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Sample records for rna bases shape

  1. SHAPE selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

    DEFF Research Database (Denmark)

    Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R

    2015-01-01

    transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES...

  2. Investigation of RNA Structure by High-Throughput SHAPE-Based Probing Methods

    DEFF Research Database (Denmark)

    Poulsen, Line Dahl

    of highthroughput SHAPE-based approaches to investigate RNA structure based on novel SHAPE reagents that permit selection of full-length cDNAs. The SHAPE Selection (SHAPES) method is applied to the foot-and-mouth disease virus (FMDV) plus strand RNA genome, and the data is used to construct a genome-wide structural...... that they are functional. The SHAPES method is further applied to the hepatitis C virus (HCV), where the data is used to refine known and predicted structures. Over the past years, the interest of studying RNA structure in their native environment has been increased, and to allow studying RNA structure inside living cells...... using the SHAPE Selection approach, I introduce a biotinylated probing reagent. This chemical can cross cell membranes and reacts with RNA inside the cells, allowing the structural conformations to be studied in the context of physiological relevant conditions in living cells. The methods and results...

  3. Shapes of interacting RNA complexes

    DEFF Research Database (Denmark)

    Fu, Benjamin Mingming; Reidys, Christian

    2014-01-01

    Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops.This shape-projection preserves the topological core of the RNA complex and for fixed topological...... genus there are only finitely many such shapes. Our main result is a new bijection that relates the shapes of RNA complexes with shapes of RNA structures. This allows to compute the shape polynomial of RNA complexes via the shape polynomial of RNA structures. We furthermore present a linear time uniform...... sampling algorithm for shapes of RNA complexes of fixed topological genus....

  4. Complete probabilistic analysis of RNA shapes

    Directory of Open Access Journals (Sweden)

    Voß Björn

    2006-02-01

    Full Text Available Abstract Background Soon after the first algorithms for RNA folding became available, it was recognised that the prediction of only one energetically optimal structure is insufficient to achieve reliable results. An in-depth analysis of the folding space as a whole appeared necessary to deduce the structural properties of a given RNA molecule reliably. Folding space analysis comprises various methods such as suboptimal folding, computation of base pair probabilities, sampling procedures and abstract shape analysis. Common to many approaches is the idea of partitioning the folding space into classes of structures, for which certain properties can be derived. Results In this paper we extend the approach of abstract shape analysis. We show how to compute the accumulated probabilities of all structures that share the same shape. While this implies a complete (non-heuristic analysis of the folding space, the computational effort depends only on the size of the shape space, which is much smaller. This approach has been integrated into the tool RNAshapes, and we apply it to various RNAs. Conclusion Analyses of conformational switches show the existence of two shapes with probabilities approximately 23 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaadaWcaaqaaiabikdaYaqaaiabiodaZaaaaaa@2EA2@ vs. 13 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaadaWcaaqaaiabigdaXaqaaiabiodaZaaaaaa@2EA0@, whereas the analysis of a microRNA precursor reveals one shape with a probability near to 1.0. Furthermore, it is shown that a shape can outperform an energetically more favourable one by

  5. Size, Shape, and Sequence-Dependent Immunogenicity of RNA Nanoparticles.

    Science.gov (United States)

    Guo, Sijin; Li, Hui; Ma, Mengshi; Fu, Jian; Dong, Yizhou; Guo, Peixuan

    2017-12-15

    RNA molecules have emerged as promising therapeutics. Like all other drugs, the safety profile and immune response are important criteria for drug evaluation. However, the literature on RNA immunogenicity has been controversial. Here, we used the approach of RNA nanotechnology to demonstrate that the immune response of RNA nanoparticles is size, shape, and sequence dependent. RNA triangle, square, pentagon, and tetrahedron with same shape but different sizes, or same size but different shapes were used as models to investigate the immune response. The levels of pro-inflammatory cytokines induced by these RNA nanoarchitectures were assessed in macrophage-like cells and animals. It was found that RNA polygons without extension at the vertexes were immune inert. However, when single-stranded RNA with a specific sequence was extended from the vertexes of RNA polygons, strong immune responses were detected. These immunostimulations are sequence specific, because some other extended sequences induced little or no immune response. Additionally, larger-size RNA square induced stronger cytokine secretion. 3D RNA tetrahedron showed stronger immunostimulation than planar RNA triangle. These results suggest that the immunogenicity of RNA nanoparticles is tunable to produce either a minimal immune response that can serve as safe therapeutic vectors, or a strong immune response for cancer immunotherapy or vaccine adjuvants. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Size, Shape, and Sequence-Dependent Immunogenicity of RNA Nanoparticles

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    Sijin Guo

    2017-12-01

    Full Text Available RNA molecules have emerged as promising therapeutics. Like all other drugs, the safety profile and immune response are important criteria for drug evaluation. However, the literature on RNA immunogenicity has been controversial. Here, we used the approach of RNA nanotechnology to demonstrate that the immune response of RNA nanoparticles is size, shape, and sequence dependent. RNA triangle, square, pentagon, and tetrahedron with same shape but different sizes, or same size but different shapes were used as models to investigate the immune response. The levels of pro-inflammatory cytokines induced by these RNA nanoarchitectures were assessed in macrophage-like cells and animals. It was found that RNA polygons without extension at the vertexes were immune inert. However, when single-stranded RNA with a specific sequence was extended from the vertexes of RNA polygons, strong immune responses were detected. These immunostimulations are sequence specific, because some other extended sequences induced little or no immune response. Additionally, larger-size RNA square induced stronger cytokine secretion. 3D RNA tetrahedron showed stronger immunostimulation than planar RNA triangle. These results suggest that the immunogenicity of RNA nanoparticles is tunable to produce either a minimal immune response that can serve as safe therapeutic vectors, or a strong immune response for cancer immunotherapy or vaccine adjuvants.

  7. Mapping RNA Structure In Vitro with SHAPE Chemistry and Next-Generation Sequencing (SHAPE-Seq).

    Science.gov (United States)

    Watters, Kyle E; Lucks, Julius B

    2016-01-01

    Mapping RNA structure with selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry has proven to be a versatile method for characterizing RNA structure in a variety of contexts. SHAPE reagents covalently modify RNAs in a structure-dependent manner to create adducts at the 2'-OH group of the ribose backbone at nucleotides that are structurally flexible. The positions of these adducts are detected using reverse transcriptase (RT) primer extension, which stops one nucleotide before the modification, to create a pool of cDNAs whose lengths reflect the location of SHAPE modification. Quantification of the cDNA pools is used to estimate the "reactivity" of each nucleotide in an RNA molecule to the SHAPE reagent. High reactivities indicate nucleotides that are structurally flexible, while low reactivities indicate nucleotides that are inflexible. These SHAPE reactivities can then be used to infer RNA structures by restraining RNA structure prediction algorithms. Here, we provide a state-of-the-art protocol describing how to perform in vitro RNA structure probing with SHAPE chemistry using next-generation sequencing to quantify cDNA pools and estimate reactivities (SHAPE-Seq). The use of next-generation sequencing allows for higher throughput, more consistent data analysis, and multiplexing capabilities. The technique described herein, SHAPE-Seq v2.0, uses a universal reverse transcription priming site that is ligated to the RNA after SHAPE modification. The introduced priming site allows for the structural analysis of an RNA independent of its sequence.

  8. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

    Science.gov (United States)

    Hajdin, Christine E; Bellaousov, Stanislav; Huggins, Wayne; Leonard, Christopher W; Mathews, David H; Weeks, Kevin M

    2013-04-02

    A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.

  9. Nuclear export of RNA: Different sizes, shapes and functions.

    Science.gov (United States)

    Williams, Tobias; Ngo, Linh H; Wickramasinghe, Vihandha O

    2018-03-01

    Export of protein-coding and non-coding RNA molecules from the nucleus to the cytoplasm is critical for gene expression. This necessitates the continuous transport of RNA species of different size, shape and function through nuclear pore complexes via export receptors and adaptor proteins. Here, we provide an overview of the major RNA export pathways in humans, highlighting the similarities and differences between each. Its importance is underscored by the growing appreciation that deregulation of RNA export pathways is associated with human diseases like cancer. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

  10. antaRNA: ant colony-based RNA sequence design.

    Science.gov (United States)

    Kleinkauf, Robert; Mann, Martin; Backofen, Rolf

    2015-10-01

    RNA sequence design is studied at least as long as the classical folding problem. Although for the latter the functional fold of an RNA molecule is to be found ,: inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology ,: reliable RNA sequence design becomes a crucial step to generate novel biochemical components. In this article ,: the computational tool antaRNA is presented. It is capable of compiling RNA sequences for a given structure that comply in addition with an adjustable full range objective GC-content distribution ,: specific sequence constraints and additional fuzzy structure constraints. antaRNA applies ant colony optimization meta-heuristics and its superior performance is shown on a biological datasets. http://www.bioinf.uni-freiburg.de/Software/antaRNA CONTACT: backofen@informatik.uni-freiburg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  11. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.

    Science.gov (United States)

    Watters, Kyle E; Abbott, Timothy R; Lucks, Julius B

    2016-01-29

    Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure-function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA-RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA-RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Advanced Design of Dumbbell-shaped Genetic Minimal Vectors Improves Non-coding and Coding RNA Expression.

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    Jiang, Xiaoou; Yu, Han; Teo, Cui Rong; Tan, Genim Siu Xian; Goh, Sok Chin; Patel, Parasvi; Chua, Yiqiang Kevin; Hameed, Nasirah Banu Sahul; Bertoletti, Antonio; Patzel, Volker

    2016-09-01

    Dumbbell-shaped DNA minimal vectors lacking nontherapeutic genes and bacterial sequences are considered a stable, safe alternative to viral, nonviral, and naked plasmid-based gene-transfer systems. We investigated novel molecular features of dumbbell vectors aiming to reduce vector size and to improve the expression of noncoding or coding RNA. We minimized small hairpin RNA (shRNA) or microRNA (miRNA) expressing dumbbell vectors in size down to 130 bp generating the smallest genetic expression vectors reported. This was achieved by using a minimal H1 promoter with integrated transcriptional terminator transcribing the RNA hairpin structure around the dumbbell loop. Such vectors were generated with high conversion yields using a novel protocol. Minimized shRNA-expressing dumbbells showed accelerated kinetics of delivery and transcription leading to enhanced gene silencing in human tissue culture cells. In primary human T cells, minimized miRNA-expressing dumbbells revealed higher stability and triggered stronger target gene suppression as compared with plasmids and miRNA mimics. Dumbbell-driven gene expression was enhanced up to 56- or 160-fold by implementation of an intron and the SV40 enhancer compared with control dumbbells or plasmids. Advanced dumbbell vectors may represent one option to close the gap between durable expression that is achievable with integrating viral vectors and short-term effects triggered by naked RNA.

  13. Reductively Responsive Hydrogel Nanoparticles with Uniform Size, Shape, and Tunable Composition for Systemic siRNA Delivery in Vivo.

    Science.gov (United States)

    Ma, Da; Tian, Shaomin; Baryza, Jeremy; Luft, J Christopher; DeSimone, Joseph M

    2015-10-05

    To achieve the great potential of siRNA based gene therapy, safe and efficient systemic delivery in vivo is essential. Here we report reductively responsive hydrogel nanoparticles with highly uniform size and shape for systemic siRNA delivery in vivo. "Blank" hydrogel nanoparticles with high aspect ratio were prepared using continuous particle fabrication based on PRINT (particle replication in nonwetting templates). Subsequently, siRNA was conjugated to "blank" nanoparticles via a disulfide linker with a high loading ratio of up to 18 wt %, followed by surface modification to enhance transfection. This fabrication process could be easily scaled up to prepare large quantity of hydrogel nanoparticles. By controlling hydrogel composition, surface modification, and siRNA loading ratio, siRNA conjugated nanoparticles were highly tunable to achieve high transfection efficiency in vitro. FVII-siRNA conjugated nanoparticles were further stabilized with surface coating for in vivo siRNA delivery to liver hepatocytes, and successful gene silencing was demonstrated at both mRNA and protein levels.

  14. Density-Based 3D Shape Descriptors

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    Schmitt Francis

    2007-01-01

    Full Text Available We propose a novel probabilistic framework for the extraction of density-based 3D shape descriptors using kernel density estimation. Our descriptors are derived from the probability density functions (pdf of local surface features characterizing the 3D object geometry. Assuming that the shape of the 3D object is represented as a mesh consisting of triangles with arbitrary size and shape, we provide efficient means to approximate the moments of geometric features on a triangle basis. Our framework produces a number of 3D shape descriptors that prove to be quite discriminative in retrieval applications. We test our descriptors and compare them with several other histogram-based methods on two 3D model databases, Princeton Shape Benchmark and Sculpteur, which are fundamentally different in semantic content and mesh quality. Experimental results show that our methodology not only improves the performance of existing descriptors, but also provides a rigorous framework to advance and to test new ones.

  15. RNA-based therapies for genodermatoses

    NARCIS (Netherlands)

    Bornert, Olivier; Peking, Patricia; Bremer, Jeroen; Koller, Ulrich; van den Akker, Peter C.; Aartsma-Rus, Annemieke; Pasmooij, Anna M. G.; Murauer, Eva M.; Nystroem, Alexander

    Genetic disorders affecting the skin, genodermatoses, constitute a large and heterogeneous group of diseases, for which treatment is generally limited to management of symptoms. RNA-based therapies are emerging as a powerful tool to treat genodermatoses. In this review, we discuss in detail RNA

  16. Ordinal-Measure Based Shape Correspondence

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    Faouzi Alaya Cheikh

    2002-04-01

    Full Text Available We present a novel approach to shape similarity estimation based on distance transformation and ordinal correlation. The proposed method operates in three steps: object alignment, contour to multilevel image transformation, and similarity evaluation. This approach is suitable for use in shape classification, content-based image retrieval and performance evaluation of segmentation algorithms. The two latter applications are addressed in this papers. Simulation results show that in both applications our proposed measure performs quite well in quantifying shape similarity. The scores obtained using this technique reflect well the correspondence between object contours as humans perceive it.

  17. Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile, and accurate RNA structure analysis

    Science.gov (United States)

    Smola, Matthew J.; Rice, Greggory M.; Busan, Steven; Siegfried, Nathan A.; Weeks, Kevin M.

    2016-01-01

    SHAPE chemistries exploit small electrophilic reagents that react with the 2′-hydroxyl group to interrogate RNA structure at single-nucleotide resolution. Mutational profiling (MaP) identifies modified residues based on the ability of reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing. The SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as for simple model RNAs. This protocol describes the experimental steps, implemented over three days, required to perform SHAPE probing and construct multiplexed SHAPE-MaP libraries suitable for deep sequencing. These steps include RNA folding and SHAPE structure probing, mutational profiling by reverse transcription, library construction, and sequencing. Automated processing of MaP sequencing data is accomplished using two software packages. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides useful troubleshooting information, often within an hour. SuperFold uses these data to model RNA secondary structures, identify regions with well-defined structures, and visualize probable and alternative helices, often in under a day. We illustrate these algorithms with the E. coli thiamine pyrophosphate riboswitch, E. coli 16S rRNA, and HIV-1 genomic RNAs. SHAPE-MaP can be used to make nucleotide-resolution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles, and entire transcriptomes. The straightforward MaP strategy greatly expands the number, length, and complexity of analyzable RNA structures. PMID:26426499

  18. Skeleton-based Hierarchical Shape Segmentation

    NARCIS (Netherlands)

    Reniers, Dennie; Telea, Alexandru

    2007-01-01

    We present an effective framework for segmenting 3D shapes into meaningful components using the curve skeleton. Our algorithm identifies a number of critical points on the curve skeleton, either fully automatically as the junctions of the curve skeleton, or based on user input. We use these points

  19. Exemplar Based Recognition of Visual Shapes

    DEFF Research Database (Denmark)

    Olsen, Søren I.

    2005-01-01

    This paper presents an approach of visual shape recognition based on exemplars of attributed keypoints. Training is performed by storing exemplars of keypoints detected in labeled training images. Recognition is made by keypoint matching and voting according to the labels for the matched keypoint....... The matching is insensitive to rotations, limited scalings and small deformations. The recognition is robust to noise, background clutter and partial occlusion. Recognition is possible from few training images and improve with the number of training images.......This paper presents an approach of visual shape recognition based on exemplars of attributed keypoints. Training is performed by storing exemplars of keypoints detected in labeled training images. Recognition is made by keypoint matching and voting according to the labels for the matched keypoints...

  20. A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA-based regulation of viral processes.

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    Baodong Wu

    2009-03-01

    Full Text Available Plus-strand RNA viruses contain RNA elements within their genomes that mediate a variety of fundamental viral processes. The traditional view of these elements is that of local RNA structures. This perspective, however, is changing due to increasing discoveries of functional viral RNA elements that are formed by long-range RNA-RNA interactions, often spanning thousands of nucleotides. The plus-strand RNA genomes of tombusviruses exemplify this concept by possessing different long-range RNA-RNA interactions that regulate both viral translation and transcription. Here we report that a third fundamental tombusvirus process, viral genome replication, requires a long-range RNA-based interaction spanning approximately 3000 nts. In vivo and in vitro analyses suggest that the discontinuous RNA platform formed by the interaction facilitates efficient assembly of the viral RNA replicase. This finding has allowed us to build an integrated model for the role of global RNA structure in regulating the reproduction of a eukaryotic RNA virus, and the insights gained have extended our understanding of the multifunctional nature of viral RNA genomes.

  1. Atomic Force Microscopy Based Cell Shape Index

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    Adia-Nimuwa, Usienemfon; Mujdat Tiryaki, Volkan; Hartz, Steven; Xie, Kan; Ayres, Virginia

    2013-03-01

    Stellation is a measure of cell physiology and pathology for several cell groups including neural, liver and pancreatic cells. In the present work, we compare the results of a conventional two-dimensional shape index study of both atomic force microscopy (AFM) and fluorescent microscopy images with the results obtained using a new three-dimensional AFM-based shape index similar to sphericity index. The stellation of astrocytes is investigated on nanofibrillar scaffolds composed of electrospun polyamide nanofibers that has demonstrated promise for central nervous system (CNS) repair. Recent work by our group has given us the ability to clearly segment the cells from nanofibrillar scaffolds in AFM images. The clear-featured AFM images indicated that the astrocyte processes were longer than previously identified at 24h. It was furthermore shown that cell spreading could vary significantly as a function of environmental parameters, and that AFM images could record these variations. The new three-dimensional AFM-based shape index incorporates the new information: longer stellate processes and cell spreading. The support of NSF PHY-095776 is acknowledged.

  2. Shielding the messenger (RNA): microRNA-based anticancer therapies

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    Sotillo, Elena; Thomas-Tikhonenko, Andrei

    2011-01-01

    It has been a decade since scientists realized that microRNAs (miRNAs) are not an oddity invented by worms to regulate gene expression at post-transcriptional levels. Rather, many of these 21–22-nucleotide-short RNAs exist in invertebrates and vertebrates alike and some of them are in fact highly conserved. miRNAs are now recognized as an important class of non-coding small RNAs that inhibit gene expression by targeting mRNA stability and translation. In the last ten years, our knowledge of the miRNAs world was expanding at vertiginous speed, propelled by the development of computational engines for miRNA identification and target prediction, biochemical tools and techniques to modulate miRNA activity, and last but not least, the emergence of miRNA-centric animal models. One important conclusion that has emerged from this effort is that many microRNAs and their cognate targets are strongly implicated in cancer, either as oncogenes or tumor and metastasis suppressors. In this review we will discuss the diverse role that miRNAs play in cancer initiation and progression and also the tools with which miRNA expression could be corrected in vivo. While the idea of targeting microRNAs towards therapeutic ends is getting considerable traction, basic, translational, and clinical research done in the next few years will tell whether this promise is well-founded. PMID:21514318

  3. Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins

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    de Beauchene, Isaure Chauvot; de Vries, Sjoerd J.; Zacharias, Martin

    2016-01-01

    Abstract Protein-RNA complexes are important for many biological processes. However, structural modeling of such complexes is hampered by the high flexibility of RNA. Particularly challenging is the docking of single-stranded RNA (ssRNA). We have developed a fragment-based approach to model the structure of ssRNA bound to a protein, based on only the protein structure, the RNA sequence and conserved contacts. The conformational diversity of each RNA fragment is sampled by an exhaustive library of trinucleotides extracted from all known experimental protein–RNA complexes. The method was applied to ssRNA with up to 12 nucleotides which bind to dimers of the RNA recognition motifs (RRMs), a highly abundant eukaryotic RNA-binding domain. The fragment based docking allows a precise de novo atomic modeling of protein-bound ssRNA chains. On a benchmark of seven experimental ssRNA–RRM complexes, near-native models (with a mean heavy-atom deviation of <3 Å from experiment) were generated for six out of seven bound RNA chains, and even more precise models (deviation < 2 Å) were obtained for five out of seven cases, a significant improvement compared to the state of the art. The method is not restricted to RRMs but was also successfully applied to Pumilio RNA binding proteins. PMID:27131381

  4. iDoRNA: An Interacting Domain-based Tool for Designing RNA-RNA Interaction Systems

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    Jittrawan Thaiprasit

    2016-03-01

    Full Text Available RNA-RNA interactions play a crucial role in gene regulation in living organisms. They have gained increasing interest in the field of synthetic biology because of their potential applications in medicine and biotechnology. However, few novel regulators based on RNA-RNA interactions with desired structures and functions have been developed due to the challenges of developing design tools. Recently, we proposed a novel tool, called iDoDe, for designing RNA-RNA interacting sequences by first decomposing RNA structures into interacting domains and then designing each domain using a stochastic algorithm. However, iDoDe did not provide an optimal solution because it still lacks a mechanism to optimize the design. In this work, we have further developed the tool by incorporating a genetic algorithm (GA to find an RNA solution with maximized structural similarity and minimized hybridized RNA energy, and renamed the tool iDoRNA. A set of suitable parameters for the genetic algorithm were determined and found to be a weighting factor of 0.7, a crossover rate of 0.9, a mutation rate of 0.1, and the number of individuals per population set to 8. We demonstrated the performance of iDoRNA in comparison with iDoDe by using six RNA-RNA interaction models. It was found that iDoRNA could efficiently generate all models of interacting RNAs with far more accuracy and required far less computational time than iDoDe. Moreover, we compared the design performance of our tool against existing design tools using forty-four RNA-RNA interaction models. The results showed that the performance of iDoRNA is better than RiboMaker when considering the ensemble defect, the fitness score and computation time usage. However, it appears that iDoRNA is outperformed by NUPACK and RNAiFold 2.0 when considering the ensemble defect. Nevertheless, iDoRNA can still be an useful alternative tool for designing novel RNA-RNA interactions in synthetic biology research. The source code of iDoRNA

  5. Fluidic-Based Virtual Aerosurface Shaping

    National Research Council Canada - National Science Library

    Glezer, Ari

    2004-01-01

    Recent work on a novel approach to the control of the aerodynamic performance of lifting surfaces by fluidic modification of their apparent aerodynamic shape, or virtual aerosurface shaping is reviewed...

  6. RNA-Based Vaccines in Cancer Immunotherapy

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    Megan A. McNamara

    2015-01-01

    Full Text Available RNA vaccines traditionally consist of messenger RNA synthesized by in vitro transcription using a bacteriophage RNA polymerase and template DNA that encodes the antigen(s of interest. Once administered and internalized by host cells, the mRNA transcripts are translated directly in the cytoplasm and then the resulting antigens are presented to antigen presenting cells to stimulate an immune response. Alternatively, dendritic cells can be loaded with either tumor associated antigen mRNA or total tumor RNA and delivered to the host to elicit a specific immune response. In this review, we will explain why RNA vaccines represent an attractive platform for cancer immunotherapy, discuss modifications to RNA structure that have been developed to optimize mRNA vaccine stability and translational efficiency, and describe strategies for nonviral delivery of mRNA vaccines, highlighting key preclinical and clinical data related to cancer immunotherapy.

  7. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.

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    Kevin A Wilkinson

    2008-04-01

    Full Text Available Replication and pathogenesis of the human immunodeficiency virus (HIV is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone flexibility at single-nucleotide resolution and from which robust structural information can be immediately derived. We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles. Remarkably, given the large number of plausible local structures, the first 10% of the HIV-1 genome exists in a single, predominant conformation in all four states. We also discover that noncoding regions functioning in a regulatory role have significantly lower (p-value < 0.0001 SHAPE reactivities, and hence more structure, than do viral coding regions that function as the template for protein synthesis. By directly monitoring protein binding inside virions, we identify the RNA recognition motif for the viral nucleocapsid protein. Seven structurally homologous binding sites occur in a well-defined domain in the genome, consistent with a role in directing specific packaging of genomic RNA into nascent virions. In addition, we identify two distinct motifs that are targets for the duplex destabilizing activity of this same protein. The nucleocapsid protein destabilizes local HIV-1 RNA structure in ways likely to facilitate initial movement both of the retroviral reverse transcriptase from its tRNA primer and of the ribosome in coding regions. Each of the three nucleocapsid interaction motifs falls in a specific genome domain, indicating that local protein interactions can be organized by the long-range architecture of an RNA. High-throughput SHAPE reveals a comprehensive view of HIV-1 RNA genome structure, and further

  8. siRNA delivery with lipid-based systems

    DEFF Research Database (Denmark)

    Foged, Camilla

    2012-01-01

    A key hurdle for the further development of RNA interference (RNAi) therapeutics like small interfering RNA (siRNA) is their safe and effective delivery. Lipids are promising and versatile carriers because they are based on Nature's own building blocks and can be provided with properties which......RNA into more hydrophobic lipoplexes, which promote passage of the siRNA across cellular membrane barriers, especially when lipids are added that facilitate membrane fusion. Despite these attractive features, siRNA delivery vehicles are facing a number of challenges such as the limited delivery efficiency...

  9. Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species.

    Science.gov (United States)

    Di Giallonardo, Francesca; Schlub, Timothy E; Shi, Mang; Holmes, Edward C

    2017-04-15

    Viruses use the cellular machinery of their hosts for replication. It has therefore been proposed that the nucleotide and dinucleotide compositions of viruses should match those of their host species. If this is upheld, it may then be possible to use dinucleotide composition to predict the true host species of viruses sampled in metagenomic surveys. However, it is also clear that different taxonomic groups of viruses tend to have distinctive patterns of dinucleotide composition that may be independent of host species. To determine the relative strength of the effect of host versus virus family in shaping dinucleotide composition, we performed a comparative analysis of 20 RNA virus families from 15 host groupings, spanning two animal phyla and more than 900 virus species. In particular, we determined the odds ratios for the 16 possible dinucleotides and performed a discriminant analysis to evaluate the capability of virus dinucleotide composition to predict the correct virus family or host taxon from which it was isolated. Notably, while 81% of the data analyzed here were predicted to the correct virus family, only 62% of these data were predicted to their correct subphylum/class host and a mere 32% to their correct mammalian order. Similarly, dinucleotide composition has a weak predictive power for different hosts within individual virus families. We therefore conclude that dinucleotide composition is generally uniform within a virus family but less well reflects that of its host species. This has obvious implications for attempts to accurately predict host species from virus genome sequences alone. IMPORTANCE Determining the processes that shape virus genomes is central to understanding virus evolution and emergence. One question of particular importance is why nucleotide and dinucleotide frequencies differ so markedly between viruses. In particular, it is currently unclear whether host species or virus family has the biggest impact on dinucleotide frequencies and

  10. The European Regulatory Environment of RNA-Based Vaccines.

    Science.gov (United States)

    Hinz, Thomas; Kallen, Kajo; Britten, Cedrik M; Flamion, Bruno; Granzer, Ulrich; Hoos, Axel; Huber, Christoph; Khleif, Samir; Kreiter, Sebastian; Rammensee, Hans-Georg; Sahin, Ugur; Singh-Jasuja, Harpreet; Türeci, Özlem; Kalinke, Ulrich

    2017-01-01

    A variety of different mRNA-based drugs are currently in development. This became possible, since major breakthroughs in RNA research during the last decades allowed impressive improvements of translation, stability and delivery of mRNA. This article focuses on antigen-encoding RNA-based vaccines that are either directed against tumors or pathogens. mRNA-encoded vaccines are developed both for preventive or therapeutic purposes. Most mRNA-based vaccines are directly administered to patients. Alternatively, primary autologous cells from cancer patients are modified ex vivo by the use of mRNA and then are adoptively transferred to patients. In the EU no regulatory guidelines presently exist that specifically address mRNA-based vaccines. The existing regulatory framework, however, clearly defines that mRNA-based vaccines in most cases have to be centrally approved. Interestingly, depending on whether RNA-based vaccines are directed against tumors or infectious disease, they are formally considered gene therapy products or not, respectively. Besides an overview on the current clinical use of mRNA vaccines in various therapeutic areas a detailed discussion of the current regulatory situation is provided and regulatory perspectives are discussed.

  11. Blocking of Goal-Location Learning Based on Shape

    Science.gov (United States)

    Alexander, Tim; Wilson, Stuart P.; Wilson, Paul N.

    2009-01-01

    Using desktop, computer-simulated virtual environments (VEs), the authors conducted 5 experiments to investigate blocking of learning about a goal location based on Shape B as a consequence of preliminary training to locate that goal using Shape A. The shapes were large 2-dimensional horizontal figures on the ground. Blocking of spatial learning…

  12. A probabilistic model for component-based shape synthesis

    KAUST Repository

    Kalogerakis, Evangelos

    2012-07-01

    We present an approach to synthesizing shapes from complex domains, by identifying new plausible combinations of components from existing shapes. Our primary contribution is a new generative model of component-based shape structure. The model represents probabilistic relationships between properties of shape components, and relates them to learned underlying causes of structural variability within the domain. These causes are treated as latent variables, leading to a compact representation that can be effectively learned without supervision from a set of compatibly segmented shapes. We evaluate the model on a number of shape datasets with complex structural variability and demonstrate its application to amplification of shape databases and to interactive shape synthesis. © 2012 ACM 0730-0301/2012/08-ART55.

  13. Histological image classification using biologically interpretable shape-based features

    International Nuclear Information System (INIS)

    Kothari, Sonal; Phan, John H; Young, Andrew N; Wang, May D

    2013-01-01

    Automatic cancer diagnostic systems based on histological image classification are important for improving therapeutic decisions. Previous studies propose textural and morphological features for such systems. These features capture patterns in histological images that are useful for both cancer grading and subtyping. However, because many of these features lack a clear biological interpretation, pathologists may be reluctant to adopt these features for clinical diagnosis. We examine the utility of biologically interpretable shape-based features for classification of histological renal tumor images. Using Fourier shape descriptors, we extract shape-based features that capture the distribution of stain-enhanced cellular and tissue structures in each image and evaluate these features using a multi-class prediction model. We compare the predictive performance of the shape-based diagnostic model to that of traditional models, i.e., using textural, morphological and topological features. The shape-based model, with an average accuracy of 77%, outperforms or complements traditional models. We identify the most informative shapes for each renal tumor subtype from the top-selected features. Results suggest that these shapes are not only accurate diagnostic features, but also correlate with known biological characteristics of renal tumors. Shape-based analysis of histological renal tumor images accurately classifies disease subtypes and reveals biologically insightful discriminatory features. This method for shape-based analysis can be extended to other histological datasets to aid pathologists in diagnostic and therapeutic decisions

  14. Morphing-Based Shape Optimization in Computational Fluid Dynamics

    Science.gov (United States)

    Rousseau, Yannick; Men'Shov, Igor; Nakamura, Yoshiaki

    In this paper, a Morphing-based Shape Optimization (MbSO) technique is presented for solving Optimum-Shape Design (OSD) problems in Computational Fluid Dynamics (CFD). The proposed method couples Free-Form Deformation (FFD) and Evolutionary Computation, and, as its name suggests, relies on the morphing of shape and computational domain, rather than direct shape parameterization. Advantages of the FFD approach compared to traditional parameterization are first discussed. Then, examples of shape and grid deformations by FFD are presented. Finally, the MbSO approach is illustrated and applied through an example: the design of an airfoil for a future Mars exploration airplane.

  15. Nanoscale magnetic ratchets based on shape anisotropy

    Science.gov (United States)

    Cui, Jizhai; Keller, Scott M.; Liang, Cheng-Yen; Carman, Gregory P.; Lynch, Christopher S.

