net result is both a multiple sequence alignment and a hierarchical clustering of the sequences. BlockMSA was tested on the subsets of the BRAliBase 2.1 benchmark suite that display high variability and on an extension to that suite to larger problem sizes. Also, alignments were evaluated of two large datasets of current biological interest, T box sequences and Group IC1 Introns. The results were compared with alignments computed by ClustalW, MAFFT, MUCLE and PROBCONS alignment programs using Sum of Pairs (SPS) and Consensus Count. Results for the benchmark suite are sensitive to problem size. On problems of 15 or greater sequences, BlockMSA is consistently the best. On none of the problems in the test suite are there appreciable differences in scores among BlockMSA, MAFFT and PROBCONS. On the T box sequences, BlockMSA does the most faithful job of reproducing known annotations. MAFFT and PROBCONS do not. On the Intron sequences, BlockMSA, MAFFT and MUSCLE are comparable at identifying conserved regions. BlockMSA is implemented in Java. Source code and supplementary datasets are available at http://aug.csres.utexas.edu/msa/
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Domain alignment within ferroelectric/dielectric PbTiO 3 /SrTiO 3 superlattice nanostructures
DOE Office of Scientific and Technical Information (OSTI.GOV)
Park, Joonkyu; Mangeri, John; Zhang, Qingteng
The ferroelectric domain pattern within lithographically defined PbTiO 3/SrTiO 3 ferroelectric/dielectric heteroepitaxial superlattice nanostructures is strongly influenced by the edges of the structures. Synchrotron X-ray nanobeam diffraction reveals that the spontaneously formed 180° ferroelectric stripe domains exhibited by such superlattices adopt a configuration in rectangular nanostructures in which domain walls are aligned with long patterned edges. The angular distribution of X-ray diffuse scattering intensity from nanodomains indicates that domains are aligned within an angular range of approximately 20° with respect to the edges. Computational studies based on a time-dependent Landau–Ginzburg–Devonshire model show that the preferred direction of the alignment resultsmore » from lowering of the bulk and electrostrictive contributions to the free energy of the system due to the release of the lateral mechanical constraint. This unexpected alignment appears to be intrinsic and not a result of distortions or defects caused by the patterning process. Thus, our work demonstrates how nanostructuring and patterning of heteroepitaxial superlattices allow for pathways to create and control ferroelectric structures that may appear counterintuitive.« less
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Domain alignment within ferroelectric/dielectric PbTiO 3 /SrTiO 3 superlattice nanostructures
Park, Joonkyu; Mangeri, John; Zhang, Qingteng; ...
2018-01-22
The ferroelectric domain pattern within lithographically defined PbTiO 3/SrTiO 3 ferroelectric/dielectric heteroepitaxial superlattice nanostructures is strongly influenced by the edges of the structures. Synchrotron X-ray nanobeam diffraction reveals that the spontaneously formed 180° ferroelectric stripe domains exhibited by such superlattices adopt a configuration in rectangular nanostructures in which domain walls are aligned with long patterned edges. The angular distribution of X-ray diffuse scattering intensity from nanodomains indicates that domains are aligned within an angular range of approximately 20° with respect to the edges. Computational studies based on a time-dependent Landau–Ginzburg–Devonshire model show that the preferred direction of the alignment resultsmore » from lowering of the bulk and electrostrictive contributions to the free energy of the system due to the release of the lateral mechanical constraint. This unexpected alignment appears to be intrinsic and not a result of distortions or defects caused by the patterning process. Thus, our work demonstrates how nanostructuring and patterning of heteroepitaxial superlattices allow for pathways to create and control ferroelectric structures that may appear counterintuitive.« less
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NASA Astrophysics Data System (ADS)
Su, Linlin; Wang, Ying; Guo, Qinglin; Li, Xiaowei; Wang, Shufang; Fu, Guangsheng; Mazur, Yuriy I.; E Ware, Morgan; Salamo, Gregory J.; Liang, Baolai; Huffaker, Diana L.
2017-08-01
Optical properties of GaAs/Al x Ga1-x As quantum rings (QRs) grown on GaAs (1 0 0) by droplet epitaxy have been investigated as a function of the Al-composition in the Al x Ga1-x As barrier. A transition from type-I to type-II band alignment is observed for the QRs via photoluminescence (PL) and time-resolved photoluminescence (TRPL) measurements. While x ⩽ 0.45, the QR PL spectra show a blue-shift and an increasing intensity with increasing Al-composition, revealing the enhancement of quantum confinement in the QRs with type-I band alignment. While x ⩾ 0.60, the characteristic large blue-shift with excitation intensity and the much longer lifetime indicate the realization of a type-II band alignment. Due to the height fluctuation of QR structures grown by droplet epitaxy mode, it is not the large blue-shift of emission energy, but the long lifetime that becomes the more important feature to identify the type-II band alignment.
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NASA Astrophysics Data System (ADS)
Okabe, Taizo; Nishimichi, Takahiro; Oguri, Masamune; Peirani, Sébastien; Kitayama, Tetsu; Sasaki, Shin; Suto, Yasushi
2018-04-01
While various observations measured ellipticities of galaxy clusters and alignments between orientations of the brightest cluster galaxies and their host clusters, there are only a handful of numerical simulations that implement realistic baryon physics to allow direct comparisons with those observations. Here we investigate ellipticities of galaxy clusters and alignments between various components of them and the central galaxies in the state-of-the-art cosmological hydrodynamical simulation Horizon-AGN, which contains dark matter, stellar, and gas components in a large simulation box of (100h-1 Mpc)3 with high spatial resolution (˜1 kpc). We estimate ellipticities of total matter, dark matter, stellar, gas surface mass density distributions, X-ray surface brightness, and the Compton y-parameter of the Sunyaev-Zel'dovich effect, as well as alignments between these components and the central galaxies for 120 projected images of galaxy clusters with masses M200 > 5 × 1013M⊙. Our results indicate that the distributions of these components are well aligned with the major-axes of the central galaxies, with the root mean square value of differences of their position angles of ˜20°, which vary little from inner to the outer regions. We also estimate alignments of these various components with total matter distributions, and find tighter alignments than those for central galaxies with the root mean square value of ˜15°. We compare our results with previous observations of ellipticities and position angle alignments and find reasonable agreements. The comprehensive analysis presented in this paper provides useful prior information for analyzing stacked lensing signals as well as designing future observations to study ellipticities and alignments of galaxy clusters.
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NASA Astrophysics Data System (ADS)
Okabe, Taizo; Nishimichi, Takahiro; Oguri, Masamune; Peirani, Sébastien; Kitayama, Tetsu; Sasaki, Shin; Suto, Yasushi
2018-07-01
While various observations measured ellipticities of galaxy clusters and alignments between orientations of the brightest cluster galaxies and their host clusters, there are only a handful of numerical simulations that implement realistic baryon physics to allow direct comparisons with those observations. Here, we investigate ellipticities of galaxy clusters and alignments between various components of them and the central galaxies in the state-of-the-art cosmological hydrodynamical simulation Horizon-AGN, which contains dark matter, stellar, and gas components in a large simulation box of (100h-1 Mpc)3 with high spatial resolution (˜1 kpc). We estimate ellipticities of total matter, dark matter, stellar, gas surface mass density distributions, X-ray surface brightness, and the Compton y-parameter of the Sunyaev-Zel'dovich effect, as well as alignments between these components and the central galaxies for 120 projected images of galaxy clusters with masses M200 > 5 × 1013 M⊙. Our results indicate that the distributions of these components are well aligned with the major axes of the central galaxies, with the root-mean-square value of differences of their position angles of ˜20°, which vary little from inner to the outer regions. We also estimate alignments of these various components with total matter distributions, and find tighter alignments than those for central galaxies with the root-mean-square value of ˜15°. We compare our results with previous observations of ellipticities and position angle alignments and find reasonable agreements. The comprehensive analysis presented in this paper provides useful prior information for analysing stacked lensing signals as well as designing future observations to study ellipticities and alignments of galaxy clusters.
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Production and perception of contrast: The case of the rise-fall contour in German
Kügler, Frank; Gollrad, Anja
2015-01-01
This study investigates the phonetics of German nuclear rise-fall contours in relation to contexts that trigger either a contrastive or a non-contrastive interpretation in the answer. A rise-fall contour can be conceived of a tonal sequence of L-H-L. A production study elicited target sentences in contrastive and non-contrastive contexts. The majority of cases realized showed a nuclear rise-fall contour. The acoustic analysis of these contours revealed a significant effect of contrastiveness on the height/alignment of the accent peak as a function of focus context. On the other hand, the height/alignment of the low turning point at the beginning of the rise did not show an effect of contrastiveness. In a series of semantic congruency perception tests participants judged the congruency of congruent and incongruent context-stimulus pairs based on three different sets of stimuli: (i) original data, (ii) manipulation of accent peak, and (iii) manipulation of the leading low. Listeners distinguished nuclear rise-fall contours as a function of focus context (Experiment 1 and 2), however not based on manipulations of the leading low (Experiment 3). The results suggest that the alignment and scaling of the accentual peak are sufficient to license a contrastive interpretation of a nuclear rise-fall contour, leaving the rising part as a phonetic onglide, or as a low tone that does not interact with the contrastivity of the context. PMID:26388795
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Effectiveness of Hip External Rotator Strengthening Exercise in Korean Postural Bowleg Women.
Park, Seong Hoon; Lee, Jun Won; Kim, Joo Hyun; Tak, Kyoung Seok; Lee, Byeong Ho; Suh, In Suck
2017-08-01
Postural bowleg is a subclinical entity with both aesthetic and functional outcomes and appears to be common in East Asian countries. Internal rotation of the hip joint is associated with varus alignment at the knee joint of the bowleg. Strengthening exercise for the hip external rotator muscles seems to be effective in improving varus alignment of bowleg, but no standardized exercise program exists. A standardized active resistance strengthening exercise for hip external rotator muscles could improve varus alignment of the lower limb in bowlegged Korean women. In this article, a case series study was conducted to observe changes following a standardized 3-month program using equipment designed for strengthening of the hip external rotator muscles. Photogrammetric and radiographic data were used to compare the gap between knees and tibiofemoral (TF) angles before and after the exercise program. As a result, on average, the knee gap decreased by 1.6 cm. The TF angle decreased by 1.5°. Regression analysis revealed a statistically significant association between changes in knee gap and TF angle. The standardized 3-month active resistance strengthening exercise program of hip external rotator muscles was effective in improving postural deviation and cosmetic outcomes in bowlegged Korean women. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .
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Michel, Audrey M.; Mullan, James P. A.; Velayudhan, Vimalkumar; O'Connor, Patrick B. F.; Donohue, Claire A.; Baranov, Pavel V.
2016-01-01
ABSTRACT Ribosome profiling (ribo-seq) is a technique that uses high-throughput sequencing to reveal the exact locations and densities of translating ribosomes at the entire transcriptome level. The technique has become very popular since its inception in 2009. Yet experimentalists who generate ribo-seq data often have to rely on bioinformaticians to process and analyze their data. We present RiboGalaxy (http://ribogalaxy.ucc.ie), a freely available Galaxy-based web server for processing and analyzing ribosome profiling data with the visualization functionality provided by GWIPS-viz (http://gwips.ucc.ie). RiboGalaxy offers researchers a suite of tools specifically tailored for processing ribo-seq and corresponding mRNA-seq data. Researchers can take advantage of the published workflows which reduce the multi-step alignment process to a minimum of inputs from the user. Users can then explore their own aligned data as custom tracks in GWIPS-viz and compare their ribosome profiles to existing ribo-seq tracks from published studies. In addition, users can assess the quality of their ribo-seq data, determine the strength of the triplet periodicity signal, generate meta-gene ribosome profiles as well as analyze the relative impact of mRNA sequence features on local read density. RiboGalaxy is accompanied by extensive documentation and tips for helping users. In addition we provide a forum (http://gwips.ucc.ie/Forum) where we encourage users to post their questions and feedback to improve the overall RiboGalaxy service. PMID:26821742
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Planes of satellite galaxies and the cosmic web
NASA Astrophysics Data System (ADS)
Libeskind, Noam I.; Hoffman, Yehuda; Tully, R. Brent; Courtois, Helene M.; Pomarède, Daniel; Gottlöber, Stefan; Steinmetz, Matthias
2015-09-01
Recent observational studies have demonstrated that the majority of satellite galaxies tend to orbit their hosts on highly flattened, vast, possibly corotating planes. Two nearly parallel planes of satellites have been confirmed around the M31 galaxy and around the Centaurus A galaxy, while the Milky Way also sports a plane of satellites. It has been argued that such an alignment of satellites on vast planes is unexpected in the standard Λ cold dark matter (ΛCDM) model of cosmology if not even in contradiction to its generic predictions. Guided by ΛCDM numerical simulations, which suggest that satellites are channelled towards hosts along the axis of the slowest collapse as dictated by the ambient velocity shear tensor, we re-examine the planes of local satellites systems within the framework of the local shear tensor derived from the Cosmicflows-2 data set. The analysis reveals that the Local Group and Centaurus A reside in a filament stretched by the Virgo cluster and compressed by the expansion of the Local Void. Four out of five thin planes of satellite galaxies are indeed closely aligned with the axis of compression induced by the Local Void. Being the less massive system, the moderate misalignment of the Milky Way's satellite plane can likely be ascribed to its greater susceptibility to tidal torques, as suggested by numerical simulations. The alignment of satellite systems in the local Universe with the ambient shear field is thus in general agreement with predictions of the ΛCDM model.
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Aligning, Bonding, and Testing Mirrors for Lightweight X-ray Telescopes
NASA Technical Reports Server (NTRS)
Chan, Kai-Wing; Zhang, William W.; Saha, Timo T.; McClelland, Ryan S.; Biskach, Michael P.; Niemeyer, Jason; Schofield, Mark J.; Mazzarella, James R.; Kolos, Linette D.; Hong, Melinda M.;
2015-01-01
High-resolution, high throughput optics for x-ray astronomy entails fabrication of well-formed mirror segments and their integration with arc-second precision. In this paper, we address issues of aligning and bonding thin glass mirrors with negligible additional distortion. Stability of the bonded mirrors and the curing of epoxy used in bonding them were tested extensively. We present results from tests of bonding mirrors onto experimental modules, and on the stability of the bonded mirrors tested in x-ray. These results demonstrate the fundamental validity of the methods used in integrating mirrors into telescope module, and reveal the areas for further investigation. The alignment and integration methods are applicable to the astronomical mission concept such as STAR-X, the Survey and Time-domain Astronomical Research Explorer.
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Ho, Czung-Yu; Lin, Fa-Hsin; Tao, Yu-Tai; Lee, Jiunn-Yih
2011-01-01
In a multicomponent nematic liquid crystal (NLC) mixture of a liquid crystal (negative-type NLC) and a photosensitive acrylic prepolymer, photopolymerization upon UV irradiation induces the separation of the LC and photosensitive acrylic prepolymer layers, thereby leading to a vertical arrangement of LC molecules. In this study, we propose a simple vertical alignment method for LC molecules, by adding a chiral smectic A (SmA∗) liquid crystal having homeotropic texture characteristics to an NLC mixture solution. Measurements of electro-optical properties revealed that the addition of the SmA∗ LC not only strengthened the anchoring force of the copolymer alignment film surface, but also significantly enhanced the contrast ratio (∼73%), response time and grayscale switching performance of the device. PMID:27877462
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Glycine activated ion channel subunits encoded by ctenophore glutamate receptor genes
Alberstein, Robert; Grey, Richard; Zimmet, Austin; ...
2015-10-12
Recent genome projects for ctenophores have revealed the presence of numerous ionotropic glutamate receptors (iGluRs) in Mnemiopsis leidyi and Pleurobrachia bachei, among our earliest metazoan ancestors. Sequence alignments and phylogenetic analysis show that these form a distinct clade from the well-characterized AMPA, kainate, and NMDA iGluR subtypes found in vertebrates. Although annotated as glutamate and kainate receptors, crystal structures of the ML032222a and PbiGluR3 ligand-binding domains (LBDs) reveal endogenous glycine in the binding pocket, whereas ligand-binding assays show that glycine binds with nanomolar affinity; biochemical assays and structural analysis establish that glutamate is occluded from the binding cavity. Further analysismore » reveals ctenophore-specific features, such as an interdomain Arg-Glu salt bridge, present only in subunits that bind glycine, but also a conserved disulfide in loop 1 of the LBD that is found in all vertebrate NMDA but not AMPA or kainate receptors. In this paper, we hypothesize that ctenophore iGluRs are related to an early ancestor of NMDA receptors, suggesting a common evolutionary path for ctenophores and bilaterian species, and finally suggest that future work should consider both glycine and glutamate as candidate neurotransmitters in ctenophore species.« less
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AGILE: Autonomous Global Integrated Language Exploitation
2009-12-01
combination, including METEOR-based alignment (with stemming and WordNet synonym matching) and GIZA ++ based alignment. So far, we have not seen any...parse trees and a detailed analysis of how function words operate in translation. This program lets us fix alignment errors that systems like GIZA ...correlates better with Pyramid than with Responsiveness scoring (i.e., it is a more precise, careful, measure) • BE generally outperforms ROUGE
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ERIC Educational Resources Information Center
Watt, Michael
2016-01-01
The purpose of this study was to inform the deliberations of a policymakers' working group by investigating what key actors in the materials' marketplace are doing to align digital and print-based materials with the Australian Curriculum and what steps need to be taken to deliver aligned materials to schools. Content analysis method was used to…
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NASA Astrophysics Data System (ADS)
Contino, Julie Anna
In a standards-based system, it is important for all components of the system to align in order to achieve the intended goals. In New York State, standards are provided to the teachers who then create individual curricula that will lead to student success on the state assessment. This mixed methods study presents an analysis of the alignment between the National Science Education Standards (NSES), New York State Physical Setting/Earth Science Core Curriculum (Core Curriculum), and New York State Earth Science Regents Examination (Regents)---the sources teachers use for creating Earth Science curricula in New York State. The NSES were found to have a 49% overlap with the Core Curriculum and a 27% overlap with the Regents. The Core Curriculum and Regents, represented by matrices consisting of performance indicators and cognitive demands, were compared using the Porter alignment index. The alignment was 0.35, categorized as slightly aligned, due to the different emphases on cognitive levels (the Core Curriculum focused on Understand and Apply while the Regents focused on Apply followed by Understand and Remember). Additionally, a purposeful sample of experienced and innovative teachers were surveyed and interviewed to gain insight on how NYS Earth Science teachers organize their scope and sequences, align their lessons with the Core Curriculum, establish internal lesson coherence, and prepare their students for the Regents Exam. Teachers' scope and sequences were well-aligned with the Core Curriculum and Regents but misalignment was found between their lessons and the Core Curriculum as well as between the stated objectives for their students and evaluation of those objectives. Based on the findings, it is suggested that the NSES be revised and the Core Curriculum updated to include quantifiable emphasis on the major understandings such as percentage of time, as well as an emphasis on alignment principles. Teacher professional development focused on alignment issues relative to the state standards and enhancing internal lesson coherence should also be provided. The insights gained from this analysis of the NYS system may be helpful to other states as they move toward standards-based systems.
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Padial, José M; Grant, Taran; Frost, Darrel R
2014-06-26
Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively. Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae. Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates that insertions and deletions occurred in twice as many aligned positions as implied by the optimal similarity-alignment, confirming previous findings that sequence turnover through insertion and deletion events plays a greater role in molecular evolution than indicated by similarity-alignments. Our results also provide a clear empirical demonstration of the different effects of wildcard taxa produced by missing data in parsimony and maximum likelihood analyses. Specifically, maximum likelihood analyses consistently (81% bootstrap frequency) provided spurious resolution despite a lack of evidence, whereas parsimony correctly depicted the ambiguity due to missing data by collapsing unsupported nodes. We provide a new taxonomy for the group that retains previously recognized Linnaean taxa except for Ceuthomantidae, Strabomantidae, and Strabomantinae. A phenotypically diagnosable superfamily is recognized formally as Brachycephaloidea, with the informal, unranked name terrarana retained as the standard common name for these frogs. We recognize three families within Brachycephaloidea that are currently diagnosable solely on molecular grounds (Brachycephalidae, Craugastoridae, and Eleutherodactylidae), as well as five subfamilies (Craugastorinae, Eleutherodactylinae, Holoadeninae, Phyzelaphryninae, and Pristimantinae) corresponding in large part to previous families and subfamilies. Our analyses upheld the monophyly of all tested genera, but we found numerous subgeneric taxa to be non-monophyletic and modified the taxonomy accordingly.
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ERIC Educational Resources Information Center
Vanfretti, Luigi; Farrokhabadi, Mostafa
2015-01-01
This article presents the implementation of the constructive alignment theory (CAT) in a power system analysis course through a consensus-based course design process. The consensus-based design process involves both the instructor and graduate-level students and it aims to develop the CAT framework in a holistic manner with the goal of including…
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Tóth, Annamária; Hausknecht, Anton; Krisai-Greilhuber, Irmgard; Papp, Tamás; Vágvölgyi, Csaba; Nagy, László G.
2013-01-01
Reconciling traditional classifications, morphology, and the phylogenetic relationships of brown-spored agaric mushrooms has proven difficult in many groups, due to extensive convergence in morphological features. Here, we address the monophyly of the Bolbitiaceae, a family with over 700 described species and examine the higher-level relationships within the family using a newly constructed multilocus dataset (ITS, nrLSU rDNA and EF1-alpha). We tested whether the fast-evolving Internal Transcribed Spacer (ITS) sequences can be accurately aligned across the family, by comparing the outcome of two iterative alignment refining approaches (an automated and a manual) and various indel-treatment strategies. We used PRANK to align sequences in both cases. Our results suggest that – although PRANK successfully evades overmatching of gapped sites, referred previously to as alignment overmatching – it infers an unrealistically high number of indel events with natively generated guide-trees. This 'alignment undermatching' could be avoided by using more rigorous (e.g. ML) guide trees. The trees inferred in this study support the monophyly of the core Bolbitiaceae, with the exclusion of Panaeolus, Agrocybe, and some of the genera formerly placed in the family. Bolbitius and Conocybe were found monophyletic, however, Pholiotina and Galerella require redefinition. The phylogeny revealed that stipe coverage type is a poor predictor of phylogenetic relationships, indicating the need for a revision of the intrageneric relationships within Conocybe. PMID:23418526
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MultiSETTER: web server for multiple RNA structure comparison.
Čech, Petr; Hoksza, David; Svozil, Daniel
2015-08-12
Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.
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First findings of duck circovirus in migrating wild ducks in China.
Niu, Xinxin; Liu, Lanlan; Han, Chunyan; Li, Jing; Zeng, Xiangwei
2018-03-01
To probe the epidemiology of duck circovirus (DuCV) in migrating wild ducks in China, 189 samples collected from 11 species of wild ducks from 2013 to 2016 were analyzed by PCR. Four positive samples were obtained from Mallard (2), Green-winged Teal (1), and Falcated Duck (1), and the positive rate was 2.12%. The homologous alignment of the complete genome shows that the homology of the wild duck strains is 81.6 to 95.1% to each other and 81.4 to 100% to the 32 strains from other origins. Amino acids alignment revealed that the mutable ORF2 gene has six major variable regions and many random mutation points. Phylogenetic analysis showed that the four sequences belong to two genotypes: wd2013017, wd2013046 and AY228555 (representative strain of genotype 1) belong to genotype 1, while wd2014012, wd2015028 and AY394721 (representative strain of genotype 2) belong to genotype 2. The results indicate that both genotypes of DuCV are distributed and common in migrating wild ducks. Further analysis shows that duck circovirus infection is mainly concentrated in the eastern coastal cities of China, which are part of the East Asian-Australian flyway. This suggests that wild ducks with circovirus may be an important factor in the epidemic and spread of DuCV. Copyright © 2018 Elsevier B.V. All rights reserved.
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Development of a Self Aligned CMOS Process for Flash Lamp Annealed Polycrystalline Silicon TFTs
NASA Astrophysics Data System (ADS)
Bischoff, Paul
The emerging active matrix liquid crystal (AMLCD) display market requires a high performing semiconductor material to meet rising standards of operation. Currently amorphous silicon (a-Si) dominates the market but it does not have the required mobility for it to be used in AMLCD manufacturing. Other materials have been developed including crystallizing a-Si into poly-silicon. A new approach to crystallization through the use of flash lamp annealing (FLA) decreases manufacturing time and greatly improves carrier mobility. Previous work on FLA silicon for the use in CMOS transistors revealed significant lateral dopant diffusion into the channel greatly increasing the minimum channel length required for a working device. This was further confounded by the gate overlap due to misalignment during lithography patterning steps. Through the use of furnace dopant activation instead of FLA dopant activation and a self aligned gate the minimum size transistor can be greatly reduced. A new lithography mask and process flow were developed for the furnace annealing and self aligned gate. Fabrication of the self aligned devices resulted in oxidation of the Molybdenum self aligned gate. Further development is needed to successfully manufacture these devices. Non-self aligned transistors were made simultaneously with self aligned devices and used the furnace activation. These devices showed an increase in sheet resistance from 250 O to 800 O and lower mobility from 380 to 40.2 V/cm2s. The lower mobility can be contributed to an increase in implanted trap density indicating furnace annealing is an inferior activation method over FLA. The minimum transistor size however was reduced from 20 to 5 mum. With improvements in the self aligned process high performing small devices can be manufactured.
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A survey and evaluations of histogram-based statistics in alignment-free sequence comparison.
Luczak, Brian B; James, Benjamin T; Girgis, Hani Z
2017-12-06
Since the dawn of the bioinformatics field, sequence alignment scores have been the main method for comparing sequences. However, alignment algorithms are quadratic, requiring long execution time. As alternatives, scientists have developed tens of alignment-free statistics for measuring the similarity between two sequences. We surveyed tens of alignment-free k-mer statistics. Additionally, we evaluated 33 statistics and multiplicative combinations between the statistics and/or their squares. These statistics are calculated on two k-mer histograms representing two sequences. Our evaluations using global alignment scores revealed that the majority of the statistics are sensitive and capable of finding similar sequences to a query sequence. Therefore, any of these statistics can filter out dissimilar sequences quickly. Further, we observed that multiplicative combinations of the statistics are highly correlated with the identity score. Furthermore, combinations involving sequence length difference or Earth Mover's distance, which takes the length difference into account, are always among the highest correlated paired statistics with identity scores. Similarly, paired statistics including length difference or Earth Mover's distance are among the best performers in finding the K-closest sequences. Interestingly, similar performance can be obtained using histograms of shorter words, resulting in reducing the memory requirement and increasing the speed remarkably. Moreover, we found that simple single statistics are sufficient for processing next-generation sequencing reads and for applications relying on local alignment. Finally, we measured the time requirement of each statistic. The survey and the evaluations will help scientists with identifying efficient alternatives to the costly alignment algorithm, saving thousands of computational hours. The source code of the benchmarking tool is available as Supplementary Materials. © The Author 2017. Published by Oxford University Press.