    2017-02-01

    Controlling magnetization using piezoelectric strain through the magnetoelectric effect offers several orders of magnitude reduction in energy consumption for spintronic applications. However strain is a uniaxial effect and, unlike directional magnetic field or spin-polarized current, cannot induce a full 180° reorientation of the magnetization vector when acting alone. We have engineered novel ‘peanut’ and ‘cat-eye’ shaped nanomagnets on piezoelectric substrates that undergo repeated deterministic 180° magnetization rotations in response to individual electric-field-induced strain pulses by breaking the uniaxial symmetry using shape anisotropy. This behavior can be likened to a magnetic ratchet, advancing magnetization clockwise with each piezostrain trigger. The results were validated using micromagnetics implemented in a multiphysics finite elements code to simulate the engineered spatial and temporal magnetic behavior. The engineering principles start from a target device function and proceed to the identification of shapes that produce the desired function. This approach opens a broad design space for next generation magnetoelectric spintronic devices.

  16. [In silico CRISPR-based sgRNA design].

    Science.gov (United States)

    Wang, Yuanli; Chuai, Guohui; Yan, Jifang; Shi, Lei; Liu, Qi

    2017-10-25

    CRISPR-based genome editing has been widely implemented in various cell types. In-silico single guide RNA (sgRNA) design is a key step for successful gene editing using CRISPR system. Continuing efforts are made to refine in-silico sgRNA design with high on-target efficacy and reduced off-target effects. In this paper, we summarize the present sgRNA design tools, and show that efficient in-silico models can be built that integrate current heterogeneous genome-editing data to derive unbiased sgRNA design rules and identify key features for improving sgRNA design. Our review shows that systematic comparisons and evaluation of on-target and off-target effects of sgRNA will allow more precise genome editing and gene therapies using the CRISPR system.

  17. Performance-based shape optimization of continuum structures

    International Nuclear Information System (INIS)

    Liang Qingquan

    2010-01-01

    This paper presents a performance-based optimization (PBO) method for optimal shape design of continuum structures with stiffness constraints. Performance-based design concepts are incorporated in the shape optimization theory to achieve optimal designs. In the PBO method, the traditional shape optimization problem of minimizing the weight of a continuum structure with displacement or mean compliance constraints is transformed to the problem of maximizing the performance of the structure. The optimal shape of a continuum structure is obtained by gradually eliminating inefficient finite elements from the structure until its performance is maximized. Performance indices are employed to monitor the performance of optimized shapes in an optimization process. Performance-based optimality criteria are incorporated in the PBO method to identify the optimum from the optimization process. The PBO method is used to produce optimal shapes of plane stress continuum structures and plates in bending. Benchmark numerical results are provided to demonstrate the effectiveness of the PBO method for generating the maximum stiffness shape design of continuum structures. It is shown that the PBO method developed overcomes the limitations of traditional shape optimization methods in optimal design of continuum structures. Performance-based optimality criteria presented can be incorporated in any shape and topology optimization methods to obtain optimal designs of continuum structures.

  18. Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

    Science.gov (United States)

    Frenkel-Morgenstern, Milana; Lacroix, Vincent; Ezkurdia, Iakes; Levin, Yishai; Gabashvili, Alexandra; Prilusky, Jaime; del Pozo, Angela; Tress, Michael; Johnson, Rory; Guigo, Roderic; Valencia, Alfonso

    2012-01-01

    Chimeric RNAs comprise exons from two or more different genes and have the potential to encode novel proteins that alter cellular phenotypes. To date, numerous putative chimeric transcripts have been identified among the ESTs isolated from several organisms and using high throughput RNA sequencing. The few corresponding protein products that have been characterized mostly result from chromosomal translocations and are associated with cancer. Here, we systematically establish that some of the putative chimeric transcripts are genuinely expressed in human cells. Using high throughput RNA sequencing, mass spectrometry experimental data, and functional annotation, we studied 7424 putative human chimeric RNAs. We confirmed the expression of 175 chimeric RNAs in 16 human tissues, with an abundance varying from 0.06 to 17 RPKM (Reads Per Kilobase per Million mapped reads). We show that these chimeric RNAs are significantly more tissue-specific than non-chimeric transcripts. Moreover, we present evidence that chimeras tend to incorporate highly expressed genes. Despite the low expression level of most chimeric RNAs, we show that 12 novel chimeras are translated into proteins detectable in multiple shotgun mass spectrometry experiments. Furthermore, we confirm the expression of three novel chimeric proteins using targeted mass spectrometry. Finally, based on our functional annotation of exon organization and preserved domains, we discuss the potential features of chimeric proteins with illustrative examples and suggest that chimeras significantly exploit signal peptides and transmembrane domains, which can alter the cellular localization of cognate proteins. Taken together, these findings establish that some chimeric RNAs are translated into potentially functional proteins in humans. PMID:22588898

  19. dsRNA silencing of an R2R3-MYB transcription factor affects flower cell shape in a Dendrobium hybrid.

    Science.gov (United States)

    Lau, Su-Ee; Schwarzacher, Trude; Othman, Rofina Yasmin; Harikrishna, Jennifer Ann

    2015-08-11

    The R2R3-MYB genes regulate pigmentation and morphogenesis of flowers, including flower and cell shape, and therefore have importance in the development of new varieties of orchids. However, new variety development is limited by the long breeding time required in orchids. In this study, we identified a cDNA, DhMYB1, that is expressed during flower development in a hybrid orchid, Dendrobium hybrida (Dendrobium bobby messina X Dendrobium chao phraya) then used the direct application of dsRNA to observe the effect of gene silencing on flower phenotype and floral epidermal cell shape. Flower bud development in the Dendrobium hybrid was characterised into seven stages and the time of meiosis was determined as between stages 3 to 5 when the bud is approximately half of the mature size. Scanning electron microscopy characterisation of adaxial epidermal cells of the flower perianth, showed that the petals and sepals each are divided into two distinct domains based on cell shape and size, while the labellum comprises seven domains. Thirty-two partial cDNA fragments representing R2R3-MYB gene sequences were isolated from D. hybrida. Phylogenetic analysis revealed that nine of the translated sequences were clustered with MYB sequences that are known to be involved in cell shape development and from these, DhMYB1 was selected for full length cDNA cloning and functional study. Direct application of a 430 bp dsRNA from the 3' region of DhMYB1 to emerging orchid flower buds reduced expression of DhMYB1 RNA compared with untreated control. Scanning electron microscopy of adaxial epidermal cells within domain one of the labellum of flowers treated with DhMYB1 dsRNA showed flattened epidermal cells whilst those of control flowers were conical. DhMYB1 is expressed throughout flower bud development and is involved in the development of the conical cell shape of the epidermal cells of the Dendrobium hybrida flower labellum. The direct application of dsRNA changed the phenotype of

  20. RNA.

    Science.gov (United States)

    Darnell, James E., Jr.

    1985-01-01

    Ribonucleic acid (RNA) converts genetic information into protein and usually must be processed to serve its function. RNA types, chemical structure, protein synthesis, translation, manufacture, and processing are discussed. Concludes that the first genes might have been spliced RNA and that humans might be closer than bacteria to primitive…

  1. Shape and Texture Based Classification of Fish Species

    DEFF Research Database (Denmark)

    Larsen, Rasmus; Ólafsdóttir, Hildur; Ersbøll, Bjarne Kjær

    2009-01-01

    In this paper we conduct a case study of ¯sh species classi- fication based on shape and texture. We consider three fish species: cod, haddock, and whiting. We derive shape and texture features from an appearance model of a set of training data. The fish in the training images were manual outlined......, and a few features including the eye and backbone contour were also annotated. From these annotations an optimal MDL curve correspondence and a subsequent image registration were derived. We have analyzed a series of shape and texture and combined shape and texture modes of variation for their ability...

  2. Shape recovery characteristics of biaxially prestrained Fe-Mn-Si-based shape memory alloy

    International Nuclear Information System (INIS)

    Wada, M.; Naoi, H.; Yasuda, H.; Maruyama, T.

    2008-01-01

    Fe-Mn-Si-based shape memory alloy has already been used practically for steel pipe joints. In most of the applications including the steel pipe joints, it is possible to estimate the reduction of diameter from the experimental data of the shape recovery after uniaxial stretching of the alloy materials. However, studies on shape recovery effects after biaxial stretching are important for the extensive applications of the alloy. In this study, we investigated the shape recovery strain after uniaxial and biaxial stretching and the microstructures of the alloy in order to see the effects of uniaxial and biaxial prestrain on the stress-induced martensitic transformation. Amounts of shape recovery strain in the biaxially prestrained specimens are smaller than those in the uniaxially prestrained specimens. Transmission electron microscopy revealed that reverse transformations of stress-induced martensitic ε-phase are prevented by slip bands formed at the same time in the biaxially prestrained specimens, but not in the uniaxially prestrained specimens. The technological data and interpretations presented in this study should be useful in forming design guidelines for promoting the extensive applications of Fe-Mn-Si-based shape memory alloy

  3. Airfoil Shape Optimization based on Surrogate Model

    Science.gov (United States)

    Mukesh, R.; Lingadurai, K.; Selvakumar, U.

    2018-02-01

    Engineering design problems always require enormous amount of real-time experiments and computational simulations in order to assess and ensure the design objectives of the problems subject to various constraints. In most of the cases, the computational resources and time required per simulation are large. In certain cases like sensitivity analysis, design optimisation etc where thousands and millions of simulations have to be carried out, it leads to have a life time of difficulty for designers. Nowadays approximation models, otherwise called as surrogate models (SM), are more widely employed in order to reduce the requirement of computational resources and time in analysing various engineering systems. Various approaches such as Kriging, neural networks, polynomials, Gaussian processes etc are used to construct the approximation models. The primary intention of this work is to employ the k-fold cross validation approach to study and evaluate the influence of various theoretical variogram models on the accuracy of the surrogate model construction. Ordinary Kriging and design of experiments (DOE) approaches are used to construct the SMs by approximating panel and viscous solution algorithms which are primarily used to solve the flow around airfoils and aircraft wings. The method of coupling the SMs with a suitable optimisation scheme to carryout an aerodynamic design optimisation process for airfoil shapes is also discussed.

  4. General enumeration of RNA secondary structures based on new ...

    African Journals Online (AJOL)

    akpobome

    coding, transferring and retrieving genetic information, and in directing cell metabolism. The nucleic acid includes DNA and RNA molecule. RNA molecule is a single-stranded nucleic acid of four different kinds of nucleotides. The four nucleotides only differ by one part, called bases. Hence, one usually identifies nucleotides.

  5. Molecular Beacon-Based MicroRNA Imaging During Neurogenesis.

    Science.gov (United States)

    Lee, Jonghwan; Kim, Soonhag

    2016-01-01

    The fluorescence monitoring system for examining endogenous microRNA (miRNA) activity in cellular level provides crucial information on not only understanding a critical role of miRNA involving a variety of biological processes, but also evaluating miRNA expression patterns in a noninvasive manner. In this protocol, we report the details of a new procedure for a molecular beacon-based miRNA monitoring system, which includes the illustration scheme for miRNA detection strategy, exogenous miRNA detection, and measurement of endogenous miRNA expression level during neurogenesis. The fluorescence signal of miR-124a beacon quenched by BHQ2 was gradually recovered as increasing concentration of the miR-124a in tube. The functional work of miR-124a beacon was examined in intracellular environment, allowing for the internalization of the miR-124a beacon by lipofectamine, which resulted in activated fluorescent signals of the miR-124a beacon in the HeLa cells after the addition of synthetic miR-124a. The endogenous miR-124a expression level was detected by miR-124a beacon system during neurogenesis, showing brighter fluorescence intensity in cytoplasmic area of P19 cells after induction of neuronal differentiation by retinoic acid. The molecular beacon based-miRNA detection technique could be applicable to the simultaneous visualization of a variety of miRNA expression patterns using different fluorescence dyes. For the study of examining endogenous miRNA expression level using miRNA-beacon system, if cellular differentiation step is already prepared, transfection step of miR-124a beacon into P19 cells, and acquisition of activated fluorescence signal measured by confocal microscope can be conducted approximately within 6 h.

  6. 3D Printed Photoresponsive Devices Based on Shape Memory Composites.

    Science.gov (United States)

    Yang, Hui; Leow, Wan Ru; Wang, Ting; Wang, Juan; Yu, Jiancan; He, Ke; Qi, Dianpeng; Wan, Changjin; Chen, Xiaodong

    2017-09-01

    Compared with traditional stimuli-responsive devices with simple planar or tubular geometries, 3D printed stimuli-responsive devices not only intimately meet the requirement of complicated shapes at macrolevel but also satisfy various conformation changes triggered by external stimuli at the microscopic scale. However, their development is limited by the lack of 3D printing functional materials. This paper demonstrates the 3D printing of photoresponsive shape memory devices through combining fused deposition modeling printing technology and photoresponsive shape memory composites based on shape memory polymers and carbon black with high photothermal conversion efficiency. External illumination triggers the shape recovery of 3D printed devices from the temporary shape to the original shape. The effect of materials thickness and light density on the shape memory behavior of 3D printed devices is quantified and calculated. Remarkably, sunlight also triggers the shape memory behavior of these 3D printed devices. This facile printing strategy would provide tremendous opportunities for the design and fabrication of biomimetic smart devices and soft robotics. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. A simple and robust vector-based shRNA expression system used for RNA interference.

    Science.gov (United States)

    Wang, Xue-jun; Li, Ying; Huang, Hai; Zhang, Xiu-juan; Xie, Pei-wen; Hu, Wei; Li, Dan-dan; Wang, Sheng-qi

    2013-01-01

    RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful genetic tool for conducting functional studies. Previously, vector-based shRNA-expression strategies capable of inducing RNAi in viable cells have been developed, however, these vector systems have some disadvantages, either because they were error-prone or cost prohibitive. In this report we described the development of a simple, robust shRNA expression system utilizing 1 long oligonucleotide or 2 short oligonucleotides for half the cost of conventional shRNA construction methods and with a >95% cloning success rate. The shRNA loop sequence and stem structure were also compared and carefully selected for better RNAi efficiency. Furthermore, an easier strategy was developed based on isocaudomers which permit rapid combination of the most efficient promoter-shRNA cassettes. Finally, using this method, the conservative target sites for hepatitis B virus (HBV) knockdown were systemically screened and HBV antigen expression shown to be successfully suppressed in the presence of connected multiple shRNAs both in vitro and in vivo. This novel design describes an inexpensive and effective way to clone and express single or multiple shRNAs from the same vector with the capacity for potent and effective silencing of target genes.

  8. A simple and robust vector-based shRNA expression system used for RNA interference.

    Directory of Open Access Journals (Sweden)

    Xue-jun Wang

    Full Text Available BACKGROUND: RNA interference (RNAi mediated by small interfering RNAs (siRNAs or short hairpin RNAs (shRNAs has become a powerful genetic tool for conducting functional studies. Previously, vector-based shRNA-expression strategies capable of inducing RNAi in viable cells have been developed, however, these vector systems have some disadvantages, either because they were error-prone or cost prohibitive. RESULTS: In this report we described the development of a simple, robust shRNA expression system utilizing 1 long oligonucleotide or 2 short oligonucleotides for half the cost of conventional shRNA construction methods and with a >95% cloning success rate. The shRNA loop sequence and stem structure were also compared and carefully selected for better RNAi efficiency. Furthermore, an easier strategy was developed based on isocaudomers which permit rapid combination of the most efficient promoter-shRNA cassettes. Finally, using this method, the conservative target sites for hepatitis B virus (HBV knockdown were systemically screened and HBV antigen expression shown to be successfully suppressed in the presence of connected multiple shRNAs both in vitro and in vivo. CONCLUSION: This novel design describes an inexpensive and effective way to clone and express single or multiple shRNAs from the same vector with the capacity for potent and effective silencing of target genes.

  9. Ti-Ni-based shape memory alloys as smart materials

    International Nuclear Information System (INIS)

    Otsuka, K.; Xu, Y.; Ren, X.

    2003-01-01

    Smart materials consist of three principal materials, ferroelectrics, shape memory alloys (SMA) and electro-active polymers (EAP). Among these SMAs, especially Ti-Ni-based alloys are important, since only they can provide large recoverable strains and high recovery stress. In the present paper the unique characteristics of Ti-Ni-based shape memory alloys are reviewed on an up-to-date basis with the aim of their applications to smart materials and structures. (orig.)

  10. SHAPE analysis of the FIV Leader RNA reveals a structural switch potentially controlling viral packaging and genome dimerization.

    Science.gov (United States)

    Kenyon, Julia C; Tanner, Sian J; Legiewicz, Michal; Phillip, Pretty S; Rizvi, Tahir A; Le Grice, Stuart F J; Lever, Andrew M L

    2011-08-01

    Feline immunodeficiency virus (FIV) infects many species of cat, and is related to HIV, causing a similar pathology. High-throughput selective 2' hydroxyl acylation analysed by primer extension (SHAPE), a technique that allows structural interrogation at each nucleotide, was used to map the secondary structure of the FIV packaging signal RNA. Previous studies of this RNA showed four conserved stem-loops, extensive long-range interactions (LRIs) and a small, palindromic stem-loop (SL5) within the gag open reading frame (ORF) that may act as a dimerization initiation site (DIS), enabling the virus to package two copies of its genome. Our analyses of wild-type (wt) and mutant RNAs suggest that although the four conserved stem-loops are static structures, the 5' and 3' regions previously shown to form LRI also adopt an alternative, yet similarly conserved conformation, in which the putative DIS is occluded, and which may thus favour translational and splicing functions over encapsidation. SHAPE and in vitro dimerization assays were used to examine SL5 mutants. Dimerization contacts appear to be made between palindromic loop sequences in SL5. As this stem-loop is located within the gag ORF, recognition of a dimeric RNA provides a possible mechanism for the specific packaging of genomic over spliced viral RNAs.

  11. Ensemble-based prediction of RNA secondary structures.

    Science.gov (United States)

    Aghaeepour, Nima; Hoos, Holger H

    2013-04-24

    Accurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile approaches, and improved methods for this task have received much attention over the past five years. Despite the impressive progress that as been achieved in this area, existing evaluations of the prediction accuracy achieved by various algorithms do not provide a comprehensive, statistically sound assessment. Furthermore, while there is increasing evidence that no prediction algorithm consistently outperforms all others, no work has been done to exploit the complementary strengths of multiple approaches. In this work, we present two contributions to the area of RNA secondary structure prediction. Firstly, we use state-of-the-art, resampling-based statistical methods together with a previously published and increasingly widely used dataset of high-quality RNA structures to conduct a comprehensive evaluation of existing RNA secondary structure prediction procedures. The results from this evaluation clarify the performance relationship between ten well-known existing energy-based pseudoknot-free RNA secondary structure prediction methods and clearly demonstrate the progress that has been achieved in recent years. Secondly, we introduce AveRNA, a generic and powerful method for combining a set of existing secondary structure prediction procedures into an ensemble-based method that achieves significantly higher prediction accuracies than obtained from any of its component procedures. Our new, ensemble-based method, AveRNA, improves the state of the art for energy-based, pseudoknot-free RNA secondary structure prediction by exploiting the complementary strengths of multiple existing prediction procedures, as demonstrated using a state-of-the-art statistical resampling approach. In addition, AveRNA allows an intuitive and effective control of the trade-off between

  12. Symmetric metamaterials based on flower-shaped structure

    International Nuclear Information System (INIS)

    Tuong, P.V.; Park, J.W.; Rhee, J.Y.; Kim, K.W.; Cheong, H.; Jang, W.H.; Lee, Y.P.

    2013-01-01

    We proposed new models of metamaterials (MMs) based on a flower-shaped structure (FSS), whose “meta-atoms” consist of two flower-shaped metallic parts separated by a dielectric layer. Like the non-symmetric MMs based on cut-wire-pairs or electric ring resonators, the symmetrical FSS demonstrates the negative permeability at GHz frequencies. Employing the results, we designed a symmetric negative-refractive-index MM [a symmetric combined structure (SCS)], which is composed of FSSs and cross continuous wires. The MM properties of the FSS and the SCS are presented numerically and experimentally. - Highlights: • A new designed of sub-wavelength metamaterial, flower-shaped structure was proposed. • Flower-shaped meta-atom illustrated effective negative permeability. • Based on the meta-atom, negative refractive index was conventionally gained. • Negative refractive index was demonstrated with symmetric properties for electromagnetic wave. • Dimensional parameters were studied under normal electromagnetic wave

  13. Cytochrome c oxidase subunit 1-based human RNA quantification to enhance mRNA profiling in forensic biology

    Directory of Open Access Journals (Sweden)

    Dong Zhao

    2017-01-01

    Full Text Available RNA analysis offers many potential applications in forensic science, and molecular identification of body fluids by analysis of cell-specific RNA markers represents a new technique for use in forensic cases. However, due to the nature of forensic materials that often admixed with nonhuman cellular components, human-specific RNA quantification is required for the forensic RNA assays. Quantification assay for human RNA has been developed in the present study with respect to body fluid samples in forensic biology. The quantitative assay is based on real-time reverse transcription-polymerase chain reaction of mitochondrial RNA cytochrome c oxidase subunit I and capable of RNA quantification with high reproducibility and a wide dynamic range. The human RNA quantification improves the quality of mRNA profiling in the identification of body fluids of saliva and semen because the quantification assay can exclude the influence of nonhuman components and reduce the adverse affection from degraded RNA fragments.

  14. Entropy-based model for miRNA isoform analysis.

    Directory of Open Access Journals (Sweden)

    Shengqin Wang

    Full Text Available MiRNAs have been widely studied due to their important post-transcriptional regulatory roles in gene expression. Many reports have demonstrated the evidence of miRNA isoform products (isomiRs in high-throughput small RNA sequencing data. However, the biological function involved in these molecules is still not well investigated. Here, we developed a Shannon entropy-based model to estimate isomiR expression profiles of high-throughput small RNA sequencing data extracted from miRBase webserver. By using the Kolmogorov-Smirnov statistical test (KS test, we demonstrated that the 5p and 3p miRNAs present more variants than the single arm miRNAs. We also found that the isomiR variant, except the 3' isomiR variant, is strongly correlated with Minimum Free Energy (MFE of pre-miRNA, suggesting the intrinsic feature of pre-miRNA should be one of the important factors for the miRNA regulation. The functional enrichment analysis showed that the miRNAs with high variation, particularly the 5' end variation, are enriched in a set of critical functions, supporting these molecules should not be randomly produced. Our results provide a probabilistic framework for miRNA isoforms analysis, and give functional insights into pre-miRNA processing.

  15. Reconstruction and analysis of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in rheumatoid arthritis.

    Science.gov (United States)

    Jiang, Hui; Ma, Rong; Zou, Shubiao; Wang, Yongzhong; Li, Zhuqing; Li, Weiping

    2017-06-01

    Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology, occurring in approximately 1.0% of general population. More and more studies have suggested that long non-coding RNAs (lncRNAs) could play important roles in various biological processes and be associated with the pathogenesis of different kinds of diseases including RA. Although a large number of lncRNAs have been found, our knowledge of their function and physiological/pathological significance is still in its infancy. In order to reveal functional lncRNAs and identify the key lncRNAs in RA, we reconstructed a global triple network based on the competitive endogenous RNA (ceRNA) theory using the data from National Center for Biotechnology Information Gene Expression Omnibus and our previous paper. Meanwhile, Gene Ontology (GO) and pathway analysis were performed using Cytoscape plug-in BinGO and Database for Annotation, Visualization, and Integration Discovery (DAVID), respectively. We found that the lncRNA-miRNA-mRNA network was composed of 7 lncRNA nodes, 90 mRNA nodes, 24 miRNA nodes, and 301 edges. The functional assay showed that 147 GO terms and 23 pathways were enriched. In addition, three lncRNAs (S5645.1, XR_006437.1, J01878) were highly related to RA, and therefore, were selected as key lncRNAs. This study suggests that specific lncRNAs are associated with the development of RA, and three lncRNAs (S5645.1, XR_006437.1, J01878) could be used as potential diagnostic biomarkers and therapeutic targets.

  16. Identification of the miRNA-mRNA regulatory network of small cell osteosarcoma based on RNA-seq.

    Science.gov (United States)

    Xie, Lin; Liao, Yedan; Shen, Lida; Hu, Fengdi; Yu, Sunlin; Zhou, Yonghong; Zhang, Ya; Yang, Yihao; Li, Dongqi; Ren, Minyan; Yuan, Zhongqin; Yang, Zuozhang

    2017-06-27

    Small cell osteosarcoma (SCO) is a rare subtype of osteosarcoma characterized by highly aggressive progression and a poor prognosis. The miRNA and mRNA expression profiles of peripheral blood mononuclear cells (PBMCs) were obtained in 3 patients with SCO and 10 healthy individuals using high-throughput RNA-sequencing. We identified 37 dysregulated miRNAs and 1636 dysregulated mRNAs in patients with SCO compared to the healthy controls. Specifically, the 37 dysregulated miRNAs consisted of 27 up-regulated miRNAs and 10 down-regulated miRNAs; the 1636 dysregulated mRNAs consisted of 555 up-regulated mRNAs and 1081 down-regulated mRNAs. The target-genes of miRNAs were predicted, and 1334 negative correlations between miRNAs and mRNAs were used to construct an miRNA-mRNA regulatory network. Dysregulated genes were significantly enriched in pathways related to cancer, mTOR signaling and cell cycle signaling. Specifically, hsa-miR-26b-5p, hsa-miR-221-3p and hsa-miR-125b-2-3p were significantly dysregulated miRNAs and exhibited a high degree of connectivity with target genes. Overall, the expression of dysregulated genes in tumor tissues and peripheral blood samples of patients with SCO measured by quantitative real-time polymerase chain reaction corroborated with our bioinformatics analyses based on the expression profiles of PBMCs from patients with SCO. Thus, hsa-miR-26b-5p, hsa-miR-221-3p and hsa-miR-125b-2-3p may be involved in SCO tumorigenesis.

  17. A path-based measurement for human miRNA functional similarities using miRNA-disease associations

    Science.gov (United States)

    Ding, Pingjian; Luo, Jiawei; Xiao, Qiu; Chen, Xiangtao

    2016-09-01

    Compared with the sequence and expression similarity, miRNA functional similarity is so important for biology researches and many applications such as miRNA clustering, miRNA function prediction, miRNA synergism identification and disease miRNA prioritization. However, the existing methods always utilized the predicted miRNA target which has high false positive and false negative to calculate the miRNA functional similarity. Meanwhile, it is difficult to achieve high reliability of miRNA functional similarity with miRNA-disease associations. Therefore, it is increasingly needed to improve the measurement of miRNA functional similarity. In this study, we develop a novel path-based calculation method of miRNA functional similarity based on miRNA-disease associations, called MFSP. Compared with other methods, our method obtains higher average functional similarity of intra-family and intra-cluster selected groups. Meanwhile, the lower average functional similarity of inter-family and inter-cluster miRNA pair is obtained. In addition, the smaller p-value is achieved, while applying Wilcoxon rank-sum test and Kruskal-Wallis test to different miRNA groups. The relationship between miRNA functional similarity and other information sources is exhibited. Furthermore, the constructed miRNA functional network based on MFSP is a scale-free and small-world network. Moreover, the higher AUC for miRNA-disease prediction indicates the ability of MFSP uncovering miRNA functional similarity.

  18. Thermoplastic shape-memory polyurethanes based on natural oils

    International Nuclear Information System (INIS)

    Saralegi, Ainara; Eceiza, Arantxa; Corcuera, Maria Angeles; Johan Foster, E; Weder, Christoph

    2014-01-01

    A new family of segmented thermoplastic polyurethanes with thermally activated shape-memory properties was synthesized and characterized. Polyols derived from castor oil with different molecular weights but similar chemical structures and a corn-sugar-based chain extender (propanediol) were used as starting materials in order to maximize the content of carbon from renewable resources in the new materials. The composition was systematically varied to establish a structure–property map and identify compositions with desirable shape-memory properties. The thermal characterization of the new polyurethanes revealed a microphase separated structure, where both the soft (by convention the high molecular weight diol) and the hard phases were highly crystalline. Cyclic thermo-mechanical tensile tests showed that these polymers are excellent candidates for use as thermally activated shape-memory polymers, in which the crystalline soft segments promote high shape fixity values (close to 100%) and the hard segment crystallites ensure high shape recovery values (80–100%, depending on the hard segment content). The high proportion of components from renewable resources used in the polyurethane formulation leads to the synthesis of bio-based polyurethanes with shape-memory properties. (paper)

  19. Shape determinative slice localization for patient-specific masseter modeling using shape-based interpolation

    Energy Technology Data Exchange (ETDEWEB)

    Ng, H.P. [NUS Graduate School for Integrative Sciences and Engineering (Singapore); Biomedical Imaging Lab., Agency for Science Technology and Research (Singapore); Foong, K.W.C. [NUS Graduate School for Integrative Sciences and Engineering (Singapore); Dept. of Preventive Dentistry, National Univ. of Singapore (Singapore); Ong, S.H. [Dept. of Electrical and Computer Engineering, National Univ. of Singapore (Singapore); Div. of Bioengineering, National Univ. of Singapore (Singapore); Liu, J.; Nowinski, W.L. [Biomedical Imaging Lab., Agency for Science Technology and Research (Singapore); Goh, P.S. [Dept. of Diagnostic Radiology, National Univ. of Singapore (Singapore)

    2007-06-15

    The masseter plays a critical role in the mastication system. A hybrid method to shape-based interpolation is used to build the masseter model from magnetic resonance (MR) data sets. The main contribution here is the localizing of determinative slices in the data sets where clinicians are required to perform manual segmentations in order for an accurate model to be built. Shape-based criteria were used to locate the candidates for determinative slices and fuzzy-c-means (FCM) clustering technique was used to establish the determinative slices. Five masseter models were built in our work and the average overlap indices ({kappa}) achieved is 85.2%. This indicates that there is good agreement between the models and the manual contour tracings. In addition, the time taken, as compared to manually segmenting all the slices, is significantly lesser. (orig.)

  20. Shape determinative slice localization for patient-specific masseter modeling using shape-based interpolation

    International Nuclear Information System (INIS)

    Ng, H.P.; Foong, K.W.C.; Ong, S.H.; Liu, J.; Nowinski, W.L.; Goh, P.S.

    2007-01-01

    The masseter plays a critical role in the mastication system. A hybrid method to shape-based interpolation is used to build the masseter model from magnetic resonance (MR) data sets. The main contribution here is the localizing of determinative slices in the data sets where clinicians are required to perform manual segmentations in order for an accurate model to be built. Shape-based criteria were used to locate the candidates for determinative slices and fuzzy-c-means (FCM) clustering technique was used to establish the determinative slices. Five masseter models were built in our work and the average overlap indices (κ) achieved is 85.2%. This indicates that there is good agreement between the models and the manual contour tracings. In addition, the time taken, as compared to manually segmenting all the slices, is significantly lesser. (orig.)

  1. Nanofibers-based nanoweb promise superhydrophobic polyaniline: from star-shaped to leaf-shaped structures.

    Science.gov (United States)

    Fan, Haosen; Wang, Hao; Guo, Jing; Zhao, Ning; Xu, Jian

    2013-11-01

    Star-shaped and leaf-shaped polyaniline (PANI) hierarchical structures with interlaced nanofibers on the surface were successfully prepared by chemical polymerization of aniline in the presence of lithium triflate (LT). Chemical structure and composition of the star-like PANI obtained were characterized by FTIR and UV-vis spectra. PANI 2D architectures can be tailored from star-shaped to leaf-shaped structures by change the concentration of LT. The synthesized star-like and leaf-like polyaniline show good superhydrophobicity with water contact angles of both above 150° due to the combination of the rough nanoweb structure and the low surface tension of fluorinated chain of dopant. This method is a facile and applicable strategy for a large-scale fabrication of 2D PANI micro/nanostructures. Many potential applications such as self-cleaning and antifouling coating can be expected based on the superhydrophobic PANI micro/nanostructures. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

  2. Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.

    Science.gov (United States)

    Smola, Matthew J; Rice, Greggory M; Busan, Steven; Siegfried, Nathan A; Weeks, Kevin M

    2015-11-01

    Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistries exploit small electrophilic reagents that react with 2'-hydroxyl groups to interrogate RNA structure at single-nucleotide resolution. Mutational profiling (MaP) identifies modified residues by using reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing. The SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as can be done for simple model RNAs. This protocol describes the experimental steps, implemented over 3 d, that are required to perform SHAPE probing and to construct multiplexed SHAPE-MaP libraries suitable for deep sequencing. Automated processing of MaP sequencing data is accomplished using two software packages. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots and provides useful troubleshooting information. SuperFold uses these data to model RNA secondary structures, identify regions with well-defined structures and visualize probable and alternative helices, often in under 1 d. SHAPE-MaP can be used to make nucleotide-resolution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles and entire transcriptomes.

  3. Regulation of Plant Microprocessor Function in Shaping microRNA Landscape

    Directory of Open Access Journals (Sweden)

    Jakub Dolata

    2018-06-01

    Full Text Available MicroRNAs are small molecules (∼21 nucleotides long that are key regulators of gene expression. They originate from long stem–loop RNAs as a product of cleavage by a protein complex called Microprocessor. The core components of the plant Microprocessor are the RNase type III enzyme Dicer-Like 1 (DCL1, the zinc finger protein Serrate (SE, and the double-stranded RNA binding protein Hyponastic Leaves 1 (HYL1. Microprocessor assembly and its processing of microRNA precursors have been reported to occur in discrete nuclear bodies called Dicing bodies. The accessibility of and modifications to Microprocessor components affect microRNA levels and may have dramatic consequences in plant development. Currently, numerous lines of evidence indicate that plant Microprocessor activity is tightly regulated. The cellular localization of HYL1 is dependent on a specific KETCH1 importin, and the E3 ubiquitin ligase COP1 indirectly protects HYL1 from degradation in a light-dependent manner. Furthermore, proper localization of HYL1 in Dicing bodies is regulated by MOS2. On the other hand, the Dicing body localization of DCL1 is regulated by NOT2b, which also interacts with SE in the nucleus. Post-translational modifications are substantial factors that contribute to protein functional diversity and provide a fine-tuning system for the regulation of protein activity. The phosphorylation status of HYL1 is crucial for its activity/stability and is a result of the interplay between kinases (MPK3 and SnRK2 and phosphatases (CPL1 and PP4. Additionally, MPK3 and SnRK2 are known to phosphorylate SE. Several other proteins (e.g., TGH, CDF2, SIC, and RCF3 that interact with Microprocessor have been found to influence its RNA-binding and processing activities. In this minireview, recent findings on the various modes of Microprocessor activity regulation are discussed.

  4. Shape-based assessment of vertebral fracture risk in postmenopausal women using discriminative shape alignment

    DEFF Research Database (Denmark)

    Crimi, Alessandro; Loog, Marco; de Bruijne, Marleen

    2012-01-01

    RATIONALE AND OBJECTIVES: Risk assessment of future osteoporotic vertebral fractures is currently based mainly on risk factors, such as bone mineral density, age, prior fragility fractures, and smoking. It can be argued that an osteoporotic vertebral fracture is not exclusively an abrupt event...... independently performed manual annotations of the vertebrae, and fracture prediction using shape features extracted from the baseline annotations was performed. This was implemented using posterior probabilities from a standard linear classifier. RESULTS: The classifier tested on the study population quantified...

  5. Shape-based grey-level image interpolation

    International Nuclear Information System (INIS)

    Keh-Shih Chuang; Chun-Yuan Chen; Ching-Kai Yeh

    1999-01-01

    The three-dimensional (3D) object data obtained from a CT scanner usually have unequal sampling frequencies in the x-, y- and z-directions. Generally, the 3D data are first interpolated between slices to obtain isotropic resolution, reconstructed, then operated on using object extraction and display algorithms. The traditional grey-level interpolation introduces a layer of intermediate substance and is not suitable for objects that are very different from the opposite background. The shape-based interpolation method transfers a pixel location to a parameter related to the object shape and the interpolation is performed on that parameter. This process is able to achieve a better interpolation but its application is limited to binary images only. In this paper, we present an improved shape-based interpolation method for grey-level images. The new method uses a polygon to approximate the object shape and performs the interpolation using polygon vertices as references. The binary images representing the shape of the object were first generated via image segmentation on the source images. The target object binary image was then created using regular shape-based interpolation. The polygon enclosing the object for each slice can be generated from the shape of that slice. We determined the relative location in the source slices of each pixel inside the target polygon using the vertices of a polygon as the reference. The target slice grey-level was interpolated from the corresponding source image pixels. The image quality of this interpolation method is better and the mean squared difference is smaller than with traditional grey-level interpolation. (author)

  6. incaRNAfbinv: a web server for the fragment-based design of RNA sequences

    Science.gov (United States)

    Drory Retwitzer, Matan; Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme; Barash, Danny

    2016-01-01

    Abstract In recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, RNAfbinv aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily exactly fold into the target, as long as the overall coarse-grained tree graph shape is preserved. Augmented by the weighted sampling algorithm of incaRNAtion, our web server called incaRNAfbinv implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs. The two complementary methodologies RNAfbinv and incaRNAtion are merged together and fully implemented in our web server incaRNAfbinv, available at http://www.cs.bgu.ac.il/incaRNAfbinv. PMID:27185893

  7. SELEX-Based Screening of Exosome-Tropic RNA.

    Science.gov (United States)

    Yamashita, Takuma; Shinotsuka, Haruka; Takahashi, Yuki; Kato, Kana; Nishikawa, Makiya; Takakura, Yoshinobu

    2017-01-01

    Cell-derived nanosized vesicles or exosomes are expected to become delivery carriers for functional RNAs, such as small interfering RNA (siRNA). A method to efficiently load functional RNAs into exosomes is required for the development of exosome-based delivery carriers of functional RNAs. However, there is no method to find exosome-tropic exogenous RNA sequences. In this study, we used a systematic evolution of ligands by exponential enrichment (SELEX) method to screen exosome-tropic RNAs that can be used to load functional RNAs into exosomes by conjugation. Pooled single stranded 80-base RNAs, each of which contains a randomized 40-base sequence, were transfected into B16-BL6 murine melanoma cells and exosomes were collected from the cells. RNAs extracted from the exosomes were subjected to next round of SELEX. Cloning and sequencing of RNAs in SELEX-screened RNA pools showed that 29 of 56 clones had a typical RNA sequence. The sequence found by SELEX was enriched in exosomes after transfection to B16-BL6 cells. The results show that the SELEX-based method can be used for screening of exosome-tropic RNAs.

  8. Size and Base Composition of RNA in Supercoiled Plasmid DNA

    Science.gov (United States)

    Williams, Peter H.; Boyer, Herbert W.; Helinski, Donald R.

    1973-01-01

    The average size and base composition of the covalently integrated RNA segment in supercoiled ColE1 DNA synthesized in Escherichia coli in the presence of chloramphenicol (CM-ColE1 DNA) have been determined by two independent methods. The two approaches yielded similar results, indicating that the RNA segment in CM-ColE1 DNA contains GMP at the 5′ end and comprises on the average 25 to 26 ribonucleotides with a base composition of 10-11 G, 3 A, 5-6 C, and 6-7 U. PMID:4359488

  9. Neurosurgery contact handheld probe based on sapphire shaped crystal

    Science.gov (United States)

    Shikunova, I. A.; Stryukov, D. O.; Rossolenko, S. N.; Kiselev, A. M.; Kurlov, V. N.

    2017-01-01

    A handheld contact probe based on sapphire shaped crystal is developed for intraoperative spectrally-resolved optical diagnostics, laser coagulation and aspiration of malignant brain tissue. The technology was integrated into the neurosurgical workflow for intraoperative real-time identification and removing of invasive brain cancer.

  10. Fe-Mn-Si based shape memory alloys

    International Nuclear Information System (INIS)

    Hsu, T.Y.

    2000-01-01

    Characteristics of martensitic transformation fcc(γ)→hcp(ε) in Fe-Mn-Si based alloys are briefly reviewed. By analyzing the influences of constituents and treatments on shape memory effect (SME) in Fe-Mn-Si, the main factors controlling SME are summarized as austenite strengthening, stacking fault energy (probability) and antiferromagnetic temperature. Contribution of thermomechanical training to SME is introduced. The Fe-Mn-Si-RE (rare earth elements) and Fe-Mn-Si-Cr-N alloys are recommended as two novel shape memory alloys with superior SME. (orig.)

  11. The predominant circular form of avocado sunblotch viroid accumulates in planta as a free RNA adopting a rod-shaped secondary structure unprotected by tightly bound host proteins.

    Science.gov (United States)

    López-Carrasco, Amparo; Flores, Ricardo

    2017-07-01

    Avocado sunblotch viroid (ASBVd), the type member of the family Avsunviroidae, replicates and accumulates in chloroplasts. Whether this minimal non-protein-coding circular RNA of 246-250 nt exists in vivo as a free nucleic acid or closely associated with host proteins remains unknown. To tackle this issue, the secondary structures of the monomeric circular (mc) (+) and (-) strands of ASBVd have been examined in silico by searching those of minimal free energy, and in vitro at single-nucleotide resolution by selective 2'-hydroxyl acylation analysed by primer extension (SHAPE). Both approaches resulted in predominant rod-like secondary structures without tertiary interactions, with the mc (+) RNA being more compact than its (-) counterpart as revealed by non-denaturing polyacryamide gel electrophoresis. Moreover, in vivo SHAPE showed that the mc ASBVd (+) form accumulates in avocado leaves as a free RNA adopting a similar rod-shaped conformation unprotected by tightly bound host proteins. Hence, the mc ASBVd (+) RNA behaves in planta like the previously studied mc (+) RNA of potato spindle tuber viroid, the type member of nuclear viroids (family Pospiviroidae), indicating that two different viroids replicating and accumulating in distinct subcellular compartments, have converged into a common structural solution. Circularity and compact secondary structures confer to these RNAs, and probably to all viroids, the intrinsic stability needed to survive in their natural habitats. However, in vivo SHAPE has not revealed the (possibly transient or loose) interactions of the mc ASBVd (+) RNA with two host proteins observed previously by UV irradiation of infected avocado leaves.

  12. Literature-based condition-specific miRNA-mRNA target prediction.

    Directory of Open Access Journals (Sweden)

    Minsik Oh

    Full Text Available miRNAs are small non-coding RNAs that regulate gene expression by binding to the 3'-UTR of genes. Many recent studies have reported that miRNAs play important biological roles by regulating specific mRNAs or genes. Many sequence-based target prediction algorithms have been developed to predict miRNA targets. However, these methods are not designed for condition-specific target predictions and produce many false positives; thus, expression-based target prediction algorithms have been developed for condition-specific target predictions. A typical strategy to utilize expression data is to leverage the negative control roles of miRNAs on genes. To control false positives, a stringent cutoff value is typically set, but in this case, these methods tend to reject many true target relationships, i.e., false negatives. To overcome these limitations, additional information should be utilized. The literature is probably the best resource that we can utilize. Recent literature mining systems compile millions of articles with experiments designed for specific biological questions, and the systems provide a function to search for specific information. To utilize the literature information, we used a literature mining system, BEST, that automatically extracts information from the literature in PubMed and that allows the user to perform searches of the literature with any English words. By integrating omics data analysis methods and BEST, we developed Context-MMIA, a miRNA-mRNA target prediction method that combines expression data analysis results and the literature information extracted based on the user-specified context. In the pathway enrichment analysis using genes included in the top 200 miRNA-targets, Context-MMIA outperformed the four existing target prediction methods that we tested. In another test on whether prediction methods can re-produce experimentally validated target relationships, Context-MMIA outperformed the four existing target prediction

  13. DNA/RNA-based formulations for treatment of breast cancer.

    Science.gov (United States)

    Xie, Zhaolu; Zeng, Xianghui

    2017-12-01

    To develop a successful formulation for the gene therapy of breast cancer, an effective therapeutic nucleic acid and a proper delivery system are essential. Increased understanding of breast cancer, and developments in biotechnology, material science and nanotechnology have provided a major impetus in the development of effective formulations for the gene therapy of breast cancer. Areas covered: We discuss DNA/RNA-based formulations that can inhibit the growth of breast cancer cells and control the progress of breast cancer. Targets for the gene therapy of breast cancer, DNA/RNA-based therapeutics and delivery systems are summarized. And examples of successful DNA/RNA-based formulations for breast cancer gene therapy are reviewed. Expert opinion: Several challenges remain in developing effective DNA/RNA-based formulations for treatment of breast cancer. Firstly, most of the currently utilized targets are not effective enough as monotherapy for breast cancer. Secondly, the requirements for co-delivery system make the preparation of formulation more complicated. Thirdly, nanoparticles with the modification of tumor-targeting ligands could be more unstable in circulation and normal tissues. Lastly, immune responses against the viral vectors are unfavorable for the gene therapy of breast cancer because of the damage to the host and the impaired therapeutic ability.

  14. Proto-ribosome: a theoretical approach based on RNA relics

    OpenAIRE

    Demongeot, Jacques

    2017-01-01

    We describe in this paper, based on already published articles, a contribution to the theory postulating the existence of a proto-ribosome, which could have appeared early at the origin of life and we discuss the interest of this notion in an evolutionary perspective, taking into account the existence of possible RNA relics of this proto-ribosome.

  15. The shape of a strain-based failure assessment diagram

    International Nuclear Information System (INIS)

    Budden, P.J.; Ainsworth, R.A.

    2012-01-01

    There have been a number of recent developments of strain-based fracture assessment approaches, including proposals by Budden [Engng Frac Mech 2006;73:537–52] for a strain-based failure assessment diagram (FAD) related to the conventional stress-based FAD. However, recent comparisons with finite element (FE) data have shown that this proposed strain-based FAD can be non-conservative in some cases, particularly for deeper cracks and materials with little strain-hardening capacity. Therefore, this paper re-examines the shape of the strain-based FAD, guided by these FE analyses and some theoretical analysis. On this basis, modified proposals for the shape of the strain-based FAD are given, including simplified and more detailed options in line with the options available for stress-based FADs in existing fitness-for-service procedures. The proposals are then illustrated by a worked example and by comparison with FE data, which demonstrate that the new proposals are generally conservative. - Highlights: ► The strain-based failure assessment diagram approach to fracture is developed. ► The new approach modifies earlier proposals by Budden. ► A new generic Option 1 strain-based failure assessment diagram is proposed. ► Validation based on finite element J data for plates and cylinders is presented. ► The new approach is generally conservative compared with the finite element data.

  16. RNA-dependent RNA polymerase: Addressing Zika outbreak by a phylogeny-based drug target study.

    Science.gov (United States)

    Stephen, Preyesh; Lin, Sheng-Xiang

    2018-01-01

    Since the first major outbreak of Zika virus (ZIKV) in 2007, ZIKV is spreading explosively through South and Central America, and recent reports in highly populated developing countries alarm the possibility of a more catastrophic outbreak. ZIKV infection in pregnant women leads to embryonic microcephaly and Guillain-Barré syndrome in adults. At present, there is limited understanding of the infectious mechanism, and no approved therapy has been reported. Despite the withdrawal of public health emergency, the WHO still considers the ZIKV as a highly significant and long-term public health challenge that the situation has to be addressed rapidly. Non-structural protein 5 is essential for capping and replication of viral RNA and comprises a methyltransferase and RNA-dependent RNA polymerase (RdRp) domain. We used molecular modeling to obtain the structure of ZIKV RdRp, and by molecular docking and phylogeny analysis, we here demonstrate the potential sites for drug screening. Two metal binding sites and an NS3-interacting region in ZIKV RdRp are demonstrated as potential drug screening sites. The docked structures reveal a remarkable degree of conservation at the substrate binding site and the potential drug screening sites. A phylogeny-based approach is provided for an emergency preparedness, where similar class of ligands could target phylogenetically related proteins. © 2017 John Wiley & Sons A/S.

  17. Shape signature based on Ricci flow and optimal mass transportation

    Science.gov (United States)

    Luo, Wei; Su, Zengyu; Zhang, Min; Zeng, Wei; Dai, Junfei; Gu, Xianfeng

    2014-11-01

    A shape signature based on surface Ricci flow and optimal mass transportation is introduced for the purpose of surface comparison. First, the surface is conformally mapped onto plane by Ricci flow, which induces a measure on the planar domain. Second, the unique optimal mass transport map is computed that transports the new measure to the canonical measure on the plane. The map is obtained by a convex optimization process. This optimal transport map encodes all the information of the Riemannian metric on the surface. The shape signature consists of the optimal transport map, together with the mean curvature, which can fully recover the original surface. The discrete theories of surface Ricci flow and optimal mass transportation are explained thoroughly. The algorithms are given in detail. The signature is tested on human facial surfaces with different expressions accquired by structured light 3-D scanner based on phase-shifting method. The experimental results demonstrate the efficiency and efficacy of the method.

  18. Beam-based alignment of C-shaped quadrupole magnets

    International Nuclear Information System (INIS)

    Portmann, G.; Robin, D.

    1998-06-01

    Many storage rings have implemented a method of finding the positional offset between the electrical center of the beam position monitors (BPM) and the magnetic center of the adjacent quadrupole magnets. The algorithm for accomplishing this is usually based on modulating the current in the quadrupole magnet and finding the beam position that minimizes the orbit perturbation. When the quadrupole magnet is C-shaped, as it is for many light sources, the modulation method can produce an erroneous measurement of the magnetic center in the horizontal plane. When the current in a C-shaped quadrupole is changed, there is an additional dipole component in the vertical field. Due to nonlinearities in the hysteresis cycle of the C-magnet geometry, the beam-based alignment technique at the Advanced Light Source (ALS) deviated horizontally by .5 mm from the actual magnetic center. By modifying the technique, the offsets were measured to an accuracy of better than 50 microm

  19. Fast-Responding Bio-Based Shape Memory Thermoplastic Polyurethanes.

    Science.gov (United States)

    Petrović, Zoran S; Milić, Jelena; Zhang, Fan; Ilavsky, Jan

    2017-07-14

    Novel fast response shape-memory polyurethanes were prepared from bio-based polyols, diphenyl methane diisocyanate and butane diol for the first time. The bio-based polyester polyols were synthesized from 9-hydroxynonanoic acid, a product obtained by ozonolysis of fatty acids extracted from soy oil and castor oil. The morphology of polyurethanes was investigated by synchrotron ultra-small angle X-ray scattering, which revealed the inter-domain spacing between the hard and soft phases, the degree of phase separation, and the level of intermixing between the hard and soft phases. We also conducted thorough investigations of the thermal, mechanical, and dielectric properties of the polyurethanes, and found that high crystallization rate of the soft segment gives these polyurethanes unique properties suitable for shape-memory applications, such as adjustable transition temperatures, high degree of elastic elongations, and good mechanical strength. These materials are also potentially biodegradable and biocompatible, therefore suitable for biomedical and environmental applications.

  20. Determination of an effective scoring function for RNA-RNA interactions with a physics-based double-iterative method.

    Science.gov (United States)

    Yan, Yumeng; Wen, Zeyu; Zhang, Di; Huang, Sheng-You

    2018-05-18

    RNA-RNA interactions play fundamental roles in gene and cell regulation. Therefore, accurate prediction of RNA-RNA interactions is critical to determine their complex structures and understand the molecular mechanism of the interactions. Here, we have developed a physics-based double-iterative strategy to determine the effective potentials for RNA-RNA interactions based on a training set of 97 diverse RNA-RNA complexes. The double-iterative strategy circumvented the reference state problem in knowledge-based scoring functions by updating the potentials through iteration and also overcame the decoy-dependent limitation in previous iterative methods by constructing the decoys iteratively. The derived scoring function, which is referred to as DITScoreRR, was evaluated on an RNA-RNA docking benchmark of 60 test cases and compared with three other scoring functions. It was shown that for bound docking, our scoring function DITScoreRR obtained the excellent success rates of 90% and 98.3% in binding mode predictions when the top 1 and 10 predictions were considered, compared to 63.3% and 71.7% for van der Waals interactions, 45.0% and 65.0% for ITScorePP, and 11.7% and 26.7% for ZDOCK 2.1, respectively. For unbound docking, DITScoreRR achieved the good success rates of 53.3% and 71.7% in binding mode predictions when the top 1 and 10 predictions were considered, compared to 13.3% and 28.3% for van der Waals interactions, 11.7% and 26.7% for our ITScorePP, and 3.3% and 6.7% for ZDOCK 2.1, respectively. DITScoreRR also performed significantly better in ranking decoys and obtained significantly higher score-RMSD correlations than the other three scoring functions. DITScoreRR will be of great value for the prediction and design of RNA structures and RNA-RNA complexes.

  1. Eye gaze tracking based on the shape of pupil image

    Science.gov (United States)

    Wang, Rui; Qiu, Jian; Luo, Kaiqing; Peng, Li; Han, Peng

    2018-01-01

    Eye tracker is an important instrument for research in psychology, widely used in attention, visual perception, reading and other fields of research. Because of its potential function in human-computer interaction, the eye gaze tracking has already been a topic of research in many fields over the last decades. Nowadays, with the development of technology, non-intrusive methods are more and more welcomed. In this paper, we will present a method based on the shape of pupil image to estimate the gaze point of human eyes without any other intrusive devices such as a hat, a pair of glasses and so on. After using the ellipse fitting algorithm to deal with the pupil image we get, we can determine the direction of the fixation by the shape of the pupil.The innovative aspect of this method is to utilize the new idea of the shape of the pupil so that we can avoid much complicated algorithm. The performance proposed is very helpful for the study of eye gaze tracking, which just needs one camera without infrared light to know the changes in the shape of the pupil to determine the direction of the eye gazing, no additional condition is required.

  2. Fast Template-based Shape Analysis using Diffeomorphic Iterative Centroid

    OpenAIRE

    Cury , Claire; Glaunès , Joan Alexis; Chupin , Marie; Colliot , Olivier

    2014-01-01

    International audience; A common approach for the analysis of anatomical variability relies on the estimation of a representative template of the population, followed by the study of this population based on the parameters of the deformations going from the template to the population. The Large Deformation Diffeomorphic Metric Mapping framework is widely used for shape analysis of anatomical structures, but computing a template with such framework is computationally expensive. In this paper w...

  3. Cleavage of influenza RNA by using a human PUF-based artificial RNA-binding protein–staphylococcal nuclease hybrid

    International Nuclear Information System (INIS)

    Mori, Tomoaki; Nakamura, Kento; Masaoka, Keisuke; Fujita, Yusuke; Morisada, Ryosuke; Mori, Koichi; Tobimatsu, Takamasa; Sera, Takashi

    2016-01-01

    Various viruses infect animals and humans and cause a variety of diseases, including cancer. However, effective methodologies to prevent virus infection have not yet been established. Therefore, development of technologies to inactivate viruses is highly desired. We have already demonstrated that cleavage of a DNA virus genome was effective to prevent its replication. Here, we expanded this methodology to RNA viruses. In the present study, we used staphylococcal nuclease (SNase) instead of the PIN domain (PilT N-terminus) of human SMG6 as an RNA-cleavage domain and fused the SNase to a human Pumilio/fem-3 binding factor (PUF)-based artificial RNA-binding protein to construct an artificial RNA restriction enzyme with enhanced RNA-cleavage rates for influenzavirus. The resulting SNase-fusion nuclease cleaved influenza RNA at rates 120-fold greater than the corresponding PIN-fusion nuclease. The cleaving ability of the PIN-fusion nuclease was not improved even though the linker moiety between the PUF and RNA-cleavage domain was changed. Gel shift assays revealed that the RNA-binding properties of the PUF derivative used was not as good as wild type PUF. Improvement of the binding properties or the design method will allow the SNase-fusion nuclease to cleave an RNA target in mammalian animal cells and/or organisms. - Highlights: • A novel RNA restriction enzyme using SNase was developed tor cleave viral RNA. • Our enzyme cleaved influenza RNA with rates >120-fold higher rates a PIN-fusion one. • Our artificial enzyme with the L5 linker showed the highest RNA cleavage rate. • Our artificial enzyme site-selectively cleaved influenza RNA in vitro.

  4. Shape-based interpolation of multidimensional grey-level images

    International Nuclear Information System (INIS)

    Grevera, G.J.; Udupa, J.K.

    1996-01-01

    Shape-based interpolation as applied to binary images causes the interpolation process to be influenced by the shape of the object. It accomplishes this by first applying a distance transform to the data. This results in the creation of a grey-level data set in which the value at each point represents the minimum distance from that point to the surface of the object. (By convention, points inside the object are assigned positive values; points outside are assigned negative values.) This distance transformed data set is then interpolated using linear or higher-order interpolation and is then thresholded at a distance value of zero to produce the interpolated binary data set. In this paper, the authors describe a new method that extends shape-based interpolation to grey-level input data sets. This generalization consists of first lifting the n-dimensional (n-D) image data to represent it as a surface, or equivalently as a binary image, in an (n + 1)-dimensional [(n + 1)-D] space. The binary shape-based method is then applied to this image to create an (n + 1)-D binary interpolated image. Finally, this image is collapsed (inverse of lifting) to create the n-D interpolated grey-level data set. The authors have conducted several evaluation studies involving patient computed tomography (CT) and magnetic resonance (MR) data as well as mathematical phantoms. They all indicate that the new method produces more accurate results than commonly used grey-level linear interpolation methods, although at the cost of increased computation

  5. Nanoparticle-based delivery of small interfering RNA: challenges for cancer therapy

    Directory of Open Access Journals (Sweden)

    Miele E

    2012-07-01

    Full Text Available Evelina Miele,1,* Gian Paolo Spinelli,2,* Ermanno Miele,3 Enzo Di Fabrizio,3,6 Elisabetta Ferretti,4 Silverio Tomao,2 Alberto Gulino,1,5 1Department of Molecular Medicine, 2Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, 3Nanostructures, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genova, 4Department of Experimental Medicine, Sapienza University of Rome, Rome, 5Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy, 6BIONEM lab, University of Magna Graecia, Campus S. Venuta, Viale Europa 88100 Catanzaro, Italy *These authors contributed equally to this workAbstract: During recent decades there have been remarkable advances and profound changes in cancer therapy. Many therapeutic strategies learned at the bench, including monoclonal antibodies and small molecule inhibitors, have been used at the bedside, leading to important successes. One of the most important advances in biology has been the discovery that small interfering RNA (siRNA is able to regulate the expression of genes, by a phenomenon known as RNA interference (RNAi. RNAi is one of the most rapidly growing fields of research in biology and therapeutics. Much research effort has gone into the application of this new discovery in the treatment of various diseases, including cancer. However, even though these molecules may have potential and strong utility, some limitations make their clinical application difficult, including delivery problems, side effects due to off-target actions, disturbance of physiological functions of the cellular machinery involved in gene silencing, and induction of the innate immune response. Many researchers have attempted to overcome these limitations and to improve the safety of potential RNAi-based therapeutics. Nanoparticles, which are nanostructured entities with tunable size, shape, and surface, as well as biological behavior, provide an ideal opportunity to modify current

  6. Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data.

    Science.gov (United States)

    Zhao, Zheng; Bai, Jing; Wu, Aiwei; Wang, Yuan; Zhang, Jinwen; Wang, Zishan; Li, Yongsheng; Xu, Juan; Li, Xia

    2015-01-01

    Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions. To facilitate such an effort, we have developed Co-LncRNA, which is a web-based computational tool that allows users to identify GO annotations and KEGG pathways that may be affected by co-expressed protein-coding genes of a single or multiple lncRNAs. LncRNA co-expressed protein-coding genes were first identified in publicly available human RNA-Seq datasets, including 241 datasets across 6560 total individuals representing 28 tissue types/cell lines. Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis. In addition, this software provides a graphical overview of pathways that are modulated by lncRNAs, as well as a specific tool to display the relevant networks between lncRNAs and their co-expressed protein-coding genes. Co-LncRNA also supports users in uploading their own lncRNA and protein-coding gene expression profiles to investigate the lncRNA combinatorial effects. It will be continuously updated with more human RNA-Seq datasets on an annual basis. Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community. Database URL: http://www.bio-bigdata.com/Co-LncRNA/. © The Author(s) 2015. Published by Oxford University Press.

  7. Research based on matlab method of digital trapezoidal shaping filter

    International Nuclear Information System (INIS)

    Zhou Qinghua; Zhang Ruanyu; Li Taihua

    2008-01-01

    In order to develop digital shaping system fast and conveniently, the paper presents the method of optimizing the trapezoidal shaping filter's parameters by using MATLAB, and discusses the affections of the parameters to the shaping result by this method. (authors)

  8. Design of nuclear pulse shaped circuit based on proportional counter

    International Nuclear Information System (INIS)

    Song Qianqian; Cheng Yi; Tuo Xianguo

    2011-01-01

    Use the self-developed proportional to sample gas tritium in environment and make the measurement. For this detector, a kind of pulse shape circuit based on second order active low pass filtering circuit realized filtering and shaping nuclear pulse by high-speed operational amplifier, with less stages that has been approved for filter Gaussian wave. Use Multisim 10.0 to simulate the different parameters of the filter circuit. The simulation result was consistent with the theoretical results. The experiments proved the feasibility of this circuit, and at the same time provided a convenient and reliable method for analysis and optimization of the nuclear pulse waveform in order for discriminating by MCA. (authors)

  9. Shape memory-based actuators and release mechanisms therefrom

    Science.gov (United States)

    Vaidyanathan, Rajan (Inventor); Snyder, Daniel W. (Inventor); Schoenwald, David K. (Inventor); Lam, Nhin S. (Inventor); Watson, Daniel S. (Inventor); Krishnan, Vinu B. (Inventor); Noebe, Ronald D. (Inventor)

    2012-01-01

    SM-based actuators (110) and release mechanisms (100) therefrom and systems (500) including one or more release mechanisms (100). The actuators (110) comprise a SM member (118) and a deformable member (140) mechanically coupled to the SM member (118) which deforms upon a shape change of the SM member triggered by a phase transition of the SM member. A retaining element (160) is mechanically coupled to the deformable member (140), wherein the retaining element (160) moves upon the shape change. Release mechanism (100) include an actuator, a rotatable mechanism (120) including at least one restraining feature (178) for restraining rotational movement of the retaining element (160) before the shape change, and at least one spring (315) that provides at least one locked spring-loaded position when the retaining element is in the restraining feature and at least one released position that is reached when the retaining element is in a position beyond the restraining feature (178). The rotatable mechanism (120) includes at least one load-bearing protrusion (310). A hitch (400) is for mechanically coupling to the load, wherein the hitch is supported on the load bearing protrusion (310) when the rotatable mechanism is in the locked spring-loaded position.

  10. A Shape Memory Alloy Based Cryogenic Thermal Conduction Switch

    Science.gov (United States)

    Notardonato, W. U.; Krishnan, V. B.; Singh, J. D.; Woodruff, T. R.; Vaidyanathan, R.

    2005-01-01

    Shape memory alloys (SMAs) can produce large strains when deformed (e.g., up to 8%). Heating results in a phase transformation and associated recovery of all the accumulated strain. This strain recovery can occur against large forces, resulting in their use as actuators. Thus an SMA element can integrate both sensory and actuation functions, by inherently sensing a change in temperature and actuating by undergoing a shape change as a result of a temperature-induced phase transformation. Two aspects of our work on cryogenic SMAs are addressed here. First - a shape memory alloy based cryogenic thermal conduction switch for operation between dewars of liquid methane and liquid oxygen in a common bulkhead arrangement is discussed. Such a switch integrates the sensor element and the actuator element and can be used to create a variable thermal sink to other cryogenic tanks for liquefaction, densification, and zero boil-off systems for advanced spaceport applications. Second - fabrication via arc-melting and subsequent materials testing of SMAs with cryogenic transformation temperatures for use in the aforementioned switch is discussed.

  11. A Shape Memory Alloy Based Cryogenic Thermal Conduction Switch

    International Nuclear Information System (INIS)

    Krishnan, V.B.; Singh, J.D.; Woodruff, T.R.; Vaidyanathan, R.; Notardonato, W.U.

    2004-01-01

    Shape memory alloys (SMAs) can produce large strains when deformed (e.g., up to 8%). Heating results in a phase transformation and associated recovery of all the accumulated strain. This strain recovery can occur against large forces, resulting in their use as actuators. Thus an SMA element can integrate both sensory and actuation functions, by inherently sensing a change in temperature and actuating by undergoing a shape change as a result of a temperature-induced phase transformation. Two aspects of our work on cryogenic SMAs are addressed here. First - a shape memory alloy based cryogenic thermal conduction switch for operation between dewars of liquid methane and liquid oxygen in a common bulkhead arrangement is discussed. Such a switch integrates the sensor element and the actuator element and can be used to create a variable thermal sink to other cryogenic tanks for liquefaction, densification, and zero boil-off systems for advanced spaceport applications. Second - fabrication via arc-melting and subsequent materials testing of SMAs with cryogenic transformation temperatures for use in the aforementioned switch is discussed

  12. Javanese Character Feature Extraction Based on Shape Energy

    Directory of Open Access Journals (Sweden)

    Galih Hendra Wibowo

    2017-07-01

    Full Text Available Javanese character is one of Indonesia's noble culture, especially in Java. However, the number of Javanese people who are able to read the letter has decreased so that there need to be conservation efforts in the form of a system that is able to recognize the characters. One solution to these problem lies in Optical Character Recognition (OCR studies, where one of its heaviest points lies in feature extraction which is to distinguish each character. Shape Energy is one of feature extraction method with the basic idea of how the character can be distinguished simply through its skeleton. Based on the basic idea, then the development of feature extraction is done based on its components to produce an angular histogram with various variations of multiples angle. Furthermore, the performance test of this method and its basic method is performed in Javanese character dataset, which has been obtained from various images, is 240 data with 19 labels by using K-Nearest Neighbors as its classification method. Performance values were obtained based on the accuracy which is generated through the Cross-Validation process of 80.83% in the angular histogram with an angle of 20 degrees, 23% better than Shape Energy. In addition, other test results show that this method is able to recognize rotated character with the lowest performance value of 86% at 180-degree rotation and the highest performance value of 96.97% at 90-degree rotation. It can be concluded that this method is able to improve the performance of Shape Energy in the form of recognition of Javanese characters as well as robust to the rotation.