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NASA Astrophysics Data System (ADS)
Gkioulidou, M.; Mitchell, D. G.; Ukhorskiy, S.; Ohtani, S.; Takahashi, K.
2017-12-01
The low-energy (eV to hundreds of eV) ion population in the inner magnetosphere, the warm plasma cloak, and in particular its heavy ion component, the O+ torus, is crucial to magnetospheric dynamics. Yet, although the effects of high latitude and cusp ionospheric O+ outflow and its subsequent transport and acceleration within the magnetotail and plasma sheet have been extensively studied, the source of low-energy O+ within the inner magnetosphere (already observed by the DE1 spacecraft in the 80s) remains a compelling open question. The HOPE instrument aboard each of the Van Allen Probes, moving in highly elliptical, equatorial orbits with apogee of 5.8 RE, has repeatedly detected low-energy O+ field-aligned enhancements. We present a comprehensive study of one such event, where low energy O+ field-aligned intensity enhancements were observed, both at small and large pitch angles, during a geomagnetic storm. The energy spectrogram exhibited a dispersive signature and a banded structure, features that our simple particle tracing simulation demonstrated are due to O+ ions outflowing from both hemispheres of the night-side ionosphere directly into the magnetosphere within L = 4, and subsequently bouncing from one hemisphere to the other. These outflows are associated with field-aligned Poynting flux enhancements and field-aligned electron beams, as observed at the Van Allen Probes location, revealing energy transport from the magnetosphere to ionosphere as well as simultaneous field-aligned electron heating. We also incorporate ionospheric measurements, such as field-aligned currents, as those are inferred by AMPERE data. The combination of unprecedented simultaneous magnetospheric and ionospheric observations allow us to investigate the processes that lead to an O+ outflow event from the low-latitude, night-side ionosphere directly into the inner magnetosphere. The ubiquity of such events in the Van Allen Probes data might reveal one of the sources for the O+ torus.
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Visualizing phylogenetic tree landscapes.
Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A
2017-02-02
Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D projections significantly increase the fit between the tree-to-tree distances and can facilitate the interpretation of the relationship among phylogenetic trees. We demonstrate that the choice of dimensionality reduction method can significantly influence the spatial relationship among a large set of competing phylogenetic trees. We highlight the importance of selecting a dimensionality reduction method to visualize large multi-locus phylogenetic landscapes and demonstrate that 3D projections of mitochondrial tree landscapes better capture the relationship among the trees being compared.
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Uribe, Juan S; Myhre, Sue Lynn; Youssef, Jim A
2016-04-01
A literature review. The purpose of this study was to review lumbar segmental and regional alignment changes following treatment with a variety of minimally invasive surgery (MIS) interbody fusion procedures for short-segment, degenerative conditions. An increasing number of lumbar fusions are being performed with minimally invasive exposures, despite a perception that minimally invasive lumbar interbody fusion procedures are unable to affect segmental and regional lordosis. Through a MEDLINE and Google Scholar search, a total of 23 articles were identified that reported alignment following minimally invasive lumbar fusion for degenerative (nondeformity) lumbar spinal conditions to examine aggregate changes in postoperative alignment. Of the 23 studies identified, 28 study cohorts were included in the analysis. Procedural cohorts included MIS ALIF (two), extreme lateral interbody fusion (XLIF) (16), and MIS posterior/transforaminal lumbar interbody fusion (P/TLIF) (11). Across 19 study cohorts and 720 patients, weighted average of lumbar lordosis preoperatively for all procedures was 43.5° (range 28.4°-52.5°) and increased 3.4° (9%) (range -2° to 7.4°) postoperatively (P < 0.001). Segmental lordosis increased, on average, by 4° from a weighted average of 8.3° preoperatively (range -0.8° to 15.8°) to 11.2° at postoperative time points (range -0.2° to 22.8°) (P < 0.001) in 1182 patient from 24 study cohorts. Simple linear regression revealed a significant relationship between preoperative lumbar lordosis and change in lumbar lordosis (r = 0.413; P = 0.003), wherein lower preoperative lumbar lordosis predicted a greater increase in postoperative lumbar lordosis. Significant gains in both weighted average lumbar lordosis and segmental lordosis were seen following MIS interbody fusion. None of the segmental lordosis cohorts and only two of the 19 lumbar lordosis cohorts showed decreases in lordosis postoperatively. These results suggest that MIS approaches are able to impact regional and local segmental alignment and that preoperative patient factors can impact the extent of correction gained (preserving vs. restoring alignment). 4.
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Galactic cosmic ray gradients, field-aligned and latitudinal, among Voyagers 1/2 and IMP-8
NASA Technical Reports Server (NTRS)
Roelof, E. C.; Decker, R. B.; Krimigis, S. M.; Venkatesan, D.; Lazarus, A. J.
1982-01-01
The present investigation represents a summary of a comprehensive analysis of the same subject conducted by Roelof et al. (1981). It is pointed out that the tandem earth-Jupiter trajectories of the Voyager 1/2 spacecraft, combined with baseline measurements from the earth-orbiting IMP 7/8 spacecraft, provide the first opportunity for unambiguously separating latitude from radial or field-aligned effects in galactic cosmic ray gradients. Attention is given to the method of data analysis, and the separation of field-aligned and latitudinal gradients. It is found that latitudinal gradients approximately equal to or greater than 1 percent per deg in the cosmic ray intensity were a common feature of the interplanetary medium between 1 and 5 AU in 1977-78. Except in the most disturbed periods, cosmic ray intensities are well-ordered in field-aligned structures.
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GATA: A graphic alignment tool for comparative sequenceanalysis
DOE Office of Scientific and Technical Information (OSTI.GOV)
Nix, David A.; Eisen, Michael B.
2005-01-01
Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dotplot analysis is often used to estimate non-coding sequence relatedness. Yet dotmore » plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments.« less
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Prosody and alignment: a sequential perspective
NASA Astrophysics Data System (ADS)
Szczepek Reed, Beatrice
2010-12-01
In their analysis of a corpus of classroom interactions in an inner city high school, Roth and Tobin describe how teachers and students accomplish interactional alignment by prosodically matching each other's turns. Prosodic matching, and specific prosodic patterns are interpreted as signs of, and contributions to successful interactional outcomes and positive emotions. Lack of prosodic matching, and other specific prosodic patterns are interpreted as features of unsuccessful interactions, and negative emotions. This forum focuses on the article's analysis of the relation between interpersonal alignment, emotion and prosody. It argues that prosodic matching, and other prosodic linking practices, play a primarily sequential role, i.e. one that displays the way in which participants place and design their turns in relation to other participants' turns. Prosodic matching, rather than being a conversational action in itself, is argued to be an interactional practice (Schegloff 1997), which is not always employed for the accomplishment of `positive', or aligning actions.
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Liu, Chuanjun; Xiao, Chengli
2018-01-01
The spatial updating and memory systems are employed during updating in both the immediate and retrieved environments. However, these dual systems seem to work differently, as the difference of pointing latency and absolute error between the two systems vary across environments. To verify this issue, the present study employed the bias analysis of signed errors based on the hypothesis that the transformed representation will bias toward the original one. Participants learned a spatial layout and then either stayed in the learning location or were transferred to a neighboring room directly or after being disoriented. After that, they performed spatial judgments from perspectives aligned with the learning direction, aligned with the direction they faced during the test, or a novel direction misaligned with the two above-mentioned directions. The patterns of signed error bias were consistent across environments. Responses for memory aligned perspectives were unbiased, whereas responses for sensorimotor aligned perspectives were biased away from the memory aligned perspective, and responses for misaligned perspectives were biased toward sensorimotor aligned perspectives. These findings indicate that the spatial updating system is consistently independent of the spatial memory system regardless of the environments, but the updating system becomes less accessible as the environment changes from immediate to a retrieved one.
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Liu, Chuanjun; Xiao, Chengli
2018-01-01
The spatial updating and memory systems are employed during updating in both the immediate and retrieved environments. However, these dual systems seem to work differently, as the difference of pointing latency and absolute error between the two systems vary across environments. To verify this issue, the present study employed the bias analysis of signed errors based on the hypothesis that the transformed representation will bias toward the original one. Participants learned a spatial layout and then either stayed in the learning location or were transferred to a neighboring room directly or after being disoriented. After that, they performed spatial judgments from perspectives aligned with the learning direction, aligned with the direction they faced during the test, or a novel direction misaligned with the two above-mentioned directions. The patterns of signed error bias were consistent across environments. Responses for memory aligned perspectives were unbiased, whereas responses for sensorimotor aligned perspectives were biased away from the memory aligned perspective, and responses for misaligned perspectives were biased toward sensorimotor aligned perspectives. These findings indicate that the spatial updating system is consistently independent of the spatial memory system regardless of the environments, but the updating system becomes less accessible as the environment changes from immediate to a retrieved one. PMID:29467698
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NASA Astrophysics Data System (ADS)
Newman, Peter; Galenano-Niño, Jorge Luis; Graney, Pamela; Razal, Joselito M.; Minett, Andrew I.; Ribas, João; Ovalle-Robles, Raquel; Biro, Maté; Zreiqat, Hala
2016-12-01
The topography of a biomaterial regulates cellular interactions and determine stem cell fate. A complete understanding of how topographical properties affect cell behavior will allow the rational design of material surfaces that elicit specified biological functions once placed in the body. To this end, we fabricate substrates with aligned or randomly organized fibrous nanostructured topographies. Culturing adipose-derived stem cells (ASCs), we explore the dynamic relationship between the alignment of topography, cell shape and cell differentiation to osteogenic and myogenic lineages. We show aligned topographies differentiate cells towards a satellite cell muscle progenitor state - a distinct cell myogenic lineage responsible for postnatal growth and repair of muscle. We analyze cell shape between the different topographies, using fluorescent time-lapse imaging over 21 days. In contrast to previous work, this allows the direct measurement of cell shape at a given time rather than defining the morphology of the underlying topography and neglecting cell shape. We report quantitative metrics of the time-based morphological behaviors of cell shape in response to differing topographies. This analysis offers insights into the relationship between topography, cell shape and cell differentiation. Cells differentiating towards a myogenic fate on aligned topographies adopt a characteristic elongated shape as well as the alignment of cells.
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Strengths weaknesses opportunities and threats of blended learning: students' perceptions.
Hande, S
2014-05-01
Blended learning (BL) in a cell biology course of the premedical program at the Kasturba Medical College International Centre, Manipal, India, commenced in 2006. The program provides training in basic sciences to students, especially from the United States and Canada. The approach to the study was phenomenographic, with a qualitative study design using an open-ended questionnaire, focused interviews and empirical observations. The aim of this study was to identify the strengths, weaknesses, opportunities and threats (SWOT) of BL in a premedical class. It was a cross-sectional study. Ninety six students in a premedical cell biology class participated in the study. SWOT analysis of students' perceptions was conducted manually. Statistical analysis included content analysis of qualitative data to classify data and aligning them into the SWOT analysis matrix. The outcomes of the study revealed student perceptions in terms of SWOT of BL and the potential uses of this strategy. The study provides background for educators and curriculum experts to plan their modules while incorporating a BL approach.
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An advanced software suite for the processing and analysis of silicon luminescence images
NASA Astrophysics Data System (ADS)
Payne, D. N. R.; Vargas, C.; Hameiri, Z.; Wenham, S. R.; Bagnall, D. M.
2017-06-01
Luminescence imaging is a versatile characterisation technique used for a broad range of research and industrial applications, particularly for the field of photovoltaics where photoluminescence and electroluminescence imaging is routinely carried out for materials analysis and quality control. Luminescence imaging can reveal a wealth of material information, as detailed in extensive literature, yet these techniques are often only used qualitatively instead of being utilised to their full potential. Part of the reason for this is the time and effort required for image processing and analysis in order to convert image data to more meaningful results. In this work, a custom built, Matlab based software suite is presented which aims to dramatically simplify luminescence image processing and analysis. The suite includes four individual programs which can be used in isolation or in conjunction to achieve a broad array of functionality, including but not limited to, point spread function determination and deconvolution, automated sample extraction, image alignment and comparison, minority carrier lifetime calibration and iron impurity concentration mapping.
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Oluwayelu, D O; Todd, D; Olaleye, O D
2008-12-01
This work reports the first molecular analysis study of chicken anaemia virus (CAV) in backyard chickens in Africa using molecular cloning and sequence analysis to characterize CAV strains obtained from commercial chickens and Nigerian backyard chickens. Partial VP1 gene sequences were determined for three CAVs from commercial chickens and for six CAV variants present in samples from a backyard chicken. Multiple alignment analysis revealed that the 6% and 4% nucleotide diversity obtained respectively for the commercial and backyard chicken strains translated to only 2% amino acid diversity for each breed. Overall, the amino acid composition of Nigerian CAVs was found to be highly conserved. Since the partial VP1 gene sequence of two backyard chicken cloned CAV strains (NGR/CI-8 and NGR/CI-9) were almost identical and evolutionarily closely related to the commercial chicken strains NGR-1, and NGR-4 and NGR-5, respectively, we concluded that CAV infections had crossed the farm boundary.
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NASA Astrophysics Data System (ADS)
Saito, Kazuya; Miyazawa, Takahito; Fujiwara, Akio; Hishida, Mafumi; Saitoh, Hideki; Massalska-Arodź, Maria; Yamamura, Yasuhisa
2013-09-01
Based on new diffraction data from aligned samples of smectic E (SmE) phase of 4-n-alkyl-4'-isothiocyanato-1,1'-biphenyls, systematics against the alkyl chain length n is analyzed. In order to perform the analysis, the molecular form factor approximated by a box-shaped distribution is calculated while taking the rounding of the distribution at corners into account. The analysis clearly shows the nano-segregated layered structure, which does not fit to the traditional structural view of SmE phase but does fit to the model the present authors proposed recently. Some implications of this conclusion are discussed in relation to the importance of the molten state of alkyl chains in most of real mesogens revealed previously through thermodynamic analyses.
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A distributed system for fast alignment of next-generation sequencing data.
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.
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Orbit Alignment in Triple Stars
NASA Astrophysics Data System (ADS)
Tokovinin, Andrei
2017-08-01
The statistics of the angle Φ between orbital angular momenta in hierarchical triple systems with known inner visual or astrometric orbits are studied. A correlation between apparent revolution directions proves the partial orbit alignment known from earlier works. The alignment is strong in triples with outer projected separation less than ˜50 au, where the average Φ is about 20^\\circ . In contrast, outer orbits wider than 1000 au are not aligned with the inner orbits. It is established that the orbit alignment decreases with the increasing mass of the primary component. The average eccentricity of inner orbits in well-aligned triples is smaller than in randomly aligned ones. These findings highlight the role of dissipative interactions with gas in defining the orbital architecture of low-mass triple systems. On the other hand, chaotic dynamics apparently played a role in shaping more massive hierarchies. The analysis of projected configurations and triples with known inner and outer orbits indicates that the distribution of Φ is likely bimodal, where 80% of triples have {{Φ }}< 70^\\circ and the remaining ones are randomly aligned.
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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
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Optimal Parameter Design of Coarse Alignment for Fiber Optic Gyro Inertial Navigation System.
Lu, Baofeng; Wang, Qiuying; Yu, Chunmei; Gao, Wei
2015-06-25
Two different coarse alignment algorithms for Fiber Optic Gyro (FOG) Inertial Navigation System (INS) based on inertial reference frame are discussed in this paper. Both of them are based on gravity vector integration, therefore, the performance of these algorithms is determined by integration time. In previous works, integration time is selected by experience. In order to give a criterion for the selection process, and make the selection of the integration time more accurate, optimal parameter design of these algorithms for FOG INS is performed in this paper. The design process is accomplished based on the analysis of the error characteristics of these two coarse alignment algorithms. Moreover, this analysis and optimal parameter design allow us to make an adequate selection of the most accurate algorithm for FOG INS according to the actual operational conditions. The analysis and simulation results show that the parameter provided by this work is the optimal value, and indicate that in different operational conditions, the coarse alignment algorithms adopted for FOG INS are different in order to achieve better performance. Lastly, the experiment results validate the effectiveness of the proposed algorithm.
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HSA: a heuristic splice alignment tool.
Bu, Jingde; Chi, Xuebin; Jin, Zhong
2013-01-01
RNA-Seq methodology is a revolutionary transcriptomics sequencing technology, which is the representative of Next generation Sequencing (NGS). With the high throughput sequencing of RNA-Seq, we can acquire much more information like differential expression and novel splice variants from deep sequence analysis and data mining. But the short read length brings a great challenge to alignment, especially when the reads span two or more exons. A two steps heuristic splice alignment tool is generated in this investigation. First, map raw reads to reference with unspliced aligner--BWA; second, split initial unmapped reads into three equal short reads (seeds), align each seed to the reference, filter hits, search possible split position of read and extend hits to a complete match. Compare with other splice alignment tools like SOAPsplice and Tophat2, HSA has a better performance in call rate and efficiency, but its results do not as accurate as the other software to some extent. HSA is an effective spliced aligner of RNA-Seq reads mapping, which is available at https://github.com/vlcc/HSA.
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Clustalnet: the joining of Clustal and CORBA.
Campagne, F
2000-07-01
Performing sequence alignment operations from a different program than the original sequence alignment code, and/or through a network connection, is often required. Interactive alignment editors and large-scale biological data analysis are common examples where such a flexibility is important. Interoperability between the alignment engine and the client should be obtained regardless of the architectures and programming languages of the server and client. Clustalnet, a Clustal alignment CORBA server is described, which was developed on the basis of Clustalw. This server brings the robustness of the algorithms and implementations of Clustal to a new level of reuse. A Clustalnet server object can be accessed from a program, transparently through the network. We present interfaces to perform the alignment operations and to control these operations via immutable contexts. The interfaces that select the contexts do not depend on the nature of the operation to be performed, making the design modular. The IDL interfaces presented here are not specific to Clustal and can be implemented on top of different sequence alignment algorithm implementations.
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BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC
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
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BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.
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/
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AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis
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
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Maleki, Ehsan; Babashah, Hossein; Koohi, Somayyeh; Kavehvash, Zahra
2017-07-01
This paper presents an optical processing approach for exploring a large number of genome sequences. Specifically, we propose an optical correlator for global alignment and an extended moiré matching technique for local analysis of spatially coded DNA, whose output is fed to a novel three-dimensional artificial neural network for local DNA alignment. All-optical implementation of the proposed 3D artificial neural network is developed and its accuracy is verified in Zemax. Thanks to its parallel processing capability, the proposed structure performs local alignment of 4 million sequences of 150 base pairs in a few seconds, which is much faster than its electrical counterparts, such as the basic local alignment search tool.
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NASA Astrophysics Data System (ADS)
Belmonte, Juan Antonio; González-García, A. César
The Nabataeans built several monuments in Petra and elsewhere displaying decoration with a certain preference for astronomical motifs. A statistical analysis of the orientation of their sacred monuments demonstrates that astronomical orientations were often part of an elaborate plan and possibly reflect traces of the astral nature of Nabataean religion. Petra and other monuments in the ancient Nabataean kingdom demonstrate the interaction between landscape features and astronomical events. Among other things, the famous Ad Deir has revealed a fascinating ensemble of light and shadow effects, perhaps connected with the bulk of Nabataean mythology, while a series of suggestive solstitial and equinoctial alignments emanate from the impressive Urn Tomb, which might have helped bring about its selection as the cathedral of the city.
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Effects of fast walking on tibiofemoral bone water content in middle-aged adults.
Ho, Kai-Yu; Standerfer, Alexa; Ngo, Suzenna; Daun, Karen; Lee, Szu-Ping
2016-08-01
Although it is believed that genu varum increases loading on the medial knee during locomotion, the acute effect of increased loading on bone stress has not been determined. This study aimed to examine the effects of locomotion and lower extremity alignment on bone water content in middle-aged adults without knee osteoarthritis. Five males and 5 females participated. Lower extremity alignment was defined as the angle between the midpoint of the anterior mid-thigh and the midpoint of the patellar tendon using the center of the patella as the fulcrum. A chemical-shift-encoded water-fat magnetic resonance imaging protocol was used to assess bone water content before and after a 30-minute fast walking session. Bone stress response was determined by quantifying water content within the weight-bearing regions of the medial and lateral compartments of the tibiofemoral joint. Paired t-tests were used to compare bone water content before and after fast walking. Pearson correlation coefficients were used to determine the associations between lower extremity alignment and changes in water content post-walking. The paired t-tests revealed no changes in water content after fast walking within medial and lateral femur/tibia (P>0.05). Pearson correlation analyses revealed a significant moderate correlation between increased bone water content of the medial femur and increased varus alignment (R=0.688, P=0.028). Although there was no significant change in bone water content following locomotion, knee varus was associated with signs of bone stress in the medial femur. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Verzotto, Davide; M Teo, Audrey S; Hillmer, Axel M; Nagarajan, Niranjan
2016-01-01
Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome-mapping technologies (for example, optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kilo base pairs (kbp) to 2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging because of the lack of efficient and sensitive map-alignment algorithms for robustly aligning error-prone maps to sequences. We introduce a novel seed-and-extend glocal (short for global-local) alignment method, OPTIMA (and a sliding-window extension for overlap alignment, OPTIMA-Overlap), which is the first to create indexes for continuous-valued mapping data while accounting for mapping errors. We also present a novel statistical model, agnostic with respect to technology-dependent error rates, for conservatively evaluating the significance of alignments without relying on expensive permutation-based tests. We show that OPTIMA and OPTIMA-Overlap outperform other state-of-the-art approaches (1.6-2 times more sensitive) and are more efficient (170-200 %) and precise in their alignments (nearly 99 % precision). These advantages are independent of the quality of the data, suggesting that our indexing approach and statistical evaluation are robust, provide improved sensitivity and guarantee high precision.
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Development and application of an algorithm to compute weighted multiple glycan alignments.
Hosoda, Masae; Akune, Yukie; Aoki-Kinoshita, Kiyoko F
2017-05-01
A glycan consists of monosaccharides linked by glycosidic bonds, has branches and forms complex molecular structures. Databases have been developed to store large amounts of glycan-binding experiments, including glycan arrays with glycan-binding proteins. However, there are few bioinformatics techniques to analyze large amounts of data for glycans because there are few tools that can handle the complexity of glycan structures. Thus, we have developed the MCAW (Multiple Carbohydrate Alignment with Weights) tool that can align multiple glycan structures, to aid in the understanding of their function as binding recognition molecules. We have described in detail the first algorithm to perform multiple glycan alignments by modeling glycans as trees. To test our tool, we prepared several data sets, and as a result, we found that the glycan motif could be successfully aligned without any prior knowledge applied to the tool, and the known recognition binding sites of glycans could be aligned at a high rate amongst all our datasets tested. We thus claim that our tool is able to find meaningful glycan recognition and binding patterns using data obtained by glycan-binding experiments. The development and availability of an effective multiple glycan alignment tool opens possibilities for many other glycoinformatics analysis, making this work a big step towards furthering glycomics analysis. http://www.rings.t.soka.ac.jp. kkiyoko@soka.ac.jp. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.
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gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances.
Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav
2016-01-01
Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos).
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gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances
Domazet-Lošo, Mirjana; Domazet-Lošo, Tomislav
2016-01-01
Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci, since the expensive computation of underlying statistical models often hinders the comparison of complete prokaryotic genomes. As an alternative, alignment-free solutions are more efficient, but cannot map (align) a query to subject genomes. To address this problem, we have developed gmos (Genome MOsaic Structure), a new program that determines the mosaic structure of query genomes when compared to a set of closely related subject genomes. The program first computes local alignments between query and subject genomes and then reconstructs the query mosaic structure by choosing the best local alignment for each query region. To accomplish the analysis quickly, the program mostly relies on pairwise alignments and constructs multiple sequence alignments over short overlapping subject regions only when necessary. This fine-tuned implementation achieves an efficiency comparable to an alignment-free tool. The program performs well for simulated and real data sets of closely related genomes and can be used for fast recombination detection; for instance, when a new prokaryotic pathogen is discovered. As an example, gmos was used to detect genome mosaicism in a pathogenic Enterococcus faecium strain compared to seven closely related genomes. The analysis took less than two minutes on a single 2.1 GHz processor. The output is available in fasta format and can be visualized using an accessory program, gmosDraw (freely available with gmos). PMID:27846272
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ERIC Educational Resources Information Center
Council of Chief State School Officers, 2009
2009-01-01
In Fall 2008, the Council of Chief State School Officers (CCSSO) conducted an alignment content analysis of the 2007 TIMSS Mathematics and Science education assessments for students at grades 4 and 8 and the 2006 PISA Mathematics and Science Literacy assessments for students at age 15 (i.e., TIMSS--Trends in Mathematics and Science Study,…
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Warp-averaging event-related potentials.
Wang, K; Begleiter, H; Porjesz, B
2001-10-01
To align the repeated single trials of the event-related potential (ERP) in order to get an improved estimate of the ERP. A new implementation of the dynamic time warping is applied to compute a warp-average of the single trials. The trilinear modeling method is applied to filter the single trials prior to alignment. Alignment is based on normalized signals and their estimated derivatives. These features reduce the misalignment due to aligning the random alpha waves, explaining amplitude differences in latency differences, or the seemingly small amplitudes of some components. Simulations and applications to visually evoked potentials show significant improvement over some commonly used methods. The new implementation of the dynamic time warping can be used to align the major components (P1, N1, P2, N2, P3) of the repeated single trials. The average of the aligned single trials is an improved estimate of the ERP. This could lead to more accurate results in subsequent analysis.