  13. Tokamak plasma shape identification based on the boundary integral equations

    International Nuclear Information System (INIS)

    Kurihara, Kenichi; Kimura, Toyoaki

    1992-05-01

    A necessary condition for tokamak plasma shape identification is discussed and a new identification method is proposed in this article. This method is based on the boundary integral equations governing a vacuum region around a plasma with only the measurement of either magnetic fluxes or magnetic flux intensities. It can identify various plasmas with low to high ellipticities with the precision determined by the number of the magnetic sensors. This method is applicable to real-time control and visualization using a 'table-look-up' procedure. (author)

  14. Plate-shaped transformation products in zirconium-base alloys

    International Nuclear Information System (INIS)

    Banerjee, S.; Dey, G.K.; Srivastava, D.

    1997-01-01

    Plate-shaped products resulting from martensitic, diffusional, and mixed mode transformations in zirconium-base alloys are compared in the present study. These alloys are particularly suitable for the comparison in view of the fact that the lattice correspondence between the parent β (bcc) and the product α (hcp) or γ-hydride (fct) phases are remarkably similar for different types of transformations. Crystallographic features such as orientation relations, habit planes, and interface structures associated with these transformations have been compared, with a view toward examining whether the transformation mechanisms have characteristic imprints on these experimental observables

  15. Body shape-based biometric recognition using millimeter wave images

    OpenAIRE

    González-Sosa, Ester; Vera-Rodríguez, Rubén; Fiérrez, Julián; Ortega-García, Javier

    2013-01-01

    Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. González-Sosa, E. ; Vera-Rodríguez, R. ; Fierrez, J. ; Ortega-García, J. "Body shape-based biometric recognition using millime...

  16. Physics-based shape matching for intraoperative image guidance

    Energy Technology Data Exchange (ETDEWEB)

    Suwelack, Stefan, E-mail: suwelack@kit.edu; Röhl, Sebastian; Bodenstedt, Sebastian; Reichard, Daniel; Dillmann, Rüdiger; Speidel, Stefanie [Institute for Anthropomatics and Robotics, Karlsruhe Institute of Technology, Adenauerring 2, Karlsruhe 76131 (Germany); Santos, Thiago dos; Maier-Hein, Lena [Computer-assisted Interventions, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120 (Germany); Wagner, Martin; Wünscher, Josephine; Kenngott, Hannes; Müller, Beat P. [General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Im Neuenheimer Feld 110, Heidelberg 69120 (Germany)

    2014-11-01

    Purpose: Soft-tissue deformations can severely degrade the validity of preoperative planning data during computer assisted interventions. Intraoperative imaging such as stereo endoscopic, time-of-flight or, laser range scanner data can be used to compensate these movements. In this context, the intraoperative surface has to be matched to the preoperative model. The shape matching is especially challenging in the intraoperative setting due to noisy sensor data, only partially visible surfaces, ambiguous shape descriptors, and real-time requirements. Methods: A novel physics-based shape matching (PBSM) approach to register intraoperatively acquired surface meshes to preoperative planning data is proposed. The key idea of the method is to describe the nonrigid registration process as an electrostatic–elastic problem, where an elastic body (preoperative model) that is electrically charged slides into an oppositely charged rigid shape (intraoperative surface). It is shown that the corresponding energy functional can be efficiently solved using the finite element (FE) method. It is also demonstrated how PBSM can be combined with rigid registration schemes for robust nonrigid registration of arbitrarily aligned surfaces. Furthermore, it is shown how the approach can be combined with landmark based methods and outline its application to image guidance in laparoscopic interventions. Results: A profound analysis of the PBSM scheme based on in silico and phantom data is presented. Simulation studies on several liver models show that the approach is robust to the initial rigid registration and to parameter variations. The studies also reveal that the method achieves submillimeter registration accuracy (mean error between 0.32 and 0.46 mm). An unoptimized, single core implementation of the approach achieves near real-time performance (2 TPS, 7–19 s total registration time). It outperforms established methods in terms of speed and accuracy. Furthermore, it is shown that the

  17. Shape control in wafer-based aperiodic 3D nanostructures

    International Nuclear Information System (INIS)

    Jeong, Hyeon-Ho; Mark, Andrew G; Gibbs, John G; Fischer, Peer; Reindl, Thomas; Waizmann, Ulrike; Weis, Jürgen

    2014-01-01

    Controlled local fabrication of three-dimensional (3D) nanostructures is important to explore and enhance the function of single nanodevices, but is experimentally challenging. We present a scheme based on e-beam lithography (EBL) written seeds, and glancing angle deposition (GLAD) grown structures to create nanoscale objects with defined shapes but in aperiodic arrangements. By using a continuous sacrificial corral surrounding the features of interest we grow isolated 3D nanostructures that have complex cross-sections and sidewall morphology that are surrounded by zones of clean substrate. (papers)

  18. Spectrum shaping of accelerator-based neutron beams for BNCT

    CERN Document Server

    Montagnini, B; Esposito, J; Giusti, V; Mattioda, F; Varone, R

    2002-01-01

    We describe Monte Carlo simulations of three facilities for the production of epithermal neutrons for Boron Neutron Capture Therapy (BNCT) and examine general aspects and problems of designing the spectrum-shaping assemblies to be used with these neutron sources. The first facility is based on an accelerator-driven low-power subcritical reactor, operating as a neutron amplifier. The other two facilities have no amplifier and rely entirely on their primary sources, a D-T fusion reaction device and a conventional 2.5 MeV proton accelerator with a Li target, respectively.

  19. Feature-Based and String-Based Models for Predicting RNA-Protein Interaction

    Directory of Open Access Journals (Sweden)

    Donald Adjeroh

    2018-03-01

    Full Text Available In this work, we study two approaches for the problem of RNA-Protein Interaction (RPI. In the first approach, we use a feature-based technique by combining extracted features from both sequences and secondary structures. The feature-based approach enhanced the prediction accuracy as it included much more available information about the RNA-protein pairs. In the second approach, we apply search algorithms and data structures to extract effective string patterns for prediction of RPI, using both sequence information (protein and RNA sequences, and structure information (protein and RNA secondary structures. This led to different string-based models for predicting interacting RNA-protein pairs. We show results that demonstrate the effectiveness of the proposed approaches, including comparative results against leading state-of-the-art methods.

  20. Shape memory-based tunable resistivity of polymer composites

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Hongsheng, E-mail: hongshengluo@163.com [Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006 (China); Zhou, Xingdong; Ma, Yuanyuan [Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006 (China); Yi, Guobin, E-mail: ygb116@163.com [Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006 (China); Cheng, Xiaoling [Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006 (China); Zhu, Yong [Shanghai Hiend Polyurethane Inc., No. 389, Jinshan District, Shanghai (China); Zu, Xihong; Zhang, Nanjun; Huang, Binghao; Yu, Lifang [Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006 (China)

    2016-02-15

    Graphical abstract: Hybrid nanofillers of the CNTs and AgNPs were embedded into a shape memory polyurethane. The composites exhibited tunable conduction, which could be facially tailored by the compositions and the thermal–mechanical programming. - Highlights: • Electrically conductive polymer composites in bi-layer structure were fabricated. • The CNTs/AgNPs layer had influence on the mechanics and thermal transitions. • The conductivity could be facially tailored via a thermo-mechanical programming. • The AgNPs contents enlarged the gauge factor of the resistivity–strain curves. • Tunneling theory was suitable for simulating the strain-dependent behaviors. - Abstract: A conductive composite in bi-layer structure was fabricated by embedding hybrid nanofillers, namely carbon nanotubes (CNTs) and silver nanoparticles (AgNPs), into a shape memory polyurethane (SMPU). The CNT/AgNP-SMPU composites exhibited a novel tunable conductivity which could be facially tailored in wide range via the compositions or a specifically designed thermo-mechanical shape memory programming. The morphologies of the conductive fillers and the composites were investigated by scanning electron microscope (SEM). The mechanical and thermal measurements were performed by tensile tests and differential scanning calorimetry (DSC). By virtue of a specifically explored shape memory programming, the composites were stretched and fixed into different temporary states. The electrical resistivity (R{sub s}) varied accordingly, which was able to be stabilized along with the shape fixing. Theoretical prediction based upon the tunneling model was performed. The R{sub s}–strain curves of the composites with different compositions were well fitted. Furthermore, the relative resistivity and the Gauge factor along with the elongation were calculated. The influence of the compositions on the strain-dependent R{sub s} was disclosed. The findings provided a new avenue to tailor the conductivity

  1. A stable RNA virus-based vector for citrus trees

    International Nuclear Information System (INIS)

    Folimonov, Alexey S.; Folimonova, Svetlana Y.; Bar-Joseph, Moshe; Dawson, William O.

    2007-01-01

    Virus-based vectors are important tools in plant molecular biology and plant genomics. A number of vectors based on viruses that infect herbaceous plants are in use for expression or silencing of genes in plants as well as screening unknown sequences for function. Yet there is a need for useful virus-based vectors for woody plants, which demand much greater stability because of the longer time required for systemic infection and analysis. We examined several strategies to develop a Citrus tristeza virus (CTV)-based vector for transient expression of foreign genes in citrus trees using a green fluorescent protein (GFP) as a reporter. These strategies included substitution of the p13 open reading frame (ORF) by the ORF of GFP, construction of a self-processing fusion of GFP in-frame with the major coat protein (CP), or expression of the GFP ORF as an extra gene from a subgenomic (sg) mRNA controlled either by a duplicated CTV CP sgRNA controller element (CE) or an introduced heterologous CE of Beet yellows virus. Engineered vector constructs were examined for replication, encapsidation, GFP expression during multiple passages in protoplasts, and for their ability to infect, move, express GFP, and be maintained in citrus plants. The most successful vectors based on the 'add-a-gene' strategy have been unusually stable, continuing to produce GFP fluorescence after more than 4 years in citrus trees

  2. Arbitrary temporal shape pulsed fiber laser based on SPGD algorithm

    Science.gov (United States)

    Jiang, Min; Su, Rongtao; Zhang, Pengfei; Zhou, Pu

    2018-06-01

    A novel adaptive pulse shaping method for a pulsed master oscillator power amplifier fiber laser to deliver an arbitrary pulse shape is demonstrated. Numerical simulation has been performed to validate the feasibility of the scheme and provide meaningful guidance for the design of the algorithm control parameters. In the proof-of-concept experiment, information on the temporal property of the laser is exchanged and evaluated through a local area network, and the laser adjusted the parameters of the seed laser according to the monitored output of the system automatically. Various pulse shapes, including a rectangular shape, ‘M’ shape, and elliptical shape are achieved through experimental iterations.

  3. DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function.

    Science.gov (United States)

    Cheng, Liang; Hu, Yang; Sun, Jie; Zhou, Meng; Jiang, Qinghua

    2018-06-01

    DincRNA aims to provide a comprehensive web-based bioinformatics toolkit to elucidate the entangled relationships among diseases and non-coding RNAs (ncRNAs) from the perspective of disease similarity. The quantitative way to illustrate relationships of pair-wise diseases always depends on their molecular mechanisms, and structures of the directed acyclic graph of Disease Ontology (DO). Corresponding methods for calculating similarity of pair-wise diseases involve Resnik's, Lin's, Wang's, PSB and SemFunSim methods. Recently, disease similarity was validated suitable for calculating functional similarities of ncRNAs and prioritizing ncRNA-disease pairs, and it has been widely applied for predicting the ncRNA function due to the limited biological knowledge from wet lab experiments of these RNAs. For this purpose, a large number of algorithms and priori knowledge need to be integrated. e.g. 'pair-wise best, pairs-average' (PBPA) and 'pair-wise all, pairs-maximum' (PAPM) methods for calculating functional similarities of ncRNAs, and random walk with restart (RWR) method for prioritizing ncRNA-disease pairs. To facilitate the exploration of disease associations and ncRNA function, DincRNA implemented all of the above eight algorithms based on DO and disease-related genes. Currently, it provides the function to query disease similarity scores, miRNA and lncRNA functional similarity scores, and the prioritization scores of lncRNA-disease and miRNA-disease pairs. http://bio-annotation.cn:18080/DincRNAClient/. biofomeng@hotmail.com or qhjiang@hit.edu.cn. Supplementary data are available at Bioinformatics online.

  4. Alar base reduction: the boomerang-shaped excision.

    Science.gov (United States)

    Foda, Hossam M T

    2011-04-01

    A boomerang-shaped alar base excision is described to narrow the nasal base and correct the excessive alar flare. The boomerang excision combined the external alar wedge resection with an internal vestibular floor excision. The internal excision was inclined 30 to 45 degrees laterally to form the inner limb of the boomerang. The study included 46 patients presenting with wide nasal base and excessive alar flaring. All cases were followed for a mean period of 18 months (range, 8 to 36 months). The laterally oriented vestibular floor excision allowed for maximum preservation of the natural curvature of the alar rim where it meets the nostril floor and upon its closure resulted in a considerable medialization of alar lobule, which significantly reduced the amount of alar flare and the amount of external alar excision needed. This external alar excision measured, on average, 3.8 mm (range, 2 to 8 mm), which is significantly less than that needed when a standard vertical internal excision was used ( P boomerang alar base excision proved to be a safe and effective technique for narrowing the nasal base and elimination of the excessive flaring and resulted in a natural, well-proportioned nasal base with no obvious scarring. © Thieme Medical Publishers.

  5. A pulse-shape discrimination method for improving Gamma-ray spectrometry based on a new digital shaping filter

    Science.gov (United States)

    Qin, Zhang-jian; Chen, Chuan; Luo, Jun-song; Xie, Xing-hong; Ge, Liang-quan; Wu, Qi-fan

    2018-04-01

    It is a usual practice for improving spectrum quality by the mean of designing a good shaping filter to improve signal-noise ratio in development of nuclear spectroscopy. Another method is proposed in the paper based on discriminating pulse-shape and discarding the bad pulse whose shape is distorted as a result of abnormal noise, unusual ballistic deficit or bad pulse pile-up. An Exponentially Decaying Pulse (EDP) generated in nuclear particle detectors can be transformed into a Mexican Hat Wavelet Pulse (MHWP) and the derivation process of the transform is given. After the transform is performed, the baseline drift is removed in the new MHWP. Moreover, the MHWP-shape can be discriminated with the three parameters: the time difference between the two minima of the MHWP, and the two ratios which are from the amplitude of the two minima respectively divided by the amplitude of the maximum in the MHWP. A new type of nuclear spectroscopy was implemented based on the new digital shaping filter and the Gamma-ray spectra were acquired with a variety of pulse-shape discrimination levels. It had manifested that the energy resolution and the peak-Compton ratio were both improved after the pulse-shape discrimination method was used.

  6. Automatic shape model building based on principal geodesic analysis bootstrapping

    DEFF Research Database (Denmark)

    Dam, Erik B; Fletcher, P Thomas; Pizer, Stephen M

    2008-01-01

    iteration are used. Thereby, we gradually capture the shape variation in the training collection better and better. Convergence of the method is explicitly enforced. The method is evaluated on collections of artificial training shapes where the expected shape mean and modes of variation are known by design...

  7. My Experience with Ti-Ni-Based and Ti-Based Shape Memory Alloys

    Science.gov (United States)

    Miyazaki, Shuichi

    2017-12-01

    The present author has been studying shape memory alloys including Cu-Al-Ni, Ti-Ni-based, and Ni-free Ti-based alloys since 1979. This paper reviews the present author's research results for the latter two materials since 1981. The topics on the Ti-Ni-based alloys include the achievement of superelasticity in Ti-Ni alloys through understanding of the role of microstructures consisting of dislocations and precipitates, followed by the contribution to the development of application market of shape memory effect and superelasticity, characterization of the R-phase and monoclinic martensitic transformations, clarification of the basic characteristics of fatigue properties, development of sputter-deposited shape memory thin films and fabrication of prototypes of microactuators utilizing thin films, development of high temperature shape memory alloys, and so on. The topics of Ni-free Ti-based shape memory alloys include the characterization of the orthorhombic phase martensitic transformation and related shape memory effect and superelasticity, the effects of texture, omega phase and adding elements on the martensitic transformation and shape memory properties, clarification of the unique effects of oxygen addition to induce non-linear large elasticity, Invar effect and heating-induced martensitic transformation, and so on.

  8. Plant oil-based shape memory polymer using acrylic monolith

    Directory of Open Access Journals (Sweden)

    T. Tsujimoto

    2015-09-01

    Full Text Available This article deals with the synthesis of a plant oil-based material using acrylic monolith. An acrylic monolith bearing oxirane groups was prepared via simple technique that involved the dissolution of poly(glycidyl methacrylate-comethyl methacrylate (PGMA in ethanolic – aqueous solution by heating and subsequent cooling. The PGMA monolith had topologically porous structure, which was attributed to the phase separation of the polymer solution. The PGMA monolith was impregnated by epoxidized soybean oil (ESO containing thermally-latent catalyst, and the subsequent curing produced a crosslinked material with relatively good transparency. The Young’s modulus and the tensile strength of polyESO/PGMA increased compared with the ESO homopolymer. The strain at break of polyESO/PGMA was larger than that of the ESO homopolymer and crosslinked PGMA. Furthermore, polyESO/PGMA exhibited good shape memory-recovery behavior.

  9. Shape Effects in Nanoparticle-Based Imaging Agents

    Science.gov (United States)

    Culver, Kayla Shani Brook

    At the nanoscale, material properties become highly size and shape dependent. These properties can be manipulated and exploited for a variety of biomedical applications, including sensing, drug delivery, diagnostics, and imaging. In particular, nanoparticles of different materials, sizes and shapes have been developed as high-performance contrast agents for optical, electron, and medical imaging. In this thesis, I focus on gold nanoparticles because they are widely used as contrast agents in multiple types of imaging modalities. Additionally, the surface of gold can be readily functionalized with ligands and the structure of the particles can be manipulated to modulate their performance as imaging agents. The properties of nanoparticles can generate contrast directly. For example, the light scattering properties of gold particles can be visualized in optical microscopy, the high electron density of gold produces contrast in electron microscopy, and the x-ray absorption properties of gold can be detected in medical x-ray and computed tomography imaging. Alternatively, the properties of the nanomaterial can be exploited to modulate the signal produced by other molecules that are bound to the particle surface. The light emission of molecular fluorophores can be quenched or dramatically increased by coupling to the optical field enhancements of gold nanoparticles, and the performance of gadolinium (Gd(III))-based magnetic resonance imaging (MRI) contrast agents can be increased by coupling to the rotational motion of nanoparticles. In this dissertation, I focus specifically on how the structure of star-shaped gold particles (nanostars) can be exploited as single-particle optical probes and to dramatically enhance the relaxivity of Gd(III) bound to the surface. Differential interference contrast (DIC) is a type of wide-field diffraction-limited optical microscopy that is commonly used by biologists to image cells without labels. Here, I demonstrate the DIC can be used

  10. Enhancement of single guide RNA transcription for efficient CRISPR/Cas-based genomic engineering.

    Science.gov (United States)

    Ui-Tei, Kumiko; Maruyama, Shohei; Nakano, Yuko

    2017-06-01

    Genomic engineering using clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) protein is a promising approach for targeting the genomic DNA of virtually any organism in a sequence-specific manner. Recent remarkable advances in CRISPR/Cas technology have made it a feasible system for use in therapeutic applications and biotechnology. In the CRISPR/Cas system, a guide RNA (gRNA), interacting with the Cas protein, recognizes a genomic region with sequence complementarity, and the double-stranded DNA at the target site is cleaved by the Cas protein. A widely used gRNA is an RNA polymerase III (pol III)-driven single gRNA (sgRNA), which is produced by artificial fusion of CRISPR RNA (crRNA) and trans-activation crRNA (tracrRNA). However, we identified a TTTT stretch, known as a termination signal of RNA pol III, in the scaffold region of the sgRNA. Here, we revealed that sgRNA carrying a TTTT stretch reduces the efficiency of sgRNA transcription due to premature transcriptional termination, and decreases the efficiency of genome editing. Unexpectedly, it was also shown that the premature terminated sgRNA may have an adverse effect of inducing RNA interference. Such disadvantageous effects were avoided by substituting one base in the TTTT stretch.

  11. Heterogeneity to Homogeneity: Synthesis, Base Pairing, and Ligation Studies of 4',3'-XyluloNA/RNA and TNA/RNA Chimeric Sequences

    Science.gov (United States)

    Bhowmik, S.; Stoop, M.; Krishnamurthy, R.

    2017-07-01

    Based on the reality of "prebiotic clutter," we herein present an alternate model for pre-RNA to RNA transition, which starts, not with homogeneous-backbone system, but rather with mixtures of heterogeneous-backbone of chimeric "pre-RNA/RNA."

  12. RNA interference-based therapeutics for human immunodeficiency virus HIV-1 treatment: synthetic siRNA or vector-based shRNA?

    Science.gov (United States)

    Subramanya, Sandesh; Kim, Sang-Soo; Manjunath, N; Shankar, Premlata

    2010-02-01

    Despite the clinical benefits of highly active antiretroviral therapy (HAART), the prospect of life-long antiretroviral treatment poses significant problems, which has spurred interest in developing new drugs and strategies to treat HIV infection and eliminate persistent viral reservoirs. RNAi has emerged as a therapeutic possibility for HIV. We discuss progress in overcoming hurdles to translating transient and stable RNAi enabling technologies to clinical application for HIV; covering the past 2 - 3 years. HIV inhibition can be achieved by transfection of chemically or enzymatically synthesized siRNAs or by DNA-based vector systems expressing short hairpin RNAs (shRNAs) that are processed intracellularly into siRNA. We compare these approaches, focusing on technical and safety issues that will guide the choice of strategy for clinical use. Introduction of synthetic siRNA into cells or its stable endogenous production using vector-driven shRNA have been shown to suppress HIV replication in vitro and, in some instances, in vivo. Each method has advantages and limitations in terms of ease of delivery, duration of silencing, emergence of escape mutants and potential toxicity. Both appear to have potential as future therapeutics for HIV, once the technical and safety issues of each approach are overcome.

  13. Phylogenetic relationships of Salmonella based on rRNA sequences

    DEFF Research Database (Denmark)

    Christensen, H.; Nordentoft, Steen; Olsen, J.E.

    1998-01-01

    separated by 16S rRNA analysis and found to be closely related to the Escherichia coli and Shigella complex by both 16S and 23S rRNA analyses. The diphasic serotypes S. enterica subspp. I and VI were separated from the monophasic serotypes subspp. IIIa and IV, including S. bongori, by 23S rRNA sequence...

  14. Shape Memory Alloy-Based Periodic Cellular Structures, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase I effort will develop and demonstrate an innovative shape memory alloy (SMA) periodic cellular structural technology. Periodic cellular structures...

  15. A thermostable messenger RNA based vaccine against rabies.

    Science.gov (United States)

    Stitz, Lothar; Vogel, Annette; Schnee, Margit; Voss, Daniel; Rauch, Susanne; Mutzke, Thorsten; Ketterer, Thomas; Kramps, Thomas; Petsch, Benjamin

    2017-12-01

    Although effective rabies virus vaccines have been existing for decades, each year, rabies virus infections still cause around 50.000 fatalities worldwide. Most of these cases occur in developing countries, where these vaccines are not available. The reasons for this are the prohibitive high costs of cell culture or egg grown rabies virus vaccines and the lack of a functional cold chain in many regions in which rabies virus is endemic. Here, we describe the excellent temperature resistance of a non-replicating mRNA based rabies virus vaccine encoding the rabies virus glycoprotein (RABV-G). Prolonged storage of the vaccine from -80°C to up to +70°C for several months did not impact the protective capacity of the mRNA vaccine. Efficacy after storage was demonstrated by the induction of rabies specific virus neutralizing antibodies and protection in mice against lethal rabies infection. Moreover, storing the vaccine at oscillating temperatures between +4° and +56°C for 20 cycles in order to simulate interruptions of the cold chain during vaccine transport, did not affect the vaccine's immunogenicity and protective characteristics, indicating that maintenance of a cold chain is not essential for this vaccine.

  16. Shape based kinetic outlier detection in real-time PCR

    Directory of Open Access Journals (Sweden)

    D'Atri Mario

    2010-04-01

    Full Text Available Abstract Background Real-time PCR has recently become the technique of choice for absolute and relative nucleic acid quantification. The gold standard quantification method in real-time PCR assumes that the compared samples have similar PCR efficiency. However, many factors present in biological samples affect PCR kinetic, confounding quantification analysis. In this work we propose a new strategy to detect outlier samples, called SOD. Results Richards function was fitted on fluorescence readings to parameterize the amplification curves. There was not a significant correlation between calculated amplification parameters (plateau, slope and y-coordinate of the inflection point and the Log of input DNA demonstrating that this approach can be used to achieve a "fingerprint" for each amplification curve. To identify the outlier runs, the calculated parameters of each unknown sample were compared to those of the standard samples. When a significant underestimation of starting DNA molecules was found, due to the presence of biological inhibitors such as tannic acid, IgG or quercitin, SOD efficiently marked these amplification profiles as outliers. SOD was subsequently compared with KOD, the current approach based on PCR efficiency estimation. The data obtained showed that SOD was more sensitive than KOD, whereas SOD and KOD were equally specific. Conclusion Our results demonstrated, for the first time, that outlier detection can be based on amplification shape instead of PCR efficiency. SOD represents an improvement in real-time PCR analysis because it decreases the variance of data thus increasing the reliability of quantification.

  17. Confidence of model based shape reconstruction from sparse data

    DEFF Research Database (Denmark)

    Baka, N.; de Bruijne, Marleen; Reiber, J. H. C.

    2010-01-01

    Statistical shape models (SSM) are commonly applied for plausible interpolation of missing data in medical imaging. However, when fitting a shape model to sparse information, many solutions may fit the available data. In this paper we derive a constrained SSM to fit noisy sparse input landmarks...

  18. Branch length similarity entropy-based descriptors for shape representation

    Science.gov (United States)

    Kwon, Ohsung; Lee, Sang-Hee

    2017-11-01

    In previous studies, we showed that the branch length similarity (BLS) entropy profile could be successfully used for the shape recognition such as battle tanks, facial expressions, and butterflies. In the present study, we proposed new descriptors, roundness, symmetry, and surface roughness, for the recognition, which are more accurate and fast in the computation than the previous descriptors. The roundness represents how closely a shape resembles to a circle, the symmetry characterizes how much one shape is similar with another when the shape is moved in flip, and the surface roughness quantifies the degree of vertical deviations of a shape boundary. To evaluate the performance of the descriptors, we used the database of leaf images with 12 species. Each species consisted of 10 - 20 leaf images and the total number of images were 160. The evaluation showed that the new descriptors successfully discriminated the leaf species. We believe that the descriptors can be a useful tool in the field of pattern recognition.

  19. Factors influencing shape memory effect and phase transformation behaviour of Fe-Mn-Si based shape memory alloys

    International Nuclear Information System (INIS)

    Li, H.; Dunne, D.; Kennon, N.

    1999-01-01

    The objective of this research work was to investigate the factors influencing the shape memory effect and phase transformation behaviour of three Fe-Mn-Si based shape memory alloys: Fe-28Mn-6Si, Fe-13Mn-5Si-10Cr-6Ni and Fe-20Mn-6Si-7Cr-1Cu. The research results show that the shape memory capacity of Fe-Mn-Si based shape memory alloys varies with annealing temperature, and this effect can be explained in terms of the effect of annealing on γ ε transformation. The nature and concentration of defects in austenite are strongly affected by annealing conditions. A high annealing temperature results in a low density of stacking faults, leading to a low nucleation rate during stress induced γ→ε transformation. The growth of ε martensite plates is favoured rather than the formation of new ε martensite plates. Coarse martensite plates produce high local transformation strains which can be accommodated by local slip deformation, leading to a reduction in the reversibility of the martensitic transformation and to a degradation of the shape memory effect. Annealing at low temperatures (≤673 K) for reasonable times does not eliminate complex defects (dislocation jogs, kinks and vacancy clusters) created by hot and cold working strains. These defects can retard the movement and rearrangement of Shockley partial dislocations, i.e. suppress γ→ε transformation, also leading to a degradation of shape memory effect. Annealing at about 873 K was found to be optimal to form the dislocation structures which are favourable for stress induced martensitic transformation, thus resulting in the best shape memory behaviour. (orig.)

  20. Correction tool for Active Shape Model based lumbar muscle segmentation.

    Science.gov (United States)

    Valenzuela, Waldo; Ferguson, Stephen J; Ignasiak, Dominika; Diserens, Gaelle; Vermathen, Peter; Boesch, Chris; Reyes, Mauricio

    2015-08-01

    In the clinical environment, accuracy and speed of the image segmentation process plays a key role in the analysis of pathological regions. Despite advances in anatomic image segmentation, time-effective correction tools are commonly needed to improve segmentation results. Therefore, these tools must provide faster corrections with a low number of interactions, and a user-independent solution. In this work we present a new interactive correction method for correcting the image segmentation. Given an initial segmentation and the original image, our tool provides a 2D/3D environment, that enables 3D shape correction through simple 2D interactions. Our scheme is based on direct manipulation of free form deformation adapted to a 2D environment. This approach enables an intuitive and natural correction of 3D segmentation results. The developed method has been implemented into a software tool and has been evaluated for the task of lumbar muscle segmentation from Magnetic Resonance Images. Experimental results show that full segmentation correction could be performed within an average correction time of 6±4 minutes and an average of 68±37 number of interactions, while maintaining the quality of the final segmentation result within an average Dice coefficient of 0.92±0.03.

  1. Shape Memory Alloy (SMA)-Based Launch Lock

    Science.gov (United States)

    Badescu, Mircea; Bao, Xiaoqi; Bar-Cohen, Yoseph

    2014-01-01

    Most NASA missions require the use of a launch lock for securing moving components during the launch or securing the payload before release. A launch lock is a device used to prevent unwanted motion and secure the controlled components. The current launch locks are based on pyrotechnic, electro mechanically or NiTi driven pin pullers and they are mostly one time use mechanisms that are usually bulky and involve a relatively high mass. Generally, the use of piezoelectric actuation provides high precession nanometer accuracy but it relies on friction to generate displacement. During launch, the generated vibrations can release the normal force between the actuator components allowing shaft's free motion which could result in damage to the actuated structures or instruments. This problem is common to other linear actuators that consist of a ball screw mechanism. The authors are exploring the development of a novel launch lock mechanism that is activated by a shape memory alloy (SMA) material ring, a rigid element and an SMA ring holding flexure. The proposed design and analytical model will be described and discussed in this paper.