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A Self-Alignment Algorithm for SINS Based on Gravitational Apparent Motion and Sensor Data Denoising
Liu, Yiting; Xu, Xiaosu; Liu, Xixiang; Yao, Yiqing; Wu, Liang; Sun, Jin
2015-01-01
Initial alignment is always a key topic and difficult to achieve in an inertial navigation system (INS). In this paper a novel self-initial alignment algorithm is proposed using gravitational apparent motion vectors at three different moments and vector-operation. Simulation and analysis showed that this method easily suffers from the random noise contained in accelerometer measurements which are used to construct apparent motion directly. Aiming to resolve this problem, an online sensor data denoising method based on a Kalman filter is proposed and a novel reconstruction method for apparent motion is designed to avoid the collinearity among vectors participating in the alignment solution. Simulation, turntable tests and vehicle tests indicate that the proposed alignment algorithm can fulfill initial alignment of strapdown INS (SINS) under both static and swinging conditions. The accuracy can either reach or approach the theoretical values determined by sensor precision under static or swinging conditions. PMID:25923932
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MULTILOCUS SEQUENCE TYPING OF BRUCELLA ISOLATES FROM THAILAND.
Chawjiraphan, Wireeya; Sonthayanon, Piengchan; Chanket, Phanita; Benjathummarak, Surachet; Kerdsin, Anusak; Kalambhaheti, Thareerat
2016-11-01
Although brucellosis outbreaks in Thailand are rare, they cause abortions and infertility in animals, resulting in significant economic loss. Because Brucella spp display > 90% DNA homology, multilocus sequence typing (MLST) was employed to categorize local Brucella isolates into sequence types (STs) and to determine their genetic relatedness. Brucella samples were isolated from vaginal secretion of cows and goats, and from blood cultures of infected individuals. Brucella species were determined by multiplex PCR of eight loci, in addition to MLST based on partial DNA sequences of nine house-keeping genes. MLST analysis of 36 isolates revealed 78 distinct novel allele types and 34 novel STs, while two isolates possessed the known ST8. Sequence alignments identified polymorphic sites in each allele, ranging from 2-6%, while overall genetic diversity was 3.6%. MLST analysis of the 36 Brucella isolates classified them into three species, namely, B. melitensis, B. abortus and B. suis, in agreement with multiplex PCR results. Genetic relatedness among ST members of B. melitensis and B. abortus determined by eBURST program revealed ST2 as founder of B. abortus isolates and ST8 the founder of B. melitensis isolates. ST 36, 41 and 50 of Thai Brucella isolates were identified as single locus variants of clonal cluster (CC) 8, while the majority of STs were diverse. The genetic diversity and relatedness identified using MLST revealed hitherto unexpected diversity among Thai Brucella isolates. Genetic classification of isolates could reveal the route of brucellosis transmission among humans and farm animals and also reveal their relationship with other isolates in the region and other parts of the world.
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Iterative refinement of structure-based sequence alignments by Seed Extension
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
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Nguyen, Ngoc N.; Nguyen, Anh V.; Dang, Liem X.
Sodium dodecyl sulfate (SDS) has been widely shown to strongly promote the formation of methane hydrate. Here we show that SDS displays an extraordinary inhibition effect on methane hydrate formation when the surfactant is used in sub-millimolar concentration (around 0.3 mM). We have also employed Sum Frequency Generation vibrational spectroscopy (SFG) and molecular dynamics simulation (MDS) to elucidate the molecular mechanism of this inhibition. The SFG and MDS results revealed a strong alignment of water molecules underneath surface adsorption of SDS in its sub-millimolar solution. Interestingly, both the alignment of water and the inhibition effect (in 0.3 mM SDS solution)more » went vanishing when an oppositely-charged surfactant (tetra-n-butylammonium bromide, TBAB) was suitably added to produce a mixed solution of 0.3 mM SDS and 3.6 mM TBAB. Combining structural and kinetic results, we pointed out that the alignment of water underneath surface adsorption of dodecyl sulfate (DS-) anions gave rise to the unexpected inhibition of methane hydration formation in sub-millimolar solution of SDS. The adoption of TBAB mitigated the SDS-induced electrostatic field at the solution’s surface and, therefore, weakened the alignment of interfacial water which, in turn, erased the inhibition effect. We discussed this finding using the concept of activation energy of the interfacial formation of gas hydrate. The main finding of this work is to reveal the interplay of interfacial water in governing gas hydrate formation which sheds light on a universal molecular-scale understanding of the influence of surfactants on gas hydrate formation. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less
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Mobile Gait Analysis System for Lower Limb Amputee High-Level Activity Rehabilitation
2012-09-01
take this data and give the clinician information they can use immediately to get more insight into existing prosthesis fit or alignment issues, help...Modification of Smart Pylon for prosthesis fit, alignment and gait training purposes – 20 In May the larger, more rugged trans-tibial (TT) Smart Pylon...data to determine metrics to indicate positive patient biomechanics factors and indicate successful prosthesis fit and alignment This will be
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Baniecki, John D.; Yamazaki, Takashi; Ricinschi, Dan; Van Overmeere, Quentin; Aso, Hiroyuki; Miyata, Yusuke; Yamada, Hiroaki; Fujimura, Norifumi; Maran, Ronald; Anazawa, Toshihisa; Valanoor, Nagarajan; Imanaka, Yoshihiko
2017-01-01
The valence band (VB) electronic structure and VB alignments at heterointerfaces of strained epitaxial stannate ASnO3 (A=Ca, Sr, and Ba) thin films are characterized using in situ X-ray and ultraviolet photoelectron spectroscopies, with band gaps evaluated using spectroscopic ellipsometry. Scanning transmission electron microscopy with geometric phase analysis is used to resolve strain at atomic resolution. The VB electronic structure is strain state dependent in a manner that correlated with a directional change in Sn-O bond lengths with strain. However, VB offsets are found not to vary significantly with strain, which resulted in ascribing most of the difference in band alignment, due to a change in the band gaps with strain, to the conduction band edge. Our results reveal significant strain tuning of conduction band offsets using epitaxial buffer layers, with strain-induced offset differences as large as 0.6 eV possible for SrSnO3. Such large conduction band offset tunability through elastic strain control may provide a pathway to minimize the loss of charge confinement in 2-dimensional electron gases and enhance the performance of photoelectrochemical stannate-based devices. PMID:28195149
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Coherent Pattern Prediction in Swarms of Delay-Coupled Agents
NASA Astrophysics Data System (ADS)
Mier-Y-Teran-Romero, Luis; Forgoston, Eric; Scwartz, Ira
2013-03-01
We consider a general swarm model of self-propelling particles interacting through a pairwise potential in the presence of a fixed communication time delay. Previous work has shown that swarms with communication time delays and noise may display pattern transitions that depend on the size of the coupling amplitude. We extend these results by completely unfolding the bifurcation structure of the mean field approximation. Our analysis reveals a direct correspondence between the different dynamical behaviors found in different regions of the coupling-time delay plane with the different classes of simulated coherent swarm patterns. We derive the spatio-temporal scales of the swarm structures, and also demonstrate how the complicated interplay of coupling strength, time delay, noise intensity, and choice of initial conditions can affect the swarm. In addition, when adding noise to the system, we find that for sufficiently large values of the coupling strength and/or the time delay, there is a noise intensity threshold that forces a transition of the swarm from a misaligned state into an aligned state. We show that this alignment transition exhibits hysteresis when the noise intensity is taken to be time dependent. Office of Naval Research, NIH (LMR and IBS) and NRL (EF)
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Rizzardi, Kristina; Winiecka-Krusnell, Jadwiga; Ramliden, Miriam; Alm, Erik; Andersson, Sabina; Byfors, Sara
2015-02-01
Fourteen isolates of an unknown species identified as belonging to the genus Legionella by selective growth on BCYE agar were isolated from the biopurification systems of three different wood processing plants. The mip gene sequence of all 14 isolates was identical and a close match alignment revealed 86 % sequence similarity with Legionella pneumophila serogroup 8. The whole genome of isolate LEGN(T) was sequenced, and a phylogenetic tree based on the alignment of 16S rRNA, mip, rpoB, rnpB and the 23S-5S intergenic region clustered LEGN(T) with L. pneumophila ATCC 33152(T). Analysis of virulence factors showed that strain LEGN(T) carries the majority of known L. pneumophila virulence factors. An amoeba infection assay performed to assess the pathogenicity of strain LEGN(T) towards Acanthamoeba castellanii showed that it can establish a replication vacuole in A. castellanii but does not significantly affect replication of amoebae. Taken together, the results confirm that strain LEGN(T) represents a novel species of the genus Legionella, for which the name Legionella norrlandica sp. nov. is proposed. The type strain is LEGN(T) ( = ATCC BAA-2678(T) = CCUG 65936(T)). © 2015 IUMS.
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Cross contrast multi-channel image registration using image synthesis for MR brain images.
Chen, Min; Carass, Aaron; Jog, Amod; Lee, Junghoon; Roy, Snehashis; Prince, Jerry L
2017-02-01
Multi-modal deformable registration is important for many medical image analysis tasks such as atlas alignment, image fusion, and distortion correction. Whereas a conventional method would register images with different modalities using modality independent features or information theoretic metrics such as mutual information, this paper presents a new framework that addresses the problem using a two-channel registration algorithm capable of using mono-modal similarity measures such as sum of squared differences or cross-correlation. To make it possible to use these same-modality measures, image synthesis is used to create proxy images for the opposite modality as well as intensity-normalized images from each of the two available images. The new deformable registration framework was evaluated by performing intra-subject deformation recovery, intra-subject boundary alignment, and inter-subject label transfer experiments using multi-contrast magnetic resonance brain imaging data. Three different multi-channel registration algorithms were evaluated, revealing that the framework is robust to the multi-channel deformable registration algorithm that is used. With a single exception, all results demonstrated improvements when compared against single channel registrations using the same algorithm with mutual information. Copyright © 2016 Elsevier B.V. All rights reserved.
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Efficient alignment-free DNA barcode analytics.
Kuksa, Pavel; Pavlovic, Vladimir
2009-11-10
In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding.
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EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity
Nahum, Laila A; Reynolds, Matthew T; Wang, Zhengyuan O; Faith, Jeremiah J; Jonna, Rahul; Jiang, Zhi J; Meyer, Thomas J; Pollock, David D
2006-01-01
Background Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed Evolutionary Genomics and Biodiversity (EGenBio; ) to begin to address this. Description EGenBio is a system for manipulation and filtering of large numbers of sequences, integrating curated sequence alignments and phylogenetic trees, managing evolutionary analyses, and visualizing their output. EGenBio is organized into three conceptual divisions, Evolution, Genomics, and Biodiversity. The Genomics division includes tools for selecting pre-aligned sequences from different genes and species, and for modifying and filtering these alignments for further analysis. Species searches are handled through queries that can be modified based on a tree-based navigation system and saved. The Biodiversity division contains tools for analyzing individual sequences or sequence alignments, whereas the Evolution division contains tools involving phylogenetic trees. Alignments are annotated with analytical results and modification history using our PRAED format. A miscellaneous Tools section and Help framework are also available. EGenBio was developed around our comparative genomic research and a prototype database of mtDNA genomes. It utilizes MySQL-relational databases and dynamic page generation, and calls numerous custom programs. Conclusion EGenBio was designed to serve as a platform for tools and resources to ease combined analysis in evolution, genomics, and biodiversity. PMID:17118150
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Li, Ying; Shi, Xiaohu; Liang, Yanchun; Xie, Juan; Zhang, Yu; Ma, Qin
2017-01-21
RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms. An alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package. RNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA comparison tools, RNApdist and RNAdistance, showcased that RNA-TVcurve can efficiently capture subtle relationships among RNAs for mutation detection and non-coding RNA classification. All the relevant results were shown in an intuitive graphical manner, and can be freely downloaded from this server. RNA-TVcurve, along with test examples and detailed documents, are available at: http://ml.jlu.edu.cn/tvcurve/ .
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O'Connor, Brian D.; Yuen, Denis; Chung, Vincent; Duncan, Andrew G.; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent
2017-01-01
As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH). PMID:28344774
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O'Connor, Brian D; Yuen, Denis; Chung, Vincent; Duncan, Andrew G; Liu, Xiang Kun; Patricia, Janice; Paten, Benedict; Stein, Lincoln; Ferretti, Vincent
2017-01-01
As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing. If run locally, an operation at this scale would have monopolized a typical academic data centre for many months, and would have presented major challenges for data storage and distribution. However, this scale is increasingly typical for genomics projects and necessitates a rethink of how analytical tools are packaged and moved to the data. For PCAWG, we embraced the use of highly portable Docker images for encapsulating and sharing complex alignment and variant calling workflows across highly variable environments. While successful, this endeavor revealed a limitation in Docker containers, namely the lack of a standardized way to describe and execute the tools encapsulated inside the container. As a result, we created the Dockstore ( https://dockstore.org), a project that brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within. This service greatly improves the sharing and reuse of genomics tools and promotes interoperability with similar projects through emerging web service standards developed by the Global Alliance for Genomics and Health (GA4GH).
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Extending unbiased stereology of brain ultrastructure to three-dimensional volumes
NASA Technical Reports Server (NTRS)
Fiala, J. C.; Harris, K. M.; Koslow, S. H. (Principal Investigator)
2001-01-01
OBJECTIVE: Analysis of brain ultrastructure is needed to reveal how neurons communicate with one another via synapses and how disease processes alter this communication. In the past, such analyses have usually been based on single or paired sections obtained by electron microscopy. Reconstruction from multiple serial sections provides a much needed, richer representation of the three-dimensional organization of the brain. This paper introduces a new reconstruction system and new methods for analyzing in three dimensions the location and ultrastructure of neuronal components, such as synapses, which are distributed non-randomly throughout the brain. DESIGN AND MEASUREMENTS: Volumes are reconstructed by defining transformations that align the entire area of adjacent sections. Whole-field alignment requires rotation, translation, skew, scaling, and second-order nonlinear deformations. Such transformations are implemented by a linear combination of bivariate polynomials. Computer software for generating transformations based on user input is described. Stereological techniques for assessing structural distributions in reconstructed volumes are the unbiased bricking, disector, unbiased ratio, and per-length counting techniques. A new general method, the fractional counter, is also described. This unbiased technique relies on the counting of fractions of objects contained in a test volume. A volume of brain tissue from stratum radiatum of hippocampal area CA1 is reconstructed and analyzed for synaptic density to demonstrate and compare the techniques. RESULTS AND CONCLUSIONS: Reconstruction makes practicable volume-oriented analysis of ultrastructure using such techniques as the unbiased bricking and fractional counter methods. These analysis methods are less sensitive to the section-to-section variations in counts and section thickness, factors that contribute to the inaccuracy of other stereological methods. In addition, volume reconstruction facilitates visualization and modeling of structures and analysis of three-dimensional relationships such as synaptic connectivity.
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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.
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Gravitational-Wave Data Analysis with Spinning Merger-Ringdown Waveforms
NASA Technical Reports Server (NTRS)
Kelly Bernard J.
2011-01-01
The recent availability of high-quality, gravitational merger-ringdown waveforms from spinning black-hole systems has made possible the development of multi-mode GW templates for use in data-analysis studies of current and proposed interferometric GW detectors. We report on recent work at NASA Goddard, analyzing the most significant modes from aligned-spin black-hole-binary mergers. From these, we have developed time-domain merger-ringdown GW templates covering the aligned-spin portion of parameter space. We also discuss how using the full information content of aligned-spin mergers can significantly reduce uncertainties in some parameters, emphasizing the significant gains possible in the last stages of merger, inaccessible to inspiral-only post-Newtonian templates.
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The Influence Of Component Alignment On The Life Of Total Knee Prostheses
NASA Astrophysics Data System (ADS)
Bugariu, Delia; Bereteu, Liviu
2012-12-01
An arthritic knee affects the patient's life by causing pain and limiting movement. If the cartilage and the bone surfaces are severely affected, the natural joint is replaced with an artificial joint. The procedure is called total knee arthroplasty (TKA). Lately, the numbers of implanted total knee prostheses grow steadily. An important factor in TKA is the perfect alignment of the total knee prosthesis (TKP) components. Component misalignment can lead to the prosthesis loss by producing wear particles. The paper proposes a study on mechanical behaviors of a TKP based on numerical analysis, using ANSYS software. The numerical analysis is based on both the normal and the changed angle of the components alignment.
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NASA Technical Reports Server (NTRS)
Asatiani, T. L.; Genina, L. E.; Zatsepin, G. T.
1985-01-01
A systematic analysis of large gamma families, detected in X-ray emulsion chambers, cases of multicore halos have been observed, and among them five events in which the halo is divided into three of four separate cores with their alignment observed in the target diagram (coplanarity of axes of corresponding electron photon cascades). The halo alignment (tendency to the straight line) leads to the aximuthal asymmetry (thrust). The analysis of lateral and momentum distributions of particles in these families shows that they also have thrust that correlates with the direction of the halo core alignment.
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Monrouxe, Lynn V; Bullock, Alison; Tseng, Hsu-Min; Wells, Stephanie E
2017-12-27
To examine how burnout across medical student to junior doctor transition relates to: measures of professional identity, team understanding, anxiety, gender, age and workplace learning (assistantship) alignment to first post. A longitudinal 1-year cohort design. Two groups of final-year medical students: (1) those undertaking end-of-year assistantships aligned in location and specialty with their first post and (2) those undertaking assistantships non-aligned. An online questionnaire included: Professional Identity Scale, Team Understanding Scale, modified Hamilton Anxiety Rating Scale and modified Copenhagen Burnout Inventory. Data were collected on four occasions: (T1) prior to graduation; (T2) 1 month post-transition; (T3) 6 months post-transition and (T4) 10 months post-transition. Questionnaires were analysed individually and using linear mixed-effect models. Medical schools and postgraduate training in one UK country. All aligned assistantship (n=182) and non-aligned assistantship students (n=319) were contacted; n=281 (56%) responded: 68% (n=183) females, 73% (n=206) 22-30 years, 46% aligned (n=129). Completion rates: aligned 72% (93/129) and non-aligned 64% (98/152). Analyses of individual scales revealed that self-reported anxiety, professional identity and patient-related burnout were stable, while team understanding, personal and work-related burnout increased, all irrespective of alignment. Three linear mixed-effect models (personal, patient-related and work-related burnout as outcome measures; age and gender as confounding variables) found that males self-reported significantly lower personal, but higher patient-related burnout, than females. Age and team understanding had no effect. Anxiety was significantly positively related and professional identity was significantly negatively related to burnout. Participants experiencing non-aligned assistantships reported higher personal and work-related burnout over time. Implications for practice include medical schools' consideration of an end-of-year workplace alignment with first-post before graduation or an extended shadowing period immediately postgraduation. How best to support undergraduate students' early professional identity development should be examined. Support systems should be in place across the transition for individuals with a predisposition for anxiety. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.
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Orientational control of block copolymer microdomains by sub-tesla magnetic fields
NASA Astrophysics Data System (ADS)
Gopinadhan, Manesh; Choo, Youngwoo; Feng, Xunda; Kawabata, Kohsuke; di, Xiaojun; Osuji, Chinedum
Magnetic fields offer a versatile approach to controlling the orientation of block copolymer (BCP) microdomains during self-assembly. To date however, such control has required the imposition of large magnetic fields (>3T), necessitating the use of complex magnet systems - either superconducting or very large conventional resistive magnets. Here we demonstrate the ability to direct BCP self-assembly using considerably smaller fields (<1T) which are accessible using simple rare-earth permanent magnets. The low field alignment is enabled by the presence of small quantities of mesogenic species that are blended into, and co-assemble with the liquid crystalline (LC) mesophase of the side-chain LC BCP under study. In situ SAXS experiments reveal a pronounced dependence of the critical alignment field strength on the stoichiometry of the blend, and the ability to generate aligned microdomains with orientational distribution coefficients exceeding 0.95 at sub-1 T fields for appropriate stoichiometries. The alignment response overall can be rationalized in terms of increased mobility and grain size due to the presence of the mesogenic additive. We use a permanent magnet to fabricate films with aligned nanopores, and the utility of this approach to generate complex BCP microdomain patterns in thin films by local field screening are highlighted. NSF DMR-1410568 and DMR-0847534.
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Variability in surface ECG morphology: signal or noise?
NASA Technical Reports Server (NTRS)
Smith, J. M.; Rosenbaum, D. S.; Cohen, R. J.
1988-01-01
Using data collected from canine models of acute myocardial ischemia, we investigated two issues of major relevance to electrocardiographic signal averaging: ECG epoch alignment, and the spectral characteristics of the beat-to-beat variability in ECG morphology. With initial digitization rates of 1 kHz, an iterative a posteriori matched filtering alignment scheme, and linear interpolation, we demonstrated that there is sufficient information in the body surface ECG to merit alignment to a precision of 0.1 msecs. Applying this technique to align QRS complexes and atrial pacing artifacts independently, we demonstrated that the conduction delay from atrial stimulus to ventricular activation may be so variable as to preclude using atrial pacing as an alignment mechanism, and that this variability in conduction time be modulated at the frequency of respiration and at a much lower frequency (0.02-0.03Hz). Using a multidimensional spectral technique, we investigated the beat-to-beat variability in ECG morphology, demonstrating that the frequency spectrum of ECG morphological variation reveals a readily discernable modulation at the frequency of respiration. In addition, this technique detects a subtle beat-to-beat alternation in surface ECG morphology which accompanies transient coronary artery occlusion. We conclude that physiologically important information may be stored in the variability in the surface electrocardiogram, and that this information is lost by conventional averaging techniques.
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Microwave and Millimeter Wave Properties of Vertically-Aligned Single Wall Carbon Nanotubes Films
NASA Astrophysics Data System (ADS)
Haddadi, K.; Tripon-Canseliet, C.; Hivin, Q.; Ducournau, G.; Teo, E.; Coquet, P.; Tay, B. K.; Lepilliet, S.; Avramovic, V.; Chazelas, J.; Decoster, D.
2016-05-01
We present the experimental determination of the complex permittivity of vertically aligned single wall carbon nanotubes (SWCNTs) films grown on quartz substrates in the microwave regime from 10 MHz up to 67 GHz, with the electrical field perpendicular to the main axis of the carbon nanotubes (CNTs), based on coplanar waveguide transmission line approach together with the measurement of the microwave impedance of top metalized vertically—aligned SWCNTs grown on conductive silicon substrates up to 26 GHz. From coplanar waveguide measurements, we obtain a real part of the permittivity almost equal to unity, which is interpreted in terms of low carbon atom density (3 × 1019 at/cm3) associated with a very low imaginary part of permittivity (<10-3) in the frequency range considered due to a very small perpendicular conductivity. The microwave impedance of a vertically aligned CNTs bundle equivalent to a low resistance reveals a good conductivity (3 S/cm) parallel to the CNTs axis. From these two kinds of data, we experimentally demonstrate the tensor nature of the vertically grown CNTs bundles.
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The kinetic regime of the Vicsek model
NASA Astrophysics Data System (ADS)
Chepizhko, A. A.; Kulinskii, V. L.
2009-12-01
We consider the dynamics of the system of self-propelling particles modeled via the Vicsek algorithm in continuum time limit. It is shown that the alignment process for the velocities can be subdivided into two regimes: "fast" kinetic and "slow" hydrodynamic ones. In fast kinetic regime the alignment of the particle velocity to the local neighborhood takes place with characteristic relaxation time. So, that the bigger regions arise with the velocity alignment. These regions align their velocities thus giving rise to hydrodynamic regime of the dynamics. We propose the mean-field-like approach in which we take into account the correlations between density and velocity. The comparison of the theoretical predictions with the numerical simulations is given. The relation between Vicsek model in the zero velocity limit and the Kuramoto model is stated. The mean-field approach accounting for the dynamic change of the neighborhood is proposed. The nature of the discontinuity of the dependence of the order parameter in case of vectorial noise revealed in Gregorie and Chaite, Phys. Rev. Lett., 92, 025702 (2004) is discussed and the explanation of it is proposed.
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Measurement and control of detailed electronic properties in a single molecule break junction.
Wang, Kun; Hamill, Joseph; Zhou, Jianfeng; Guo, Cunlan; Xu, Bingqian
2014-01-01
The lack of detailed experimental controls has been one of the major obstacles hindering progress in molecular electronics. While large fluctuations have been occurring in the experimental data, specific details, related mechanisms, and data analysis techniques are in high demand to promote our physical understanding at the single-molecule level. A series of modulations we recently developed, based on traditional scanning probe microscopy break junctions (SPMBJs), have helped to discover significant properties in detail which are hidden in the contact interfaces of a single-molecule break junction (SMBJ). For example, in the past we have shown that the correlated force and conductance changes under the saw tooth modulation and stretch-hold mode of PZT movement revealed inherent differences in the contact geometries of a molecular junction. In this paper, using a bias-modulated SPMBJ and utilizing emerging data analysis techniques, we report on the measurement of the altered alignment of the HOMO of benzene molecules with changing the anchoring group which coupled the molecule to metal electrodes. Further calculations based on Landauer fitting and transition voltage spectroscopy (TVS) demonstrated the effects of modulated bias on the location of the frontier molecular orbitals. Understanding the alignment of the molecular orbitals with the Fermi level of the electrodes is essential for understanding the behaviour of SMBJs and for the future design of more complex devices. With these modulations and analysis techniques, fruitful information has been found about the nature of the metal-molecule junction, providing us insightful clues towards the next step for in-depth study.
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Ventura, Marco; Jankovic, Ivana; Walker, D. Carey; Pridmore, R. David; Zink, Ralf
2002-01-01
We have identified and sequenced the genes encoding the aggregation-promoting factor (APF) protein from six different strains of Lactobacillus johnsonii and Lactobacillus gasseri. Both species harbor two apf genes, apf1 and apf2, which are in the same orientation and encode proteins of 257 to 326 amino acids. Multiple alignments of the deduced amino acid sequences of these apf genes demonstrate a very strong sequence conservation of all of the genes with the exception of their central regions. Northern blot analysis showed that both genes are transcribed, reaching their maximum expression during the exponential phase. Primer extension analysis revealed that apf1 and apf2 harbor a putative promoter sequence that is conserved in all of the genes. Western blot analysis of the LiCl cell extracts showed that APF proteins are located on the cell surface. Intact cells of L. johnsonii revealed the typical cell wall architecture of S-layer-carrying gram-positive eubacteria, which could be selectively removed with LiCl treatment. In addition, the amino acid composition, physical properties, and genetic organization were found to be quite similar to those of S-layer proteins. These results suggest that APF is a novel surface protein of the Lactobacillus acidophilus B-homology group which might belong to an S-layer-like family. PMID:12450842
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Chung, H Y; Choi, Y C; Park, H N
2015-05-18
We investigated the phylogenetic relationships between pig breeds, compared the genetic similarity between humans and pigs, and provided basic genetic information on Korean native pigs (KNPs), using genetic variants of the swine leukocyte antigen 3 (SLA-3) gene. Primers were based on sequences from GenBank (accession Nos. AF464010 and AF464009). Polymerase chain reaction analysis amplified approximately 1727 bp of segments, which contained 1086 bp of coding regions and 641 bp of the 3'- and 5'-untranslated regions. Bacterial artificial chromosome clones of miniature pigs were used for sequencing the SLA-3 genomic region, which was 3114 bp in total length, including the coding (1086 bp) and non-coding (2028 bp) regions. Sequence analysis detected 53 single nucleotide polymorphisms (SNPs), based on a minor allele frequency greater than 0.01, which is low compared with other pig breeds, and the results suggest that there is low genetic variability in KNPs. Comparative analysis revealed that humans possess approximately three times more genetic variation than do pigs. Approximately 71% of SNPs in exons 2 and 3 were detected in KNPs, and exon 5 in humans is a highly polymorphic region. Newly identified sequences of SLA-3 using KNPs were submitted to GenBank (accession No. DQ992512-18). Cluster analysis revealed that KNPs were grouped according to three major alleles: SLA-3*0502 (DQ992518), SLA-3*0302 (DQ992513 and DQ992516), and SLA-3*0303 (DQ992512, DQ992514, DQ992515, and DQ992517). Alignments revealed that humans have a relatively close genetic relationship with pigs and chimpanzees. The information provided by this study may be useful in KNP management.
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Lippolis, Giuseppe; Edsjö, Anders; Helczynski, Leszek; Bjartell, Anders; Overgaard, Niels Chr
2013-09-05
Prostate cancer is one of the leading causes of cancer related deaths. For diagnosis, predicting the outcome of the disease, and for assessing potential new biomarkers, pathologists and researchers routinely analyze histological samples. Morphological and molecular information may be integrated by aligning microscopic histological images in a multiplex fashion. This process is usually time-consuming and results in intra- and inter-user variability. The aim of this study is to investigate the feasibility of using modern image analysis methods for automated alignment of microscopic images from differently stained adjacent paraffin sections from prostatic tissue specimens. Tissue samples, obtained from biopsy or radical prostatectomy, were sectioned and stained with either hematoxylin & eosin (H&E), immunohistochemistry for p63 and AMACR or Time Resolved Fluorescence (TRF) for androgen receptor (AR). Image pairs were aligned allowing for translation, rotation and scaling. The registration was performed automatically by first detecting landmarks in both images, using the scale invariant image transform (SIFT), followed by the well-known RANSAC protocol for finding point correspondences and finally aligned by Procrustes fit. The Registration results were evaluated using both visual and quantitative criteria as defined in the text. Three experiments were carried out. First, images of consecutive tissue sections stained with H&E and p63/AMACR were successfully aligned in 85 of 88 cases (96.6%). The failures occurred in 3 out of 13 cores with highly aggressive cancer (Gleason score ≥ 8). Second, TRF and H&E image pairs were aligned correctly in 103 out of 106 cases (97%).The third experiment considered the alignment of image pairs with the same staining (H&E) coming from a stack of 4 sections. The success rate for alignment dropped from 93.8% in adjacent sections to 22% for sections furthest away. The proposed method is both reliable and fast and therefore well suited for automatic segmentation and analysis of specific areas of interest, combining morphological information with protein expression data from three consecutive tissue sections. Finally, the performance of the algorithm seems to be largely unaffected by the Gleason grade of the prostate tissue samples examined, at least up to Gleason score 7.
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Chen, Yikai; Wang, Kai; Xu, Chengcheng; Shi, Qin; He, Jie; Li, Peiqing; Shi, Ting
2018-05-19
To overcome the limitations of previous highway alignment safety evaluation methods, this article presents a highway alignment safety evaluation method based on fault tree analysis (FTA) and the characteristics of vehicle safety boundaries, within the framework of dynamic modeling of the driver-vehicle-road system. Approaches for categorizing the vehicle failure modes while driving on highways and the corresponding safety boundaries were comprehensively investigated based on vehicle system dynamics theory. Then, an overall crash probability model was formulated based on FTA considering the risks of 3 failure modes: losing steering capability, losing track-holding capability, and rear-end collision. The proposed method was implemented on a highway segment between Bengbu and Nanjing in China. A driver-vehicle-road multibody dynamics model was developed based on the 3D alignments of the Bengbu to Nanjing section of Ning-Luo expressway using Carsim, and the dynamics indices, such as sideslip angle and, yaw rate were obtained. Then, the average crash probability of each road section was calculated with a fixed-length method. Finally, the average crash probability was validated against the crash frequency per kilometer to demonstrate the accuracy of the proposed method. The results of the regression analysis and correlation analysis indicated good consistency between the results of the safety evaluation and the crash data and that it outperformed the safety evaluation methods used in previous studies. The proposed method has the potential to be used in practical engineering applications to identify crash-prone locations and alignment deficiencies on highways in the planning and design phases, as well as those in service.
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NASA Astrophysics Data System (ADS)
Thomson, Mark D.; Zouaghi, Wissem; Meng, Fanqi; Wiecha, Matthias M.; Rabia, Kaneez; Heinlein, Thorsten; Hussein, Laith; Babu, Deepu; Yadav, Sandeep; Engstler, Jörg; Schneider, Jörg J.; Nicoloso, Norbert; Rychetský, Ivan; Kužel, Petr; Roskos, Hartmut G.
2018-01-01
We investigate the broadband dielectric properties of vertically aligned, multi-wall carbon nanotubes (VACNT), over both the terahertz (THz) and mid-infrared spectral ranges. The nominally undoped, metallic VACNT samples are probed at normal incidence, i.e. the response is predominantly due to polarisation perpendicular to the CNT axis. A detailed comparison of various conductivity models and previously reported results is presented for the non-Drude behaviour we observe in the conventional THz range (up to 2.5 THz). Extension to the mid-infrared range reveals an absorption peak at \
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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.
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Treangen, Todd J; Ondov, Brian D; Koren, Sergey; Phillippy, Adam M
2014-01-01
Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.
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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
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Schroeder, Lennart; Martin, Gregory
2018-05-25
In total knee arthroplasty (TKA), surgeons often face the decision of maximizing tibial component fit and achieving correct rotational alignment at the same time. Customized implants (CIMs) address this difficulty by aiming to replicate the anatomical joint structure, utilizing data from patient-specific knee geometry during the manufacturing. We intraoperatively compared component fit in four tibial zones of a CIM to that of three different off-the-shelf (OTS) TKA designs in 44 knees. Additionally, we assessed the rotational alignment of the tibia using computed tomography (CT)-based computer aided design model analysis. Overall the CIM device showed significantly better component fit than the OTS TKAs. While 18% of OTS designs presented an implant overhang of 3 mm or more, none of the CIM components did ( p < 0.05). There was a larger percentage of CIMs seen with optimal fit (≤1 mm implant overhang to ≤1 mm tibial bone undercoverage) than in OTS TKAs. Also, OTS implants showed significantly more component underhang of ≥3 mm than the CIM design (37 vs. 18%). The rotational analysis revealed that 45% of the OTS tibial components showed a rotational deviation of more than 5 degrees and 4% of more than 10 degrees to a tibial rotational axis described by Cobb et al. No deviation was seen for the CIM, as the device is designed along this axis. Using the medial one-third of the tibial tubercle as the rotational landmark, 95% of the OTS trays demonstrated a rotational deviation of more than 5 degrees and 73% of more than 10 degrees compared with 73% of CIM tibial trays with more than 5 degrees and 27% with more than 10 degrees. Based on our findings, we believe that the CIM TKA provides both better rotational alignment and tibial fit without causing overhang of the tibial tray than the three examined OTS implants. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.
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Jain, Varsha; Patel, Brijesh; Umar, Farhat Paul; Ajithakumar, H. M.; Gurjar, Suraj K.; Gupta, I. D.; Verma, Archana
2017-01-01
Aim: This study was conducted with the objective to identify single nucleotide polymorphism (SNP) in protein phosphatase 1 regulatory subunit 11 (PPP1R11) gene in Murrah bulls. Materials and Methods: Genomic DNA was isolated by phenol–chloroform extraction method from the frozen semen samples of 65 Murrah bulls maintained at Artificial Breeding Research Centre, ICAR-National Dairy Research Institute, Karnal. The quality and concentration of DNA was checked by spectrophotometer reading and agarose gel electrophoresis. The target region of PPP1R11 gene was amplified using four sets of primer designed based on Bos taurus reference sequence. The amplified products were sequenced and aligned using Clustal Omega for identification of SNPs. Animals were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using EcoNI restriction enzyme. Results: The sequences in the NCBI accession number NW_005785016.1 for Bubalus bubalis were compared and aligned with the edited sequences of Murrah bulls with Clustal Omega software. A total of 10 SNPs were found, out of which 1 at 5’UTR, 3 at intron 1, and 6 at intron 2 region. PCR-RFLP using restriction enzyme EcoNI revealed only AA genotype indicating monomorphism in PPP1R11 gene of all Murrah animals included in the study. Conclusion: A total of 10 SNPs were found. PCR-RFLP revealed only AA genotype indicating monomorphism in PPP1R11 gene of all Murrah animals included in the study, due to which association analysis with conception rate was not feasible. PMID:28344410
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Functionally conserved cis-regulatory elements of COL18A1 identified through zebrafish transgenesis.
Kague, Erika; Bessling, Seneca L; Lee, Josephine; Hu, Gui; Passos-Bueno, Maria Rita; Fisher, Shannon
2010-01-15
Type XVIII collagen is a component of basement membranes, and expressed prominently in the eye, blood vessels, liver, and the central nervous system. Homozygous mutations in COL18A1 lead to Knobloch Syndrome, characterized by ocular defects and occipital encephalocele. However, relatively little has been described on the role of type XVIII collagen in development, and nothing is known about the regulation of its tissue-specific expression pattern. We have used zebrafish transgenesis to identify and characterize cis-regulatory sequences controlling expression of the human gene. Candidate enhancers were selected from non-coding sequence associated with COL18A1 based on sequence conservation among mammals. Although these displayed no overt conservation with orthologous zebrafish sequences, four regions nonetheless acted as tissue-specific transcriptional enhancers in the zebrafish embryo, and together recapitulated the major aspects of col18a1 expression. Additional post-hoc computational analysis on positive enhancer sequences revealed alignments between mammalian and teleost sequences, which we hypothesize predict the corresponding zebrafish enhancers; for one of these, we demonstrate functional overlap with the orthologous human enhancer sequence. Our results provide important insight into the biological function and regulation of COL18A1, and point to additional sequences that may contribute to complex diseases involving COL18A1. More generally, we show that combining functional data with targeted analyses for phylogenetic conservation can reveal conserved cis-regulatory elements in the large number of cases where computational alignment alone falls short. Copyright 2009 Elsevier Inc. All rights reserved.
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NASA Astrophysics Data System (ADS)
Lalit, Manisha; Gangwal, Rahul P.; Dhoke, Gaurao V.; Damre, Mangesh V.; Khandelwal, Kanchan; Sangamwar, Abhay T.
2013-10-01
A combined pharmacophore modelling, 3D-QSAR and molecular docking approach was employed to reveal structural and chemical features essential for the development of small molecules as LRH-1 agonists. The best HypoGen pharmacophore hypothesis (Hypo1) consists of one hydrogen-bond donor (HBD), two general hydrophobic (H), one hydrophobic aromatic (HYAr) and one hydrophobic aliphatic (HYA) feature. It has exhibited high correlation coefficient of 0.927, cost difference of 85.178 bit and low RMS value of 1.411. This pharmacophore hypothesis was cross-validated using test set, decoy set and Cat-Scramble methodology. Subsequently, validated pharmacophore hypothesis was used in the screening of small chemical databases. Further, 3D-QSAR models were developed based on the alignment obtained using substructure alignment. The best CoMFA and CoMSIA model has exhibited excellent rncv2 values of 0.991 and 0.987, and rcv2 values of 0.767 and 0.703, respectively. CoMFA predicted rpred2 of 0.87 and CoMSIA predicted rpred2 of 0.78 showed that the predicted values were in good agreement with the experimental values. Molecular docking analysis reveals that π-π interaction with His390 and hydrogen bond interaction with His390/Arg393 is essential for LRH-1 agonistic activity. The results from pharmacophore modelling, 3D-QSAR and molecular docking are complementary to each other and could serve as a powerful tool for the discovery of potent small molecules as LRH-1 agonists.
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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.
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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.
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Lommen, Arjen
2009-04-15
Hyphenated full-scan MS technology creates large amounts of data. A versatile easy to handle automation tool aiding in the data analysis is very important in handling such a data stream. MetAlign softwareas described in this manuscripthandles a broad range of accurate mass and nominal mass GC/MS and LC/MS data. It is capable of automatic format conversions, accurate mass calculations, baseline corrections, peak-picking, saturation and mass-peak artifact filtering, as well as alignment of up to 1000 data sets. A 100 to 1000-fold data reduction is achieved. MetAlign software output is compatible with most multivariate statistics programs.
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NASA Astrophysics Data System (ADS)
Olczak, Gene; Fischer, David J.; Connelly, Mark; Wells, Conrad
2011-09-01
The James Webb Space Telescope (JWST) integration includes a center of curvature test on its 18 primary mirror segment assemblies (PMSAs). This important test is the only ground test that will demonstrate the ability to align all 18 PMSAs. Using a multi-wavelength interferometer (MWIF) integrated to the test bed telescope (TBT), a one-sixth scale model of the JWST, we verify our ability to align and phase the 18 PMSAs. In this paper we will discuss data analysis and test results when using the MWIF to align the segments of the TBT in preparation for alignment of the JWST.
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Zhang, Zhongbao; Zhang, Jiewei; Chen, Yajuan; Li, Ruifen; Wang, Hongzhi; Ding, Liping; Wei, Jianhua
2014-09-01
Hexokinases (HXKs, EC 2.7.1.1) play important roles in metabolism, glucose (Glc) signaling, and phosphorylation of Glc and fructose and are ubiquitous in all organisms. Despite their physiological importance, the maize HXK (ZmHXK) genes have not been analyzed systematically. We isolated and characterized nine members of the ZmHXK gene family which were distributed on 3 of the 10 maize chromosomes. A multiple sequence alignment and motif analysis revealed that the maize ZmHXK proteins share three conserved domains. Phylogenetic analysis revealed that the ZmHXK family can be divided into four subfamilies. We identified putative cis-elements in the ZmHXK promoter sequences potentially involved in phytohormone and abiotic stress responses, sugar repression, light and circadian rhythm regulation, Ca(2+) responses, seed development and germination, and CO2-responsive transcriptional activation. To study the functions of maize HXK isoforms, we characterized the expression of the ZmHXK5 and ZmHXK6 genes, which are evolutionarily related to the OsHXK5 and OsHXK6 genes from rice. Analysis of tissue-specific expression patterns using quantitative real time-PCR showed that ZmHXK5 was highly expressed in tassels, while ZmHXK6 was expressed in both tassels and leaves. ZmHXK5 and ZmHXK6 expression levels were upregulated by phytohormones and by abiotic stress.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Brown, D. J. A.; Collier Cameron, A.; Enoch, B.
We present measurements of the spin-orbit alignment angle, {lambda}, for the hot Jupiter systems WASP-32, WASP-38, and HAT-P-27/WASP-40, based on data obtained using the HARPS spectrograph. We analyze the Rossiter-McLaughlin effect for all three systems and also carry out Doppler tomography for WASP-32 and WASP-38. We find that WASP-32 (T {sub eff} = 6140{sup +90} {sub -100} K) is aligned, with an alignment angle of {lambda} = 10.{sup 0}5{sup +6.4} {sub -6.5} obtained through tomography, and that WASP-38 (T {sub eff} = 6180{sup +40} {sub -60} K) is also aligned, with tomographic analysis yielding {lambda} = 7.{sup 0}5{sup +4.7} {submore » -6.1}. The latter result provides an order-of-magnitude improvement in the uncertainty in {lambda} compared to the previous analysis of Simpson et al. We are only able to loosely constrain the angle for HAT-P-27/WASP-40 (T{sub eff} = 5190{sup +160} {sub -170} K) to {lambda} = 24.{sup 0}2{sup +76.0}{sub -44.5}, owing to the poor signal-to-noise ratio of our data. We consider this result a non-detection under a slightly updated version of the alignment test of Brown et al. We place our results in the context of the full sample of spin-orbit alignment measurements, finding that they provide further support for previously established trends.« less
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Fast alignment-free sequence comparison using spaced-word frequencies.
Leimeister, Chris-Andre; Boden, Marcus; Horwege, Sebastian; Lindner, Sebastian; Morgenstern, Burkhard
2014-07-15
Alignment-free methods for sequence comparison are increasingly used for genome analysis and phylogeny reconstruction; they circumvent various difficulties of traditional alignment-based approaches. In particular, alignment-free methods are much faster than pairwise or multiple alignments. They are, however, less accurate than methods based on sequence alignment. Most alignment-free approaches work by comparing the word composition of sequences. A well-known problem with these methods is that neighbouring word matches are far from independent. To reduce the statistical dependency between adjacent word matches, we propose to use 'spaced words', defined by patterns of 'match' and 'don't care' positions, for alignment-free sequence comparison. We describe a fast implementation of this approach using recursive hashing and bit operations, and we show that further improvements can be achieved by using multiple patterns instead of single patterns. To evaluate our approach, we use spaced-word frequencies as a basis for fast phylogeny reconstruction. Using real-world and simulated sequence data, we demonstrate that our multiple-pattern approach produces better phylogenies than approaches relying on contiguous words. Our program is freely available at http://spaced.gobics.de/. © The Author 2014. Published by Oxford University Press.
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"Performance Of A Wafer Stepper With Automatic Intra-Die Registration Correction."
NASA Astrophysics Data System (ADS)
van den Brink, M. A.; Wittekoek, S.; Linders, H. F. D.; van Hout, F. J.; George, R. A.
1987-01-01
An evaluation of a wafer stepper with the new improved Philips/ASM-L phase grating alignment system is reported. It is shown that an accurate alignment system needs an accurate X-Y-0 wafer stage and an accurate reticle Z stage to realize optimum overlay accuracy. This follows from a discussion of the overlay budget and an alignment procedure model. The accurate wafer stage permits high overlay accuracy using global alignment only, thus eliminating the throughput penalty of align-by-field schemes. The accurate reticle Z stage enables an intra-die magnification control with respect to the wafer scale. Various overlay data are reported, which have been measured with the automatic metrology program of the stepper. It is demonstrated that the new dual alignment system (with the external spatial filter) has improved the ability to align to weakly reflecting layers. The results are supported by a Fourier analysis of the alignment signal. Resolution data are given for the PAS 2500 projection lenses, which show that the high overlay accuracy of the system is properly matched with submicron linewidth control. The results of a recently introduced 20mm i-line lens with a numerical aperture of 0.4 (Zeiss 10-78-58) are included.
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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.
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Development of Optical System for ARGO-M
NASA Astrophysics Data System (ADS)
Nah, Jakyoung; Jang, Jung-Guen; Jang, Bi-Ho; Han, In-Woo; Han, Jeong-Yeol; Park, Kwijong; Lim, Hyung-Chul; Yu, Sung-Yeol; Park, Eunseo; Seo, Yoon-Kyung; Moon, Il-Kwon; Choi, Byung-Kyu; Na, Eunjoo; Nam, Uk-Won
2013-03-01
ARGO-M is a satellite laser ranging (SLR) system developed by the Korea Astronomy and Space Science Institute with the consideration of mobility and daytime and nighttime satellite observation. The ARGO-M optical system consists of 40 cm receiving telescope, 10 cm transmitting telescope, and detecting optics. For the development of ARGO-M optical system, the structural analysis was performed with regard to the optics and optomechanics design and the optical components. To ensure the optical performance, the quality was tested at the level of parts using the laser interferometer and ultra-high-precision measuring instruments. The assembly and alignment of ARGO-M optical system were conducted at an auto-collimation facility. As the transmission and reception are separated in the ARGO-M optical system, the pointing alignment between the transmitting telescope and receiving telescope is critical for precise target pointing. Thus, the alignment using the ground target and the radiant point observation of transmitting laser beam was carried out, and the lines of sight for the two telescopes were aligned within the required pointing precision. This paper describes the design, structural analysis, manufacture and assembly of parts, and entire process related with the alignment for the ARGO-M optical system.
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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.
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Reference-guided assembly of four diverse Arabidopsis thaliana genomes
Schneeberger, Korbinian; Ossowski, Stephan; Ott, Felix; Klein, Juliane D.; Wang, Xi; Lanz, Christa; Smith, Lisa M.; Cao, Jun; Fitz, Joffrey; Warthmann, Norman; Henz, Stefan R.; Huson, Daniel H.; Weigel, Detlef
2011-01-01
We present whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago. Using a newly developed reference-guided approach, we assembled large contigs from 9 to 42 Gb of Illumina short-read data from the Landsberg erecta (Ler-1), C24, Bur-0, and Kro-0 strains, which have been sequenced as part of the 1,001 Genomes Project for this species. Using alignments against the reference sequence, we first reduced the complexity of the de novo assembly and later integrated reads without similarity to the reference sequence. As an example, half of the noncentromeric C24 genome was covered by scaffolds that are longer than 260 kb, with a maximum of 2.2 Mb. Moreover, over 96% of the reference genome was covered by the reference-guided assembly, compared with only 87% with a complete de novo assembly. Comparisons with 2 Mb of dideoxy sequence reveal that the per-base error rate of the reference-guided assemblies was below 1 in 10,000. Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html. PMID:21646520
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Terminator field-aligned current system: A new finding from model-assimilated data set (MADS)
NASA Astrophysics Data System (ADS)
Zhu, L.; Schunk, R. W.; Scherliess, L.; Sojka, J. J.; Gardner, L. C.; Eccles, J. V.; Rice, D.
2013-12-01
Physics-based data assimilation models have been recognized by the space science community as the most accurate approach to specify and forecast the space weather of the solar-terrestrial environment. The model-assimilated data sets (MADS) produced by these models constitute an internally consistent time series of global three-dimensional fields whose accuracy can be estimated. Because of its internal consistency of physics and completeness of descriptions on the status of global systems, the MADS has also been a powerful tool to identify the systematic errors in measurements, reveal the missing physics in physical models, and discover the important dynamical physical processes that are inadequately observed or missed by measurements due to observational limitations. In the past years, we developed a data assimilation model for the high-latitude ionospheric plasma dynamics and electrodynamics. With a set of physical models, an ensemble Kalman filter, and the ingestion of data from multiple observations, the data assimilation model can produce a self-consistent time-series of the complete descriptions of the global high-latitude ionosphere, which includes the convection electric field, horizontal and field-aligned currents, conductivity, as well as 3-D plasma densities and temperatures, In this presentation, we will show a new field-aligned current system discovered from the analysis of the MADS produced by our data assimilation model. This new current system appears and develops near the ionospheric terminator. The dynamical features of this current system will be described and its connection to the active role of the ionosphere in the M-I coupling will be discussed.
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A new statistical framework to assess structural alignment quality using information compression
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
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Electrostatically Induced Carbon Nanotube Alignment for Polymer Composite Applications
NASA Astrophysics Data System (ADS)
Chapkin, Wesley Aaron
We have developed a non-invasive technique utilizing polarized Raman spectroscopy to measure changes in carbon nanotube (CNT) alignment in situ and in real time in a polymer matrix. With this technique, we have confirmed the prediction of faster alignment for CNTs in higher electric fields. Real-time polarized Raman spectroscopy also allows us to demonstrate the loss of CNT alignment that occurs after the electric field is removed, which reveals the need for fast polymerization steps or the continued application of the aligning force during polymerization to lock in CNT alignment. Through a study on the effect of polymer viscosity on the rate of CNT alignment, we have determined that shear viscosity serves as the controlling mechanism for CNT rotation. This finding matches literature modeling of rigid rod mobility in a polymer melt and demonstrates that the rotational mobility of CNTs can be explained by a continuum model even though the diameters of single-walled CNTs are 1-2 nm. The viscosity dependence indicates that the manipulation of temperature (and indirectly viscosity) will have a direct effect on the rate of CNT alignment, which could prove useful in expediting the manufacturing of CNT-reinforced composites cured at elevated temperatures. Using real-time polarized Raman spectroscopy, we also demonstrate that electric fields of various strengths lead not only to different speeds of CNT rotation but also to different degrees of alignment. We hypothesize that this difference in achievable alignment results from discrete populations of nanotubes based on their length. The results are then explained by balancing the alignment energy for a given electric field strength with the randomizing thermal energy of the system. By studying the alignment dynamics of different CNT length distributions, we show that different degrees of alignment achieved as a function of the applied electric field strength are directly related to the square of the nanotube length. This finding matches an electrostatic potential energy model for CNT rotation. Lastly, we investigate the effects of conductive carbon fibers on electrostatically induced alignment of CNTs within carbon fiber composites. The relative electric field strength throughout the composite is modeled using COMSOL Multiphysics. We show the ability to generate enhanced electric field gradients within the gaps between carbon fibers for various fiber orientations. Using polarized Raman spectroscopy, increased levels of CNT alignment are observed between carbon fiber tows, which is consistent with the modeled higher electric field strengths in these regions. These findings could potentially lead to the development of carbon fiber composites with CNT additions that selectively enhance the composite properties outside the carbon fiber interphase in the neat epoxy.
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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
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An extensive assessment of network alignment algorithms for comparison of brain connectomes.
Milano, Marianna; Guzzi, Pietro Hiram; Tymofieva, Olga; Xu, Duan; Hess, Christofer; Veltri, Pierangelo; Cannataro, Mario
2017-06-06
Recently the study of the complex system of connections in neural systems, i.e. the connectome, has gained a central role in neurosciences. The modeling and analysis of connectomes are therefore a growing area. Here we focus on the representation of connectomes by using graph theory formalisms. Macroscopic human brain connectomes are usually derived from neuroimages; the analyzed brains are co-registered in the image domain and brought to a common anatomical space. An atlas is then applied in order to define anatomically meaningful regions that will serve as the nodes of the network - this process is referred to as parcellation. The atlas-based parcellations present some known limitations in cases of early brain development and abnormal anatomy. Consequently, it has been recently proposed to perform atlas-free random brain parcellation into nodes and align brains in the network space instead of the anatomical image space, as a way to deal with the unknown correspondences of the parcels. Such process requires modeling of the brain using graph theory and the subsequent comparison of the structure of graphs. The latter step may be modeled as a network alignment (NA) problem. In this work, we first define the problem formally, then we test six existing state of the art of network aligners on diffusion MRI-derived brain networks. We compare the performances of algorithms by assessing six topological measures. We also evaluated the robustness of algorithms to alterations of the dataset. The results confirm that NA algorithms may be applied in cases of atlas-free parcellation for a fully network-driven comparison of connectomes. The analysis shows MAGNA++ is the best global alignment algorithm. The paper presented a new analysis methodology that uses network alignment for validating atlas-free parcellation brain connectomes. The methodology has been experimented on several brain datasets.