  2. Knowledge and method base for shape memory alloys

    Energy Technology Data Exchange (ETDEWEB)

    Welp, E.G.; Breidert, J. [Ruhr-University Bochum, Institute of Engineering Design, 44780 Bochum (Germany)

    2004-05-01

    It is often impossible for design engineers to decide whether it is possible to use shape memory alloys (SMA) for a particular task. In case of a decision to use SMA for product development, design engineers normally do not know in detail how to proceed in a correct and beneficial way. In order to support design engineers who have no previous knowledge about SMA and to assist in the transfer of results from basic research to industrial practice, an essential knowledge and method base has been developed. Through carefully conducted literature studies and patent analysis material and design information could be collected. All information is implemented into a computer supported knowledge and method base that provides design information with a particular focus on the conceptual and embodiment design phase. The knowledge and method base contains solution principles and data about effects, material and manufacturing as well as design guidelines and calculation methods for dimensioning and optimization. A browser-based user interface ensures that design engineers have immediate access to the latest version of the knowledge and method base. In order to ensure a user friendly application, an evaluation with several test users has been carried out. Reactions of design engineers from the industrial sector underline the need for support related to knowledge on SMA. (Abstract Copyright [2004], Wiley Periodicals, Inc.) [German] Fuer Konstrukteure ist es haeufig schwierig zu entscheiden, ob sich der Einsatz von Formgedaechtnislegierungen (FGL) fuer eine bestimmte Aufgabe eignet. Fuer den Fall, dass FGL fuer die Produktentwicklung genutzt werden sollen, besitzen Ingenieure zumeist nur unzureichende Detailkenntnisse, um Formgedaechtnislegierungen richtig und in vorteilhafter Weise anwenden zu koennen. Zur Unterstuetzung von Konstrukteuren, die ueber kein Vorwissen und keine Erfahrungen zu FGL verfuegen und zum Transfer von Forschungsergebnissen in die industrielle Praxis, ist eine

  3. Shape memory alloy wire-based smart natural rubber bearing

    International Nuclear Information System (INIS)

    Hedayati Dezfuli, F; Shahria Alam, M

    2013-01-01

    In this study, two types of smart elastomeric bearings are presented using shape memory alloy (SMA) wires. Due to the unique characteristics of SMAs, such as the superelastic effect and the recentering capability, the residual deformation in SMA-based natural rubber bearings (SMA-NRBs) is significantly reduced whereas the energy dissipation capacity is increased. Two different configurations of SMA wires incorporated in elastomeric bearings are considered. The effect of several parameters, including the shear strain amplitude, the type of SMA, the aspect ratio of the base isolator, the thickness of SMA wire, and the amount of pre-strain in the wires on the performance of SMA-NRBs is investigated. Rubber bearings are composed of natural rubber layers bonded to steel shims as reinforcement. Results show that ferrous SMA wire, FeNiCuAlTaB, with 13.5% superelastic strain and a very low austenite finish temperature (−62 °C), is the best candidate to be used in SMA-NRBs subjected to high shear strain amplitudes. In terms of the lateral flexibility and wire strain level, the smart rubber bearing with a cross configuration of SMA wires is more efficient. Moreover, the cross configuration can be implemented in high-aspect-ratio elastomeric bearings since the strain induced in the wire does not exceed the superelastic range. When cross SMA wires with 2% pre-strain are used in a smart NRB, the dissipated energy is increased by 74% and the residual deformation is decreased by 15%. (paper)

  4. RNA Detection Based on Graphene Field-Effect Transistor Biosensor

    Directory of Open Access Journals (Sweden)

    Meng Tian

    2018-01-01

    Full Text Available Graphene has attracted much attention in biosensing applications due to its unique properties. In this paper, the monolayer graphene was grown by chemical vapor deposition (CVD method. Using the graphene as the electric channel, we have fabricated a graphene field-effect transistor (G-FET biosensor that can be used for label-free detection of RNA. Compared with conventional method, the G-FET RNA biosensor can be run in low cost, be time-saving, and be miniaturized for RNA measurement. The sensors show high performance and achieve the RNA detection sensitivity as low as 0.1 fM, which is two orders of magnitude lower than the previously reports. Moreover, the G-FET biosensor can readily distinguish target RNA from noncomplementary RNA, showing high selectivity for RNA detection. The developed G-FET RNA biosensor with high sensitivity, fast analysis speed, and simple operation may provide a new feasible direction for RNA research and biosensing.

  5. Mechanism of action of mRNA-based vaccines.

    Science.gov (United States)

    Iavarone, Carlo; O'hagan, Derek T; Yu, Dong; Delahaye, Nicolas F; Ulmer, Jeffrey B

    2017-09-01

    The present review summarizes the growing body of work defining the mechanisms of action of this exciting new vaccine technology that should allow rational approaches in the design of next generation mRNA vaccines. Areas covered: Bio-distribution of mRNA, localization of antigen production, role of the innate immunity, priming of the adaptive immune response, route of administration and effects of mRNA delivery systems. Expert commentary: In the last few years, the development of RNA vaccines had a fast growth, the rising number of proof will enable rational approaches to improving the effectiveness and safety of this modern class of medicine.

  6. A probabilistic model for component-based shape synthesis

    KAUST Repository

    Kalogerakis, Evangelos; Chaudhuri, Siddhartha; Koller, Daphne; Koltun, Vladlen

    2012-01-01

    represents probabilistic relationships between properties of shape components, and relates them to learned underlying causes of structural variability within the domain. These causes are treated as latent variables, leading to a compact representation

  7. Shape Memory Alloy-Based Periodic Cellular Structures, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase II effort will continue to develop and demonstrate an innovative shape memory alloy (SMA) periodic cellular structural technology. Periodic cellular...

  8. TiAu based shape memory alloys for high temperature applications

    International Nuclear Information System (INIS)

    Wadood, Abdul; Yamabe-Mitarai, Yoko; Hosoda, Hideki

    2014-01-01

    TiAu (equiatomic) exhibits phase transformaion from B2 (ordered bcc) to thermo-elastic orthorhombic B19 martensite at about 875K and thus TiAu is categorized as high temperature shape memory alloy. In this study, recent research and developments related to TiAu based high temperature shape memory alloys will be discussed in the Introduction part. Then some results of our research group related to strengthening of TiAu based high temperature shape memory alloys will be presented. Potential of TiAu based shape memory alloys for high temperature shape memory materials applications will also be discussed

  9. RNA interference-based resistance against a legume mastrevirus

    Directory of Open Access Journals (Sweden)

    Mansoor Shahid

    2011-11-01

    Full Text Available Abstract Background RNA interference (RNAi is a homology-dependant gene silencing mechanism and has been widely used to engineer resistance in plants against RNA viruses. However, its usefulness in delivering resistance against plant DNA viruses belonging to family Geminiviridae is still being debated. Although the RNAi approach has been shown, using a transient assay, to be useful in countering monocotyledonous plant-infecting geminiviruses of the genus Mastrevirus, it has yet to be investigated as a means of delivering resistance to dicot-infecting mastreviruses. Chickpea chlorotic dwarf Pakistan virus (CpCDPKV is a legume-infecting mastrevirus that affects chickpea and other leguminous crops in Pakistan. Results Here a hairpin (hpRNAi construct containing sequences encompassing part of replication-associated protein gene, intergenic region and part of the movement protein gene of CpCDPKV under the control of the Cauliflower mosaic virus 35S promoter has been produced and stably transformed into Nicotiana benthamiana. Plants harboring the hairpin construct were challenged with CpCDPKV. All non-transgenic N. benthamiana plants developed symptoms of CpCDPKV infection within two weeks post-inoculation. In contrast, none of the inoculated transgenic plants showed symptoms of infection and no viral DNA could be detected by Southern hybridization. A real-time quantitative PCR analysis identified very low-level accumulation of viral DNA in the inoculated transgenic plants. Conclusions The results presented show that the RNAi-based resistance strategy is useful in protecting plants from a dicot-infecting mastrevirus. The very low levels of virus detected in plant tissue of transgenic plants distal to the inoculation site suggest that virus movement and/or viral replication was impaired leading to plants that showed no discernible signs of virus infection.

  10. Slices: A shape-proxy based on planar sections

    KAUST Repository

    McCrae, James

    2011-12-01

    Minimalist object representations or shape-proxies that spark and inspire human perception of shape remain an incompletely understood, yet powerful aspect of visual communication. We explore the use of planar sections, i.e., the contours of intersection of planes with a 3D object, for creating shape abstractions, motivated by their popularity in art and engineering. We first perform a user study to show that humans do define consistent and similar planar section proxies for common objects. Interestingly, we observe a strong correlation between user-defined planes and geometric features of objects. Further we show that the problem of finding the minimum set of planes that capture a set of 3D geometric shape features is both NP-hard and not always the proxy a user would pick. Guided by the principles inferred from our user study, we present an algorithm that progressively selects planes to maximize feature coverage, which in turn influence the selection of subsequent planes. The algorithmic framework easily incorporates various shape features, while their relative importance values are computed and validated from the user study data. We use our algorithm to compute planar slices for various objects, validate their utility towards object abstraction using a second user study, and conclude showing the potential applications of the extracted planar slice shape proxies.

  11. Design of digital trapezoidal shaping filter based on LabVIEW

    International Nuclear Information System (INIS)

    Liu Yujuan; Qin Guoxiu; Yang Zhihui; Zhang Xiaodong

    2013-01-01

    It describes the design of a digital trapezoidal shaping filter to nuclear signals based on LabVIEW. A method of optimizing the trapezoidal shaping filter's parameters was presented and tested, and the test results of the effect of shaping filter algorithm were studied. (authors)

  12. Ultrasound Common Carotid Artery Segmentation Based on Active Shape Model

    Science.gov (United States)

    Yang, Xin; Jin, Jiaoying; Xu, Mengling; Wu, Huihui; He, Wanji; Yuchi, Ming; Ding, Mingyue

    2013-01-01

    Carotid atherosclerosis is a major reason of stroke, a leading cause of death and disability. In this paper, a segmentation method based on Active Shape Model (ASM) is developed and evaluated to outline common carotid artery (CCA) for carotid atherosclerosis computer-aided evaluation and diagnosis. The proposed method is used to segment both media-adventitia-boundary (MAB) and lumen-intima-boundary (LIB) on transverse views slices from three-dimensional ultrasound (3D US) images. The data set consists of sixty-eight, 17 × 2 × 2, 3D US volume data acquired from the left and right carotid arteries of seventeen patients (eight treated with 80 mg atorvastatin and nine with placebo), who had carotid stenosis of 60% or more, at baseline and after three months of treatment. Manually outlined boundaries by expert are adopted as the ground truth for evaluation. For the MAB and LIB segmentations, respectively, the algorithm yielded Dice Similarity Coefficient (DSC) of 94.4% ± 3.2% and 92.8% ± 3.3%, mean absolute distances (MAD) of 0.26 ± 0.18 mm and 0.33 ± 0.21 mm, and maximum absolute distances (MAXD) of 0.75 ± 0.46 mm and 0.84 ± 0.39 mm. It took 4.3 ± 0.5 mins to segment single 3D US images, while it took 11.7 ± 1.2 mins for manual segmentation. The method would promote the translation of carotid 3D US to clinical care for the monitoring of the atherosclerotic disease progression and regression. PMID:23533535

  13. Ultrasound Common Carotid Artery Segmentation Based on Active Shape Model

    Directory of Open Access Journals (Sweden)

    Xin Yang

    2013-01-01

    Full Text Available Carotid atherosclerosis is a major reason of stroke, a leading cause of death and disability. In this paper, a segmentation method based on Active Shape Model (ASM is developed and evaluated to outline common carotid artery (CCA for carotid atherosclerosis computer-aided evaluation and diagnosis. The proposed method is used to segment both media-adventitia-boundary (MAB and lumen-intima-boundary (LIB on transverse views slices from three-dimensional ultrasound (3D US images. The data set consists of sixty-eight, 17 × 2 × 2, 3D US volume data acquired from the left and right carotid arteries of seventeen patients (eight treated with 80 mg atorvastatin and nine with placebo, who had carotid stenosis of 60% or more, at baseline and after three months of treatment. Manually outlined boundaries by expert are adopted as the ground truth for evaluation. For the MAB and LIB segmentations, respectively, the algorithm yielded Dice Similarity Coefficient (DSC of 94.4% ± 3.2% and 92.8% ± 3.3%, mean absolute distances (MAD of 0.26 ± 0.18 mm and 0.33 ± 0.21 mm, and maximum absolute distances (MAXD of 0.75 ± 0.46 mm and 0.84 ± 0.39 mm. It took 4.3 ± 0.5 mins to segment single 3D US images, while it took 11.7 ± 1.2 mins for manual segmentation. The method would promote the translation of carotid 3D US to clinical care for the monitoring of the atherosclerotic disease progression and regression.

  14. Laser beam shaping design based on micromirror array

    Science.gov (United States)

    Fang, Han; Su, Bida; Liu, Jiaguo; Fan, Xiaoli; Jing, Wang

    2017-10-01

    In the practical application of the laser, it is necessary to use the laser beam shaping technology to shape the output beam of laser device to the uniform light intensity distribution. The shaping divergent optical system of compound eye integrator way is composed of beam expanding mirror group and lens array. Its working principle is to expand the output laser to a certain size of caliber, and then divide the beam with lens array into multiple sub beam, where the lens unit of lens array can control the divergence angle of sub beam through the design of focal length, with mutual superposition of the sub beam in far field, to make up for the nonuniformity of beam, so that the radiant exitance on the radiated surface may become uniform. In this paper, we use a reflective microlens array to realize the laser beam shaping. By through of the practical optical path model established, the ray tracing is carried out and the simulation results for single-mode Gaussian beam with noise circumstance is provided. The analysis results show that the laser beam shaping under different inputs can be effectively realized by use of microlens array. All the energy is within the signal window, with a high energy efficiency of more than 90%; The measured surface has a better uniformity, and the uniformity is better than 99.5% at 150m.

  15. Phases stability of shape memory alloys Cu based under irradiation

    International Nuclear Information System (INIS)

    Zelaya, Maria Eugenia

    2006-01-01

    The effects of irradiation on the relative phase stability of phases related by a martensitic transformation in copper based shape memory alloys were studied in this work.Different kind of particles and energies were employed in the irradiation experiments.The first kind of irradiation was performed with 2,6 MeV electrons, the second one with 170 keV and 300 keV Cu ions and the third one with swift heavy ions (Kr, Xe, Au) with energies between 200 and 600 MeV.Stabilization of the 18 R martensite in Cu-Zn-Al-Ni induced by electron irradiation was studied.The results were compared to those of the stabilization induced by quenching and ageing in the same alloy, and the ones obtained by irradiation in 18 R-Cu-Zn-Al alloys.The effects of Cu irradiation over b phase were analyzed with several electron microscopy techniques including: scanning electron microscopy (S E M), high resolution electron microscopy (H R E M), micro diffraction and X-ray energy dispersive spectroscopy (E D S). Structural changes in Cu-Zn-Al b phase into a closed packed structure were induced by Cu ion implantation.The closed packed structures depend on the irradiation fluence.Based on these results, the interface between these structures (closed packed and b) and the stability of disordered phases were analyzed. It was also compared the evolution of long range order in the Cu-Zn-Al and in the Cu-Zn-Al-Ni b phase as a function of fluence.The evolution of the g phase was also compared. Both results were discussed in terms of the mobility of irradiation induced point defects.Finally, the effects induced by swift heavy ions in b phase and 18 R martensite were studied. The results of the irradiation in b phase were qualitatively similar to those produced by irradiation with lower energies. On the contrary, nano metric defects were found in the irradiated 18 R martensite.These defects were characterized by H R E M.The characteristic contrast of the defects was associated to a local change in the

  16. An efficient and robutst method for shape-based image retrieval

    International Nuclear Information System (INIS)

    Salih, N.D.; Besar, R.; Abas, F.S.

    2007-01-01

    Shapes can be thought as being the words oft he visual language. Shape boundaries need to be simplified and estimated in a wide variety of image analysis applications. Representation and description of Shapes is one of the major problems in content-based image retrieval (CBIR). This paper present an a novel method for shape representation and description named block-based shape representation (BSR), which is capable of extracting reliable information of the object outline in a concise manner. Our technique is translation, scale, and rotation invariant. It works well on different types of shapes and fast enough for use in real-time. This technique has been implemented and evaluated in order to analyze its accuracy and Efficiency. Based on the experimental results, we urge that the proposed BSR is a compact and reliable shape representation method. (author)

  17. Shape analysis of isoseismals based on empirical and synthetic data

    International Nuclear Information System (INIS)

    Molchan, G.; Panza, G.F.

    2000-11-01

    We present an attempt to compare modeled ground motion acceleration fields with macroseismic observations. Two techniques for the representation of the observed intensities by isoseismals, a smoothing technique and one which visualizes the local uncertainty of an isoseismal, are tested with synthetic and observed data. We show how noise in the data and irregularities in the distribution of observation sites affect the resolution of the isoseismal's shape. In addition to ''standard'' elongated shapes, we identify cross-like patterns in the macroseismic observations for two Italian earthquakes of strike-slip type; similar patterns are displayed by the theoretical peak acceleration fields calculated assuming the point source models given in the literature. (author)

  18. Engineered ribosomal RNA operon copy-number variants of E. coli reveal the evolutionary trade-offs shaping rRNA operon number

    Science.gov (United States)

    Gyorfy, Zsuzsanna; Draskovits, Gabor; Vernyik, Viktor; Blattner, Frederick F.; Gaal, Tamas; Posfai, Gyorgy

    2015-01-01

    Ribosomal RNA (rrn) operons, characteristically present in several copies in bacterial genomes (7 in E. coli), play a central role in cellular physiology. We investigated the factors determining the optimal number of rrn operons in E. coli by constructing isogenic variants with 5–10 operons. We found that the total RNA and protein content, as well as the size of the cells reflected the number of rrn operons. While growth parameters showed only minor differences, competition experiments revealed a clear pattern: 7–8 copies were optimal under conditions of fluctuating, occasionally rich nutrient influx and lower numbers were favored in stable, nutrient-limited environments. We found that the advantages of quick adjustment to nutrient availability, rapid growth and economic regulation of ribosome number all contribute to the selection of the optimal rrn operon number. Our results suggest that the wt rrn operon number of E. coli reflects the natural, ‘feast and famine’ life-style of the bacterium, however, different copy numbers might be beneficial under different environmental conditions. Understanding the impact of the copy number of rrn operons on the fitness of the cell is an important step towards the creation of functional and robust genomes, the ultimate goal of synthetic biology. PMID:25618851

  19. Shortcomings of short hairpin RNA-based transgenic RNA interference in mouse oocytes

    Czech Academy of Sciences Publication Activity Database

    Sarnová, Lenka; Malík, Radek; Sedláček, Radislav; Svoboda, Petr

    2010-01-01

    Roč. 9, č. 8 (2010), s. 1-10 ISSN 1477-5751 R&D Project s: GA MŠk ME09039 Grant - others:EMBO SDIG(DE) project 1483 Institutional research plan: CEZ:AV0Z50520514 Keywords : transgenic RNAi * shRNA * oocyte Subject RIV: EB - Genetics ; Molecular Biology http://www.jnrbm.com/content/9/1/8

  20. Shortcomings of short hairpin RNA-based transgenic RNA interference in mouse oocytes

    Czech Academy of Sciences Publication Activity Database

    Sarnová, Lenka; Malík, Radek; Sedláček, Radislav; Svoboda, Petr

    2010-01-01

    Roč. 9, č. 8 (2010), s. 1-10 ISSN 1477-5751 R&D Projects: GA MŠk ME09039 Grant - others:EMBO SDIG(DE) project 1483 Institutional research plan: CEZ:AV0Z50520514 Keywords : transgenic RNAi * shRNA * oocyte Subject RIV: EB - Genetics ; Molecular Biology http://www.jnrbm.com/content/9/1/8

  1. High-Throughput Sequencing Based Methods of RNA Structure Investigation

    DEFF Research Database (Denmark)

    Kielpinski, Lukasz Jan

    In this thesis we describe the development of four related methods for RNA structure probing that utilize massive parallel sequencing. Using them, we were able to gather structural data for multiple, long molecules simultaneously. First, we have established an easy to follow experimental...... and computational protocol for detecting the reverse transcription termination sites (RTTS-Seq). This protocol was subsequently applied to hydroxyl radical footprinting of three dimensional RNA structures to give a probing signal that correlates well with the RNA backbone solvent accessibility. Moreover, we applied...

  2. Adaptive Shape Kernel-Based Mean Shift Tracker in Robot Vision System

    Directory of Open Access Journals (Sweden)

    Chunmei Liu

    2016-01-01

    Full Text Available This paper proposes an adaptive shape kernel-based mean shift tracker using a single static camera for the robot vision system. The question that we address in this paper is how to construct such a kernel shape that is adaptive to the object shape. We perform nonlinear manifold learning technique to obtain the low-dimensional shape space which is trained by training data with the same view as the tracking video. The proposed kernel searches the shape in the low-dimensional shape space obtained by nonlinear manifold learning technique and constructs the adaptive kernel shape in the high-dimensional shape space. It can improve mean shift tracker performance to track object position and object contour and avoid the background clutter. In the experimental part, we take the walking human as example to validate that our method is accurate and robust to track human position and describe human contour.

  3. Adaptive Shape Kernel-Based Mean Shift Tracker in Robot Vision System

    Science.gov (United States)

    2016-01-01

    This paper proposes an adaptive shape kernel-based mean shift tracker using a single static camera for the robot vision system. The question that we address in this paper is how to construct such a kernel shape that is adaptive to the object shape. We perform nonlinear manifold learning technique to obtain the low-dimensional shape space which is trained by training data with the same view as the tracking video. The proposed kernel searches the shape in the low-dimensional shape space obtained by nonlinear manifold learning technique and constructs the adaptive kernel shape in the high-dimensional shape space. It can improve mean shift tracker performance to track object position and object contour and avoid the background clutter. In the experimental part, we take the walking human as example to validate that our method is accurate and robust to track human position and describe human contour. PMID:27379165

  4. Slices: A shape-proxy based on planar sections

    KAUST Repository

    McCrae, James; Singh, Karan S.; Mitra, Niloy J.

    2011-01-01

    of intersection of planes with a 3D object, for creating shape abstractions, motivated by their popularity in art and engineering. We first perform a user study to show that humans do define consistent and similar planar section proxies for common objects

  5. A Shape-Based Account for Holistic Face Processing

    Science.gov (United States)

    Zhao, Mintao; Bülthoff, Heinrich H.; Bülthoff, Isabelle

    2016-01-01

    Faces are processed holistically, so selective attention to 1 face part without any influence of the others often fails. In this study, 3 experiments investigated what type of facial information (shape or surface) underlies holistic face processing and whether generalization of holistic processing to nonexperienced faces requires extensive…

  6. PseudoBase: a database with RNA pseudoknots.

    Science.gov (United States)

    van Batenburg, F H; Gultyaev, A P; Pleij, C W; Ng, J; Oliehoek, J

    2000-01-01

    PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo-knots. It can be reached at http://wwwbio. Leiden Univ.nl/ approximately Batenburg/PKB.html. This page will direct the user to a retrieval page from where a particular pseudoknot can be chosen, or to a submission page which enables the user to add pseudoknot information to the database or to an informative page that elaborates on the various aspects of the database. For each pseudoknot, 12 items are stored, e.g. the nucleotides of the region that contains the pseudoknot, the stem positions of the pseudoknot, the EMBL accession number of the sequence that contains this pseudoknot and the support that can be given regarding the reliability of the pseudoknot. Access is via a small number of steps, using 16 different categories. The development process was done by applying the evolutionary methodology for software development rather than by applying the methodology of the classical waterfall model or the more modern spiral model.

  7. Quantitative Outline-based Shape Analysis and Classification of Planetary Craterforms using Supervised Learning Models

    Science.gov (United States)

    Slezak, Thomas Joseph; Radebaugh, Jani; Christiansen, Eric

    2017-10-01

    The shapes of craterform morphology on planetary surfaces provides rich information about their origins and evolution. While morphologic information provides rich visual clues to geologic processes and properties, the ability to quantitatively communicate this information is less easily accomplished. This study examines the morphology of craterforms using the quantitative outline-based shape methods of geometric morphometrics, commonly used in biology and paleontology. We examine and compare landforms on planetary surfaces using shape, a property of morphology that is invariant to translation, rotation, and size. We quantify the shapes of paterae on Io, martian calderas, terrestrial basaltic shield calderas, terrestrial ash-flow calderas, and lunar impact craters using elliptic Fourier analysis (EFA) and the Zahn and Roskies (Z-R) shape function, or tangent angle approach to produce multivariate shape descriptors. These shape descriptors are subjected to multivariate statistical analysis including canonical variate analysis (CVA), a multiple-comparison variant of discriminant analysis, to investigate the link between craterform shape and classification. Paterae on Io are most similar in shape to terrestrial ash-flow calderas and the shapes of terrestrial basaltic shield volcanoes are most similar to martian calderas. The shapes of lunar impact craters, including simple, transitional, and complex morphology, are classified with a 100% rate of success in all models. Multiple CVA models effectively predict and classify different craterforms using shape-based identification and demonstrate significant potential for use in the analysis of planetary surfaces.

  8. Shape based automated detection of pulmonary nodules with surface feature based false positive reduction

    International Nuclear Information System (INIS)

    Nomura, Y.; Itoh, H.; Masutani, Y.; Ohtomo, K.; Maeda, E.; Yoshikawa, T.; Hayashi, N.

    2007-01-01

    We proposed a shape based automated detection of pulmonary nodules with surface feature based false positive (FP) reduction. In the proposed system, the FP existing in internal of vessel bifurcation is removed using extracted surface of vessels and nodules. From the validation with 16 chest CT scans, we find that the proposed CAD system achieves 18.7 FPs/scan at 90% sensitivity, and 7.8 FPs/scan at 80% sensitivity. (orig.)

  9. In Silico Meets In Vivo: Towards Computational CRISPR-Based sgRNA Design.

    Science.gov (United States)

    Chuai, Guo-Hui; Wang, Qi-Long; Liu, Qi

    2017-01-01

    CRISPR-based genome editing has been widely implemented in various cell types. In silico single guide RNA (sgRNA) design is a key step for successful gene editing using the CRISPR system, and continuing efforts are aimed at refining in silico sgRNA design with high on-target efficacy and reduced off-target effects. Many sgRNA design tools are available, but careful assessments of their application scenarios and performance benchmarks across different types of genome-editing data are needed. Efficient in silico models can be built that integrate current heterogeneous genome-editing data to derive unbiased sgRNA design rules and identify key features for improving sgRNA design. Comprehensive evaluation of on-target and off-target effects of sgRNA will allow more precise genome editing and gene therapies using the CRISPR system. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Active contour-based visual tracking by integrating colors, shapes, and motions.

    Science.gov (United States)

    Hu, Weiming; Zhou, Xue; Li, Wei; Luo, Wenhan; Zhang, Xiaoqin; Maybank, Stephen

    2013-05-01

    In this paper, we present a framework for active contour-based visual tracking using level sets. The main components of our framework include contour-based tracking initialization, color-based contour evolution, adaptive shape-based contour evolution for non-periodic motions, dynamic shape-based contour evolution for periodic motions, and the handling of abrupt motions. For the initialization of contour-based tracking, we develop an optical flow-based algorithm for automatically initializing contours at the first frame. For the color-based contour evolution, Markov random field theory is used to measure correlations between values of neighboring pixels for posterior probability estimation. For adaptive shape-based contour evolution, the global shape information and the local color information are combined to hierarchically evolve the contour, and a flexible shape updating model is constructed. For the dynamic shape-based contour evolution, a shape mode transition matrix is learnt to characterize the temporal correlations of object shapes. For the handling of abrupt motions, particle swarm optimization is adopted to capture the global motion which is applied to the contour in the current frame to produce an initial contour in the next frame.

  11. Fatigue crack shape prediction based on vertex singularity

    Czech Academy of Sciences Publication Activity Database

    Hutař, Pavel; Náhlík, Luboš

    2008-01-01

    Roč. 2, č. 1 (2008), s. 45-52 ISSN 1802-680X R&D Projects: GA ČR GA101/08/1623; GA ČR GP106/06/P239 Institutional research plan: CEZ:AV0Z20410507 Keywords : 3D vertex singularity * crack shape * fatigue crack propagation Subject RIV: JL - Materials Fatigue, Friction Mechanics

  12. Tracking fungal community responses to maize plants by DNA- and RNA-based pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Eiko E Kuramae

    Full Text Available We assessed soil fungal diversity and community structure at two sampling times (t1 = 47 days and t2 = 104 days of plant age in pots associated with four maize cultivars, including two genetically modified (GM cultivars by high-throughput pyrosequencing of the 18S rRNA gene using DNA and RNA templates. We detected no significant differences in soil fungal diversity and community structure associated with different plant cultivars. However, DNA-based analyses yielded lower fungal OTU richness as compared to RNA-based analyses. Clear differences in fungal community structure were also observed in relation to sampling time and the nucleic acid pool targeted (DNA versus RNA. The most abundant soil fungi, as recovered by DNA-based methods, did not necessary represent the most "active" fungi (as recovered via RNA. Interestingly, RNA-derived community compositions at t1 were highly similar to DNA-derived communities at t2, based on presence/absence measures of OTUs. We recovered large proportions of fungal sequences belonging to arbuscular mycorrhizal fungi and Basidiomycota, especially at the RNA level, suggesting that these important and potentially beneficial fungi are not affected by the plant cultivars nor by GM traits (Bt toxin production. Our results suggest that even though DNA- and RNA-derived soil fungal communities can be very different at a given time, RNA composition may have a predictive power of fungal community development through time.

  13. Synthetic biology devices and circuits for RNA-based 'smart vaccines': a propositional review.

    Science.gov (United States)

    Andries, Oliwia; Kitada, Tasuku; Bodner, Katie; Sanders, Niek N; Weiss, Ron

    2015-02-01

    Nucleic acid vaccines have been gaining attention as an alternative to the standard attenuated pathogen or protein based vaccine. However, an unrealized advantage of using such DNA or RNA based vaccination modalities is the ability to program within these nucleic acids regulatory devices that would provide an immunologist with the power to control the production of antigens and adjuvants in a desirable manner by administering small molecule drugs as chemical triggers. Advances in synthetic biology have resulted in the creation of highly predictable and modular genetic parts and devices that can be composed into synthetic gene circuits with complex behaviors. With the recent advent of modified RNA gene delivery methods and developments in the RNA replicon platform, we foresee a future in which mammalian synthetic biologists will create genetic circuits encoded exclusively on RNA. Here, we review the current repertoire of devices used in RNA synthetic biology and propose how programmable 'smart vaccines' will revolutionize the field of RNA vaccination.

  14. GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

    Science.gov (United States)

    Boudard, Mélanie; Bernauer, Julie; Barth, Dominique; Cohen, Johanne; Denise, Alain

    2015-01-01

    Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is predicting the spatial arrangement of the various structural elements of RNA. As RNA folding is generally hierarchical, methods involving coarse-grained models hold great promise for this purpose. We present here a novel coarse-grained method for sampling, based on game theory and knowledge-based potentials. This strategy, GARN (Game Algorithm for RNa sampling), is often much faster than previously described techniques and generates large sets of solutions closely resembling the native structure. GARN is thus a suitable starting point for the molecular modeling of large RNAs, particularly those with experimental constraints. GARN is available from: http://garn.lri.fr/.

  15. RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.

    Science.gov (United States)

    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

  16. A Small RNA-Based Immune System Defends Germ Cells against Mobile Genetic Elements

    Directory of Open Access Journals (Sweden)

    Astrid D. Haase

    2016-01-01

    Full Text Available Transposons are mobile genetic elements that threaten the survival of species by destabilizing the germline genomes. Limiting the spread of these selfish elements is imperative. Germ cells employ specialized small regulatory RNA pathways to restrain transposon activity. PIWI proteins and Piwi-interacting RNAs (piRNAs silence transposons at the transcriptional and posttranscriptional level with loss-of-function mutant animals universally exhibiting sterility often associated with germ cell defects. This short review aims to illustrate basic strategies of piRNA-guided defense against transposons. Mechanisms of piRNA silencing are most readily studied in Drosophila melanogaster, which serves as a model to delineate molecular concepts and as a reference for mammalian piRNA systems. PiRNA pathways utilize two major strategies to handle the challenges of transposon control: (1 the hard-wired molecular memory of prior transpositions enables recognition of mobile genetic elements and discriminates transposons from host genes; (2 a feed-forward adaptation mechanism shapes piRNA populations to selectively combat the immediate threat of transposon transcripts. In flies, maternally contributed PIWI-piRNA complexes bolster both of these lines of defense and ensure transgenerational immunity. While recent studies have provided a conceptual framework of what could be viewed as an ancient immune system, we are just beginning to appreciate its many molecular innovations.