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NASA Astrophysics Data System (ADS)
Yoo, Byung-Wook; Park, Jae-Hyoung; Jin, Joo-Young; Jang, Yun-Ho; Kim, Yong-Kweon
2009-05-01
This paper describes a self-alignment method whereby a mirror actuation voltage, corresponding to a specific tilting angle, is unvarying in terms of misalignment during fabrication. A deep silicon etching process is proposed to penetrate the top silicon layer (the micromirror layer) and an amorphous silicon layer (the addressing electrode layer) together, through an aluminum mask pattern, in order to minimize the misalignment effect on the micromirror actuation. The size of a fabricated mirror plate is 250 × 250 × 4 µm3. A pair of amorphous silicon electrodes under the mirror plate is about half the size of the mirror plate individually. Numerical analysis associated with calculating the pull-in voltage and the bonding misalignment is performed to verify the self-alignment concepts focused upon in this paper. Curves of the applied voltage versus the tilt angle of the self-aligned micromirror are observed using a position sensing detector in order to compare the measurement results with MATLAB analysis of the expected static deflections. Although a 3.7 µm misalignment is found between the mirror plate and the electrodes, in the direction perpendicular to the shallow trench of the electrodes, before the self-alignment process, the measured pull-in voltage has been found to be 103.4 V on average; this differs from the pull-in voltage of a perfectly aligned micromirror by only 0.67%. Regardless of the unpredictable misalignments in repetitive photolithography and bonding, the tilting angles corresponding to the driving voltages are proved to be uniform along the single axis as well as conform to the results of analytical analysis.
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Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment
2013-01-01
Background Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. Results In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Conclusion Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA. PMID:24564200
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Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.
Nagar, Anurag; Hahsler, Michael
2013-01-01
Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA.
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Development of a molecular approach to describe the composition of Trichoderma communities.
Meincke, Remo; Weinert, Nicole; Radl, Viviane; Schloter, Michael; Smalla, Kornelia; Berg, Gabriele
2010-01-01
Trichoderma and its teleomorphic stage Hypocrea play a key role for ecosystem functioning in terrestrial habitats. However, little is known about the ecology of the fungus. In this study we developed a novel Trichoderma-specific primer pair for diversity analysis. Based on a broad range master alignment, specific Trichoderma primers (ITSTrF/ITSTrR) were designed that comprise an approximate 650bp fragment of the internal transcribed spacer region from all taxonomic clades of the genus Trichoderma. This amplicon is suitable for identification with TrichoKey and TrichoBLAST. Moreover, this primer system was successfully applied to study the Trichoderma communities in the rhizosphere of different potato genotypes grown at two field sites in Germany. Cloning and sequencing confirmed the specificity of the primer and revealed a site-dependent Trichoderma composition. Based on the new primer system a semi-nested approach was used to generate amplicons suitable for denaturing gradient gel electrophoresis (DGGE) analysis and applied to analyse Trichoderma communities in the rhizosphere of potatoes. High field heterogeneity of Trichoderma communities was revealed by both DGGE. Furthermore, qPCR showed significantly different Trichoderma copy numbers between the sites. Copyright 2009 Elsevier B.V. All rights reserved.
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In silico analysis of L-asparaginase from different source organisms.
Dwivedi, Vivek Dhar; Mishra, Sarad Kumar
2014-06-01
L-asparaginases are widely distributed enzymes among plants, fungi and bacteria. This enzyme catalyzes the conversion of l-asparagine to l-aspartate and ammonia and to a lesser extent the formation of l-glutamate from l-glutamine. In the present study, forty-five full-length amino acid sequences of L-asparaginases from bacteria, fungi and plants were collected and subjected to multiple sequence alignment (MSA), domain identification, discovering individual amino acid composition, and phylogenetic tree construction. MSA revealed that two glycine residues were identically found in all analyzed species, two glycine residues were also identically found in all the fungal and bacterial sources and three glycine residues were identically found in all plant and bacterial sources while no residue was identically found in plant and fungal L-asparaginases. Two major sequence clusters were constructed by phylogenetic analysis. One cluster contains eleven species of fungi, twelve species of bacteria, and one species of plant, whereas the other one contains fourteen species of plant, four species of fungi and three species bacteria. The amino acid composition result revealed that the average frequency of amino acid alanine is 10.77 percent that is very high in comparison to other amino acids in all analyzed species.
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Adewoye, L O; Worobec, E A
2000-08-08
The Pseudomonas aeruginosa oprB gene encodes the carbohydrate-selective OprB porin, which translocates substrate molecules across the outer membrane to the periplasmic glucose-binding protein. We identified and cloned two open reading frames (ORFs) flanking the oprB gene but are not in operonic arrangement with the oprB gene. The downstream ORF encodes a putative polypeptide homologous to members of a family of transcriptional repressors, whereas the oprB gene is preceded by an ORF encoding a putative product, which exhibits strong homology to several carbohydrate transport ATP-binding cassette (ABC) proteins. The genomic copy of the upstream ORF was mutagenized by homologous recombination. Analysis of the deletion mutant in comparison with the wild type revealed a significant reduction in [14C] glucose transport activity in the mutant strain, suggesting that this ORF likely encodes the inner membrane component of the glucose ABC transporter. It is thus designated gltK gene to reflect its homology to the Pseudomona fluorescens mtlK and its involvement in the high-affinity glucose transport system. Multiple alignment analysis revealed that the P. aeruginosa gltK gene product is a member of the MalK subfamily of ABC proteins.
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In, Jung Bin; Cho, Kang Rae; Tran, Tung Xuan; Kim, Seok-Min; Wang, Yinmin; Grigoropoulos, Costas P; Noy, Aleksandr; Fornasiero, Francesco
2018-06-07
We investigate the thermal stability of alumina supporting layers sputtered at different conditions and its effect on the growth of aligned single-walled carbon nanotube arrays. Radio frequency magnetron sputtering of alumina under oxygen-argon atmosphere produces a Si-rich alumina alloy film on a silicon substrate. Atomic force microscopy on the annealed catalysts reveals that Si-rich alumina films are more stable than alumina layers with low Si content at the elevated temperatures at which the growth of single-walled carbon nanotubes is initiated. The enhanced thermal stability of the Si-rich alumina layer results in a narrower (< 2.2 nm) diameter distribution of the single-walled carbon nanotubes. Thanks to the smaller diameters of their nanotube pores, membranes fabricated with vertically aligned nanotubes grown on the stable layers display improved ion selectivity.
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NASA Astrophysics Data System (ADS)
In, Jung Bin; Cho, Kang Rae; Tran, Tung Xuan; Kim, Seok-Min; Wang, Yinmin; Grigoropoulos, Costas P.; Noy, Aleksandr; Fornasiero, Francesco
2018-06-01
We investigate the thermal stability of alumina supporting layers sputtered at different conditions and its effect on the growth of aligned single-walled carbon nanotube arrays. Radio frequency magnetron sputtering of alumina under oxygen-argon atmosphere produces a Si-rich alumina alloy film on a silicon substrate. Atomic force microscopy on the annealed catalysts reveals that Si-rich alumina films are more stable than alumina layers with low Si content at the elevated temperatures at which the growth of single-walled carbon nanotubes is initiated. The enhanced thermal stability of the Si-rich alumina layer results in a narrower (< 2.2 nm) diameter distribution of the single-walled carbon nanotubes. Thanks to the smaller diameters of their nanotube pores, membranes fabricated with vertically aligned nanotubes grown on the stable layers display improved ion selectivity.
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Dense Vertically Aligned Copper Nanowire Composites as High Performance Thermal Interface Materials.
Barako, Michael T; Isaacson, Scott G; Lian, Feifei; Pop, Eric; Dauskardt, Reinhold H; Goodson, Kenneth E; Tice, Jesse
2017-12-06
Thermal interface materials (TIMs) are essential for managing heat in modern electronics, and nanocomposite TIMs can offer critical improvements. Here, we demonstrate thermally conductive, mechanically compliant TIMs based on dense, vertically aligned copper nanowires (CuNWs) embedded into polymer matrices. We evaluate the thermal and mechanical characteristics of 20-25% dense CuNW arrays with and without polydimethylsiloxane infiltration. The thermal resistance achieved is below 5 mm 2 K W -1 , over an order of magnitude lower than commercial heat sink compounds. Nanoindentation reveals that the nonlinear deformation mechanics of this TIM are influenced by both the CuNW morphology and the polymer matrix. We also implement a flip-chip bonding protocol to directly attach CuNW composites to copper surfaces, as required in many thermal architectures. Thus, we demonstrate a rational design strategy for nanocomposite TIMs that simultaneously retain the high thermal conductivity of aligned CuNWs and the mechanical compliance of a polymer.
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Selvan, A. Sakthivel; Gupta, I. D.; Verma, A.; Chaudhari, M. V.; Magotra, A.
2016-01-01
Aim: The present study was undertaken with the objectives to characterize and to analyze combined genotypes of cluster of differentiation 14 (CD14) gene to explore its association with clinical mastitis in Karan Fries (KF) cows maintained in the National Dairy Research Institute herd, Karnal. Materials and Methods: Genomic DNA was extracted using blood of randomly selected 94 KF lactating cattle by phenol-chloroform method. After checking its quality and quantity, polymerase chain reaction (PCR) was carried out using six sets of reported gene-specific primers to amplify complete KF CD14 gene. The forward and reverse sequences for each PCR fragments were assembled to form complete sequence for the respective region of KF CD14 gene. The multiple sequence alignments of the edited sequence with the corresponding reference with reported Bos taurus sequence (EU148610.1) were performed with ClustalW software to identify single nucleotide polymorphisms (SNPs). Basic Local Alignment Search Tool analysis was performed to compare the sequence identity of KF CD14 gene with other species. The restriction fragment length polymorphism (RFLP) analysis was carried out in all KF cows using Helicobacter pylori 188I (Hpy188I) (contig 2) and Haemophilus influenzae I (HinfI) (contig 4) restriction enzyme (RE). Cows were assigned genotypes obtained by PCR-RFLP analysis, and association study was done using Chi-square (χ2) test. The genotypes of both contigs (loci) number 2 and 4 were combined with respect to each animal to construct combined genotype patterns. Results: Two types of sequences of KF were obtained: One with 2630 bp having one insertion at 616 nucleotide (nt) position and one deletion at 1117 nt position, and the another sequence was of 2629 bp having only one deletion at 615 nt position. ClustalW, multiple alignments of KF CD14 gene sequence with B. taurus cattle sequence (EU148610.1), revealed 24 nt changes (SNPs). Cows were also screened using PCR-RFLP with Hpy188I (contig 2) and HinfI (contig 4) RE, which revealed three genotypes each that differed significantly regarding mastitis incidence. The maximum possible combination of these two loci shown nine combined genotype patterns and it was observed only eight combined genotypes out of nine: AACC, AACD, AADD, ABCD, ABDD, BBCC, BBCD, and BBDD. The combined genotype ABCC was not observed in the studied population of KF cows. Out of 94 animals, AACD combined genotype animals (10.63%) were found to be not affected with mastitis, and ABDD combined genotyped animals was observed having the highest mastitis incidence of 15.96%. Conclusion: AACD typed cows were found to be least susceptible to mastitis incidence as compared to other combined genotypes. PMID:27536026
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Selvan, A Sakthivel; Gupta, I D; Verma, A; Chaudhari, M V; Magotra, A
2016-07-01
The present study was undertaken with the objectives to characterize and to analyze combined genotypes of cluster of differentiation 14 (CD14) gene to explore its association with clinical mastitis in Karan Fries (KF) cows maintained in the National Dairy Research Institute herd, Karnal. Genomic DNA was extracted using blood of randomly selected 94 KF lactating cattle by phenol-chloroform method. After checking its quality and quantity, polymerase chain reaction (PCR) was carried out using six sets of reported gene-specific primers to amplify complete KF CD14 gene. The forward and reverse sequences for each PCR fragments were assembled to form complete sequence for the respective region of KF CD14 gene. The multiple sequence alignments of the edited sequence with the corresponding reference with reported Bos taurus sequence (EU148610.1) were performed with ClustalW software to identify single nucleotide polymorphisms (SNPs). Basic Local Alignment Search Tool analysis was performed to compare the sequence identity of KF CD14 gene with other species. The restriction fragment length polymorphism (RFLP) analysis was carried out in all KF cows using Helicobacter pylori 188I (Hpy188I) (contig 2) and Haemophilus influenzae I (HinfI) (contig 4) restriction enzyme (RE). Cows were assigned genotypes obtained by PCR-RFLP analysis, and association study was done using Chi-square (χ (2)) test. The genotypes of both contigs (loci) number 2 and 4 were combined with respect to each animal to construct combined genotype patterns. Two types of sequences of KF were obtained: One with 2630 bp having one insertion at 616 nucleotide (nt) position and one deletion at 1117 nt position, and the another sequence was of 2629 bp having only one deletion at 615 nt position. ClustalW, multiple alignments of KF CD14 gene sequence with B. taurus cattle sequence (EU148610.1), revealed 24 nt changes (SNPs). Cows were also screened using PCR-RFLP with Hpy188I (contig 2) and HinfI (contig 4) RE, which revealed three genotypes each that differed significantly regarding mastitis incidence. The maximum possible combination of these two loci shown nine combined genotype patterns and it was observed only eight combined genotypes out of nine: AACC, AACD, AADD, ABCD, ABDD, BBCC, BBCD, and BBDD. The combined genotype ABCC was not observed in the studied population of KF cows. Out of 94 animals, AACD combined genotype animals (10.63%) were found to be not affected with mastitis, and ABDD combined genotyped animals was observed having the highest mastitis incidence of 15.96%. AACD typed cows were found to be least susceptible to mastitis incidence as compared to other combined genotypes.
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NASA Astrophysics Data System (ADS)
Iqbal, Z.; Azhar, Ehtsham; Mehmood, Zaffar; Maraj, E. N.
2018-01-01
Boundary layer stagnation point flow of Casson fluid over a Riga plate of variable thickness is investigated in present article. Riga plate is an electromagnetic actuator consists of enduring magnets and gyrated aligned array of alternating electrodes mounted on a plane surface. Physical problem is modeled and simplified under appropriate transformations. Effects of thermal radiation and viscous dissipation are incorporated. These differential equations are solved by Keller Box Scheme using MATLAB. Comparison is given with shooting techniques along with Range-Kutta Fehlberg method of order 5. Graphical and tabulated analysis is drawn. The results reveal that Eckert number, radiation and fluid parameters enhance temperature whereas they contribute in lowering rate of heat transfer. The numerical outcomes of present analysis depicts that Keller Box Method is capable and consistent to solve proposed nonlinear problem with high accuracy.
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Global Electricity Trade Network: Structures and Implications
Ji, Ling; Jia, Xiaoping; Chiu, Anthony S. F.; Xu, Ming
2016-01-01
Nations increasingly trade electricity, and understanding the structure of the global power grid can help identify nations that are critical for its reliability. This study examines the global grid as a network with nations as nodes and international electricity trade as links. We analyze the structure of the global electricity trade network and find that the network consists of four sub-networks, and provide a detailed analysis of the largest network, Eurasia. Russia, China, Ukraine, and Azerbaijan have high betweenness measures in the Eurasian sub-network, indicating the degrees of centrality of the positions they hold. The analysis reveals that the Eurasian sub-network consists of seven communities based on the network structure. We find that the communities do not fully align with geographical proximity, and that the present international electricity trade in the Eurasian sub-network causes an approximately 11 million additional tons of CO2 emissions. PMID:27504825
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Global Electricity Trade Network: Structures and Implications.
Ji, Ling; Jia, Xiaoping; Chiu, Anthony S F; Xu, Ming
2016-01-01
Nations increasingly trade electricity, and understanding the structure of the global power grid can help identify nations that are critical for its reliability. This study examines the global grid as a network with nations as nodes and international electricity trade as links. We analyze the structure of the global electricity trade network and find that the network consists of four sub-networks, and provide a detailed analysis of the largest network, Eurasia. Russia, China, Ukraine, and Azerbaijan have high betweenness measures in the Eurasian sub-network, indicating the degrees of centrality of the positions they hold. The analysis reveals that the Eurasian sub-network consists of seven communities based on the network structure. We find that the communities do not fully align with geographical proximity, and that the present international electricity trade in the Eurasian sub-network causes an approximately 11 million additional tons of CO2 emissions.
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Yadav, Saurabh; Kumari, Pragati; Kushwaha, Hemant Ritturaj
2013-01-01
Glutaredoxins are enzymatic antioxidants which are small, ubiquitous, glutathione dependent and essentially classified under thioredoxin-fold superfamily. Glutaredoxins are classified into two types: dithiol and monothiol. Monothiol glutaredoxins which carry the signature "CGFS" as a redox active motif is known for its role in oxidative stress, inside the cell. In the present analysis, the 138 amino acid long monothiol glutaredoxin, AgGRX1 from Ashbya gossypii was identified and has been used for the analysis. The multiple sequence alignment of the AgGRX1 protein sequence revealed the characteristic motif of typical monothiol glutaredoxin as observed in various other organisms. The proposed structure of the AgGRX1 protein was used to analyze signature folds related to the thioredoxin superfamily. Further, the study highlighted the structural features pertaining to the complex mechanism of glutathione docking and interacting residues.
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Design and analysis of magneto rheological fluid brake for an all terrain vehicle
NASA Astrophysics Data System (ADS)
George, Luckachan K.; Tamilarasan, N.; Thirumalini, S.
2018-02-01
This work presents an optimised design for a magneto rheological fluid brake for all terrain vehicles. The actuator consists of a disk which is immersed in the magneto rheological fluid surrounded by an electromagnet. The braking torque is controlled by varying the DC current applied to the electromagnet. In the presence of a magnetic field, the magneto rheological fluid particle aligns in a chain like structure, thus increasing the viscosity. The shear stress generated causes friction in the surfaces of the rotating disk. Electromagnetic analysis of the proposed system is carried out using finite element based COMSOL multi-physics software and the amount of magnetic field generated is calculated with the help of COMSOL. The geometry is optimised and performance of the system in terms of braking torque is carried out. Proposed design reveals better performance in terms of braking torque from the existing literature.
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Revealing the glass transition in shape memory polymers using Brillouin spectroscopy.
Steelman, Zachary A; Weems, Andrew C; Traverso, Andrew J; Szafron, Jason M; Maitland, Duncan J; Yakovlev, Vladislav V
2017-12-11
Emerging medical devices which employ shape memory polymers (SMPs) require precise measurements of the glass transition temperature (T g ) to ensure highly controlled shape recovery kinetics. Conventional techniques like differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA) have limitations that prevent utilization for certain devices, including limited accuracy and the need for sacrificial samples. In this report, we employ an approach based on Brillouin spectroscopy to probe the glass transition of SMPs rapidly, remotely, and nondestructively. Further, we compare the T g obtained from Brillouin scattering with DMA- and DSC-measured T g to demonstrate the accuracy of Brillouin scattering for this application. We conclude that Brillouin spectroscopy is an accurate technique for obtaining the glass transition temperature of SMPs, aligning closely with the most common laboratory standards while providing a rapid, remote, and nondestructive method for the analysis of unique polymeric medical devices.
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MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
Wang, Yupeng; Tang, Haibao; DeBarry, Jeremy D.; Tan, Xu; Li, Jingping; Wang, Xiyin; Lee, Tae-ho; Jin, Huizhe; Marler, Barry; Guo, Hui; Kissinger, Jessica C.; Paterson, Andrew H.
2012-01-01
MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/. PMID:22217600
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Chirkov, Sergei; Ivanov, Peter; Sheveleva, Anna
2013-06-01
Atypical isolates of plum pox virus (PPV) were discovered in naturally infected sour cherry in urban ornamental plantings in Moscow, Russia. The isolates were detected by polyclonal double antibody sandwich ELISA and RT-PCR using universal primers specific for the 3'-non-coding and coat protein (CP) regions of the genome but failed to be recognized by triple antibody sandwich ELISA with the universal monoclonal antibody 5B and by RT-PCR using primers specific to for PPV strains D, M, C and W. Sequence analysis of the CP genes of nine isolates revealed 99.2-100 % within-group identity and 62-85 % identity to conventional PPV strains. Phylogenetic analysis showed that the atypical isolates represent a group that is distinct from the known PPV strains. Alignment of the N-terminal amino acid sequences of CP demonstrated their close similarity to those of a new tentative PPV strain, CR.
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Ion blocking dip shape analysis around a LaAlO3/SrTiO3 interface
NASA Astrophysics Data System (ADS)
Jalabert, D.; Zaid, H.; Berger, M. H.; Fongkaew, I.; Lambrecht, W. R. L.; Sehirlioglu, A.
2018-05-01
We present an analysis of the widths of the blocking dips obtained in MEIS ion blocking experiments of two LaAlO3/SrTiO3 heterostructures differing in their LaAlO3 layer thicknesses. In the LaAlO3 layers, the observed blocking dips are larger than expected. This enlargement is the result of the superposition of individual dips at slightly different angular positions revealing a local disorder in the atomic alignment, i.e., layer buckling. By contrast, in the SrTiO3 substrate, just below the interface, the obtained blocking dips are thinner than expected. This thinning indicates that the blocking atoms stand at a larger distance from the scattering center than expected. This is attributed to an accumulation of Sr vacancies at the layer/substrate interface which induces lattice distortions shifting the atoms off the scattering plane.
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Genome analysis of the platypus reveals unique signatures of evolution.
Warren, Wesley C; Hillier, LaDeana W; Marshall Graves, Jennifer A; Birney, Ewan; Ponting, Chris P; Grützner, Frank; Belov, Katherine; Miller, Webb; Clarke, Laura; Chinwalla, Asif T; Yang, Shiaw-Pyng; Heger, Andreas; Locke, Devin P; Miethke, Pat; Waters, Paul D; Veyrunes, Frédéric; Fulton, Lucinda; Fulton, Bob; Graves, Tina; Wallis, John; Puente, Xose S; López-Otín, Carlos; Ordóñez, Gonzalo R; Eichler, Evan E; Chen, Lin; Cheng, Ze; Deakin, Janine E; Alsop, Amber; Thompson, Katherine; Kirby, Patrick; Papenfuss, Anthony T; Wakefield, Matthew J; Olender, Tsviya; Lancet, Doron; Huttley, Gavin A; Smit, Arian F A; Pask, Andrew; Temple-Smith, Peter; Batzer, Mark A; Walker, Jerilyn A; Konkel, Miriam K; Harris, Robert S; Whittington, Camilla M; Wong, Emily S W; Gemmell, Neil J; Buschiazzo, Emmanuel; Vargas Jentzsch, Iris M; Merkel, Angelika; Schmitz, Juergen; Zemann, Anja; Churakov, Gennady; Kriegs, Jan Ole; Brosius, Juergen; Murchison, Elizabeth P; Sachidanandam, Ravi; Smith, Carly; Hannon, Gregory J; Tsend-Ayush, Enkhjargal; McMillan, Daniel; Attenborough, Rosalind; Rens, Willem; Ferguson-Smith, Malcolm; Lefèvre, Christophe M; Sharp, Julie A; Nicholas, Kevin R; Ray, David A; Kube, Michael; Reinhardt, Richard; Pringle, Thomas H; Taylor, James; Jones, Russell C; Nixon, Brett; Dacheux, Jean-Louis; Niwa, Hitoshi; Sekita, Yoko; Huang, Xiaoqiu; Stark, Alexander; Kheradpour, Pouya; Kellis, Manolis; Flicek, Paul; Chen, Yuan; Webber, Caleb; Hardison, Ross; Nelson, Joanne; Hallsworth-Pepin, Kym; Delehaunty, Kim; Markovic, Chris; Minx, Pat; Feng, Yucheng; Kremitzki, Colin; Mitreva, Makedonka; Glasscock, Jarret; Wylie, Todd; Wohldmann, Patricia; Thiru, Prathapan; Nhan, Michael N; Pohl, Craig S; Smith, Scott M; Hou, Shunfeng; Nefedov, Mikhail; de Jong, Pieter J; Renfree, Marilyn B; Mardis, Elaine R; Wilson, Richard K
2008-05-08
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.
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Genome analysis of the platypus reveals unique signatures of evolution
Warren, Wesley C.; Hillier, LaDeana W.; Marshall Graves, Jennifer A.; Birney, Ewan; Ponting, Chris P.; Grützner, Frank; Belov, Katherine; Miller, Webb; Clarke, Laura; Chinwalla, Asif T.; Yang, Shiaw-Pyng; Heger, Andreas; Locke, Devin P.; Miethke, Pat; Waters, Paul D.; Veyrunes, Frédéric; Fulton, Lucinda; Fulton, Bob; Graves, Tina; Wallis, John; Puente, Xose S.; López-Otín, Carlos; Ordóñez, Gonzalo R.; Eichler, Evan E.; Chen, Lin; Cheng, Ze; Deakin, Janine E.; Alsop, Amber; Thompson, Katherine; Kirby, Patrick; Papenfuss, Anthony T.; Wakefield, Matthew J.; Olender, Tsviya; Lancet, Doron; Huttley, Gavin A.; Smit, Arian F. A.; Pask, Andrew; Temple-Smith, Peter; Batzer, Mark A.; Walker, Jerilyn A.; Konkel, Miriam K.; Harris, Robert S.; Whittington, Camilla M.; Wong, Emily S. W.; Gemmell, Neil J.; Buschiazzo, Emmanuel; Vargas Jentzsch, Iris M.; Merkel, Angelika; Schmitz, Juergen; Zemann, Anja; Churakov, Gennady; Kriegs, Jan Ole; Brosius, Juergen; Murchison, Elizabeth P.; Sachidanandam, Ravi; Smith, Carly; Hannon, Gregory J.; Tsend-Ayush, Enkhjargal; McMillan, Daniel; Attenborough, Rosalind; Rens, Willem; Ferguson-Smith, Malcolm; Lefèvre, Christophe M.; Sharp, Julie A.; Nicholas, Kevin R.; Ray, David A.; Kube, Michael; Reinhardt, Richard; Pringle, Thomas H.; Taylor, James; Jones, Russell C.; Nixon, Brett; Dacheux, Jean-Louis; Niwa, Hitoshi; Sekita, Yoko; Huang, Xiaoqiu; Stark, Alexander; Kheradpour, Pouya; Kellis, Manolis; Flicek, Paul; Chen, Yuan; Webber, Caleb; Hardison, Ross; Nelson, Joanne; Hallsworth-Pepin, Kym; Delehaunty, Kim; Markovic, Chris; Minx, Pat; Feng, Yucheng; Kremitzki, Colin; Mitreva, Makedonka; Glasscock, Jarret; Wylie, Todd; Wohldmann, Patricia; Thiru, Prathapan; Nhan, Michael N.; Pohl, Craig S.; Smith, Scott M.; Hou, Shunfeng; Renfree, Marilyn B.; Mardis, Elaine R.; Wilson, Richard K.
2009-01-01
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation. PMID:18464734
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Revealing the glass transition in shape memory polymers using Brillouin spectroscopy
NASA Astrophysics Data System (ADS)
Steelman, Zachary A.; Weems, Andrew C.; Traverso, Andrew J.; Szafron, Jason M.; Maitland, Duncan J.; Yakovlev, Vladislav V.
2017-12-01
Emerging medical devices which employ shape memory polymers (SMPs) require precise measurements of the glass transition temperature (Tg) to ensure highly controlled shape recovery kinetics. Conventional techniques like differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA) have limitations that prevent utilization for certain devices, including limited accuracy and the need for sacrificial samples. In this report, we employ an approach based on Brillouin spectroscopy to probe the glass transition of SMPs rapidly, remotely, and nondestructively. Further, we compare the Tg obtained from Brillouin scattering with DMA- and DSC-measured Tg to demonstrate the accuracy of Brillouin scattering for this application. We conclude that Brillouin spectroscopy is an accurate technique for obtaining the glass transition temperature of SMPs, aligning closely with the most common laboratory standards while providing a rapid, remote, and nondestructive method for the analysis of unique polymeric medical devices.
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Bahador, Fateme; Sharifian, Roxana; Farhadi, Payam; Jafari, Abdosaleh; Nematolahi, Mohtram; Shokrpour, Nasrin
This study aimed to develop and test a research model that examined 7effective factors on the effectiveness of laboratory information system (LIS) through strategic planning. This research was carried out on total laboratory staff, information technology staff, and laboratory managers in Shiraz (a city in the south of Iran) teaching hospitals by structural equation modeling approach in 2015. The results revealed that there was no significant positive relationship between decisions based on cost-benefit analysis and LIS functionality with LIS effectiveness, but there was a significant positive relationship between other factors and LIS effectiveness. As expected, high levels of strategic information system planning result in increasing LIS effectiveness. The results also showed that the relationship between cost-benefit analysis, LIS functionality, end-user involvement, and information technology-business alignment with strategic information system planning was significant and positive.
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Kernel-aligned multi-view canonical correlation analysis for image recognition
NASA Astrophysics Data System (ADS)
Su, Shuzhi; Ge, Hongwei; Yuan, Yun-Hao
2016-09-01
Existing kernel-based correlation analysis methods mainly adopt a single kernel in each view. However, only a single kernel is usually insufficient to characterize nonlinear distribution information of a view. To solve the problem, we transform each original feature vector into a 2-dimensional feature matrix by means of kernel alignment, and then propose a novel kernel-aligned multi-view canonical correlation analysis (KAMCCA) method on the basis of the feature matrices. Our proposed method can simultaneously employ multiple kernels to better capture the nonlinear distribution information of each view, so that correlation features learned by KAMCCA can have well discriminating power in real-world image recognition. Extensive experiments are designed on five real-world image datasets, including NIR face images, thermal face images, visible face images, handwritten digit images, and object images. Promising experimental results on the datasets have manifested the effectiveness of our proposed method.
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Time Alignment as a Necessary Step in the Analysis of Sleep Probabilistic Curves
NASA Astrophysics Data System (ADS)
Rošt'áková, Zuzana; Rosipal, Roman
2018-02-01
Sleep can be characterised as a dynamic process that has a finite set of sleep stages during the night. The standard Rechtschaffen and Kales sleep model produces discrete representation of sleep and does not take into account its dynamic structure. In contrast, the continuous sleep representation provided by the probabilistic sleep model accounts for the dynamics of the sleep process. However, analysis of the sleep probabilistic curves is problematic when time misalignment is present. In this study, we highlight the necessity of curve synchronisation before further analysis. Original and in time aligned sleep probabilistic curves were transformed into a finite dimensional vector space, and their ability to predict subjects' age or daily measures is evaluated. We conclude that curve alignment significantly improves the prediction of the daily measures, especially in the case of the S2-related sleep states or slow wave sleep.
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Algama, Manjula; Tasker, Edward; Williams, Caitlin; Parslow, Adam C; Bryson-Richardson, Robert J; Keith, Jonathan M
2017-03-27
Computational identification of non-coding RNAs (ncRNAs) is a challenging problem. We describe a genome-wide analysis using Bayesian segmentation to identify intronic elements highly conserved between three evolutionarily distant vertebrate species: human, mouse and zebrafish. We investigate the extent to which these elements include ncRNAs (or conserved domains of ncRNAs) and regulatory sequences. We identified 655 deeply conserved intronic sequences in a genome-wide analysis. We also performed a pathway-focussed analysis on genes involved in muscle development, detecting 27 intronic elements, of which 22 were not detected in the genome-wide analysis. At least 87% of the genome-wide and 70% of the pathway-focussed elements have existing annotations indicative of conserved RNA secondary structure. The expression of 26 of the pathway-focused elements was examined using RT-PCR, providing confirmation that they include expressed ncRNAs. Consistent with previous studies, these elements are significantly over-represented in the introns of transcription factors. This study demonstrates a novel, highly effective, Bayesian approach to identifying conserved non-coding sequences. Our results complement previous findings that these sequences are enriched in transcription factors. However, in contrast to previous studies which suggest the majority of conserved sequences are regulatory factor binding sites, the majority of conserved sequences identified using our approach contain evidence of conserved RNA secondary structures, and our laboratory results suggest most are expressed. Functional roles at DNA and RNA levels are not mutually exclusive, and many of our elements possess evidence of both. Moreover, ncRNAs play roles in transcriptional and post-transcriptional regulation, and this may contribute to the over-representation of these elements in introns of transcription factors. We attribute the higher sensitivity of the pathway-focussed analysis compared to the genome-wide analysis to improved alignment quality, suggesting that enhanced genomic alignments may reveal many more conserved intronic sequences.
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Bertaccini, Edward J.; Yoluk, Ozge; Lindahl, Erik R.; Trudell, James R.
2013-01-01
Background Anesthetics mediate portions of their activity via modulation of the γ-aminobutyric acid receptor (GABAaR). While its molecular structure remains unknown, significant progress has been made towards understanding its interactions with anesthetics via molecular modeling. Methods The structure of the torpedo acetylcholine receptor (nAChRα), the structures of the α4 and β2 subunits of the human nAChR, the structures of the eukaryotic glutamate-gated chloride channel (GluCl), and the prokaryotic pH sensing channels, from Gloeobacter violaceus and Erwinia chrysanthemi, were aligned with the SAlign and 3DMA algorithms. A multiple sequence alignment from these structures and those of the GABAaR was performed with ClustalW. The Modeler and Rosetta algorithms independently created three-dimensional constructs of the GABAaR from the GluCl template. The CDocker algorithm docked a congeneric series of propofol derivatives into the binding pocket and scored calculated binding affinities for correlation with known GABAaR potentiation EC50’s. Results Multiple structure alignments of templates revealed a clear consensus of residue locations relevant to anesthetic effects except for torpedo nAChR. Within the GABAaR models generated from GluCl, the residues notable for modulating anesthetic action within transmembrane segments 1, 2, and 3 converged on the intersubunit interface between alpha and beta subunits. Docking scores of a propofol derivative series into this binding site showed strong linear correlation with GABAaR potentiation EC50. Conclusion Consensus structural alignment based on homologous templates revealed an intersubunit anesthetic binding cavity within the transmembrane domain of the GABAaR, which showed correlation of ligand docking scores with experimentally measured GABAaR potentiation. PMID:23770602
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Bertaccini, Edward J; Yoluk, Ozge; Lindahl, Erik R; Trudell, James R
2013-11-01
Anesthetics mediate portions of their activity via modulation of the γ-aminobutyric acid receptor (GABAaR). Although its molecular structure remains unknown, significant progress has been made toward understanding its interactions with anesthetics via molecular modeling. The structure of the torpedo acetylcholine receptor (nAChRα), the structures of the α4 and β2 subunits of the human nAChR, the structures of the eukaryotic glutamate-gated chloride channel (GluCl), and the prokaryotic pH-sensing channels, from Gloeobacter violaceus and Erwinia chrysanthemi, were aligned with the SAlign and 3DMA algorithms. A multiple sequence alignment from these structures and those of the GABAaR was performed with ClustalW. The Modeler and Rosetta algorithms independently created three-dimensional constructs of the GABAaR from the GluCl template. The CDocker algorithm docked a congeneric series of propofol derivatives into the binding pocket and scored calculated binding affinities for correlation with known GABAaR potentiation EC50s. Multiple structure alignments of templates revealed a clear consensus of residue locations relevant to anesthetic effects except for torpedo nAChR. Within the GABAaR models generated from GluCl, the residues notable for modulating anesthetic action within transmembrane segments 1, 2, and 3 converged on the intersubunit interface between α and β subunits. Docking scores of a propofol derivative series into this binding site showed strong linear correlation with GABAaR potentiation EC50. Consensus structural alignment based on homologous templates revealed an intersubunit anesthetic binding cavity within the transmembrane domain of the GABAaR, which showed a correlation of ligand docking scores with experimentally measured GABAaR potentiation.
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Rajesh, P S; Rai, V Ravishankar
2014-01-03
The aiiA homologous gene known to encode AHL- lactonase enzyme which hydrolyze the N-acylhomoserine lactone (AHL) quorum sensing signaling molecules produced by Gram negative bacteria. In this study, the degradation of AHL molecules was determined by cell-free lysate of endophytic Enterobacter species. The percentage of quorum quenching was confirmed and quantified by HPLC method (p<0.0001). Amplification and sequence BLAST analysis showed the presence of aiiA homologous gene in endophytic Enterobacter asburiae VT65, Enterobacter aerogenes VT66 and Enterobacter ludwigii VT70 strains. Sequence alignment analysis revealed the presence of two zinc binding sites, "HXHXDH" motif as well as tyrosine residue at the position 194. Based on known template available at Swiss-Model, putative tertiary structure of AHL-lactonase was constructed. The result showed that novel endophytic strains of Enterobacter genera encode the novel aiiA homologous gene and its structural importance for future study. Copyright © 2013 Elsevier Inc. All rights reserved.
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Genetic analysis of a novel nidovirus from fathead minnows
Batts, William N.; Goodwin, Andrew E.; Winton, James R.
2012-01-01
A bacilliform virus was isolated from diseased fathead minnows (Pimephales promelas). Analysis of the complete genome coding for the polyprotein (pp1ab), spike (S), membrane (M) and nucleocapsid (N) proteins revealed that the virus was most like white bream virus (WBV), another bacilliform virus isolated from white bream (Blicca bjoerkna L.) and the type species of the genus Bafinivirus within the order Nidovirales. In addition to similar gene order and size, alignment of deduced amino acid sequences of the pp1ab, M, N and S proteins of the fathead minnow nidovirus (FHMNV) with those of WBV showed 46, 44, 39 and 15 % identities, respectively. Phylogenetic analysis using the conserved helicase domain of the replicase showed FHMNV was distinct from WBV, yet the closest relative identified to date. Thus, FHMNV appears to represent a second species in the genus Bafinivirus. A PCR assay was developed for the identification of future FHMNV-like isolates.
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Trigo-Mouriño, Pablo; Navarro-Vázquez, Armando; Sánchez-Pedregal, Víctor M
2012-12-01
The dependence of molecular alignment with solvent nature and salt concentration has been investigated for mechanically stretched polyacrylamide copolymer gels. Residual dipolar couplings (RDCs) were recorded for D(2)O, DMSO-d(6), and DMSO-d(6)/D(2)O solutions containing different proportions of the solvents and different sodium chloride concentrations. Alignment tensors were determined by fitting the experimental RDCs to the DFT-computed structure of N-methylcodeinium ion. Analysis of the tensors shows that the degree of alignment decreases with the proportion of DMSO-d(6) as well as with the concentration of sodium chloride, most likely due to enhanced ion-pair aggregation. Furthermore, rotation of the alignment tensor is observed when increasing the salt concentration. Copyright © 2012 John Wiley & Sons, Ltd.
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A mean-field theory for self-propelled particles interacting by velocity alignment mechanisms
NASA Astrophysics Data System (ADS)
Peruani, F.; Deutsch, A.; Bär, M.
2008-04-01
A mean-field approach (MFA) is proposed for the analysis of orientational order in a two-dimensional system of stochastic self-propelled particles interacting by local velocity alignment mechanism. The treatment is applied to the cases of ferromagnetic (F) and liquid-crystal (LC) alignment. In both cases, MFA yields a second order phase transition for a critical noise strength and a scaling exponent of 1/2 for the respective order parameters. We find that the critical noise amplitude ηc at which orientational order emerges in the LC case is smaller than in the F-alignment case, i.e. ηLC C<ηF C. A comparison with simulations of individual-based models with F- resp. LC-alignment shows that the predictions about the critical behavior and the qualitative relation between the respective critical noise amplitudes are correct.
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Ren, Liqiang; Wu, Di; Li, Yuhua; Zheng, Bin; Chen, Yong; Yang, Kai; Liu, Hong
2016-06-01
This study presents a practical alignment method for X-ray spectral measurement in a rotating gantry based micro-computed tomography (micro-CT) system using three-dimensional (3D) printing technology. In order to facilitate the spectrometer placement inside the gantry, supporting structures including a cover and a stand were dedicatedly designed and printed using a 3D printer. According to the relative position between the spectrometer and the stand, the upright projection of the spectrometer collimator onto the stand was determined and then marked by a tungsten pinhole. Thus, a visible alignment indicator of the X-ray central beam and the spectrometer collimator represented by the pinhole was established in the micro-CT live mode. Then, a rough alignment could be achieved through repeatedly adjusting and imaging the stand until the pinhole was located at the center of the acquired projection image. With the spectrometer being positioned back onto the stand, the precise alignment was completed by slightly translating the spectrometer-stand assembly around the rough location, until finding a "sweet spot" with the highest photon rate and proper distribution of the X-ray photons in the resultant spectrum. The spectra were acquired under precise alignment and misalignment of approximately 0.2, 0.5, and 1.0mm away from the precise alignment position, and then were compared in qualitative and quantitative analyses. Qualitative analysis results show that, with slight misalignment, the photon rate is reduced from 1302 to 1098, 1031, and 416 photons/second (p/s), respectively, and the characteristic peaks in the acquired spectra are gradually deteriorated. Quantitative analysis indicates that the energy resolutions for characteristic peak of K α1 were calculated as 1.56% for precise alignment, while were 1.84% and 2.40% for slight misalignment of 0.2mm and 0.5mm. The mean energies were reduced from 43.93keV under precise alignment condition to 40.97, 39.63 and 37.78keV when misaligned. Accurate spectral measurements in micro-CT systems are significantly influenced by the alignment precision. This practical alignment method using 3D printing technology could be readily applied to other rotating gantry based micro-CT systems with modified design of the supporting structures and careful considerations of the spectrometer and gantry dimensions.
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Ren, Liqiang; Wu, Di; Li, Yuhua; Zheng, Bin; Chen, Yong; Yang, Kai; Liu, Hong
2016-01-01
This study presents a practical alignment method for X-ray spectral measurement in a rotating gantry based micro-computed tomography (micro-CT) system using three-dimensional (3D) printing technology. In order to facilitate the spectrometer placement inside the gantry, supporting structures including a cover and a stand were dedicatedly designed and printed using a 3D printer. According to the relative position between the spectrometer and the stand, the upright projection of the spectrometer collimator onto the stand was determined and then marked by a tungsten pinhole. Thus, a visible alignment indicator of the X-ray central beam and the spectrometer collimator represented by the pinhole was established in the micro-CT live mode. Then, a rough alignment could be achieved through repeatedly adjusting and imaging the stand until the pinhole was located at the center of the acquired projection image. With the spectrometer being positioned back onto the stand, the precise alignment was completed by slightly translating the spectrometer-stand assembly around the rough location, until finding a “sweet spot” with the highest photon rate and proper distribution of the X-ray photons in the resultant spectrum. The spectra were acquired under precise alignment and misalignment of approximately 0.2, 0.5, and 1.0mm away from the precise alignment position, and then were compared in qualitative and quantitative analyses. Qualitative analysis results show that, with slight misalignment, the photon rate is reduced from 1302 to 1098, 1031, and 416 photons/second (p/s), respectively, and the characteristic peaks in the acquired spectra are gradually deteriorated. Quantitative analysis indicates that the energy resolutions for characteristic peak of Kα1 were calculated as 1.56% for precise alignment, while were 1.84% and 2.40% for slight misalignment of 0.2mm and 0.5mm. The mean energies were reduced from 43.93keV under precise alignment condition to 40.97, 39.63 and 37.78keV when misaligned. Accurate spectral measurements in micro-CT systems are significantly influenced by the alignment precision. This practical alignment method using 3D printing technology could be readily applied to other rotating gantry based micro-CT systems with modified design of the supporting structures and careful considerations of the spectrometer and gantry dimensions. PMID:27777787
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Hal: an automated pipeline for phylogenetic analyses of genomic data.
Robbertse, Barbara; Yoder, Ryan J; Boyd, Alex; Reeves, John; Spatafora, Joseph W
2011-02-07
The rapid increase in genomic and genome-scale data is resulting in unprecedented levels of discrete sequence data available for phylogenetic analyses. Major analytical impasses exist, however, prior to analyzing these data with existing phylogenetic software. Obstacles include the management of large data sets without standardized naming conventions, identification and filtering of orthologous clusters of proteins or genes, and the assembly of alignments of orthologous sequence data into individual and concatenated super alignments. Here we report the production of an automated pipeline, Hal that produces multiple alignments and trees from genomic data. These alignments can be produced by a choice of four alignment programs and analyzed by a variety of phylogenetic programs. In short, the Hal pipeline connects the programs BLASTP, MCL, user specified alignment programs, GBlocks, ProtTest and user specified phylogenetic programs to produce species trees. The script is available at sourceforge (http://sourceforge.net/projects/bio-hal/). The results from an example analysis of Kingdom Fungi are briefly discussed.
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Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS.
Warris, Sven; Yalcin, Feyruz; Jackson, Katherine J L; Nap, Jan Peter
2015-01-01
To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis. With the Parallel SW Alignment Software (PaSWAS) it is possible (a) to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs) to perform high-speed sequence alignments, and (b) retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1) tag recovery in next generation sequence data and (2) isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.
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Li, Peipei; Piao, Yongjun; Shon, Ho Sun; Ryu, Keun Ho
2015-10-28
Recently, rapid improvements in technology and decrease in sequencing costs have made RNA-Seq a widely used technique to quantify gene expression levels. Various normalization approaches have been proposed, owing to the importance of normalization in the analysis of RNA-Seq data. A comparison of recently proposed normalization methods is required to generate suitable guidelines for the selection of the most appropriate approach for future experiments. In this paper, we compared eight non-abundance (RC, UQ, Med, TMM, DESeq, Q, RPKM, and ERPKM) and two abundance estimation normalization methods (RSEM and Sailfish). The experiments were based on real Illumina high-throughput RNA-Seq of 35- and 76-nucleotide sequences produced in the MAQC project and simulation reads. Reads were mapped with human genome obtained from UCSC Genome Browser Database. For precise evaluation, we investigated Spearman correlation between the normalization results from RNA-Seq and MAQC qRT-PCR values for 996 genes. Based on this work, we showed that out of the eight non-abundance estimation normalization methods, RC, UQ, Med, TMM, DESeq, and Q gave similar normalization results for all data sets. For RNA-Seq of a 35-nucleotide sequence, RPKM showed the highest correlation results, but for RNA-Seq of a 76-nucleotide sequence, least correlation was observed than the other methods. ERPKM did not improve results than RPKM. Between two abundance estimation normalization methods, for RNA-Seq of a 35-nucleotide sequence, higher correlation was obtained with Sailfish than that with RSEM, which was better than without using abundance estimation methods. However, for RNA-Seq of a 76-nucleotide sequence, the results achieved by RSEM were similar to without applying abundance estimation methods, and were much better than with Sailfish. Furthermore, we found that adding a poly-A tail increased alignment numbers, but did not improve normalization results. Spearman correlation analysis revealed that RC, UQ, Med, TMM, DESeq, and Q did not noticeably improve gene expression normalization, regardless of read length. Other normalization methods were more efficient when alignment accuracy was low; Sailfish with RPKM gave the best normalization results. When alignment accuracy was high, RC was sufficient for gene expression calculation. And we suggest ignoring poly-A tail during differential gene expression analysis.
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Efficient alignment-free DNA barcode analytics
Kuksa, Pavel; Pavlovic, Vladimir
2009-01-01
Background In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. Results New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Conclusion Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding. PMID:19900305
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Persson, Nils E; Rafshoon, Joshua; Naghshpour, Kaylie; Fast, Tony; Chu, Ping-Hsun; McBride, Michael; Risteen, Bailey; Grover, Martha; Reichmanis, Elsa
2017-10-18
High-throughput discovery of process-structure-property relationships in materials through an informatics-enabled empirical approach is an increasingly utilized technique in materials research due to the rapidly expanding availability of data. Here, process-structure-property relationships are extracted for the nucleation, growth, and deposition of semiconducting poly(3-hexylthiophene) (P3HT) nanofibers used in organic field effect transistors, via high-throughput image analysis. This study is performed using an automated image analysis pipeline combining existing open-source software and new algorithms, enabling the rapid evaluation of structural metrics for images of fibrillar materials, including local orientational order, fiber length density, and fiber length distributions. We observe that microfluidic processing leads to fibers that pack with unusually high density, while sonication yields fibers that pack sparsely with low alignment. This is attributed to differences in their crystallization mechanisms. P3HT nanofiber packing during thin film deposition exhibits behavior suggesting that fibers are confined to packing in two-dimensional layers. We find that fiber alignment, a feature correlated with charge carrier mobility, is driven by increasing fiber length, and that shorter fibers tend to segregate to the buried dielectric interface during deposition, creating potentially performance-limiting defects in alignment. Another barrier to perfect alignment is the curvature of P3HT fibers; we propose a mechanistic simulation of fiber growth that reconciles both this curvature and the log-normal distribution of fiber lengths inherent to the fiber populations under consideration.
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Customisation of the exome data analysis pipeline using a combinatorial approach.
Pattnaik, Swetansu; Vaidyanathan, Srividya; Pooja, Durgad G; Deepak, Sa; Panda, Binay
2012-01-01
The advent of next generation sequencing (NGS) technologies have revolutionised the way biologists produce, analyse and interpret data. Although NGS platforms provide a cost-effective way to discover genome-wide variants from a single experiment, variants discovered by NGS need follow up validation due to the high error rates associated with various sequencing chemistries. Recently, whole exome sequencing has been proposed as an affordable option compared to whole genome runs but it still requires follow up validation of all the novel exomic variants. Customarily, a consensus approach is used to overcome the systematic errors inherent to the sequencing technology, alignment and post alignment variant detection algorithms. However, the aforementioned approach warrants the use of multiple sequencing chemistry, multiple alignment tools, multiple variant callers which may not be viable in terms of time and money for individual investigators with limited informatics know-how. Biologists often lack the requisite training to deal with the huge amount of data produced by NGS runs and face difficulty in choosing from the list of freely available analytical tools for NGS data analysis. Hence, there is a need to customise the NGS data analysis pipeline to preferentially retain true variants by minimising the incidence of false positives and make the choice of right analytical tools easier. To this end, we have sampled different freely available tools used at the alignment and post alignment stage suggesting the use of the most suitable combination determined by a simple framework of pre-existing metrics to create significant datasets.
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Yun, Dong-Jin; Shin, Weon-Ho; Bulliard, Xavier; Park, Jong Hwan; Kim, Seyun; Chung, Jae Gwan; Kim, Yongsu; Heo, Sung; Kim, Seong Heon
2016-08-26
A novel, direct method for the characterization of the energy level alignments at bulk-heterojunction (BHJ)/electrode interfaces on the basis of electronic spectroscopy measurements is proposed. The home-made in situ photoemission system is used to perform x-ray/ultraviolet photoemission spectroscopy (XPS/UPS), reflection electron energy loss spectroscopy (REELS) and inverse photoemission spectroscopy of organic-semiconductors (OSCs) deposited onto a Au substrate. Through this analysis system, we are able to obtain the electronic structures of a boron subphthalocyanine chloride:fullerene (SubPC:C60) BHJ and those of the separate OSC/electrode structures (SubPC/Au and C60/Au). Morphology and chemical composition analyses confirm that the original SubPC and C60 electronic structures remain unchanged in the electrodes prepared. Using this technique, we ascertain that the position and area of the nearest peak to the Fermi energy (EF = 0 eV) in the UPS (REELS) spectra of SubPC:C60 BHJ provide information on the highest occupied molecular orbital level (optical band gap) and combination ratio of the materials, respectively. Thus, extracting the adjusted spectrum from the corresponding SubPC:C60 BHJ UPS (REELS) spectrum reveals its electronic structure, equivalent to that of the C60 materials. This novel analytical approach allows complete energy-level determination for each combination ratio by separating its electronic structure information from the BHJ spectrum.
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Cellulose in Cyanobacteria. Origin of Vascular Plant Cellulose Synthase?