  17. Martensitic transformation in Co-based ferromagnetic shape memory alloy

    Czech Academy of Sciences Publication Activity Database

    Kopeček, Jaromír; Yokaichiya, F.; Laufek, F.; Jarošová, Markéta; Jurek, Karel; Drahokoupil, Jan; Sedláková-Ignácová, Silvia; Molnár, Peter; Heczko, Oleg

    2012-01-01

    Roč. 122, č. 3 (2012), s. 475-477 ISSN 0587-4246. [International Symposium on Physics of Materials, ISPMA /12./. Praha, 04.09.2011-08.09.2011] R&D Projects: GA ČR(CZ) GA101/09/0702; GA ČR GAP107/10/0824; GA AV ČR IAA100100920 Institutional research plan: CEZ:AV0Z10100520; CEZ:AV0Z10100521 Keywords : microstructure * shape memory alloys * neutron diffraction * cobalt alloys Subject RIV: JG - Metallurgy Impact factor: 0.531, year: 2012

  18. Shape memory polymers based on uniform aliphatic urethane networks

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, T S; Bearinger, J P; Herberg, J L; Marion III, J E; Wright, W J; Evans, C L; Maitland, D J

    2007-01-19

    Aliphatic urethane polymers have been synthesized and characterized, using monomers with high molecular symmetry, in order to form amorphous networks with very uniform supermolecular structures which can be used as photo-thermally actuable shape memory polymers (SMPs). The monomers used include hexamethylene diisocyanate (HDI), trimethylhexamethylenediamine (TMHDI), N,N,N{prime},N{prime}-tetrakis(hydroxypropyl)ethylenediamine (HPED), triethanolamine (TEA), and 1,3-butanediol (BD). The new polymers were characterized by solvent extraction, NMR, XPS, UV/VIS, DSC, DMTA, and tensile testing. The resulting polymers were found to be single phase amorphous networks with very high gel fraction, excellent optical clarity, and extremely sharp single glass transitions in the range of 34 to 153 C. Thermomechanical testing of these materials confirms their excellent shape memory behavior, high recovery force, and low mechanical hysteresis (especially on multiple cycles), effectively behaving as ideal elastomers above T{sub g}. We believe these materials represent a new and potentially important class of SMPs, and should be especially useful in applications such as biomedical microdevices.

  19. Triangle bipolar pulse shaping and pileup correction based on DSP

    International Nuclear Information System (INIS)

    Esmaeili-sani, Vahid; Moussavi-zarandi, Ali; Akbar-ashrafi, Nafiseh; Boghrati, Behzad

    2011-01-01

    Programmable Digital Signal Processing (DSP) microprocessors are capable of doing complex discrete signal processing algorithms with clock rates above 50 MHz. This combined with their low expense, ease of use and selected dedicated hardware make them an ideal option for spectrometer data acquisition systems. For this generation of spectrometers, functions that are typically performed in dedicated circuits, or offline, are being migrated to the field programmable gate array (FPGA). This will not only reduce the electronics, but the features of modern FPGAs can be utilized to add considerable signal processing power to produce higher resolution spectra. In this paper we report on an all-digital triangle bipolar pulse shaping and pileup correction algorithm that is being developed for the DSP. The pileup mitigation algorithm will allow the spectrometers to run at higher count rates or with multiple sources without imposing large data losses due to the overlapping of scintillation signals. This correction technique utilizes a very narrow bipolar triangle digital pulse shaping algorithm to extract energy information for most pileup events.

  20. Triangle bipolar pulse shaping and pileup correction based on DSP

    Energy Technology Data Exchange (ETDEWEB)

    Esmaeili-sani, Vahid, E-mail: vaheed_esmaeely80@yahoo.com [Department of Nuclear Engineering and Physics, Amirkabir University of Technology, P.O. Box 4155-4494, Tehran (Iran, Islamic Republic of); Moussavi-zarandi, Ali; Akbar-ashrafi, Nafiseh; Boghrati, Behzad [Department of Nuclear Engineering and Physics, Amirkabir University of Technology, P.O. Box 4155-4494, Tehran (Iran, Islamic Republic of)

    2011-02-11

    Programmable Digital Signal Processing (DSP) microprocessors are capable of doing complex discrete signal processing algorithms with clock rates above 50 MHz. This combined with their low expense, ease of use and selected dedicated hardware make them an ideal option for spectrometer data acquisition systems. For this generation of spectrometers, functions that are typically performed in dedicated circuits, or offline, are being migrated to the field programmable gate array (FPGA). This will not only reduce the electronics, but the features of modern FPGAs can be utilized to add considerable signal processing power to produce higher resolution spectra. In this paper we report on an all-digital triangle bipolar pulse shaping and pileup correction algorithm that is being developed for the DSP. The pileup mitigation algorithm will allow the spectrometers to run at higher count rates or with multiple sources without imposing large data losses due to the overlapping of scintillation signals. This correction technique utilizes a very narrow bipolar triangle digital pulse shaping algorithm to extract energy information for most pileup events.

  1. Determination of Resistant Starch Assimilating Bacteria in Fecal Samples of Mice by In vitro RNA-Based Stable Isotope Probing

    Science.gov (United States)

    Herrmann, Elena; Young, Wayne; Rosendale, Douglas; Conrad, Ralf; Riedel, Christian U.; Egert, Markus

    2017-01-01

    The impact of the intestinal microbiota on human health is becoming increasingly appreciated in recent years. In consequence, and fueled by major technological advances, the composition of the intestinal microbiota in health and disease has been intensively studied by high throughput sequencing approaches. Observations linking dysbiosis of the intestinal microbiota with a number of serious medical conditions including chronic inflammatory disorders and allergic diseases suggest that restoration of the composition and activity of the intestinal microbiota may be a treatment option at least for some of these diseases. One possibility to shape the intestinal microbiota is the administration of prebiotic carbohydrates such as resistant starch (RS). In the present study, we aim at establishing RNA-based stable isotope probing (RNA-SIP) to identify bacterial populations that are involved in the assimilation of RS using anaerobic in vitro fermentation of murine fecal material with stable [U13C] isotope-labeled potato starch. Total RNA from these incubations was extracted, processed by gradient ultracentrifugation and fractionated by density. 16S rRNA gene sequences were amplified from reverse transcribed RNA of high and low density fractions suspected to contain labeled and unlabeled RNA, respectively. Phylogenetic analysis of the obtained sequences revealed a distinct subset of the intestinal microbiota involved in starch metabolism. The results suggest Bacteroidetes, in particular genera affiliated with Prevotellaceae, as well as members of the Ruminococcacea family to be primary assimilators of resistant starch due to a significantly higher relative abundance in higher density fractions in RNA samples isolated after 2 h of incubation. Using high performance liquid chromatography coupled to isotope ratio mass spectrometry (HPLC-IRMS) analysis, some stable isotope label was recovered from acetate, propionate and butyrate. Here, we demonstrate the suitability of RNA

  2. Determination of Resistant Starch Assimilating Bacteria in Fecal Samples of Mice by In vitro RNA-Based Stable Isotope Probing

    Directory of Open Access Journals (Sweden)

    Elena Herrmann

    2017-07-01

    Full Text Available The impact of the intestinal microbiota on human health is becoming increasingly appreciated in recent years. In consequence, and fueled by major technological advances, the composition of the intestinal microbiota in health and disease has been intensively studied by high throughput sequencing approaches. Observations linking dysbiosis of the intestinal microbiota with a number of serious medical conditions including chronic inflammatory disorders and allergic diseases suggest that restoration of the composition and activity of the intestinal microbiota may be a treatment option at least for some of these diseases. One possibility to shape the intestinal microbiota is the administration of prebiotic carbohydrates such as resistant starch (RS. In the present study, we aim at establishing RNA-based stable isotope probing (RNA-SIP to identify bacterial populations that are involved in the assimilation of RS using anaerobic in vitro fermentation of murine fecal material with stable [U13C] isotope-labeled potato starch. Total RNA from these incubations was extracted, processed by gradient ultracentrifugation and fractionated by density. 16S rRNA gene sequences were amplified from reverse transcribed RNA of high and low density fractions suspected to contain labeled and unlabeled RNA, respectively. Phylogenetic analysis of the obtained sequences revealed a distinct subset of the intestinal microbiota involved in starch metabolism. The results suggest Bacteroidetes, in particular genera affiliated with Prevotellaceae, as well as members of the Ruminococcacea family to be primary assimilators of resistant starch due to a significantly higher relative abundance in higher density fractions in RNA samples isolated after 2 h of incubation. Using high performance liquid chromatography coupled to isotope ratio mass spectrometry (HPLC-IRMS analysis, some stable isotope label was recovered from acetate, propionate and butyrate. Here, we demonstrate the

  3. INVESTIGATING SHAPE REPRESENTATION USING SENSITIVITY TO PART- AND AXIS-BASED TRANSFORMATIONS

    OpenAIRE

    Denisova, Kristina; Feldman, Jacob; Su, Xiaotao; Singh, Manish

    2016-01-01

    Part -and axis-based approaches organize shape representations in terms of simple parts and their spatial relationships. Shape transformations that alter qualitative part structure have been shown to be more detectable than those that preserve it. We compared sensitivity to various transformations that change quantitative properties of parts and their spatial relationships, while preserving qualitative part structure. Shape transformations involving changes in length, width, curvature, orient...

  4. Cationic star-shaped polymer as an siRNA carrier for reducing MMP-9 expression in skin fibroblast cells and promoting wound healing in diabetic rats

    Directory of Open Access Journals (Sweden)

    Li N

    2014-07-01

    Full Text Available Na Li,1,* Heng-Cong Luo,1,* Chuan Yang,1 Jun-Jie Deng,2 Meng Ren,1 Xiao-Ying Xie,1 Diao-Zhu Lin,1 Li Yan,1 Li-Ming Zhang2 1Department of Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China; 2DSAPM Lab and PCFM Lab, Institute of Polymer Science, Department of Polymer and Materials Science, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, People’s Republic of China *These authors contributed equally to this work Background: Excessive expression of matrix metalloproteinase-9 (MMP-9 is deleterious to the cutaneous wound-healing process in the context of diabetes. The aim of the present study was to explore whether a cationic star-shaped polymer consisting of ß-cyclodextrin (ß-CD core and poly(amidoamine dendron arms (ß-CD-[D3]7 could be used as the gene carrier of small interfering RNA (siRNA to reduce MMP-9 expression for enhanced diabetic wound healing. Methods: The cytotoxicity of ß-CD-(D37 was investigated by 3-(4,5-Dimethylthiazol-2-yl-2,5-diphenyltetrazolium bromide assay (MMT method in the rat CRL1213 skin fibroblast cell line. The transfection efficiency of ß-CD-(D37/MMP-9-small interfering RNA (siRNA complexes was determined by confocal microscopy and flow cytometry. Quantitative real time (RT polymerase chain reaction was performed to measure the gene expression of MMP-9 after the transfection by ß-CD-(D37/MMP-9-siRNA complexes. The ß-CD-(D37/MMP-9-siRNA complexes were injected on the wounds of streptozocin-induced diabetic rats. Wound closure was measured on days 4 and 7 post-wounding. Results: ß-CD-(D37 exhibited low cytotoxicity in fibroblast cells, and easily formed the complexes with MMP-9-siRNA. The ß-CD-(D37/MMP-9-siRNA complexes were readily taken up by fibroblast cells, resulting in the downregulation of MMP-9 gene expression (P<0.01. Animal experiments revealed that the treatment by ß-CD-(D37/MMP-9-siRNA complexes enhanced wound

  5. Posterior variability of inclusion shape based on tomographic measurement data

    International Nuclear Information System (INIS)

    Watzenig, Daniel; Fox, Colin

    2008-01-01

    We treat the problem of recovering the unknown shape of a single inclusion with unknown constant permittivity in an otherwise uniform background material, from uncertain measurements of trans-capacitance at electrodes outside the material. The ubiquitous presence of measurement noise implies that the practical measurement process is probabilistic, and the inverse problem is naturally stated as statistical inference. Formulating the inverse problem in a Bayesian inferential framework requires accurately modelling the forward map, measurement noise, and specifying a prior distribution for the cross-sectional material distribution. Numerical implementation of the forward map is via the boundary element method (BEM) taking advantage of a piecewise constant representation. Summary statistics are calculated using MCMC sampling to characterize posterior variability for synthetic and measured data sets.

  6. Thermally controlled femtosecond pulse shaping using metasurface based optical filters

    Science.gov (United States)

    Rahimi, Eesa; Şendur, Kürşat

    2018-02-01

    Shaping of the temporal distribution of the ultrashort pulses, compensation of pulse deformations due to phase shift in transmission and amplification are of interest in various optical applications. To address these problems, in this study, we have demonstrated an ultra-thin reconfigurable localized surface plasmon (LSP) band-stop optical filter driven by insulator-metal phase transition of vanadium dioxide. A Joule heating mechanism is proposed to control the thermal phase transition of the material. The resulting permittivity variation of vanadium dioxide tailors spectral response of the transmitted pulse from the stack. Depending on how the pulse's spectrum is located with respect to the resonance of the band-stop filter, the thin film stack can dynamically compress/expand the output pulse span up to 20% or shift its phase up to 360°. Multi-stacked filters have shown the ability to dynamically compensate input carrier frequency shifts and pulse span variations besides their higher span expansion rates.

  7. Metamaterials based on wedge-shaped electrodynamic structures

    Directory of Open Access Journals (Sweden)

    Mitrokhin Vladimir

    2017-01-01

    Full Text Available The paper studies a possibility of simulation of artificial composite media with negative values of the real part of the equivalent dielectric (magnetic permittivity, by the use of segments of hollow composite waveguides with cylindrical guided waves in evanescent mode. Reactive evanescent fields of wedge-shaped waveguide eigenmodes are formed in the evanescent region before the critical section of the waveguide which separates the quasistatic field region from the distributing field of the evanescent waveguide mode. The possibility of simulation is determined by the equivalence of dispersion equation of the eigenmode propagation constant and the dispersion equation for the electric (magnetic permittivity of plasma-like medium if cut-off frequency and electric (magnetic plasma frequency of the medium are equal.

  8. New method of contour-based mask-shape compiler

    Science.gov (United States)

    Matsuoka, Ryoichi; Sugiyama, Akiyuki; Onizawa, Akira; Sato, Hidetoshi; Toyoda, Yasutaka

    2007-10-01

    We have developed a new method of accurately profiling a mask shape by utilizing a Mask CD-SEM. The method is intended to realize high accuracy, stability and reproducibility of the Mask CD-SEM adopting an edge detection algorithm as the key technology used in CD-SEM for high accuracy CD measurement. In comparison with a conventional image processing method for contour profiling, it is possible to create the profiles with much higher accuracy which is comparable with CD-SEM for semiconductor device CD measurement. In this report, we will introduce the algorithm in general, the experimental results and the application in practice. As shrinkage of design rule for semiconductor device has further advanced, an aggressive OPC (Optical Proximity Correction) is indispensable in RET (Resolution Enhancement Technology). From the view point of DFM (Design for Manufacturability), a dramatic increase of data processing cost for advanced MDP (Mask Data Preparation) for instance and surge of mask making cost have become a big concern to the device manufacturers. In a sense, it is a trade-off between the high accuracy RET and the mask production cost, while it gives a significant impact on the semiconductor market centered around the mask business. To cope with the problem, we propose the best method for a DFM solution in which two dimensional data are extracted for an error free practical simulation by precise reproduction of a real mask shape in addition to the mask data simulation. The flow centering around the design data is fully automated and provides an environment where optimization and verification for fully automated model calibration with much less error is available. It also allows complete consolidation of input and output functions with an EDA system by constructing a design data oriented system structure. This method therefore is regarded as a strategic DFM approach in the semiconductor metrology.

  9. Statistical shape modeling based renal volume measurement using tracked ultrasound

    Science.gov (United States)

    Pai Raikar, Vipul; Kwartowitz, David M.

    2017-03-01

    Autosomal dominant polycystic kidney disease (ADPKD) is the fourth most common cause of kidney transplant worldwide accounting for 7-10% of all cases. Although ADPKD usually progresses over many decades, accurate risk prediction is an important task.1 Identifying patients with progressive disease is vital to providing new treatments being developed and enable them to enter clinical trials for new therapy. Among other factors, total kidney volume (TKV) is a major biomarker predicting the progression of ADPKD. Consortium for Radiologic Imaging Studies in Polycystic Kidney Disease (CRISP)2 have shown that TKV is an early, and accurate measure of cystic burden and likely growth rate. It is strongly associated with loss of renal function.3 While ultrasound (US) has proven as an excellent tool for diagnosing the disease; monitoring short-term changes using ultrasound has been shown to not be accurate. This is attributed to high operator variability and reproducibility as compared to tomographic modalities such as CT and MR (Gold standard). Ultrasound has emerged as one of the standout modality for intra-procedural imaging and with methods for spatial localization has afforded us the ability to track 2D ultrasound in physical space which it is being used. In addition to this, the vast amount of recorded tomographic data can be used to generate statistical shape models that allow us to extract clinical value from archived image sets. In this work, we aim at improving the prognostic value of US in managing ADPKD by assessing the accuracy of using statistical shape model augmented US data, to predict TKV, with the end goal of monitoring short-term changes.

  10. Lipid-Based Liquid Crystalline Nanoparticles Facilitate Cytosolic Delivery of siRNA via Structural Transformation.

    Science.gov (United States)

    He, Shufang; Fan, Weiwei; Wu, Na; Zhu, Jingjing; Miao, Yunqiu; Miao, Xiaran; Li, Feifei; Zhang, Xinxin; Gan, Yong

    2018-04-11

    RNA interference (RNAi) technology has shown great promise for the treatment of cancer and other genetic disorders. Despite the efforts to increase the target tissue distribution, the safe and effective delivery of siRNA to the diseased cells with sufficient cytosolic transport is another critical factor for successful RNAi clinical application. Here, the constructed lipid-based liquid crystalline nanoparticles, called nano-Transformers, can transform thestructure in the intracellular acidic environment and perform high-efficient siRNA delivery for cancer treatment. The developed nano-Transformers have satisfactory siRNA loading efficiency and low cytotoxicity. Different from the traditional cationic nanocarriers, the endosomal membrane fusion induced by the conformational transition of lipids contributes to the easy dissociation of siRNA from nanocarriers and direct release of free siRNA into cytoplasm. We show that transfection with cyclin-dependent kinase 1 (CDK1)-siRNA-loaded nano-Transformers causes up to 95% reduction of relevant mRNA in vitro and greatly inhibits the tumor growth without causing any immunogenic response in vivo. This work highlights that the lipid-based nano-Transformers may become the next generation of siRNA delivery system with higher efficacy and improved safety profiles.

  11. Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

    Science.gov (United States)

    Zhang, Wenqian; Yu, Ying; Hertwig, Falk; Thierry-Mieg, Jean; Zhang, Wenwei; Thierry-Mieg, Danielle; Wang, Jian; Furlanello, Cesare; Devanarayan, Viswanath; Cheng, Jie; Deng, Youping; Hero, Barbara; Hong, Huixiao; Jia, Meiwen; Li, Li; Lin, Simon M; Nikolsky, Yuri; Oberthuer, André; Qing, Tao; Su, Zhenqiang; Volland, Ruth; Wang, Charles; Wang, May D; Ai, Junmei; Albanese, Davide; Asgharzadeh, Shahab; Avigad, Smadar; Bao, Wenjun; Bessarabova, Marina; Brilliant, Murray H; Brors, Benedikt; Chierici, Marco; Chu, Tzu-Ming; Zhang, Jibin; Grundy, Richard G; He, Min Max; Hebbring, Scott; Kaufman, Howard L; Lababidi, Samir; Lancashire, Lee J; Li, Yan; Lu, Xin X; Luo, Heng; Ma, Xiwen; Ning, Baitang; Noguera, Rosa; Peifer, Martin; Phan, John H; Roels, Frederik; Rosswog, Carolina; Shao, Susan; Shen, Jie; Theissen, Jessica; Tonini, Gian Paolo; Vandesompele, Jo; Wu, Po-Yen; Xiao, Wenzhong; Xu, Joshua; Xu, Weihong; Xuan, Jiekun; Yang, Yong; Ye, Zhan; Dong, Zirui; Zhang, Ke K; Yin, Ye; Zhao, Chen; Zheng, Yuanting; Wolfinger, Russell D; Shi, Tieliu; Malkas, Linda H; Berthold, Frank; Wang, Jun; Tong, Weida; Shi, Leming; Peng, Zhiyu; Fischer, Matthias

    2015-06-25

    Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. We generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being expressed in this malignancy. We also find that RNA-seq provides much more detailed information on specific transcript expression patterns in clinico-genetic neuroblastoma subgroups than microarrays. To systematically compare the power of RNA-seq and microarray-based models in predicting clinical endpoints, we divide the cohort randomly into training and validation sets and develop 360 predictive models on six clinical endpoints of varying predictability. Evaluation of factors potentially affecting model performances reveals that prediction accuracies are most strongly influenced by the nature of the clinical endpoint, whereas technological platforms (RNA-seq vs. microarrays), RNA-seq data analysis pipelines, and feature levels (gene vs. transcript vs. exon-junction level) do not significantly affect performances of the models. We demonstrate that RNA-seq outperforms microarrays in determining the transcriptomic characteristics of cancer, while RNA-seq and microarray-based models perform similarly in clinical endpoint prediction. Our findings may be valuable to guide future studies on the development of gene expression-based predictive models and their implementation in clinical practice.

  12. Role of samarium additions on the shape memory behavior of iron based alloys

    International Nuclear Information System (INIS)

    Shakoor, R.A.; Khalid, F. Ahmad; Kang, Kisuk

    2011-01-01

    Research highlights: → The effect of samarium contents on shape memory behavior has been studied. → Addition of samarium increases the strength, c/a ratio and ε (hcp martensite). → Addition of samarium retards the nucleation of α (bcc martensite). → Improvement in shape memory effect with the increase in samarium contents. - Abstract: The effect of samarium contents on shape memory behavior of iron based shape memory alloys has been studied. It is found that the strength of the alloys increases with the increase in samarium contents. This effect can be attributed to the solid solution strengthening of austenite by samarium addition. It is also noticed that the shape memory effect increases with the increase in samarium contents. This improvement in shape memory effect presumably can be regarded as the effect of improvement in strength, increase in c/a ratio and obstruction of nucleation of α in the microstructure.

  13. Quantitation of base substitutions in eukaryotic 5S rRNA: selection for the maintenance of RNA secondary structure.

    Science.gov (United States)

    Curtiss, W C; Vournakis, J N

    1984-01-01

    Eukaryotic 5S rRNA sequences from 34 diverse species were compared by the following method: (1) The sequences were aligned; (2) the positions of substitutions were located by comparison of all possible pairs of sequences; (3) the substitution sites were mapped to an assumed general base pairing model; and (4) the R-Y model of base stacking was used to study stacking pattern relationships in the structure. An analysis of the sequence and structure variability in each region of the molecule is presented. It was found that the degree of base substitution varies over a wide range, from absolute conservation to occurrence of over 90% of the possible observable substitutions. The substitutions are located primarily in stem regions of the 5S rRNA secondary structure. More than 88% of the substitutions in helical regions maintain base pairing. The disruptive substitutions are primarily located at the edges of helical regions, resulting in shortening of the helical regions and lengthening of the adjacent nonpaired regions. Base stacking patterns determined by the R-Y model are mapped onto the general secondary structure. Intrastrand and interstrand stacking could stabilize alternative coaxial structures and limit the conformational flexibility of nonpaired regions. Two short contiguous regions are 100% conserved in all species. This may reflect evolutionary constraints imposed at the DNA level by the requirement for binding of a 5S gene transcription initiation factor during gene expression.

  14. Thermally controlled femtosecond pulse shaping using metasurface based optical filters

    Directory of Open Access Journals (Sweden)

    Rahimi Eesa

    2018-02-01

    Full Text Available Shaping of the temporal distribution of the ultrashort pulses, compensation of pulse deformations due to phase shift in transmission and amplification are of interest in various optical applications. To address these problems, in this study, we have demonstrated an ultra-thin reconfigurable localized surface plasmon (LSP band-stop optical filter driven by insulator-metal phase transition of vanadium dioxide. A Joule heating mechanism is proposed to control the thermal phase transition of the material. The resulting permittivity variation of vanadium dioxide tailors spectral response of the transmitted pulse from the stack. Depending on how the pulse’s spectrum is located with respect to the resonance of the band-stop filter, the thin film stack can dynamically compress/expand the output pulse span up to 20% or shift its phase up to 360°. Multi-stacked filters have shown the ability to dynamically compensate input carrier frequency shifts and pulse span variations besides their higher span expansion rates.

  15. Automatic anatomical structures location based on dynamic shape measurement

    Science.gov (United States)

    Witkowski, Marcin; Rapp, Walter; Sitnik, Robert; Kujawinska, Malgorzata; Vander Sloten, Jos; Haex, Bart; Bogaert, Nico; Heitmann, Kjell

    2005-09-01

    New image processing methods and active photonics apparatus have made possible the development of relatively inexpensive optical systems for complex shape and object measurements. We present dynamic 360° scanning method for analysis of human lower body biomechanics, with an emphasis on the analysis of the knee joint. The anatomical structure (of high medical interest) that is possible to scan and analyze, is patella. Tracking of patella position and orientation under dynamic conditions may lead to detect pathological patella movements and help in knee joint disease diagnosis. The processed data is obtained from a dynamic laser triangulation surface measurement system, able to capture slow to normal movements with a scan frequency between 15 and 30 Hz. These frequency rates are enough to capture controlled movements used e.g. for medical examination purposes. The purpose of the work presented is to develop surface analysis methods that may be used as support of diagnosis of motoric abilities of lower limbs. The paper presents algorithms used to process acquired lower limbs surface data in order to find the position and orientation of patella. The algorithms implemented include input data preparation, curvature description methods, knee region discrimination and patella assumed position/orientation calculation. Additionally, a method of 4D (3D + time) medical data visualization is proposed. Also some exemplary results are presented.

  16. Smart Inulin-Based Polycationic Nanodevices for siRNA Delivery.

    Science.gov (United States)

    Cavallaro, G; Sardo, C; Scialabba, C; Licciardi, M; Giammona, G

    2017-01-01

    The advances of short interfering RNA (siRNA) mediated therapy provide a powerful option for the treatment of many diseases by silencing the expression of targeted genes including cancer development and progression. Inulin is a very simple and biocompatible polysaccharide proposed by our groups to produce interesting delivery systems for Nucleic Acid Based Drugs (NABDs), such as siRNA, either as polycations able to give polyplexes and polymeric coatings for nanosystems having a metallic core. In this research field, different functionalizing groups were linked to the inulin backbone with specific aims including oligoamine such as Ethylendiammine (EDA), Diethylediamine (DETA), Spermine, (SPM) etc. In this contribution the main Inulin-based nanodevices for the delivery of siRNA have been reported, analysed and compared with particular reference to their chemical design and structure, biocompatibility, siRNA complexing ability, silencing ability. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Pulse shape discrimination based on fast signals from silicon photomultipliers

    Science.gov (United States)

    Yu, Junhao; Wei, Zhiyong; Fang, Meihua; Zhang, Zixia; Cheng, Can; Wang, Yi; Su, Huiwen; Ran, Youquan; Zhu, Qingwei; Zhang, He; Duan, Kai; Chen, Ming; Liu, Meng

    2018-06-01

    Recent developments in organic plastic scintillators capable of pulse shape discrimination (PSD) enable a breakthrough in discrimination between neutrons and gammas. Plastic scintillator detectors coupled with silicon photomultipliers (SiPMs) offer many advantages, such as lower power consumption, smaller volume, and especially insensitivity to magnetic fields, compared with conventional photomultiplier tubes (PMTs). A SensL SiPM has two outputs: a standard output and a fast output. It is known that the charge injected into the fast output electrode is typically approximately 2% of the total charge generated during the avalanche, whereas the charge injected into the standard output electrode is nearly 98% of the total. Fast signals from SiPMs exhibit better performance in terms of timing and time-correlated measurements compared with standard signals. The pulse duration of a standard signal is on the order of hundreds of nanoseconds, whereas the pulse duration of the main monopole waveform of a fast signal is a few tens of nanoseconds. Fast signals are traditionally thought to be suitable for photon counting at very high speeds but unsuitable for PSD due to the partial charge collection. Meanwhile, the standard outputs of SiPMs coupled with discriminating scintillators have yielded nice PSD performances, but there have been no reports on PSD using fast signals. Our analysis shows that fast signals can also provide discrimination if the rate of charge injection into the fast output electrode is fixed for each event, even though only a portion of the charge is collected. In this work, we achieved successful PSD using fast signals; meanwhile, using a coincidence timing window of less 3 nanoseconds between the readouts from both ends of the detector reduced the influence of the high SiPM dark current. We experimentally achieved good timing performance and PSD capability simultaneously.

  18. RNA secondary structures in a polymer-zeta model how foldings should be shaped for sparsification to establish a linear speedup

    DEFF Research Database (Denmark)

    Jin, Emma Yu; Nebel, M. E.

    2016-01-01

    that the corresponding conditional probabilities behave according to a polymer-zeta probability model. We show that even if some of the structural parameters exhibit an almost realistic behavior on average, the expected shape of a folding in that model must be assumed to highly differ from those observed in nature. More...... sparsification) may reduce the runtime to n2 on average, assuming that nucleotides of distance d form a hydrogen bond (i.e. are paired) with probability (Formula Presented.) for some constants b > 0, c > 1. The latter is called the polymer-zeta model and plays a crucial role in speeding up the above mentioned...... algorithm. In this paper we discuss the application of the polymer-zeta property for the analysis of sparsification, showing that it must be applied conditionally on first and last positions to pair. Afterwards, we will investigate the combinatorics of RNA secondary structures assuming...

  19. Chess games: a model for RNA based computation.

    Science.gov (United States)

    Cukras, A R; Faulhammer, D; Lipton, R J; Landweber, L F

    1999-10-01

    Here we develop the theory of RNA computing and a method for solving the 'knight problem' as an instance of a satisfiability (SAT) problem. Using only biological molecules and enzymes as tools, we developed an algorithm for solving the knight problem (3 x 3 chess board) using a 10-bit combinatorial pool and sequential RNase H digestions. The results of preliminary experiments presented here reveal that the protocol recovers far more correct solutions than expected at random, but the persistence of errors still presents the greatest challenge.

  20. A novel fruit shape classification method based on multi-scale analysis

    Science.gov (United States)

    Gui, Jiangsheng; Ying, Yibin; Rao, Xiuqin

    2005-11-01

    Shape is one of the major concerns and which is still a difficult problem in automated inspection and sorting of fruits. In this research, we proposed the multi-scale energy distribution (MSED) for object shape description, the relationship between objects shape and its boundary energy distribution at multi-scale was explored for shape extraction. MSED offers not only the mainly energy which represent primary shape information at the lower scales, but also subordinate energy which represent local shape information at higher differential scales. Thus, it provides a natural tool for multi resolution representation and can be used as a feature for shape classification. We addressed the three main processing steps in the MSED-based shape classification. They are namely, 1) image preprocessing and citrus shape extraction, 2) shape resample and shape feature normalization, 3) energy decomposition by wavelet and classification by BP neural network. Hereinto, shape resample is resample 256 boundary pixel from a curve which is approximated original boundary by using cubic spline in order to get uniform raw data. A probability function was defined and an effective method to select a start point was given through maximal expectation, which overcame the inconvenience of traditional methods in order to have a property of rotation invariants. The experiment result is relatively well normal citrus and serious abnormality, with a classification rate superior to 91.2%. The global correct classification rate is 89.77%, and our method is more effective than traditional method. The global result can meet the request of fruit grading.

  1. New Kids on the Block: RNA-Based Influenza Virus Vaccines.

    Science.gov (United States)

    Scorza, Francesco Berlanda; Pardi, Norbert

    2018-04-01

    RNA-based immunization strategies have emerged as promising alternatives to conventional vaccine approaches. A substantial body of published work demonstrates that RNA vaccines can elicit potent, protective immune responses against various pathogens. Consonant with its huge impact on public health, influenza virus is one of the best studied targets of RNA vaccine research. Currently licensed influenza vaccines show variable levels of protection against seasonal influenza virus strains but are inadequate against drifted and pandemic viruses. In recent years, several types of RNA vaccines demonstrated efficacy against influenza virus infections in preclinical models. Additionally, comparative studies demonstrated the superiority of some RNA vaccines over the currently used inactivated influenza virus vaccines in animal models. Based on these promising preclinical results, clinical trials have been initiated and should provide valuable information about the translatability of the impressive preclinical data to humans. This review briefly describes RNA-based vaccination strategies, summarizes published preclinical and clinical data, highlights the roadblocks that need to be overcome for clinical applications, discusses the landscape of industrial development, and shares the authors' personal perspectives about the future of RNA-based influenza virus vaccines.

  2. In vitro base modification of Escherichia coli glutamate 2 transfer-RNA and phenylalanine transfer-RNA gene transcripts

    International Nuclear Information System (INIS)

    Shahan, M.N.

    1989-01-01

    Plasmids were constructed that contain an E. Coli tRNA 2 Glu or tRNA Phe gene in a system transcribable by T7 or SP6 RNA polymerase. Selectively 32 P-labeled transcripts of these plasmids were used to study tRNA base modification in vitro in crude extracts by nearest neighbor analysis. The synthesis of 5-methyl-aminomethyl-2-thiouridine (mnm 5 s 2 U) was studied. Complete synthesis of mnm 5 s 2 2U is not observed. Instead, 2-thiouridine (s 2 U) is synthesized. Synthesis requires ATP, cysteine, Mg + , and monovalent cation concentrations below 50 mM. The reaction has a pH optimum above 7.0. Sulfide ion will substitute for cysteine in the reaction but sulfate, sulfite, methionine, homocysteine, and β-mercaptopyruvate will not. Extracts from E. coli strains carrying either the asuE or asuF mutations have reduced s 2 U synthetic activity which supports in vivo evidence that the wild type genes are involved in 2-thiolation of uridine. The enzyme is shown to be unstable both upon storage at -80 degree C and during the modification reaction. A method was developed to study the synthesis of any one of four pseudouridines ψ found at different positions of the tRNA cloverleaf. Synthesis of ψ is observed at three of the four positions-positions 32, 39, and 55. The asuC mutation is shown to affect ψ synthesis only at position 39 confirming that it is an allele of hisT and that the hisT mutations do not affect ψ synthesis at position 32 in E. coli. Synthesis of ψ32, ψ39, and ψ55 does not require any prior modification. Synthesis of dihydrouridine, 7-methylguanosine, and 3(3-amino-3-carboxypropyl)uridine is also observed. Synthesis of 2-methyladenosine and ψ 13 is not seen. Removal of part of the aminoacyl stem reduces synthesis of all modifications examined by 3' fold or more

  3. Direct-write fabrication of 4D active shape-changing behavior based on a shape memory polymer and its nanocomposite (Conference Presentation)

    Science.gov (United States)

    Wei, Hongqiu; Zhang, Qiwei; Yao, Yongtao; Liu, Liwu; Liu, Yanju; Leng, Jinsong

    2017-04-01

    Shape memory polymers (SMPs), a typical class of smart materials, have been witnessed significant advances in the past decades. Based on the unique performance to recover the initial shape after going through a shape deformation, the applications of SMPs have aroused growing interests. However, most of the researches are hindered by traditional processing technologies which limit the design space of SMPs-based structures. Three-dimension (3D) printing as an emerging technology endows design freedom to manufacture materials with complex structures. In present article, we show that by employing direct-write printing method; one can realize the printing of SMPs to achieve 4D active shape-changing structures. We first fabricated a kind of 3D printable polylactide (PLA)-based SMPs and characterized the overall properties of such materials. Results demonstrated the prepared PLA-based SMPs presenting excellent shape memory effect. In what follows, the rheological properties of such PLA-based SMP ink during printing process were discussed in detail. Finally, we designed and printed several 3D configurations for investigation. By combining 3D printing with shape memory behavior, these printed structures achieve 4D active shape-changing performance under heat stimuli. This research presents a high flexible method to realize the fabrication of SMP-based 4D active shape-changing structures, which opens the way for further developments and improvements of high-tech fields like 4D printing, soft robotics, micro-systems and biomedical devices.

  4. Non-Watson Crick base pairs might stabilize RNA structural motifs in ...

    Indian Academy of Sciences (India)

    Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural ...

  5. A high-performance flexible fibre-shaped electrochemical capacitor based on electrochemically reduced graphene oxide.

    Science.gov (United States)

    Li, Yingru; Sheng, Kaixuan; Yuan, Wenjing; Shi, Gaoquan

    2013-01-11

    A fibre-shaped solid electrochemical capacitor based on electrochemically reduced graphene oxide has been fabricated, exhibiting high specific capacitance and rate capability, long cycling life and attractive flexibility.

  6. L-shaped benzimidazole fluorophores: synthesis, characterization and optical response to bases, acids and anions.

    Science.gov (United States)

    Lirag, Rio Carlo; Le, Ha T M; Miljanić, Ognjen Š

    2013-05-14

    Nine L-shaped benzimidazole fluorophores have been synthesized, computationally evaluated and spectroscopically characterized. These "half-cruciform" fluorophores respond to bases, acids and anions through changes in fluorescence that vary from moderate to dramatic.

  7. Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures

    Directory of Open Access Journals (Sweden)

    Carugo Oliviero

    2011-10-01

    Full Text Available Abstract Background Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing. Results A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed. Conclusions The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs.

  8. RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

    Directory of Open Access Journals (Sweden)

    Chen Chun

    2008-03-01

    Full Text Available Abstract Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1 present a robust and effective way for RNA structural data compression; (2 design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool

  9. Preclinical and clinical development of siRNA-based therapeutics.

    Science.gov (United States)

    Ozcan, Gulnihal; Ozpolat, Bulent; Coleman, Robert L; Sood, Anil K; Lopez-Berestein, Gabriel

    2015-06-29

    The discovery of RNA interference, first in plants and Caenorhabditis elegans and later in mammalian cells, led to the emergence of a transformative view in biomedical research. Knowledge of the multiple actions of non-coding RNAs has truly allowed viewing DNA, RNA and proteins in novel ways. Small interfering RNAs (siRNAs) can be used as tools to study single gene function both in vitro and in vivo and are an attractive new class of therapeutics, especially against undruggable targets for the treatment of cancer and other diseases. Despite the potential of siRNAs in cancer therapy, many challenges remain, including rapid degradation, poor cellular uptake and off-target effects. Rational design strategies, selection algorithms, chemical modifications and nanocarriers offer significant opportunities to overcome these challenges. Here, we review the development of siRNAs as therapeutic agents from early design to clinical trial, with special emphasis on the development of EphA2-targeting siRNAs for ovarian cancer treatment. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. nRC: non-coding RNA Classifier based on structural features.

    Science.gov (United States)

    Fiannaca, Antonino; La Rosa, Massimo; La Paglia, Laura; Rizzo, Riccardo; Urso, Alfonso

    2017-01-01

    Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes. Moreover, the lack of knowledge about the complete mechanisms in regulative processes, together with the development of high-throughput technologies, has required the help of bioinformatics tools in addressing biologists and clinicians with a deeper comprehension of the functional roles of ncRNAs. In this work, we introduce a new ncRNA classification tool, nRC (non-coding RNA Classifier). Our approach is based on features extraction from the ncRNA secondary structure together with a supervised classification algorithm implementing a deep learning architecture based on convolutional neural networks. We tested our approach for the classification of 13 different ncRNA classes. We obtained classification scores, using the most common statistical measures. In particular, we reach an accuracy and sensitivity score of about 74%. The proposed method outperforms other similar classification methods based on secondary structure features and machine learning algorithms, including the RNAcon tool that, to date, is the reference classifier. nRC tool is freely available as a docker image at https://hub.docker.com/r/tblab/nrc/. The source code of nRC tool is also available at https://github.com/IcarPA-TBlab/nrc.

  11. Novel Shape-Memory Polymer with Two Transition Temperature Based on Two Different Memory Mechanism

    Institute of Scientific and Technical Information of China (English)

    Liu Guoqin; Ding Xiaobing; Cao Yiping; Zheng Zhaohui; Peng Yuxing

    2004-01-01

    As an important kind of intelligent materials, shape-memory materials have been received increasing attention on account of their interesting properties and potential applications in recent years. Particularly, the rise of shape-memory polymers by far surpasses well-known metallic shape-memory alloys in their shape-memory properties. The advantages of polymers compared to other materials are their easier availability and their wide range of mechanical and physical properties. The polymers designed to exhibit a shape-memory effect require two components on the molecular level: crosslinks to determine the permanent shape and switching segments with Ttrans to fix the temporary shape. Up to now almost all papers on shape-memory polymers introduce switching segments with the covalent linking method. On the other hand, only several cases concern non-covalent interaction. However, the research works mentioned above is based on a single Ttrans (i.e., Tm or Tg).Following our previous work, here, we first report a novel kind of polymer consisted of PMMA-PEG semi-interpenetrating polymer networks (semi-IPN), which exhibiting independently two shape memory effects based on Tm and Tg, respectively. This result can also extend the shape memory polymer categories from one Ttrans to two Ttrans, and the combination of Tm and Tg give rise to an extremely excellent shape-memory effect.Two different shape memory behaviors of this material based on two transition temperatures were evaluated by bending test as follows: a straight strip of the specimen was folded at a temperature above Ttrans and kept in this shape. The so-deformed sample was cooled down to a temperature Tlow< Ttrans and the deforming stress were released. When the sample was heated up to the measuring temperature Thigh > Ttrans, it recovered its initial shape. The deformation angle θ f varied as a function of time and the ratio of the recovery was defined as θ f /180. The PMMA-PEG polymer behaved as a hard plastic

  12. Metrics for comparing neuronal tree shapes based on persistent homology.

    Directory of Open Access Journals (Sweden)

    Yanjie Li

    Full Text Available As more and more neuroanatomical data are made available through efforts such as NeuroMorpho.Org and FlyCircuit.org, the need to develop computational tools to facilitate automatic knowledge discovery from such large datasets becomes more urgent. One fundamental question is how best to compare neuron structures, for instance to organize and classify large collection of neurons. We aim to develop a flexible yet powerful framework to support comparison and classification of large collection of neuron structures efficiently. Specifically we propose to use a topological persistence-based feature vectorization framework. Existing methods to vectorize a neuron (i.e, convert a neuron to a feature vector so as to support efficient comparison and/or searching typically rely on statistics or summaries of morphometric information, such as the average or maximum local torque angle or partition asymmetry. These simple summaries have limited power in encoding global tree structures. Based on the concept of topological persistence recently developed in the field of computational topology, we vectorize each neuron structure into a simple yet informative summary. In particular, each type of information of interest can be represented as a descriptor function defined on the neuron tree, which is then mapped to a simple persistence-signature. Our framework can encode both local and global tree structure, as well as other information of interest (electrophysiological or dynamical measures, by considering multiple descriptor functions on the neuron. The resulting persistence-based signature is potentially more informative than simple statistical summaries (such as average/mean/max of morphometric quantities-Indeed, we show that using a certain descriptor function will give a persistence-based signature containing strictly more information than the classical Sholl analysis. At the same time, our framework retains the efficiency associated with treating neurons as

  13. A collaborative European exercise on mRNA-based body fluid/skin typing and interpretation of DNA and RNA results

    DEFF Research Database (Denmark)

    van den Berge, M; Carracedo, A; Gomes, I

    2014-01-01

    The European Forensic Genetics Network of Excellence (EUROFORGEN-NoE) undertook a collaborative project on mRNA-based body fluid/skin typing and the interpretation of the resulting RNA and DNA data. Although both body fluids and skin are composed of a variety of cell types with different function...

  14. Shape-Controlled Fabrication of the Polymer-Based Micromotor Based on the Polydimethylsiloxane Template.

    Science.gov (United States)

    Su, Miaoda; Liu, Mei; Liu, Limei; Sun, Yunyu; Li, Mingtong; Wang, Dalei; Zhang, Hui; Dong, Bin

    2015-11-03

    We report the utilization of the polydimethylsiloxane template to construct polymer-based autonomous micromotors with various structures. Solid or hollow micromotors, which consist of polycaprolactone and platinum nanoparticles, can be obtained with controllable sizes and shapes. The resulting micromotor can not only be self-propelled in solution based on the bubble propulsion mechanism in the presence of the hydrogen peroxide fuel, but also exhibit structure-dependent motion behavior. In addition, the micromotors can exhibit various functions, ranging from fluorescence, magnetic control to cargo transportation. Since the current method can be extended to a variety of organic and inorganic materials, we thus believe it may have great potential in the fabrication of different functional micromotors for diverse applications.

  15. Base pairing and structural insights into the 5-formylcytosine in RNA duplex

    Science.gov (United States)

    Wang, Rui; Luo, Zhipu; He, Kaizhang; Delaney, Michael O.; Chen, Doris; Sheng, Jia

    2016-01-01

    Abstract 5-Formylcytidine (f5C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m5C) through 5-hydroxymethylcytidine (hm5C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f5C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5′-GUA(f5C)GUAC-3′]2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f5C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex. PMID:27079978

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

    Directory of Open Access Journals (Sweden)

    Michael F Sloma

    2017-11-01

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

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

    Science.gov (United States)

    Sloma, Michael F; Mathews, David H

    2017-11-01

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

  18. Analysis of current and alternative phenol based RNA extraction methodologies for cyanobacteria

    Directory of Open Access Journals (Sweden)

    Lindblad Peter

    2009-08-01

    Full Text Available Abstract Background The validity and reproducibility of gene expression studies depend on the quality of extracted RNA and the degree of genomic DNA contamination. Cyanobacteria are gram-negative prokaryotes that synthesize chlorophyll a and carry out photosynthetic water oxidation. These organisms possess an extended array of secondary metabolites that impair cell lysis, presenting particular challenges when it comes to nucleic acid isolation. Therefore, we used the NHM5 strain of Nostoc punctiforme ATCC 29133 to compare and improve existing phenol based chemistry and procedures for RNA extraction. Results With this work we identify and explore strategies for improved and lower cost high quality RNA isolation from cyanobacteria. All the methods studied are suitable for RNA isolation and its use for downstream applications. We analyse different Trizol based protocols, introduce procedural changes and describe an alternative RNA extraction solution. Conclusion It was possible to improve purity of isolated RNA by modifying protocol procedures. Further improvements, both in RNA purity and experimental cost, were achieved by using a new extraction solution, PGTX.

  19. Mapping Optimal Charge Density and Length of ROMP-Based PTDMs for siRNA Internalization.

    Science.gov (United States)

    Caffrey, Leah M; deRonde, Brittany M; Minter, Lisa M; Tew, Gregory N

    2016-10-10

    A fundamental understanding of how polymer structure impacts internalization and delivery of biologically relevant cargoes, particularly small interfering ribonucleic acid (siRNA), is of critical importance to the successful design of improved delivery reagents. Herein we report the use of ring-opening metathesis polymerization (ROMP) methods to synthesize two series of guanidinium-rich protein transduction domain mimics (PTDMs): one based on an imide scaffold that contains one guanidinium moiety per repeat unit, and another based on a diester scaffold that contains two guanidinium moieties per repeat unit. By varying both the degree of polymerization and, in effect, the relative number of cationic charges in each PTDM, the performances of the two ROMP backbones for siRNA internalization were evaluated and compared. Internalization of fluorescently labeled siRNA into Jurkat T cells demonstrated that fluorescein isothiocyanate (FITC)-siRNA internalization had a charge content dependence, with PTDMs containing approximately 40 to 60 cationic charges facilitating the most internalization. Despite this charge content dependence, the imide scaffold yielded much lower viabilities in Jurkat T cells than the corresponding diester PTDMs with similar numbers of cationic charges, suggesting that the diester scaffold is preferred for siRNA internalization and delivery applications. These developments will not only improve our understanding of the structural factors necessary for optimal siRNA internalization, but will also guide the future development of optimized PTDMs for siRNA internalization and delivery.

  20. Optimal consistency in microRNA expression analysis using reference-gene-based normalization.

    Science.gov (United States)

    Wang, Xi; Gardiner, Erin J; Cairns, Murray J

    2015-05-01

    Normalization of high-throughput molecular expression profiles secures differential expression analysis between samples of different phenotypes or biological conditions, and facilitates comparison between experimental batches. While the same general principles apply to microRNA (miRNA) normalization, there is mounting evidence that global shifts in their expression patterns occur in specific circumstances, which pose a challenge for normalizing miRNA expression data. As an alternative to global normalization, which has the propensity to flatten large trends, normalization against constitutively expressed reference genes presents an advantage through their relative independence. Here we investigated the performance of reference-gene-based (RGB) normalization for differential miRNA expression analysis of microarray expression data, and compared the results with other normalization methods, including: quantile, variance stabilization, robust spline, simple scaling, rank invariant, and Loess regression. The comparative analyses were executed using miRNA expression in tissue samples derived from subjects with schizophrenia and non-psychiatric controls. We proposed a consistency criterion for evaluating methods by examining the overlapping of differentially expressed miRNAs detected using different partitions of the whole data. Based on this criterion, we found that RGB normalization generally outperformed global normalization methods. Thus we recommend the application of RGB normalization for miRNA expression data sets, and believe that this will yield a more consistent and useful readout of differentially expressed miRNAs, particularly in biological conditions characterized by large shifts in miRNA expression.

  1. Drawbacks of the ancient RNA-based life-like system under primitive earth conditions.

    Science.gov (United States)

    Kawamura, Kunio

    2012-07-01

    Following the discovery of ribozymes, the "RNA world" hypothesis has become the most accepted hypothesis concerning the origin of life and genetic information. However, this hypothesis has several drawbacks. Verification of the hypothesis from different viewpoints led us to proposals from the viewpoint of the hydrothermal origin of life, solubility of RNA and related biopolymers, and the possibility of creating an evolutionary system comparable to the in vitro selection technique for functional RNA molecules based on molecular biology. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  2. Chinese wine classification system based on micrograph using combination of shape and structure features

    Science.gov (United States)

    Wan, Yi

    2011-06-01

    Chinese wines can be classification or graded by the micrographs. Micrographs of Chinese wines show floccules, stick and granule of variant shape and size. Different wines have variant microstructure and micrographs, we study the classification of Chinese wines based on the micrographs. Shape and structure of wines' particles in microstructure is the most important feature for recognition and classification of wines. So we introduce a feature extraction method which can describe the structure and region shape of micrograph efficiently. First, the micrographs are enhanced using total variation denoising, and segmented using a modified Otsu's method based on the Rayleigh Distribution. Then features are extracted using proposed method in the paper based on area, perimeter and traditional shape feature. Eight kinds total 26 features are selected. Finally, Chinese wine classification system based on micrograph using combination of shape and structure features and BP neural network have been presented. We compare the recognition results for different choices of features (traditional shape features or proposed features). The experimental results show that the better classification rate have been achieved using the combinational features proposed in this paper.

  3. A novel knowledge-based potential for RNA 3D structure evaluation

    Science.gov (United States)

    Yang, Yi; Gu, Qi; Zhang, Ben-Gong; Shi, Ya-Zhou; Shao, Zhi-Gang

    2018-03-01

    Ribonucleic acids (RNAs) play a vital role in biology, and knowledge of their three-dimensional (3D) structure is required to understand their biological functions. Recently structural prediction methods have been developed to address this issue, but a series of RNA 3D structures are generally predicted by most existing methods. Therefore, the evaluation of the predicted structures is generally indispensable. Although several methods have been proposed to assess RNA 3D structures, the existing methods are not precise enough. In this work, a new all-atom knowledge-based potential is developed for more accurately evaluating RNA 3D structures. The potential not only includes local and nonlocal interactions but also fully considers the specificity of each RNA by introducing a retraining mechanism. Based on extensive test sets generated from independent methods, the proposed potential correctly distinguished the native state and ranked near-native conformations to effectively select the best. Furthermore, the proposed potential precisely captured RNA structural features such as base-stacking and base-pairing. Comparisons with existing potential methods show that the proposed potential is very reliable and accurate in RNA 3D structure evaluation. Project supported by the National Science Foundation of China (Grants Nos. 11605125, 11105054, 11274124, and 11401448).

  4. Biosensor-based microRNA detection: techniques, design, performance, and challenges.

    Science.gov (United States)

    Johnson, Blake N; Mutharasan, Raj

    2014-04-07

    The current state of biosensor-based techniques for amplification-free microRNA (miRNA) detection is critically reviewed. Comparison with non-sensor and amplification-based molecular techniques (MTs), such as polymerase-based methods, is made in terms of transduction mechanism, associated protocol, and sensitivity. Challenges associated with miRNA hybridization thermodynamics which affect assay selectivity and amplification bias are briefly discussed. Electrochemical, electromechanical, and optical classes of miRNA biosensors are reviewed in terms of transduction mechanism, limit of detection (LOD), time-to-results (TTR), multiplexing potential, and measurement robustness. Current trends suggest that biosensor-based techniques (BTs) for miRNA assay will complement MTs due to the advantages of amplification-free detection, LOD being femtomolar (fM)-attomolar (aM), short TTR, multiplexing capability, and minimal sample preparation requirement. Areas of future importance in miRNA BT development are presented which include focus on achieving high measurement confidence and multiplexing capabilities.

  5. Shape memory and pseudoelastic properties of Fe-Mn-Si and Ti-Ni based alloys

    International Nuclear Information System (INIS)

    Guenin, G.

    1997-01-01

    The aim of this presentation is to analyse and discuss some recent advances in shape memory and pseudoelastic properties of different alloys. Experimental work in connection with theoretical ones will be reviewed. The first part is devoted to the microstructural origin of shape memory properties of Fe-Mn-Si based alloys (γ-ε transformation); the second part is a synthetic analysis of the effects of thermomechanical treatments on shape memory and pseudoelastic effects in Ti-Ni alloys, with some focus on the behaviour of the R phase introduced. (orig.)

  6. Context based Coding of Binary Shapes by Object Boundary Straightness Analysis

    DEFF Research Database (Denmark)

    Aghito, Shankar Manuel; Forchhammer, Søren

    2004-01-01

    A new lossless compression scheme for bilevel images targeted at binary shapes of image and video objects is presented. The scheme is based on a local analysis of the digital straightness of the causal part of the object boundary, which is used in the context definition for arithmetic encoding....... Tested on individual images of binary shapes and binary layers of digital maps the algorithm outperforms PWC, JBIG and MPEG-4 CAE. On the binary shapes the code lengths are reduced by 21%, 25%, and 42%, respectively. On the maps the reductions are 34%, 32%, and 59%, respectively. The algorithm is also...

  7. Adaptive Square-Shaped Trajectory-Based Service Location Protocol in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Hwa-Jung Lim

    2010-04-01

    Full Text Available In this paper we propose an adaptive square-shaped trajectory (ASST-based service location method to ensure load scalability in wireless sensor networks. This first establishes a square-shaped trajectory over the nodes that surround a target point computed by the hash function and any user can access it, using the hash. Both the width and the size of the trajectory are dynamically adjustable, depending on the number of queries made to the service information on the trajectory. The number of sensor nodes on the trajectory varies in proportion to the changing trajectory shape, allowing high loads to be distributed around the hot spot area.

  8. eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.

    Science.gov (United States)

    Yuan, Tiezheng; Huang, Xiaoyi; Dittmar, Rachel L; Du, Meijun; Kohli, Manish; Boardman, Lisa; Thibodeau, Stephen N; Wang, Liang

    2014-03-05

    RNA sequencing (RNA-seq) is emerging as a critical approach in biological research. However, its high-throughput advantage is significantly limited by the capacity of bioinformatics tools. The research community urgently needs user-friendly tools to efficiently analyze the complicated data generated by high throughput sequencers. We developed a standalone tool with graphic user interface (GUI)-based analytic modules, known as eRNA. The capacity of performing parallel processing and sample management facilitates large data analyses by maximizing hardware usage and freeing users from tediously handling sequencing data. The module miRNA identification" includes GUIs for raw data reading, adapter removal, sequence alignment, and read counting. The module "mRNA identification" includes GUIs for reference sequences, genome mapping, transcript assembling, and differential expression. The module "Target screening" provides expression profiling analyses and graphic visualization. The module "Self-testing" offers the directory setups, sample management, and a check for third-party package dependency. Integration of other GUIs including Bowtie, miRDeep2, and miRspring extend the program's functionality. eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. eRNA is available for free download at https://sourceforge.net/projects/erna/?source=directory.

  9. Visualizing RNA Secondary Structure Base Pair Binding Probabilities using Nested Concave Hulls

    OpenAIRE

    Sansen , Joris; Bourqui , Romain; Thebault , Patricia; Allali , Julien; Auber , David

    2015-01-01

    International audience; The challenge 1 of the BIOVIS 2015 design contest consists in designing an intuitive visual depiction of base pairs binding probabilities for secondary structure of ncRNA. Our representation depicts the potential nucleotide pairs binding using nested concave hulls over the computed MFE ncRNA secondary structure. Thus, it allows to identify regions with a high level of uncertainty in the MFE computation and the structures which seem to match to reality.

  10. Investigating shape representation using sensitivity to part- and axis-based transformations.

    Science.gov (United States)

    Denisova, Kristina; Feldman, Jacob; Su, Xiaotao; Singh, Manish

    2016-09-01

    Part- and axis-based approaches organize shape representations in terms of simple parts and their spatial relationships. Shape transformations that alter qualitative part structure have been shown to be more detectable than those that preserve it. We compared sensitivity to various transformations that change quantitative properties of parts and their spatial relationships, while preserving qualitative part structure. Shape transformations involving changes in length, width, curvature, orientation and location were applied to a small part attached to a larger base of a two-part shape. Increment thresholds were estimated for each transformation using a 2IFC procedure. Thresholds were converted into common units of shape difference to enable comparisons across transformations. Higher sensitivity was consistently found for transformations involving a parameter of a single part (length, width, curvature) than those involving spatial relations between two parts (relative orientation and location), suggesting a single-part superiority effect. Moreover, sensitivity to shifts in part location - a biomechanically implausible shape transformation - was consistently poorest. The influence of region-based geometry was investigated via stereoscopic manipulation of figure and ground. Sensitivity was compared across positive parts (protrusions) and negative parts (indentations) for transformations involving a change in orientation or location. For changes in part orientation (biomechanically plausible), sensitivity was better for positive than negative parts; whereas for changes in part location (biomechanically implausible), no systematic difference was observed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. A Meta-Path-Based Prediction Method for Human miRNA-Target Association

    Directory of Open Access Journals (Sweden)

    Jiawei Luo

    2016-01-01

    Full Text Available MicroRNAs (miRNAs are short noncoding RNAs that play important roles in regulating gene expressing, and the perturbed miRNAs are often associated with development and tumorigenesis as they have effects on their target mRNA. Predicting potential miRNA-target associations from multiple types of genomic data is a considerable problem in the bioinformatics research. However, most of the existing methods did not fully use the experimentally validated miRNA-mRNA interactions. Here, we developed RMLM and RMLMSe to predict the relationship between miRNAs and their targets. RMLM and RMLMSe are global approaches as they can reconstruct the missing associations for all the miRNA-target simultaneously and RMLMSe demonstrates that the integration of sequence information can improve the performance of RMLM. In RMLM, we use RM measure to evaluate different relatedness between miRNA and its target based on different meta-paths; logistic regression and MLE method are employed to estimate the weight of different meta-paths. In RMLMSe, sequence information is utilized to improve the performance of RMLM. Here, we carry on fivefold cross validation and pathway enrichment analysis to prove the performance of our methods. The fivefold experiments show that our methods have higher AUC scores compared with other methods and the integration of sequence information can improve the performance of miRNA-target association prediction.

  12. Application of support vector machine to three-dimensional shape-based virtual screening using comprehensive three-dimensional molecular shape overlay with known inhibitors.

    Science.gov (United States)

    Sato, Tomohiro; Yuki, Hitomi; Takaya, Daisuke; Sasaki, Shunta; Tanaka, Akiko; Honma, Teruki

    2012-04-23

    In this study, machine learning using support vector machine was combined with three-dimensional (3D) molecular shape overlay, to improve the screening efficiency. Since the 3D molecular shape overlay does not use fingerprints or descriptors to compare two compounds, unlike 2D similarity methods, the application of machine learning to a 3D shape-based method has not been extensively investigated. The 3D similarity profile of a compound is defined as the array of 3D shape similarities with multiple known active compounds of the target protein and is used as the explanatory variable of support vector machine. As the measures of 3D shape similarity for our new prediction models, the prediction performances of the 3D shape similarity metrics implemented in ROCS, such as ShapeTanimoto and ScaledColor, were validated, using the known inhibitors of 15 target proteins derived from the ChEMBL database. The learning models based on the 3D similarity profiles stably outperformed the original ROCS when more than 10 known inhibitors were available as the queries. The results demonstrated the advantages of combining machine learning with the 3D similarity profile to process the 3D shape information of plural active compounds.

  13. Textural Maturity Analysis and Sedimentary Environment Discrimination Based on Grain Shape Data

    Science.gov (United States)

    Tunwal, M.; Mulchrone, K. F.; Meere, P. A.

    2017-12-01

    Morphological analysis of clastic sedimentary grains is an important source of information regarding the processes involved in their formation, transportation and deposition. However, a standardised approach for quantitative grain shape analysis is generally lacking. In this contribution we report on a study where fully automated image analysis techniques were applied to loose sediment samples collected from glacial, aeolian, beach and fluvial environments. A range of shape parameters are evaluated for their usefulness in textural characterisation of populations of grains. The utility of grain shape data in ranking textural maturity of samples within a given sedimentary environment is evaluated. Furthermore, discrimination of sedimentary environment on the basis of grain shape information is explored. The data gathered demonstrates a clear progression in textural maturity in terms of roundness, angularity, irregularity, fractal dimension, convexity, solidity and rectangularity. Textural maturity can be readily categorised using automated grain shape parameter analysis. However, absolute discrimination between different depositional environments on the basis of shape parameters alone is less certain. For example, the aeolian environment is quite distinct whereas fluvial, glacial and beach samples are inherently variable and tend to overlap each other in terms of textural maturity. This is most likely due to a collection of similar processes and sources operating within these environments. This study strongly demonstrates the merit of quantitative population-based shape parameter analysis of texture and indicates that it can play a key role in characterising both loose and consolidated sediments. This project is funded by the Irish Petroleum Infrastructure Programme (www.pip.ie)

  14. A Circulating microRNA Signature Predicts Age-Based Development of Lymphoma.

    Directory of Open Access Journals (Sweden)

    Afshin Beheshti

    Full Text Available Extensive epidemiological data have demonstrated an exponential rise in the incidence of non-Hodgkin lymphoma (NHL that is associated with increasing age. The molecular etiology of this remains largely unknown, which impacts the effectiveness of treatment for patients. We proposed that age-dependent circulating microRNA (miRNA signatures in the host influence diffuse large B cell lymphoma (DLBCL development. Our objective was to examine tumor development in an age-based DLBCL system using an inventive systems biology approach. We harnessed a novel murine model of spontaneous DLBCL initiation (Smurf2-deficient at two age groups: 3 and 15 months old. All Smurf2-deficient mice develop visible DLBCL tumor starting at 15 months of age. Total miRNA was isolated from serum, bone marrow and spleen and were collected for all age groups for Smurf2-deficient mice and age-matched wild-type C57BL/6 mice. Using systems biology techniques, we identified a list of 10 circulating miRNAs being regulated in both the spleen and bone marrow that were present in DLBCL forming mice starting at 3 months of age that were not present in the control mice. Furthermore, this miRNA signature was found to occur circulating in the blood and it strongly impacted JUN and MYC oncogenic signaling. In addition, quantification of the miRNA signature was performed via Droplet Digital PCR technology. It was discovered that a key miRNA signature circulates throughout a host prior to the formation of a tumor starting at 3 months old, which becomes further modulated by age and yielded calculation of a 'carcinogenic risk score'. This novel age-based circulating miRNA signature may potentially be leveraged as a DLBCL risk profile at a young age to predict future lymphoma development or disease progression as well as for potential innovative miRNA-based targeted therapeutic strategies in lymphoma.

  15. Biomarker MicroRNAs for Diagnosis of Oral Squamous Cell Carcinoma Identified Based on Gene Expression Data and MicroRNA-mRNA Network Analysis

    Science.gov (United States)

    Zhang, Hui; Li, Tangxin; Zheng, Linqing

    2017-01-01

    Oral squamous cell carcinoma is one of the most malignant tumors with high mortality rate worldwide. Biomarker discovery is critical for early diagnosis and precision treatment of this disease. MicroRNAs are small noncoding RNA molecules which often regulate essential biological processes and are good candidates for biomarkers. By integrative analysis of both the cancer-associated gene expression data and microRNA-mRNA network, miR-148b-3p, miR-629-3p, miR-27a-3p, and miR-142-3p were screened as novel diagnostic biomarkers for oral squamous cell carcinoma based on their unique regulatory abilities in the network structure of the conditional microRNA-mRNA network and their important functions. These findings were confirmed by literature verification and functional enrichment analysis. Future experimental validation is expected for the further investigation of their molecular mechanisms. PMID:29098014

  16. Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.

    Science.gov (United States)

    Al-Khatib, Ra'ed M; Rashid, Nur'Aini Abdul; Abdullah, Rosni

    2011-08-01

    The secondary structure of RNA pseudoknots has been extensively inferred and scrutinized by computational approaches. Experimental methods for determining RNA structure are time consuming and tedious; therefore, predictive computational approaches are required. Predicting the most accurate and energy-stable pseudoknot RNA secondary structure has been proven to be an NP-hard problem. In this paper, a new RNA folding approach, termed MSeeker, is presented; it includes KnotSeeker (a heuristic method) and Mfold (a thermodynamic algorithm). The global optimization of this thermodynamic heuristic approach was further enhanced by using a case-based reasoning technique as a local optimization method. MSeeker is a proposed algorithm for predicting RNA pseudoknot structure from individual sequences, especially long ones. This research demonstrates that MSeeker improves the sensitivity and specificity of existing RNA pseudoknot structure predictions. The performance and structural results from this proposed method were evaluated against seven other state-of-the-art pseudoknot prediction methods. The MSeeker method had better sensitivity than the DotKnot, FlexStem, HotKnots, pknotsRG, ILM, NUPACK and pknotsRE methods, with 79% of the predicted pseudoknot base-pairs being correct.