Nobles, David R.; Romanovicz, Dwight K.; Brown, R. Malcolm
2001-01-01
Although cellulose biosynthesis among the cyanobacteria has been suggested previously, we present the first conclusive evidence, to our knowledge, of the presence of cellulose in these organisms. Based on the results of x-ray diffraction, electron microscopy of microfibrils, and cellobiohydrolase I-gold labeling, we report the occurrence of cellulose biosynthesis in nine species representing three of the five sections of cyanobacteria. Sequence analysis of the genomes of four cyanobacteria revealed the presence of multiple amino acid sequences bearing the DDD35QXXRW motif conserved in all cellulose synthases. Pairwise alignments demonstrated that CesAs from plants were more similar to putative cellulose synthases from Anabaena sp. Pasteur Culture Collection 7120 and Nostoc punctiforme American Type Culture Collection 29133 than any other cellulose synthases in the database. Multiple alignments of putative cellulose synthases from Anabaena sp. Pasteur Culture Collection 7120 and N. punctiforme American Type Culture Collection 29133 with the cellulose synthases of other prokaryotes, Arabidopsis, Gossypium hirsutum, Populus alba × Populus tremula, corn (Zea mays), and Dictyostelium discoideum showed that cyanobacteria share an insertion between conserved regions U1 and U2 found previously only in eukaryotic sequences. Furthermore, phylogenetic analysis indicates that the cyanobacterial cellulose synthases share a common branch with CesAs of vascular plants in a manner similar to the relationship observed with cyanobacterial and chloroplast 16s rRNAs, implying endosymbiotic transfer of CesA from cyanobacteria to plants and an ancient origin for cellulose synthase in eukaryotes. PMID:11598227
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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.
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Prosody and Alignment: A Sequential Perspective
ERIC Educational Resources Information Center
Reed, Beatrice Szczepek
2010-01-01
In their analysis of a corpus of classroom interactions in an inner city high school, Roth and Tobin describe how teachers and students accomplish interactional alignment by prosodically matching each other's turns. Prosodic matching, and specific prosodic patterns are interpreted as signs of, and contributions to successful interactional outcomes…
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Solving the problem of Trans-Genomic Query with alignment tables.
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.
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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.
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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.
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The biological features and genetic diversity of novel fish rhabdovirus isolates in China.
Fu, Xiaozhe; Lin, Qiang; Liang, Hongru; Liu, Lihui; Huang, Zhibin; Li, Ningqiu; Su, Jianguo
2017-09-01
The Rhabdoviridae is a diverse family of negative-sense single-stranded RNA viruses which infects mammals, birds, reptiles, fish, insects and plants. Herein, we reported the isolation and characterization of 6 novel viruses from diseased fish collected from China including SCRV-QY, SCRV-SS, SCRV-GM, CmRV-FS, MsRV-SS, OmbRV-JM. The typical clinical symptom of diseased fish was hemorrhaging. Efficient propagation of these isolates in a Chinese perch brain cell line was determined by means of observation of cytopathic effect, RT-PCR and electron microscopy. Sequence alignment and phylogenetic analysis of the complete G protein sequences revealed that these isolates were clustered into one monophyletic lineage belonging to the species Siniperca chuatsi rhabdovirus.
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Bridgework ahead! Innovation ecosystems vis-à-vis responsible innovation
NASA Astrophysics Data System (ADS)
Foley, Rider; Wiek, Arnim
2017-02-01
Public funding agencies largely support academic research as an effort to stimulate future product commercialization and foster broader societal benefits. Yet, translating research nurtured in academic settings into such outcomes is complex and demands functional interactions between government, academic, and industry, i.e., "triple helix," organizations within an innovation ecosystem. This article argues that in the spirit of responsible innovation, research funding should build bridges that extend beyond the triple helix stakeholders to connect to peripheral organizations. To support that argument, evidence from agent network analysis gathered from two case studies reveals strong and weak connections, as well as gaps within innovation ecosystems in Switzerland and metropolitan Phoenix, USA. This article offers insights on how innovation ecosystems are aligned or misaligned with responsible innovation.
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Interdiscplinary team processes within an in-home service delivery organization.
Gantert, Thomas W; McWilliam, Carol L
2004-01-01
Interdisciplinary teamwork is particularly difficult to achieve in the community context where geographical separateness and solo practices impede face to face contact and collaborative practice. Understanding the processes that occur within interdisciplinary teams is imperative, since client outcomes are influenced by interdisciplinary teamwork. The purpose of this exploratory study was to describe the processes that occur within interdisciplinary teams that deliver in-home care. Applying grounded theory methodology, the researcher conducted unstructured in-depth interviews with a purposeful sample of healthcare providers and used constant comparative analysis to elicit the findings. Findings revealed three key team processes: networking, navigating, and aligning. The descriptions afford several insights that are applicable to in-home healthcare agencies attempting to achieve effective interdisciplinary team functioning.
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NASA Astrophysics Data System (ADS)
Wang, P.; Yang, L.; Dai, B.; Yang, Z.; Guo, S.; Zhu, J.
2017-07-01
Vertically-aligned WO3 nanoplates on transparent conducting fluorine-doped tin oxide (FTO) glass were prepared by a facile template-free crystal-seed-assisted hydrothermal method. The effects of the hydrothermal temperature and reaction time on the crystal structure and morphology of the products were investigated by XRD and SEM. The XRD results showed that the as-prepared thin films obtained below 150∘C comprised orthorhombic WO3 ṡ H2O and completely converted to monoclinic WO3 at 180∘C. It was also noted that there was a phase transformation from orthorhombic to monoclinic by increasing the reaction time from 1 to 12 h. SEM analysis revealed that WO3 thin films are composed of plate-like nanostructures.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Calabrese, Gabriele, E-mail: calabrese@pdi-berlin.de; Corfdir, Pierre; Gao, Guanhui
We demonstrate the self-assembled growth of vertically aligned GaN nanowire ensembles on a flexible Ti foil by plasma-assisted molecular beam epitaxy. The analysis of single nanowires by transmission electron microscopy reveals that they are single crystalline. Low-temperature photoluminescence spectroscopy demonstrates that in comparison to standard GaN nanowires grown on Si, the nanowires prepared on the Ti foil exhibit an equivalent crystalline perfection, a higher density of basal-plane stacking faults, but a reduced density of inversion domain boundaries. The room-temperature photoluminescence spectrum of the nanowire ensemble is not influenced or degraded by the bending of the substrate. The present results pavemore » the way for the fabrication of flexible optoelectronic devices based on GaN nanowires on metal foils.« less
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Geographic variation in marine turtle fibropapillomatosis
Greenblatt, R.J.; Work, Thierry M.; Dutton, P.; Sutton, C.A.; Spraker, T.R.; Casey, R.N.; Diez, C.E.; Parker, Dana C.; St. Ledger, J.; Balazs, G.H.; Casey, J.W.
2005-01-01
We document three examples of fibropapillomatosis by histology, quantitative polymerase chain reaction (qPCR), and sequence analysis from three different geographic areas. Tumors compatible in morphology with fibropapillomatosis were seen in green turtles from Puerto Rico and San Diego (California) and in a hybrid loggerhead/ hawksbill turtle from Florida Bay (Florida). Tumors were confirmed as fibropapillomas on histology, although severity of disease varied between cases. Polymerase chain reaction (PCR) analyses revealed infection with the fibropapilloma-associated turtle herpesvirus (FPTHV) in all cases, albeit at highly variable copy numbers per cell. Alignment of a portion of the polymerase gene from each fibropapilloma-associated turtle herpesvirus isolate demonstrated geographic variation in sequence. These cases illustrate geographic variation in both the pathology and the virology of fibropapillomatosis.
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Geographic variation in marine turtle fibropapillomatosis.
Greenblatt, Rebecca J; Work, Thierry M; Dutton, Peter; Sutton, Claudia A; Spraker, Terry R; Casey, Rufina N; Diez, Carlos E; Parker, Denise; St Leger, Judy; Balazs, George H; Casey, James W
2005-09-01
We document three examples of fibropapillomatosis by histology, quantitative polymerase chain reaction (qPCR), and sequence analysis from three different geographic areas. Tumors compatible in morphology with fibropapillomatosis were seen in green turtles from Puerto Rico and San Diego (California) and in a hybrid loggerhead/ hawksbill turtle from Florida Bay (Florida). Tumors were confirmed as fibropapillomas on histology, although severity of disease varied between cases. Polymerase chain reaction (PCR) analyses revealed infection with the fibropapilloma-associated turtle herpesvirus (FPTHV) in all cases, albeit at highly variable copy numbers per cell. Alignment of a portion of the polymerase gene from each fibropapilloma-associated turtle herpesvirus isolate demonstrated geographic variation in sequence. These cases illustrate geographic variation in both the pathology and the virology of fibropapillomatosis.
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Gupta, Vikas; Bustamante, Mariana; Fredriksson, Alexandru; Carlhäll, Carl-Johan; Ebbers, Tino
2018-01-01
Assessment of blood flow in the left ventricle using four-dimensional flow MRI requires accurate left ventricle segmentation that is often hampered by the low contrast between blood and the myocardium. The purpose of this work is to improve left-ventricular segmentation in four-dimensional flow MRI for reliable blood flow analysis. The left ventricle segmentations are first obtained using morphological cine-MRI with better in-plane resolution and contrast, and then aligned to four-dimensional flow MRI data. This alignment is, however, not trivial due to inter-slice misalignment errors caused by patient motion and respiratory drift during breath-hold based cine-MRI acquisition. A robust image registration based framework is proposed to mitigate such errors automatically. Data from 20 subjects, including healthy volunteers and patients, was used to evaluate its geometric accuracy and impact on blood flow analysis. High spatial correspondence was observed between manually and automatically aligned segmentations, and the improvements in alignment compared to uncorrected segmentations were significant (P < 0.01). Blood flow analysis from manual and automatically corrected segmentations did not differ significantly (P > 0.05). Our results demonstrate the efficacy of the proposed approach in improving left-ventricular segmentation in four-dimensional flow MRI, and its potential for reliable blood flow analysis. Magn Reson Med 79:554-560, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.
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Sparse alignment for robust tensor learning.
Lai, Zhihui; Wong, Wai Keung; Xu, Yong; Zhao, Cairong; Sun, Mingming
2014-10-01
Multilinear/tensor extensions of manifold learning based algorithms have been widely used in computer vision and pattern recognition. This paper first provides a systematic analysis of the multilinear extensions for the most popular methods by using alignment techniques, thereby obtaining a general tensor alignment framework. From this framework, it is easy to show that the manifold learning based tensor learning methods are intrinsically different from the alignment techniques. Based on the alignment framework, a robust tensor learning method called sparse tensor alignment (STA) is then proposed for unsupervised tensor feature extraction. Different from the existing tensor learning methods, L1- and L2-norms are introduced to enhance the robustness in the alignment step of the STA. The advantage of the proposed technique is that the difficulty in selecting the size of the local neighborhood can be avoided in the manifold learning based tensor feature extraction algorithms. Although STA is an unsupervised learning method, the sparsity encodes the discriminative information in the alignment step and provides the robustness of STA. Extensive experiments on the well-known image databases as well as action and hand gesture databases by encoding object images as tensors demonstrate that the proposed STA algorithm gives the most competitive performance when compared with the tensor-based unsupervised learning methods.
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Abaka, Gamze; Bıyıkoğlu, Türker; Erten, Cesim
2013-07-01
Given a pair of metabolic pathways, an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree reconstruction, drug design and overall may enhance our understanding of cellular metabolism. We consider the problem of providing one-to-many alignments of reactions in a pair of metabolic pathways. We first provide a constrained alignment framework applicable to the problem. We show that the constrained alignment problem even in a primitive setting is computationally intractable, which justifies efforts for designing efficient heuristics. We present our Constrained Alignment of Metabolic Pathways (CAMPways) algorithm designed for this purpose. Through extensive experiments involving a large pathway database, we demonstrate that when compared with a state-of-the-art alternative, the CAMPways algorithm provides better alignment results on metabolic networks as far as measures based on same-pathway inclusion and biochemical significance are concerned. The execution speed of our algorithm constitutes yet another important improvement over alternative algorithms. Open source codes, executable binary, useful scripts, all the experimental data and the results are freely available as part of the Supplementary Material at http://code.google.com/p/campways/. Supplementary data are available at Bioinformatics online.
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Radio-Optical Alignments in a Low Radio Luminosity Sample
NASA Technical Reports Server (NTRS)
Lacy, Mark; Ridgway, Susan E.; Wold, Margrethe; Lilje, Per B.; Rawlings, Steve
1999-01-01
We present an optically-based study of the alignment between the radio axes and the optical major axes of eight z approximately 0.7 radio galaxies in a 7C sample. The radio galaxies in this sample are approximately 20-times less radio luminous than 3C galaxies at the same redshift, and are significantly less radio-luminous than any other well-defined samples studied to date. Using Nordic Optical Telescope images taken in good seeing conditions at rest-frame wavelengths just longward of the 4000A break, we find a statistically significant alignment effect in the 7C sample. Furthermore, in two cases where the aligned components are well separated from the host we have been able to confirm spectroscopically that they are indeed at the same redshift as the radio galaxy. However, a quantitative analysis of the alignment in this sample and in a corresponding 3C sample from HST (Hubble Space Telescope) archival data indicates that the percentage of aligned flux may be lower and of smaller spatial scale in the 7C sample. Our study suggests that alignments on the 50-kpc scale are probably closely related to the radio luminosity, whereas those on the 15 kpc scale are not. We discuss these results in the context of popular models for the alignment effect.
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MANGO: a new approach to multiple sequence alignment.
Zhang, Zefeng; Lin, Hao; Li, Ming
2007-01-01
Multiple sequence alignment is a classical and challenging task for biological sequence analysis. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state of the art multiple sequence alignment programs suffer from the 'once a gap, always a gap' phenomenon. Is there a radically new way to do multiple sequence alignment? This paper introduces a novel and orthogonal multiple sequence alignment method, using multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds are provably significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks showing that MANGO compares favorably, in both accuracy and speed, against state-of-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, Prob-ConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0 and Kalign 2.0.
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Accelerated probabilistic inference of RNA structure evolution
Holmes, Ian
2005-01-01
Background Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage. The same problem is faced by other RNA alignment-and-folding algorithms based on Sankoff's 1985 algorithm. It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered. Results We demonstrate how flexible classes of constraint can be imposed, greatly reducing the computational costs while maintaining a high quality of structural homology prediction. Any score-attributed context-free grammar (e.g. energy-based scoring schemes, or conditionally normalized Pair SCFGs) is amenable to this treatment. It is now possible to combine independent structural and alignment constraints of unprecedented general flexibility in Pair SCFG alignment algorithms. We outline several applications to the bioinformatics of RNA sequence and structure, including Waterman-Eggert N-best alignments and progressive multiple alignment. We evaluate the performance of the algorithm on test examples from the RFAM database. Conclusion A program, Stemloc, that implements these algorithms for efficient RNA sequence alignment and structure prediction is available under the GNU General Public License. PMID:15790387
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Articular chondrocyte alignment in the rat after surgically induced osteoarthritis
Takahashi, Hideaki; Tamaki, Hiroyuki; Yamamoto, Noriaki; Onishi, Hideaki
2017-01-01
[Purpose] Chondrocytes in articular cartilage are aligned as columns from the joint surface. Notably, loss of chondrocyte and abnormalities of differentiation factors give rise to osteoarthritis (OA). However, the relationship between chondrocyte alignment and OA progression remains unclear. This study was performed to investigate temporal alterations in surgically-induced OA rats. [Subjects and Methods] Thirteen-week-old Wistar rats (n=30) underwent destabilized medial meniscus surgery in their right knee and sham surgery in their left knee. Specimens (n=5) were collected at 0, 1, 2, 4 and 8 weeks after surgery. Histological analysis with Osteoarthritis Research Society International (OARSI) scores, cell density ratios, cell alignments and correlation between OARSI scores and cell density/alignment was performed. [Results] OARSI scores were significantly higher at 1, 2, 4 and 8 weeks in the DMM group than in the control. Cell density ratios were decreased significantly in the DMM group at 2, 4 and 8 weeks compared with the control. Chondrocyte alignment was decreased significantly in the DMM group at 4 and 8 weeks. There were negative correlations between OA severity and cell density / cell alignment. [Conclusion] The results suggest a relationship between chondrocyte alignment and cartilage homeostasis, which plays an important role in OA progression. PMID:28533592
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Goodrich, Zachary J; Norby, Bo; Eichelberger, Bunita M; Friedeck, Wade O; Callis, Hollye N; Hulse, Don A; Kerwin, Sharon C; Fox, Derek B; Saunders, W Brian
2014-10-01
To report thoracic limb alignment values in healthy dogs; to determine if limb alignment values are significantly different when obtained from standing versus recumbent radiographic projections. Prospective cross-sectional study. Labrador Retrievers (n = 45) >15 months of age. Standing and recumbent radiographs were obtained and limb montages were randomized before analysis by a single investigator blinded to dog, limb, and limb position. Twelve limb alignment values were determined using the CORA methodology. Measurements were performed in triplicate and intra-observer variability was evaluated by intra-class correlation coefficient (ICC). Limb alignment values were reported as mean ± SD and 95% confidence intervals. Linear mixed models were used to determine if significant associations existed between limb alignment values and limb, limb position, gender, age, weight, and body condition score. There were significant differences in standing and recumbent limb alignment values for all values except elbow mechanical axis deviation (eMAD). Limb, gender, age, body weight, and body condition score had no effect. ICC values ranged from 0.522 to 0.758, indicating moderate to substantial agreement for repeated measurements by a single investigator. Limb alignment values are significantly different when determined from standing versus recumbent radiographs in healthy Labrador Retrievers. © Copyright 2014 by The American College of Veterinary Surgeons.
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A Molecular Phylogeny of the Chalcidoidea (Hymenoptera)
Munro, James B.; Heraty, John M.; Burks, Roger A.; Hawks, David; Mottern, Jason; Cruaud, Astrid; Rasplus, Jean-Yves; Jansta, Petr
2011-01-01
Chalcidoidea (Hymenoptera) are extremely diverse with more than 23,000 species described and over 500,000 species estimated to exist. This is the first comprehensive phylogenetic analysis of the superfamily based on a molecular analysis of 18S and 28S ribosomal gene regions for 19 families, 72 subfamilies, 343 genera and 649 species. The 56 outgroups are comprised of Ceraphronoidea and most proctotrupomorph families, including Mymarommatidae. Data alignment and the impact of ambiguous regions are explored using a secondary structure analysis and automated (MAFFT) alignments of the core and pairing regions and regions of ambiguous alignment. Both likelihood and parsimony approaches are used to analyze the data. Overall there is no impact of alignment method, and few but substantial differences between likelihood and parsimony approaches. Monophyly of Chalcidoidea and a sister group relationship between Mymaridae and the remaining Chalcidoidea is strongly supported in all analyses. Either Mymarommatoidea or Diaprioidea are the sister group of Chalcidoidea depending on the analysis. Likelihood analyses place Rotoitidae as the sister group of the remaining Chalcidoidea after Mymaridae, whereas parsimony nests them within Chalcidoidea. Some traditional family groups are supported as monophyletic (Agaonidae, Eucharitidae, Encyrtidae, Eulophidae, Leucospidae, Mymaridae, Ormyridae, Signiphoridae, Tanaostigmatidae and Trichogrammatidae). Several other families are paraphyletic (Perilampidae) or polyphyletic (Aphelinidae, Chalcididae, Eupelmidae, Eurytomidae, Pteromalidae, Tetracampidae and Torymidae). Evolutionary scenarios discussed for Chalcidoidea include the evolution of phytophagy, egg parasitism, sternorrhynchan parasitism, hypermetamorphic development and heteronomy. PMID:22087244
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Nucleon Alignment and Shape Competition at High Spin in ^180Hf
NASA Astrophysics Data System (ADS)
Tandel, U. S.; Chowdhury, P.; Tandel, S. K.; Sheppard, S.; Cline, D.; Wu, C. Y.; Carpenter, M. P.; Janssens, R. V. F.; Khoo, T. L.; Lauritsen, T.; Lister, C. J.; Seweryniak, D.; Zhu, S.
2006-10-01
In light even-N Hf isotopes (N = 96-106), the first i13/2 neutron alignment occurs at hφ< 0.3 MeV. In contrast, no alignment was observed up to ˜ 0.4 MeV in ^180,182Hf (N = 108,110) [1]. Theoretical calculations predict that oblate collective rotation becomes yrast at high spins in ^180Hf [2, 3]. In the present work, the yrast band of ^180Hf has been extended to high spins, via inelastic excitation, using a 1300 MeV ^180Hf beam incident on a thin ^232Th target. The γ rays were detected by Gammasphere, with event by event Doppler correction and Q-value selectivity provided by CHICO. The data reveal onset of the first nucleon alignment in ^180Hf at hφ ˜ 0.43 MeV, which is significantly higher than predictions (˜ 0.35 MeV). Interestingly, the γ-vibrational band is crossed by a band with apparent high moment-of-inertia at ˜ 0.25 MeV. This structure, which becomes near yrast at the highest observed spins will be discussed in the context of nucleon alignment and shape competition at high spin in ^180Hf. [1] E. Ngijoi-Yogo, Ph.D. thesis, U.Mass. Lowell (2004) [2] R.R. Hilton and H.J. Mang, Phys. Rev. Lett. 43, 1979 (1979). [3] F.R. Xu et al., Phys. Rev. C62, 014301 (2000).
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NASA Astrophysics Data System (ADS)
Afraimovich, E. L.; Ishin, A. B.; Tinin, M. V.; Yasyukevich, Yu. V.; Jin, S. G.
2011-05-01
The mid-latitude field-aligned irregularity (FAI) along the magnetic field line is a common phenomenon in the ionosphere. However, few data reveal the field-aligned ionospheric irregularities. They are insufficient to identify FAIs effects so far, particularly effect on global positioning system (GPS) signals. In this paper, the mid-latitude FAIs by line-of-sight angular scanning relative to the local magnetic field vector are investigated using the denser GPS network observations in Japan. It has been the first found that total GPS L2 phase slips over Japan, during the recovery phase of the 12 Feb 2000 geomagnetic storm were caused by GPS signal scattering on FAIs both for the lines-of-sight aligned to the magnetic field line (the field of aligned scattering, FALS) and across the magnetic field line (the field of across scattering, FACS). The FALS results are also in a good agreement with the data of the magnetic field orientation control of GPS occultation observations of equatorial scintillation during thorough low earth orbit (LEO) satellites measurements, e.g. Challenging Minisatellite Payload (CHAMP) and Satellite de Aplicaciones Cientificas-C (SAC-C). The role of large-angle scattering almost along the normal to the magnetic field line in GPS scintillation is determined by attenuation of the irregularity anisotropy factor as compared with the other factors.
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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.
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Electrospun fibrinogen-PLA nanofibres for vascular tissue engineering.
Gugutkov, D; Gustavsson, J; Cantini, M; Salmeron-Sánchez, M; Altankov, G
2017-10-01
Here we report on the development of a new type of hybrid fibrinogen-polylactic acid (FBG-PLA) nanofibres (NFs) with improved stiffness, combining the good mechanical properties of PLA with the excellent cell recognition properties of native FBG. We were particularly interested in the dorsal and ventral cell response to the nanofibres' organization (random or aligned), using human umbilical endothelial cells (HUVECs) as a model system. Upon ventral contact with random NFs, the cells developed a stellate-like morphology with multiple projections. The well-developed focal adhesion complexes suggested a successful cellular interaction. However, time-lapse analysis shows significantly lowered cell movements, resulting in the cells traversing a relatively short distance in multiple directions. Conversely, an elongated cell shape and significantly increased cell mobility were observed in aligned NFs. To follow the dorsal cell response, artificial wounds were created on confluent cell layers previously grown on glass slides and covered with either random or aligned NFs. Time-lapse analysis showed significantly faster wound coverage (within 12 h) of HUVECs on aligned samples vs. almost absent directional migration on random ones. However, nitric oxide (NO) release shows that endothelial cells possess lowered functionality on aligned NFs compared to random ones, where significantly higher NO production was found. Collectively, our studies show that randomly organized NFs could support the endothelization of implants while aligned NFs would rather direct cell locomotion for guided neovascularization. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.
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Comparison of landmark-based and automatic methods for cortical surface registration
Pantazis, Dimitrios; Joshi, Anand; Jiang, Jintao; Shattuck, David; Bernstein, Lynne E.; Damasio, Hanna; Leahy, Richard M.
2009-01-01
Group analysis of structure or function in cerebral cortex typically involves as a first step the alignment of the cortices. A surface based approach to this problem treats the cortex as a convoluted surface and coregisters across subjects so that cortical landmarks or features are aligned. This registration can be performed using curves representing sulcal fundi and gyral crowns to constrain the mapping. Alternatively, registration can be based on the alignment of curvature metrics computed over the entire cortical surface. The former approach typically involves some degree of user interaction in defining the sulcal and gyral landmarks while the latter methods can be completely automated. Here we introduce a cortical delineation protocol consisting of 26 consistent landmarks spanning the entire cortical surface. We then compare the performance of a landmark-based registration method that uses this protocol with that of two automatic methods implemented in the software packages FreeSurfer and BrainVoyager. We compare performance in terms of discrepancy maps between the different methods, the accuracy with which regions of interest are aligned, and the ability of the automated methods to correctly align standard cortical landmarks. Our results show similar performance for ROIs in the perisylvian region for the landmark based method and FreeSurfer. However, the discrepancy maps showed larger variability between methods in occipital and frontal cortex and also that automated methods often produce misalignment of standard cortical landmarks. Consequently, selection of the registration approach should consider the importance of accurate sulcal alignment for the specific task for which coregistration is being performed. When automatic methods are used, the users should ensure that sulci in regions of interest in their studies are adequately aligned before proceeding with subsequent analysis. PMID:19796696
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Aguirre, Luis E.; de Oliveira, Alexandre; Seč, David; Čopar, Simon; Almeida, Pedro L.; Ravnik, Miha; Godinho, Maria Helena; Žumer, Slobodan
2016-01-01
Probing the surface morphology of microthin fibers such as naturally occurring biofibers is essential for understanding their structural properties, biological function, and mechanical performance. The state-of-the-art methods for studying the surfaces of biofibers are atomic force microscopy imaging and scanning electron microscopy, which well characterize surface geometry of the fibers but provide little information on the local interaction potential of the fibers with the surrounding material. In contrast, complex nematic fluids respond very well to external fields and change their optical properties upon such stimuli. Here we demonstrate that liquid crystal droplets deposited on microthin biofibers—including spider silk and cellulosic fibers—reveal characteristics of the fibers’ surface, performing as simple but sensitive surface sensors. By combining experiments and numerical modeling, different types of fibers are identified through the fiber-to-nematic droplet interactions, including perpendicular and axial or helicoidal planar molecular alignment. Spider silks align nematic molecules parallel to fibers or perpendicular to them, whereas cellulose aligns the molecules unidirectionally or helicoidally along the fibers, indicating notably different surface interactions. The nematic droplets as sensors thus directly reveal chirality of cellulosic fibers. Different fiber entanglements can be identified by depositing droplets exactly at the fiber crossings. More generally, the presented method can be used as a simple but powerful approach for probing the surface properties of small-size bioobjects, opening a route to their precise characterization. PMID:26768844
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Aguirre, Luis E; de Oliveira, Alexandre; Seč, David; Čopar, Simon; Almeida, Pedro L; Ravnik, Miha; Godinho, Maria Helena; Žumer, Slobodan
2016-02-02
Probing the surface morphology of microthin fibers such as naturally occurring biofibers is essential for understanding their structural properties, biological function, and mechanical performance. The state-of-the-art methods for studying the surfaces of biofibers are atomic force microscopy imaging and scanning electron microscopy, which well characterize surface geometry of the fibers but provide little information on the local interaction potential of the fibers with the surrounding material. In contrast, complex nematic fluids respond very well to external fields and change their optical properties upon such stimuli. Here we demonstrate that liquid crystal droplets deposited on microthin biofibers--including spider silk and cellulosic fibers--reveal characteristics of the fibers' surface, performing as simple but sensitive surface sensors. By combining experiments and numerical modeling, different types of fibers are identified through the fiber-to-nematic droplet interactions, including perpendicular and axial or helicoidal planar molecular alignment. Spider silks align nematic molecules parallel to fibers or perpendicular to them, whereas cellulose aligns the molecules unidirectionally or helicoidally along the fibers, indicating notably different surface interactions. The nematic droplets as sensors thus directly reveal chirality of cellulosic fibers. Different fiber entanglements can be identified by depositing droplets exactly at the fiber crossings. More generally, the presented method can be used as a simple but powerful approach for probing the surface properties of small-size bioobjects, opening a route to their precise characterization.
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Molecular Characterization of a Novel Bovine Viral Diarrhea Virus Isolate SD-15
Zhu, Lisai; Lu, Haibing; Cao, Yufeng; Gai, Xiaochun; Guo, Changming; Liu, Yajing; Liu, Jiaxu; Wang, Xinping
2016-01-01
As one of the major pathogens, bovine viral diarrhea virus caused a significant economic loss to the livestock industry worldwide. Although BVDV infections have increasingly been reported in China in recent years, the molecular aspects of those BVDV strains were barely characterized. In this study, we reported the identification and characterization of a novel BVDV isolate designated as SD-15 from cattle, which is associated with an outbreak characterized by severe hemorrhagic and mucous diarrhea with high morbidity and mortality in Shandong, China. SD-15 was revealed to be a noncytopathic BVDV, and has a complete genomic sequence of 12,285 nucleotides that contains a large open reading frame encoding 3900 amino acids. Alignment analysis showed that SD-15 has 93.8% nucleotide sequence identity with BVDV ZM-95 isolate, a previous BVDV strain isolated from pigs manifesting clinical signs and lesions resembling to classical swine fever. Phylogenetic analysis clustered SD-15 to a BVDV-1m subgenotype. Analysis of the deduced amino acid sequence of glycoproteins revealed that E2 has several highly conserved and variable regions within BVDV-1 genotypes. An additional N-glycosylation site (240NTT) was revealed exclusively in SD-15-encoded E2 in addition to four potential glycosylation sites (Asn-X-Ser/Thr) shared by all BVDV-1 genotypes. Furthermore, unique amino acid and linear epitope mutations were revealed in SD-15-encoded Erns glycoprotein compared with known BVDV-1 genotype. In conclusion, we have isolated a noncytopathic BVDV-1m strain that is associated with a disease characterized by high morbidity and mortality, revealed the complete genome sequence of the first BVDV-1m virus originated from cattle, and found a unique glycosylation site in E2 and a linear epitope mutation in Erns encoded by SD-15 strain. Those results will broaden the current understanding of BVDV infection and lay a basis for future investigation on SD-15-related pathogenesis. PMID:27764206
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Nadeau, Jeremy S.; Wright, Bob W.; Synovec, Robert E.
2010-04-15
A critical comparison of methods for correcting severely retention time shifted gas chromatography-mass spectrometry (GC-MS) data is presented. The method reported herein is an adaptation to the Piecewise Alignment Algorithm to quickly align severely shifted one-dimensional (1D) total ion current (TIC) data, then applying these shifts to broadly align all mass channels throughout the separation, referred to as a TIC shift function (SF). The maximum shift varied from (-) 5 s in the beginning of the chromatographic separation to (+) 20 s toward the end of the separation, equivalent to a maximum shift of over 5 peak widths. Implementing themore » TIC shift function (TIC SF) prior to Fisher Ratio (F-Ratio) feature selection and then principal component analysis (PCA) was found to be a viable approach to classify complex chromatograms, that in this study were obtained from GC-MS separations of three gasoline samples serving as complex test mixtures, referred to as types C, M and S. The reported alignment algorithm via the TIC SF approach corrects for large dynamic shifting in the data as well as subtle peak-to-peak shifts. The benefits of the overall TIC SF alignment and feature selection approach were quantified using the degree-of-class separation (DCS) metric of the PCA scores plots using the type C and M samples, since they were the most similar, and thus the most challenging samples to properly classify. The DCS values showed an increase from an initial value of essentially zero for the unaligned GC-TIC data to a value of 7.9 following alignment; however, the DCS was unchanged by feature selection using F-Ratios for the GC-TIC data. The full mass spectral data provided an increase to a final DCS of 13.7 after alignment and two-dimensional (2D) F-Ratio feature selection.« less
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Phylo-VISTA: Interactive visualization of multiple DNA sequence alignments
DOE Office of Scientific and Technical Information (OSTI.GOV)
Shah, Nameeta; Couronne, Olivier; Pennacchio, Len A.
The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing number of genomic sequence datasets being generated for an ever-increasing number of organisms. To be efficient these visualization algorithms must support the ability to accommodate consistently a wide range of evolutionary distances in a comparison framework based upon phylogenetic relationships. Results: We have developed Phylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure for multiple DNA sequences. The complexity of visual presentation is effectively organized using a frameworkmore » based upon interspecies phylogenetic relationships. The phylogenetic organization supports rapid, user-guided interspecies comparison. To aid in navigation through large sequence datasets, Phylo-VISTA leverages concepts from VISTA that provide a user with the ability to select and view data at varying resolutions. The combination of multiresolution data visualization and analysis, combined with the phylogenetic framework for interspecies comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments. Availability: Phylo-VISTA is available at http://www-gsd.lbl. gov/phylovista. It requires an Internet browser with Java Plugin 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu« less
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NASA Astrophysics Data System (ADS)
Lee, Sang Jin; Heo, Min; Lee, Donghyun; Heo, Dong Nyoung; Lim, Ho-Nam; Kwon, Il Keun
2017-12-01
In this study, we designed highly-aligned thermoplastic polycarbonate urethane (PCU) fibrous scaffolds coated with bioactive compounds, such as Poly-L-Lysine (PLL) and Poly-L-Ornithine (PLO), to enhance cellular adhesion and directivity. These products were characterized by scanning electron microscope (SEM) analysis which demonstrated that highly aligned fiber strands were formed without beads when coated onto a mandrel rotating at 1800 rpm. During in vitro cell test, PLO-coated, aligned PCU scaffolds were found to have significantly higher proliferation rates than PLL coated and bare PCU scaffolds. Interestingly, dental pulp stem cells (DPSCs) were observed to stretch along the longitudinal axis parallel to the cell direction on highly aligned scaffolds. These results clearly confirm that our strategy may suggest a useful paradigm by inducing neural tissue repair as a means to remodeling and healing of tissue for restorative procedures in neural tissue engineering.
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Yu, Jia; Blom, Jochen; Sczyrba, Alexander; Goesmann, Alexander
2017-09-10
The introduction of next generation sequencing has caused a steady increase in the amounts of data that have to be processed in modern life science. Sequence alignment plays a key role in the analysis of sequencing data e.g. within whole genome sequencing or metagenome projects. BLAST is a commonly used alignment tool that was the standard approach for more than two decades, but in the last years faster alternatives have been proposed including RapSearch, GHOSTX, and DIAMOND. Here we introduce HAMOND, an application that uses Apache Hadoop to parallelize DIAMOND computation in order to scale-out the calculation of alignments. HAMOND is fault tolerant and scalable by utilizing large cloud computing infrastructures like Amazon Web Services. HAMOND has been tested in comparative genomics analyses and showed promising results both in efficiency and accuracy. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.
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AmpliVar: mutation detection in high-throughput sequence from amplicon-based libraries.
Hsu, Arthur L; Kondrashova, Olga; Lunke, Sebastian; Love, Clare J; Meldrum, Cliff; Marquis-Nicholson, Renate; Corboy, Greg; Pham, Kym; Wakefield, Matthew; Waring, Paul M; Taylor, Graham R
2015-04-01
Conventional means of identifying variants in high-throughput sequencing align each read against a reference sequence, and then call variants at each position. Here, we demonstrate an orthogonal means of identifying sequence variation by grouping the reads as amplicons prior to any alignment. We used AmpliVar to make key-value hashes of sequence reads and group reads as individual amplicons using a table of flanking sequences. Low-abundance reads were removed according to a selectable threshold, and reads above this threshold were aligned as groups, rather than as individual reads, permitting the use of sensitive alignment tools. We show that this approach is more sensitive, more specific, and more computationally efficient than comparable methods for the analysis of amplicon-based high-throughput sequencing data. The method can be extended to enable alignment-free confirmation of variants seen in hybridization capture target-enrichment data. © 2015 WILEY PERIODICALS, INC.
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Industrial metrology as applied to large physics experiments
DOE Office of Scientific and Technical Information (OSTI.GOV)
Veal, D.
1993-05-01
A physics experiment is a large complex 3-D object (typ. 1200 m{sup 3}, 35000 tonnes), with sub-millimetric alignment requirements. Two generic survey alignment tasks can be identified; first, an iterative positioning of the apparatus subsystems in space and, second, a quantification of as-built parameters. The most convenient measurement technique is industrial triangulation but the complexity of the measured object and measurement environment constraints frequently requires a more sophisticated approach. To enlarge the ``survey alignment toolbox`` measurement techniques commonly associated with other disciplines such as geodesy, applied geodesy for accelerator alignment, and mechanical engineering are also used. Disparate observables require amore » heavy reliance on least squares programs for campaign pre-analysis and calculation. This paper will offer an introduction to the alignment of physics experiments and will identify trends for the next generation of SSC experiments.« less
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Infant-Mother Acoustic-Prosodic Alignment and Developmental Risk.
Seidl, Amanda; Cristia, Alejandrina; Soderstrom, Melanie; Ko, Eon-Suk; Abel, Emily A; Kellerman, Ashleigh; Schwichtenberg, A J
2018-06-19
One promising early marker for autism and other communicative and language disorders is early infant speech production. Here we used daylong recordings of high- and low-risk infant-mother dyads to examine whether acoustic-prosodic alignment as well as two automated measures of infant vocalization are related to developmental risk status indexed via familial risk and developmental progress at 36 months of age. Automated analyses of the acoustics of daylong real-world interactions were used to examine whether pitch characteristics of one vocalization by the mother or the child predicted those of the vocalization response by the other speaker and whether other features of infants' speech in daylong recordings were associated with developmental risk status or outcomes. Low-risk and high-risk dyads did not differ in the level of acoustic-prosodic alignment, which was overall not significant. Further analyses revealed that acoustic-prosodic alignment did not predict infants' later developmental progress, which was, however, associated with two automated measures of infant vocalizations (daily vocalizations and conversational turns). Although further research is needed, these findings suggest that automated measures of vocalizations drawn from daylong recordings are a possible early identification tool for later developmental progress/concerns. https://osf.io/cdn3v/.
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Sleep, circadian rhythm and body weight: parallel developments.
Westerterp-Plantenga, Margriet S
2016-11-01
Circadian alignment is crucial for body-weight management, and for metabolic health. In this context, circadian alignment consists of alignment of sleep, meal patterns and physical activity. During puberty a significant reduction in sleep duration occurs, and pubertal status is inversely associated with sleep duration. A consistent inverse association between habitual sleep duration and body-weight development occurs, independent of possible confounders. Research on misalignment reveals that circadian misalignment affects sleep-architecture and subsequently disturbs glucose-insulin metabolism, substrate oxidation, leptin- and ghrelin concentrations, appetite, food reward, hypothalamic-pituitary-adrenal-axis activity and gut-peptide concentrations enhancing positive energy balance and metabolic disturbance. Not only aligning meals and sleep in a circadian way is crucial, also regular physical activity during the day strongly promotes the stability and amplitude of circadian rhythm, and thus may serve as an instrument to restore poor circadian rhythms. Endogenicity may play a role in interaction of these environmental variables with a genetic predisposition. In conclusion, notwithstanding the separate favourable effects of sufficient daily physical activity, regular meal patterns, sufficient sleep duration and quality sleep on energy balance, the overall effect of the amplitude and stability of the circadian rhythm, perhaps including genetic predisposition, may integrate the separate effects in an additive way.
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Lee, Young Jun; Lee, Joo Kang; Jung, Soo Chang; Lee, Hwang-woo; Yin, Chang Shik; Lee, Young Jin
2013-01-01
Objective. The objective of this study was to investigate the effect of a holistic intraoral appliance (OA) on cervical spine alignment and subjective symptom severity. Design. An observational study on case series with holistic OA therapy. Setting. An outpatient clinic for holistic temporomandibular joint (TMJ) therapy under the supervision of the Pain Center, CHA Biomedical center, CHA University. Subjects. Ambulatory patients presenting with diverse chief complaints in the holistic TMJ clinic. Main Measures. Any immediate change in the curvature of cervical spine and the degree of atlantoaxial rotation was investigated in the images of simple X-ray and computed tomography of cervical spine with or without OA. Changes of subjective symptom severity were also analyzed for the holistic OA therapy cases. Results. A total of 59 cases were reviewed. Alignment of upper cervical spine rotation showed an immediate improvement (P < 0.001). Changes of subjective symptom severity also showed significant improvement (P < 0.05). Conclusion. These cases revealed rudimentary clinical evidence that holistic OA therapy may be related to an alleviated symptom severity and an improved cervical spinal alignment. These results show that further researches may warrant for the holistic TMJ therapy. PMID:23935655
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Educational silos in nursing education: a critical review of practical nurse education in Canada.
Butcher, Diane L; MacKinnon, Karen A
2015-09-01
Changes to practical nurse education (with expanded scopes of practice) align with the increasing need for nurses and assistive personnel in global acute care contexts. A case in point is this critical exploration of Canadian practical nursing literature, undertaken to reveal predominating discourses and relationships to nursing disciplinary knowledge. The objectives of this poststructural critical review were to identify dominant discourses in practical nurse education literature and to analyze these discourses to uncover underlying beliefs, constructed truths, assumptions, ambiguities and sources of knowledge within the discursive landscape. Predominant themes in the discourses surrounding practical nurse education included conversations about the nurse shortage, expanded roles, collaboration, evidence-based practice, role confusion, cost/efficiency, the history of practical nurse education and employer interests. The complex relationships between practical nursing and the disciplinary landscape of nursing are revealed in the analysis of discourses related to the purpose(s) of practical nurse education, curricula/educational programming, relationships between RN and PN education and the role of nursing knowledge. Power dynamics related to employer needs and interests, as well as educational silos and the nature of women's work, are also revealed within the intersection of various discourses. © 2014 John Wiley & Sons Ltd.
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Optimization of bicelle lipid composition and temperature for EPR spectroscopy of aligned membranes.
McCaffrey, Jesse E; James, Zachary M; Thomas, David D
2015-01-01
We have optimized the magnetic alignment of phospholipid bilayered micelles (bicelles) for EPR spectroscopy, by varying lipid composition and temperature. Bicelles have been extensively used in NMR spectroscopy for several decades, in order to obtain aligned samples in a near-native membrane environment and take advantage of the intrinsic sensitivity of magnetic resonance to molecular orientation. Recently, bicelles have also seen increasing use in EPR, which offers superior sensitivity and orientational resolution. However, the low magnetic field strength (less than 1 T) of most conventional EPR spectrometers results in homogeneously oriented bicelles only at a temperature well above physiological. To optimize bicelle composition for magnetic alignment at reduced temperature, we prepared bicelles containing varying ratios of saturated (DMPC) and unsaturated (POPC) phospholipids, using EPR spectra of a spin-labeled fatty acid to assess alignment as a function of lipid composition and temperature. Spectral analysis showed that bicelles containing an equimolar mixture of DMPC and POPC homogeneously align at 298 K, 20 K lower than conventional DMPC-only bicelles. It is now possible to perform EPR studies of membrane protein structure and dynamics in well-aligned bicelles at physiological temperatures and below. Copyright © 2014 Elsevier Inc. All rights reserved.
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Aligning Biomolecular Networks Using Modular Graph Kernels
NASA Astrophysics Data System (ADS)
Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant
Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.
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AlignNemo: a local network alignment method to integrate homology and topology.
Ciriello, Giovanni; Mina, Marco; Guzzi, Pietro H; Cannataro, Mario; Guerra, Concettina
2012-01-01
Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo.
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Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns
Tian, Wenhong; Samatova, Nagiza F.
2013-01-01
A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach based onmore » a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (fly), E. coli K12 and S. typhimurium , E. coli K12 and C. crescenttus , we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily.« less
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Kowalski, William J; Yuan, Fangping; Nakane, Takeichiro; Masumoto, Hidetoshi; Dwenger, Marc; Ye, Fei; Tinney, Joseph P; Keller, Bradley B
2017-08-01
Biological tissues have complex, three-dimensional (3D) organizations of cells and matrix factors that provide the architecture necessary to meet morphogenic and functional demands. Disordered cell alignment is associated with congenital heart disease, cardiomyopathy, and neurodegenerative diseases and repairing or replacing these tissues using engineered constructs may improve regenerative capacity. However, optimizing cell alignment within engineered tissues requires quantitative 3D data on cell orientations and both efficient and validated processing algorithms. We developed an automated method to measure local 3D orientations based on structure tensor analysis and incorporated an adaptive subregion size to account for multiple scales. Our method calculates the statistical concentration parameter, κ, to quantify alignment, as well as the traditional orientational order parameter. We validated our method using synthetic images and accurately measured principal axis and concentration. We then applied our method to confocal stacks of cleared, whole-mount engineered cardiac tissues generated from human-induced pluripotent stem cells or embryonic chick cardiac cells and quantified cardiomyocyte alignment. We found significant differences in alignment based on cellular composition and tissue geometry. These results from our synthetic images and confocal data demonstrate the efficiency and accuracy of our method to measure alignment in 3D tissues.
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Kernel Manifold Alignment for Domain Adaptation.
Tuia, Devis; Camps-Valls, Gustau
2016-01-01
The wealth of sensory data coming from different modalities has opened numerous opportunities for data analysis. The data are of increasing volume, complexity and dimensionality, thus calling for new methodological innovations towards multimodal data processing. However, multimodal architectures must rely on models able to adapt to changes in the data distribution. Differences in the density functions can be due to changes in acquisition conditions (pose, illumination), sensors characteristics (number of channels, resolution) or different views (e.g. street level vs. aerial views of a same building). We call these different acquisition modes domains, and refer to the adaptation problem as domain adaptation. In this paper, instead of adapting the trained models themselves, we alternatively focus on finding mappings of the data sources into a common, semantically meaningful, representation domain. This field of manifold alignment extends traditional techniques in statistics such as canonical correlation analysis (CCA) to deal with nonlinear adaptation and possibly non-corresponding data pairs between the domains. We introduce a kernel method for manifold alignment (KEMA) that can match an arbitrary number of data sources without needing corresponding pairs, just few labeled examples in all domains. KEMA has interesting properties: 1) it generalizes other manifold alignment methods, 2) it can align manifolds of very different complexities, performing a discriminative alignment preserving each manifold inner structure, 3) it can define a domain-specific metric to cope with multimodal specificities, 4) it can align data spaces of different dimensionality, 5) it is robust to strong nonlinear feature deformations, and 6) it is closed-form invertible, which allows transfer across-domains and data synthesis. To authors' knowledge this is the first method addressing all these important issues at once. We also present a reduced-rank version of KEMA for computational efficiency, and discuss the generalization performance of KEMA under Rademacher principles of stability. Aligning multimodal data with KEMA reports outstanding benefits when used as a data pre-conditioner step in the standard data analysis processing chain. KEMA exhibits very good performance over competing methods in synthetic controlled examples, visual object recognition and recognition of facial expressions tasks. KEMA is especially well-suited to deal with high-dimensional problems, such as images and videos, and under complicated distortions, twists and warpings of the data manifolds. A fully functional toolbox is available at https://github.com/dtuia/KEMA.git.
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Strengths Weaknesses Opportunities and Threats of Blended Learning: Students’ Perceptions
Hande, S
2014-01-01
Background: Blended learning (BL) in a cell biology course of the premedical program at the Kasturba Medical College International Centre, Manipal, India, commenced in 2006. The program provides training in basic sciences to students, especially from the United States and Canada. The approach to the study was phenomenographic, with a qualitative study design using an open-ended questionnaire, focused interviews and empirical observations. Aim: The aim of this study was to identify the strengths, weaknesses, opportunities and threats (SWOT) of BL in a premedical class. Subjects and Methods: It was a cross-sectional study. Ninety six students in a premedical cell biology class participated in the study. SWOT analysis of students’ perceptions was conducted manually. Statistical analysis included content analysis of qualitative data to classify data and aligning them into the SWOT analysis matrix. Results: The outcomes of the study revealed student perceptions in terms of SWOT of BL and the potential uses of this strategy. Conclusions: The study provides background for educators and curriculum experts to plan their modules while incorporating a BL approach. PMID:24971204
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USDA-ARS?s Scientific Manuscript database
Water buffalo (Bubalus bubalis L.) represent a significant livestock species with high economic importance and promising characteristics for production; however, like many other livestock species, they lack a highly polished and contiguous reference genome assembly for use in high-resolution compara...
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Hegger, Ingrid; Marks, Lisanne K; Janssen, Susan W J; Schuit, Albertine J; Keijsers, Jolanda F M; van Oers, Hans A M
2016-09-30
To improve knowledge utilization in policymaking, alignment between researchers and policymakers during knowledge production is essential, but difficult to maintain. In three previously reported case studies, we extensively evaluated complex research projects commissioned by policymakers to investigate how alignment is achieved in a research process and to discover ways to enhance knowledge contributions to health policy. In the present study, we investigated how the findings of these three research projects could be integrated into a practical tool for researchers to enhance their contribution to evidence-based policy. A cross-case analysis was conducted to integrate the findings of the evaluation of the three research projects and to identify important alignment areas in these projects. By means of an iterative process, we prepared a tool that includes reflection questions for researchers. The "Research for Policy" tool was tested with input from the project managers of three new research projects. Based on the findings, the final version of the Research for Policy tool was prepared. By cross-case analysis of the three case studies, the following important alignment areas were identified: the goal, quality, relevance, timing, and presentation of research, the tasks and authorities of actors, the consultative structure and vertical alignment within organizations, and the organizational environment. The project managers regarded the Research for Policy tool as a useful checklist for addressing the important alignment areas in a research project. Based on their feedback, the illustrative examples from the case studies were added to the reflection questions. The project managers suggested making the tool accessible not only to researchers but also to policymakers. The format of the Research for Policy tool was further adjusted to users' needs by adding clickable links. Alignment between research and policymaking requires continuous efforts and a clear understanding of process issues in the research project. The Research for Policy tool offers practical alignment guidance and facilitates reflection on process issues, which supports researchers in aligning with policymakers and in acting in a context-sensitive way.
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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.
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Computational design and engineering of polymeric orthodontic aligners.
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.
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Ren, Xiaozhi; Han, Yiming; Wang, Jie; Jiang, Yuqi; Yi, Zhengfang; Xu, He; Ke, Qinfei
2018-04-01
A chronic wound in diabetic patients is usually characterized by poor angiogenesis and delayed wound closure. The exploration of efficient strategy to significantly improve angiogenesis in the diabetic wound bed and thereby accelerate wound healing is still a significant challenge. Herein, we reported a kind of aligned porous poly (l-lactic acid) (PlLA) electrospun fibrous membranes containing dimethyloxalylglycine (DMOG)-loaded mesoporous silica nanoparticles (DS) for diabetic wound healing. The PlLA electrospun fibers aligned in a single direction and there were ellipse-shaped nano-pores in situ generated onto the surface of fibers, while the DS were well distributed in the fibers and the DMOG as well as Si ion could be controlled released from the nanopores on the fibers. The in vitro results revealed that the aligned porous composite membranes (DS-PL) could stimulate the proliferation, migration and angiogenesis-related gene expression of human umbilical vein endothelial cells (HUVECs) compared with the pure PlLA membranes. The in vivo study further demonstrated that the prepared DS-PL membranes significantly improved neo-vascularization, re-epithelialization and collagen formation as well as inhibited inflammatory reaction in the diabetic wound bed, which eventually stimulated the healing of the diabetic wound. Collectively, these results suggest that the combination of hierarchical structures (nanopores on the aligned fibers) with the controllable released DMOG drugs as well as Si ions from the membranes, which could create a synergetic effect on the rapid stimulation of angiogenesis in the diabetic wound bed, is a potential novel therapeutic strategy for highly efficient diabetic wound healing. A chronic wound in diabetic patients is usually characterized by the poor angiogenesis and the delayed wound closure. The main innovation of this study is to design a new kind of skin tissue engineered scaffold, aligned porous poly (l-lactic acid) (PlLA) electrospun membranes containing dimethyloxalylglycine (DMOG)-loaded mesoporous silica nanoparticles (DS), which could significantly improve angiogenesis in the diabetic wound bed and thereby accelerate diabetic wound healing. The results revealed that the electrospun fibers with ellipse-shaped nano-pores on the surface were aligned in a single direction, while there were DS particles distributed in the fibers and the DMOG as well as Si ions could be controllably released from the nanopores on the fibers. The in vitro studies demonstrated that the hierarchical nanostructures (nanopores on the aligned fibers) and the controllable released chemical active agents (DMOG drugs and Si ions) from the DS-PL membranes could exert a synergistic effect on inducing the endothelial cell proliferation, migration and differentiation. Above all, the scaffolds distinctly induced the angiogenesis, collagen deposition and re-epithelialization as well as inhibited inflammation reaction in the wound sites, which eventually stimulated the healing of diabetic wounds in vivo. The significance of the current study is that the combination of the hierarchical aligned porous nanofibrous structure with DMOG-loaded MSNs incorporated in electrospun fibers may suggest a high-efficiency strategy for chronic wound healing. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.