  17. Sequence-based heuristics for faster annotation of non-coding RNA families.

    Science.gov (United States)

    Weinberg, Zasha; Ruzzo, Walter L

    2006-01-01

    Non-coding RNAs (ncRNAs) are functional RNA molecules that do not code for proteins. Covariance Models (CMs) are a useful statistical tool to find new members of an ncRNA gene family in a large genome database, using both sequence and, importantly, RNA secondary structure information. Unfortunately, CM searches are extremely slow. Previously, we created rigorous filters, which provably sacrifice none of a CM's accuracy, while making searches significantly faster for virtually all ncRNA families. However, these rigorous filters make searches slower than heuristics could be. In this paper we introduce profile HMM-based heuristic filters. We show that their accuracy is usually superior to heuristics based on BLAST. Moreover, we compared our heuristics with those used in tRNAscan-SE, whose heuristics incorporate a significant amount of work specific to tRNAs, where our heuristics are generic to any ncRNA. Performance was roughly comparable, so we expect that our heuristics provide a high-quality solution that--unlike family-specific solutions--can scale to hundreds of ncRNA families. The source code is available under GNU Public License at the supplementary web site.

  18. General enumeration of RNA secondary structures based on new ...

    African Journals Online (AJOL)

    Crick base pairs between AU and GC. Based on the new representation, this paper also computes the number of various types of constrained secondary structures taking the minimum stack length 1 and minimum size m for each bonding loop as ...

  19. Growth inhibition of head and neck squamous cell carcinoma cells by sgRNA targeting the cyclin D1 mRNA based on TRUE gene silencing.

    Directory of Open Access Journals (Sweden)

    Satoshi Iizuka

    Full Text Available Head and neck squamous cell carcinoma (HNSCC exhibits increased expression of cyclin D1 (CCND1. Previous studies have shown a correlation between poor prognosis of HNSCC and cyclin D1 overexpression. tRNase ZL-utilizing efficacious gene silencing (TRUE gene silencing is one of the RNA-mediated gene expression control technologies that have therapeutic potential. This technology is based on a unique enzymatic property of mammalian tRNase ZL, which is that it can cleave any target RNA at any desired site by recognizing a pre-tRNA-like complex formed between the target RNA and an artificial small guide RNA (sgRNA. In this study, we designed several sgRNAs targeting human cyclin D1 mRNA to examine growth inhibition of HNSCC cells. Transfection of certain sgRNAs decreased levels of cyclin D1 mRNA and protein in HSC-2 and HSC-3 cells, and also inhibited their proliferation. The combination of these sgRNAs and cisplatin showed more than additive inhibition of cancer cell growth. These findings demonstrate that TRUE gene silencing of cyclin D1 leads to inhibition of the growth of HNSCC cells and suggest that these sgRNAs alone or combined with cisplatin may be a useful new therapy for HNSCCs.

  20. Application of 3D Zernike descriptors to shape-based ligand similarity searching

    Directory of Open Access Journals (Sweden)

    Venkatraman Vishwesh

    2009-12-01

    Full Text Available Abstract Background The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed. Results In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR and SIMCOMP, a graph matching algorithm that compares atom environments. Three benchmark datasets are used to thoroughly test the methods in terms of their ability for molecular classification, retrieval rate, and performance under the situation that simulates actual virtual screening tasks over a large pharmaceutical database. The 3DZD performed better than or comparable to the other methods examined, depending on the datasets and evaluation metrics used. Reasons for the success and the failure of the shape based methods for specific cases are investigated. Based on the results for the three datasets, general conclusions are drawn with regard to their efficiency and applicability. Conclusion The 3DZD has unique ability for fast comparison of three-dimensional shape of compounds. Examples analyzed illustrate the advantages and the room for improvements for the 3DZD.

  1. Application of 3D Zernike descriptors to shape-based ligand similarity searching.

    Science.gov (United States)

    Venkatraman, Vishwesh; Chakravarthy, Padmasini Ramji; Kihara, Daisuke

    2009-12-17

    The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed. In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD) for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR) and SIMCOMP, a graph matching algorithm that compares atom environments. Three benchmark datasets are used to thoroughly test the methods in terms of their ability for molecular classification, retrieval rate, and performance under the situation that simulates actual virtual screening tasks over a large pharmaceutical database. The 3DZD performed better than or comparable to the other methods examined, depending on the datasets and evaluation metrics used. Reasons for the success and the failure of the shape based methods for specific cases are investigated. Based on the results for the three datasets, general conclusions are drawn with regard to their efficiency and applicability. The 3DZD has unique ability for fast comparison of three-dimensional shape of compounds. Examples analyzed illustrate the advantages and the room for improvements for the 3DZD.

  2. The optimal input optical pulse shape for the self-phase modulation based chirp generator

    Science.gov (United States)

    Zachinyaev, Yuriy; Rumyantsev, Konstantin

    2018-04-01

    The work is aimed to obtain the optimal shape of the input optical pulse for the proper functioning of the self-phase modulation based chirp generator allowing to achieve high values of chirp frequency deviation. During the research, the structure of the device based on self-phase modulation effect using has been analyzed. The influence of the input optical pulse shape of the transmitting optical module on the chirp frequency deviation has been studied. The relationship between the frequency deviation of the generated chirp and frequency linearity for the three options for implementation of the pulse shape has been also estimated. The results of research are related to the development of the theory of radio processors based on fiber-optic structures and can be used in radars, secure communications, geolocation and tomography.

  3. Stability of RNA silencing-based traits after virus infection

    DEFF Research Database (Denmark)

    Jørgensen, Bodil; Albrechtsen, Merete

    2007-01-01

    with constructs based on virus coat protein (CP) genes or other viral genes has been successfully used to engineer PTGS-mediated virus resistance into a large number of crop plants and some transgenic lines have been commercially exploited. However the discovery that plant viruses encode suppressors of gene...... silencing has raised concerns that virus infection of crop plants might reverse the new silencing-based traits. Most studies of virus suppression of silencing have used model systems based on silencing of reporter genes. A few studies have analysed the effects of virus infections on plants with genetically...... engineered virus resistance based on either a simple sense or an inverted repeat construct. We decided to use genetically engineered virus resistance in potato as a model system for further studies of the effect of virus infection on genetically engineered traits. We present for the first time a comparison...

  4. Probing electronic coupling between adenine bases in RNA strands from synchrotron radiation circular dichroism experiments

    DEFF Research Database (Denmark)

    Nielsen, Lisbeth Munksgård; Hoffmann, Søren Vrønning; Nielsen, Steen Brøndsted

    2012-01-01

    Circular dichroism spectra (176–330 nm) of RNA adenine oligomers, (rA)n (n = 1–10, 12, 15, and 20), reveal electronic coupling between two bases in short strands. The number of interacting bases in long strands is more and larger than that reported previously for the corresponding DNA strands....

  5. A computer graphics based model for scattering from objects of arbitrary shapes in the optical region

    Science.gov (United States)

    Goel, Narendra S.; Rozehnal, Ivan; Thompson, Richard L.

    1991-01-01

    A computer-graphics-based model, named DIANA, is presented for generation of objects of arbitrary shape and for calculating bidirectional reflectances and scattering from them, in the visible and infrared region. The computer generation is based on a modified Lindenmayer system approach which makes it possible to generate objects of arbitrary shapes and to simulate their growth, dynamics, and movement. Rendering techniques are used to display an object on a computer screen with appropriate shading and shadowing and to calculate the scattering and reflectance from the object. The technique is illustrated with scattering from canopies of simulated corn plants.

  6. Research on Sustainable Development Level Evaluation of Resource-based Cities Based on Shapely Entropy and Chouqet Integral

    Science.gov (United States)

    Zhao, Hui; Qu, Weilu; Qiu, Weiting

    2018-03-01

    In order to evaluate sustainable development level of resource-based cities, an evaluation method with Shapely entropy and Choquet integral is proposed. First of all, a systematic index system is constructed, the importance of each attribute is calculated based on the maximum Shapely entropy principle, and then the Choquet integral is introduced to calculate the comprehensive evaluation value of each city from the bottom up, finally apply this method to 10 typical resource-based cities in China. The empirical results show that the evaluation method is scientific and reasonable, which provides theoretical support for the sustainable development path and reform direction of resource-based cities.

  7. Atlas-based analysis of cardiac shape and function: correction of regional shape bias due to imaging protocol for population studies.

    Science.gov (United States)

    Medrano-Gracia, Pau; Cowan, Brett R; Bluemke, David A; Finn, J Paul; Kadish, Alan H; Lee, Daniel C; Lima, Joao A C; Suinesiaputra, Avan; Young, Alistair A

    2013-09-13

    Cardiovascular imaging studies generate a wealth of data which is typically used only for individual study endpoints. By pooling data from multiple sources, quantitative comparisons can be made of regional wall motion abnormalities between different cohorts, enabling reuse of valuable data. Atlas-based analysis provides precise quantification of shape and motion differences between disease groups and normal subjects. However, subtle shape differences may arise due to differences in imaging protocol between studies. A mathematical model describing regional wall motion and shape was used to establish a coordinate system registered to the cardiac anatomy. The atlas was applied to data contributed to the Cardiac Atlas Project from two independent studies which used different imaging protocols: steady state free precession (SSFP) and gradient recalled echo (GRE) cardiovascular magnetic resonance (CMR). Shape bias due to imaging protocol was corrected using an atlas-based transformation which was generated from a set of 46 volunteers who were imaged with both protocols. Shape bias between GRE and SSFP was regionally variable, and was effectively removed using the atlas-based transformation. Global mass and volume bias was also corrected by this method. Regional shape differences between cohorts were more statistically significant after removing regional artifacts due to imaging protocol bias. Bias arising from imaging protocol can be both global and regional in nature, and is effectively corrected using an atlas-based transformation, enabling direct comparison of regional wall motion abnormalities between cohorts acquired in separate studies.

  8. Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2015-12-01

    Full Text Available High-throughput mRNA sequencing (RNA-Seq is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-Seq data. We introduce a Network-based method for RNA-Seq-based Transcript Quantification (Net-RSTQ to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation. Based on our observation that the abundances of the neighboring isoforms by domain-domain interactions in the network are positively correlated, Net-RSTQ models the expression of the neighboring transcripts as Dirichlet priors on the likelihood of the observed read alignments against the transcripts in one gene. The transcript abundances of all the genes are then jointly estimated with alternating optimization of multiple EM problems. In simulation Net-RSTQ effectively improved isoform transcript quantifications when isoform co-expressions correlate with their interactions. qRT-PCR results on 25 multi-isoform genes in a stem cell line, an ovarian cancer cell line, and a breast cancer cell line also showed that Net-RSTQ estimated more consistent isoform proportions with RNA-Seq data. In the experiments on the RNA-Seq data in The Cancer Genome Atlas (TCGA, the transcript abundances estimated by Net-RSTQ are more informative for patient sample classification of ovarian cancer, breast cancer and lung cancer. All experimental results collectively support that Net-RSTQ is a promising approach for isoform quantification. Net-RSTQ toolbox is available at http://compbio.cs.umn.edu/Net-RSTQ/.

  9. Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

    Science.gov (United States)

    Song, Yinglei; Liu, Chunmei; Malmberg, Russell; Pan, Fangfang; Cai, Liming

    2005-01-01

    Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

  10. Mechanical properties and shape memory effect of thermal-responsive polymer based on PVA

    Science.gov (United States)

    Lin, Liulan; Zhang, Lingfeng; Guo, Yanwei

    2018-01-01

    In this study, the effect of content of glutaraldehyde (GA) on the shape memory behavior of a shape memory polymer based on polyvinyl alcohol chemically cross-linked with GA was investigated. Thermal-responsive shape memory composites with three different GA levels, GA-PVA (3 wt%, 5 wt%, 7 wt%), were prepared by particle melting, mold forming and freeze-drying technique. The mechanical properties, thermal properties and shape memory behavior were measured by differential scanning calorimeter, physical bending test and cyclic thermo-mechanical test. The addition of GA to PVA led to a steady shape memory transition temperature and an improved mechanical compressive strength. The composite with 5 wt% of GA exhibited the best shape recoverability. Further increase in the crosslinking agent content of GA would reduce the recovery force and prolong the recovery time due to restriction in the movement of the soft PVA chain segments. These results provide important information for the study on materials in 4D printing.

  11. Multistable wireless micro-actuator based on antagonistic pre-shaped double beams

    International Nuclear Information System (INIS)

    Liu, X; Lamarque, F; Doré, E; Pouille, P

    2015-01-01

    This paper presents a monolithic multistable micro-actuator based on antagonistic pre-shaped double beams. The designed micro-actuator is formed by two rows of bistable micro-actuators providing four stable positions. The bistable mechanism for each row is a pair of antagonistic pre-shaped beams. This bistable mechanism has an easier pre-load operation compared to the pre-compressed bistable beams method. Furthermore, it solves the asymmetrical force output problem of parallel pre-shaped bistable double beams. At the same time, the geometrical limit is lower than parallel pre-shaped bistable double beams, which ensures a smaller stroke of the micro-actuator with the same dimensions. The designed micro-actuator is fabricated using laser cutting machine on medium density fiberboard (MDF). The bistability and merits of antagonistic pre-shaped double beams are experimentally validated. Finally, a contactless actuation test is performed using 660 nm wavelength laser heating shape memory alloy (SMA) active elements. (paper)

  12. Multistable wireless micro-actuator based on antagonistic pre-shaped double beams

    Science.gov (United States)

    Liu, X.; Lamarque, F.; Doré, E.; Pouille, P.

    2015-07-01

    This paper presents a monolithic multistable micro-actuator based on antagonistic pre-shaped double beams. The designed micro-actuator is formed by two rows of bistable micro-actuators providing four stable positions. The bistable mechanism for each row is a pair of antagonistic pre-shaped beams. This bistable mechanism has an easier pre-load operation compared to the pre-compressed bistable beams method. Furthermore, it solves the asymmetrical force output problem of parallel pre-shaped bistable double beams. At the same time, the geometrical limit is lower than parallel pre-shaped bistable double beams, which ensures a smaller stroke of the micro-actuator with the same dimensions. The designed micro-actuator is fabricated using laser cutting machine on medium density fiberboard (MDF). The bistability and merits of antagonistic pre-shaped double beams are experimentally validated. Finally, a contactless actuation test is performed using 660 nm wavelength laser heating shape memory alloy (SMA) active elements.

  13. RNA-based, transient modulation of gene expression in human haematopoietic stem and progenitor cells

    Science.gov (United States)

    Diener, Yvonne; Jurk, Marion; Kandil, Britta; Choi, Yeong-Hoon; Wild, Stefan; Bissels, Ute; Bosio, Andreas

    2015-01-01

    Modulation of gene expression is a useful tool to study the biology of haematopoietic stem and progenitor cells (HSPCs) and might also be instrumental to expand these cells for therapeutic approaches. Most of the studies so far have employed stable gene modification by viral vectors that are burdensome when translating protocols into clinical settings. Our study aimed at exploring new ways to transiently modify HSPC gene expression using non-integrating, RNA-based molecules. First, we tested different methods to deliver these molecules into HSPCs. The delivery of siRNAs with chemical transfection methods such as lipofection or cationic polymers did not lead to target knockdown, although we observed more than 90% fluorescent cells using a fluorochrome-coupled siRNA. Confocal microscopic analysis revealed that despite extensive washing, siRNA stuck to or in the cell surface, thereby mimicking a transfection event. In contrast, electroporation resulted in efficient, siRNA-mediated protein knockdown. For transient overexpression of proteins, we used optimised mRNA molecules with modified 5′- and 3′-UTRs. Electroporation of mRNA encoding GFP resulted in fast, efficient and persistent protein expression for at least seven days. Our data provide a broad-ranging comparison of transfection methods for hard-to-transfect cells and offer new opportunities for DNA-free, non-integrating gene modulation in HSPCs. PMID:26599627

  14. Nanosystems based on siRNA silencing HuR expression counteract diabetic retinopathy in rat.

    Science.gov (United States)

    Amadio, Marialaura; Pascale, Alessia; Cupri, Sarha; Pignatello, Rosario; Osera, Cecilia; D Agata, Velia; D Amico, Agata Grazia; Leggio, Gian Marco; Ruozi, Barbara; Govoni, Stefano; Drago, Filippo; Bucolo, Claudio

    2016-09-01

    We evaluated whether specifically and directly targeting human antigen R (HuR), a member of embryonic lethal abnormal vision (ELAV) proteins family, may represent a new potential therapeutic strategy to manage diabetic retinopathy. Nanosystems loaded with siRNA silencing HuR expression (lipoplexes), consisting of solid lipid nanoparticles (SLN) and liposomes (SUV) were prepared. Photon correlation spectroscopy analysis, Zeta potential measurement and atomic force microscopy (AFM) studies were carried out to characterize the complexation of siRNA with the lipid nanocarriers. Nanosystems were evaluated by using AFM and scanning electron microscopy. The lipoplexes were injected into the eye of streptozotocin (STZ)-induced diabetic rats. Retinal HuR and VEGF levels were detected by Western blot and ELISA, respectively. Retinal histology was also carried out. The results demonstrated that retinal HuR and VEGF are significantly increased in STZ-rats and are blunted by HuR siRNA treatment. Lipoplexes with a weak positive surface charge and with a 4:1 N/P (cationic lipid nitrogen to siRNA phosphate) ratio exert a better transfection efficiency, significantly dumping retinal HuR and VEGF levels. In conclusion, we demonstrated that siRNA can be efficiently delivered into the rat retina using lipid-based nanocarriers, and some of the lipoplexes loaded with siRNA silencing HuR expression are potential candidates to manage retinal diseases. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Sensitive voltammetric detection of yeast RNA based on its interaction with Victoria Blue B

    Directory of Open Access Journals (Sweden)

    WEI SUN

    2009-12-01

    Full Text Available Voltammetric studies of the interaction of yeast RNA (y-RNA with Victoria Blue B (VBB are described in this paper. Furthermore, a linear sweep voltammetric method for the detection of y-RNA was established. The reaction conditions, such as acidity and amount of buffer solution, the concentration of VBB, the reaction time and temperature, etc., were carefully investigated by second order derivative linear sweep voltammetry. Under the optimal conditions, the reduction peak current of VBB at –0.75 V decreased greatly after the addition of y-RNA to the solution without any shift of the reduction peak potential. Based on the decrease of the peak current, a new quantitative method for the determination of y-RNA was developed. The effects of co-existing substances on the determination were carefully investigated and three synthetic samples were determined with satisfactory results. The stoichiometry of the VBB–y-RNA complex was calculated by linear sweep voltammetry and the interaction mechanism is discussed.

  16. tRNA acceptor-stem and anticodon bases embed separate features of amino acid chemistry

    Science.gov (United States)

    Carter, Charles W.; Wolfenden, Richard

    2016-01-01

    abstract The universal genetic code is a translation table by which nucleic acid sequences can be interpreted as polypeptides with a wide range of biological functions. That information is used by aminoacyl-tRNA synthetases to translate the code. Moreover, amino acid properties dictate protein folding. We recently reported that digital correlation techniques could identify patterns in tRNA identity elements that govern recognition by synthetases. Our analysis, and the functionality of truncated synthetases that cannot recognize the tRNA anticodon, support the conclusion that the tRNA acceptor stem houses an independent code for the same 20 amino acids that likely functioned earlier in the emergence of genetics. The acceptor-stem code, related to amino acid size, is distinct from a code in the anticodon that is related to amino acid polarity. Details of the acceptor-stem code suggest that it was useful in preserving key properties of stereochemically-encoded peptides that had developed the capacity to interact catalytically with RNA. The quantitative embedding of the chemical properties of amino acids into tRNA bases has implications for the origins of molecular biology. PMID:26595350

  17. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

    KAUST Repository

    Chawla, Mohit

    2015-06-27

    Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.

  18. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

    KAUST Repository

    Chawla, Mohit; Oliva, R.; Bujnicki, J. M.; Cavallo, Luigi

    2015-01-01

    Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.

  19. Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities.

    Science.gov (United States)

    Hagio, Taichi; Sakuraba, Shun; Iwakiri, Junichi; Mori, Ryota; Asai, Kiyoshi

    2018-02-19

    It is known that functional RNAs often switch their functions by forming different secondary structures. Popular tools for RNA secondary structures prediction, however, predict the single 'best' structures, and do not produce alternative structures. There are bioinformatics tools to predict suboptimal structures, but it is difficult to detect which alternative secondary structures are essential. We proposed a new computational method to detect essential alternative secondary structures from RNA sequences by decomposing the base-pairing probability matrix. The decomposition is calculated by a newly implemented software tool, RintW, which efficiently computes the base-pairing probability distributions over the Hamming distance from arbitrary reference secondary structures. The proposed approach has been demonstrated on ROSE element RNA thermometer sequence and Lysine RNA ribo-switch, showing that the proposed approach captures conformational changes in secondary structures. We have shown that alternative secondary structures are captured by decomposing base-paring probabilities over Hamming distance. Source code is available from http://www.ncRNA.org/RintW .

  20. URS DataBase: universe of RNA structures and their motifs.

    Science.gov (United States)

    Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

    2016-01-01

    The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA-protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.Database URL: http://server3.lpm.org.ru/urs/. © The Author(s) 2016. Published by Oxford University Press.

  1. Support vector machine-based facial-expression recognition method combining shape and appearance

    Science.gov (United States)

    Han, Eun Jung; Kang, Byung Jun; Park, Kang Ryoung; Lee, Sangyoun

    2010-11-01

    Facial expression recognition can be widely used for various applications, such as emotion-based human-machine interaction, intelligent robot interfaces, face recognition robust to expression variation, etc. Previous studies have been classified as either shape- or appearance-based recognition. The shape-based method has the disadvantage that the individual variance of facial feature points exists irrespective of similar expressions, which can cause a reduction of the recognition accuracy. The appearance-based method has a limitation in that the textural information of the face is very sensitive to variations in illumination. To overcome these problems, a new facial-expression recognition method is proposed, which combines both shape and appearance information, based on the support vector machine (SVM). This research is novel in the following three ways as compared to previous works. First, the facial feature points are automatically detected by using an active appearance model. From these, the shape-based recognition is performed by using the ratios between the facial feature points based on the facial-action coding system. Second, the SVM, which is trained to recognize the same and different expression classes, is proposed to combine two matching scores obtained from the shape- and appearance-based recognitions. Finally, a single SVM is trained to discriminate four different expressions, such as neutral, a smile, anger, and a scream. By determining the expression of the input facial image whose SVM output is at a minimum, the accuracy of the expression recognition is much enhanced. The experimental results showed that the recognition accuracy of the proposed method was better than previous researches and other fusion methods.

  2. An explanation for the shape of nanoindentation unloading curves based on finite element simulation

    International Nuclear Information System (INIS)

    Bolshakov, A.; Pharr, G.M.

    1995-01-01

    Current methods for measuring hardness and modulus from nanoindentation load-displacement data are based on Sneddon's equations for the indentation of an elastic half-space by an axially symmetric rigid punch. Recent experiments have shown that nanoindentation unloading data are distinctly curved in a manner which is not consistent with either the flat punch or the conical indenter geometries frequently used in modeling, but are more closely approximated by a parabola of revolution. Finite element simulations for conical indentation of an elastic-plastic material are presented which corroborate the experimental observations, and from which a simple explanation for the shape of the unloading curve is derived. The explanation is based on the concept of an effective indenter shape whose geometry is determined by the shape of the plastic hardness impression formed during indentation

  3. Automated mode shape estimation in agent-based wireless sensor networks

    Science.gov (United States)

    Zimmerman, Andrew T.; Lynch, Jerome P.

    2010-04-01

    Recent advances in wireless sensing technology have made it possible to deploy dense networks of sensing transducers within large structural systems. Because these networks leverage the embedded computing power and agent-based abilities integral to many wireless sensing devices, it is possible to analyze sensor data autonomously and in-network. In this study, market-based techniques are used to autonomously estimate mode shapes within a network of agent-based wireless sensors. Specifically, recent work in both decentralized Frequency Domain Decomposition and market-based resource allocation is leveraged to create a mode shape estimation algorithm derived from free-market principles. This algorithm allows an agent-based wireless sensor network to autonomously shift emphasis between improving mode shape accuracy and limiting the consumption of certain scarce network resources: processing time, storage capacity, and power consumption. The developed algorithm is validated by successfully estimating mode shapes using a network of wireless sensor prototypes deployed on the mezzanine balcony of Hill Auditorium, located on the University of Michigan campus.

  4. Systematic Development Strategy for Smart Devices Based on Shape-Memory Polymers

    Directory of Open Access Journals (Sweden)

    Andrés Díaz Lantada

    2017-10-01

    Full Text Available Shape-memory polymers are outstanding “smart” materials, which can perform important geometrical changes, when activated by several types of external stimuli, and which can be applied to several emerging engineering fields, from aerospace applications, to the development of biomedical devices. The fact that several shape-memory polymers can be structured in an additive way is an especially noteworthy advantage, as the development of advanced actuators with complex geometries for improved performance can be achieved, if adequate design and manufacturing considerations are taken into consideration. Present study presents a review of challenges and good practices, leading to a straightforward methodology (or integration of strategies, for the development of “smart” actuators based on shape-memory polymers. The combination of computer-aided design, computer-aided engineering and additive manufacturing technologies is analyzed and applied to the complete development of interesting shape-memory polymer-based actuators. Aspects such as geometrical design and optimization, development of the activation system, selection of the adequate materials and related manufacturing technologies, training of the shape-memory effect, final integration and testing are considered, as key processes of the methodology. Current trends, including the use of low-cost 3D and 4D printing, and main challenges, including process eco-efficiency and biocompatibility, are also discussed and their impact on the proposed methodology is considered.

  5. Image segmentation with a novel regularized composite shape prior based on surrogate study

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Tingting, E-mail: tingtingzhao@mednet.ucla.edu; Ruan, Dan, E-mail: druan@mednet.ucla.edu [The Department of Radiation Oncology, University of California, Los Angeles, California 90095 (United States)

    2016-05-15

    Purpose: Incorporating training into image segmentation is a good approach to achieve additional robustness. This work aims to develop an effective strategy to utilize shape prior knowledge, so that the segmentation label evolution can be driven toward the desired global optimum. Methods: In the variational image segmentation framework, a regularization for the composite shape prior is designed to incorporate the geometric relevance of individual training data to the target, which is inferred by an image-based surrogate relevance metric. Specifically, this regularization is imposed on the linear weights of composite shapes and serves as a hyperprior. The overall problem is formulated in a unified optimization setting and a variational block-descent algorithm is derived. Results: The performance of the proposed scheme is assessed in both corpus callosum segmentation from an MR image set and clavicle segmentation based on CT images. The resulted shape composition provides a proper preference for the geometrically relevant training data. A paired Wilcoxon signed rank test demonstrates statistically significant improvement of image segmentation accuracy, when compared to multiatlas label fusion method and three other benchmark active contour schemes. Conclusions: This work has developed a novel composite shape prior regularization, which achieves superior segmentation performance than typical benchmark schemes.

  6. Image segmentation with a novel regularized composite shape prior based on surrogate study

    International Nuclear Information System (INIS)

    Zhao, Tingting; Ruan, Dan

    2016-01-01

    Purpose: Incorporating training into image segmentation is a good approach to achieve additional robustness. This work aims to develop an effective strategy to utilize shape prior knowledge, so that the segmentation label evolution can be driven toward the desired global optimum. Methods: In the variational image segmentation framework, a regularization for the composite shape prior is designed to incorporate the geometric relevance of individual training data to the target, which is inferred by an image-based surrogate relevance metric. Specifically, this regularization is imposed on the linear weights of composite shapes and serves as a hyperprior. The overall problem is formulated in a unified optimization setting and a variational block-descent algorithm is derived. Results: The performance of the proposed scheme is assessed in both corpus callosum segmentation from an MR image set and clavicle segmentation based on CT images. The resulted shape composition provides a proper preference for the geometrically relevant training data. A paired Wilcoxon signed rank test demonstrates statistically significant improvement of image segmentation accuracy, when compared to multiatlas label fusion method and three other benchmark active contour schemes. Conclusions: This work has developed a novel composite shape prior regularization, which achieves superior segmentation performance than typical benchmark schemes.

  7. Cavitation erosion of Ti-Ni shape memory alloy deposited coatings and Fe base shape memory alloy solid

    International Nuclear Information System (INIS)

    Hattori, Shuji; Fujisawa, Seiji; Owa, Tomonobu

    2007-01-01

    In this study, cavitation erosion tests were carried out by using thermal spraying and deposition of Ti-Ni shape memory alloy for the surface coating. The results show the test speciment of Ti-Ni thermal spraying has many initial defects, so that the erosion resistance is very low. The erosion resistance of Ti-Ni deposit is about 5-10 times higher than that of SUS 304, thus erosion resistance of Ti-Ni deposit is better than that of Ti-Ni thermal spraying. The cavitation erosion tests were carried out by using Fe-Mn-Si with shape memory and gunmetal with low elastic modulus. The erosion resistance of Fe-Mn-Si shape memory alloy solid is about 9 times higher than that of SUS 304. The erosion resistance of gunmetal is almost the same as SUS 304, because the test specimen of gunmetal has many small defects on the original surface. (author)

  8. Nanotechnology based approaches for detection and delivery of microRNA in healthcare and crop protection.

    Science.gov (United States)

    Chaudhary, Vrantika; Jangra, Sumit; Yadav, Neelam R

    2018-04-13

    Nanobiotechnology has the potential to revolutionize diverse sectors including medicine, agriculture, food, textile and pharmaceuticals. Disease diagnostics, therapeutics and crop protection strategies are fast emerging using nanomaterials preferably nanobiomaterials. It has potential for development of novel nanobiomolecules which offer several advantages over conventional treatment methods. RNA nanoparticles with many unique features are promising candidates in disease treatment. The miRNAs are involved in many biochemical and developmental pathways and their regulation in plants and animals. These appear to be a powerful tool for controlling various pathological diseases in human, plants and animals, however there are challenges associated with miRNA based nanotechnology. Several advancements made in the field of miRNA therapeutics make it an attractive approach, but a lot more has to be explored in nanotechnology assisted miRNA therapy. The miRNA based technologies can be employed for detection and combating crop diseases as well. Despite these potential advantages, nanobiotechnology applications in the agricultural sector are still in its infancy and have not yet made its mark in comparison with healthcare sector. The review provides a platform to discuss nature, role and use of miRNAs in nanobiotechnology applications.

  9. RNA-Based TWIST1 Inhibition via Dendrimer Complex to Reduce Breast Cancer Cell Metastasis

    Directory of Open Access Journals (Sweden)

    James Finlay

    2015-01-01

    Full Text Available Breast cancer is the leading cause of cancer-related deaths among women in the United States, and survival rates are lower for patients with metastases and/or triple-negative breast cancer (TNBC; ER, PR, and Her2 negative. Understanding the mechanisms of cancer metastasis is therefore crucial to identify new therapeutic targets and develop novel treatments to improve patient outcomes. A potential target is the TWIST1 transcription factor, which is often overexpressed in aggressive breast cancers and is a master regulator of cellular migration through epithelial-mesenchymal transition (EMT. Here, we demonstrate an siRNA-based TWIST1 silencing approach with delivery using a modified poly(amidoamine (PAMAM dendrimer. Our results demonstrate that SUM1315 TNBC cells efficiently take up PAMAM-siRNA complexes, leading to significant knockdown of TWIST1 and EMT-related target genes. Knockdown lasts up to one week after transfection and leads to a reduction in migration and invasion, as determined by wound healing and transwell assays. Furthermore, we demonstrate that PAMAM dendrimers can deliver siRNA to xenograft orthotopic tumors and siRNA remains in the tumor for at least four hours after treatment. These results suggest that further development of dendrimer-based delivery of siRNA for TWIST1 silencing may lead to a valuable adjunctive therapy for patients with TNBC.

  10. RNA-Based Assessment of Diversity and Composition of Active Archaeal Communities in the German Bight

    Directory of Open Access Journals (Sweden)

    Bernd Wemheuer

    2012-01-01

    Full Text Available Archaea play an important role in various biogeochemical cycles. They are known extremophiles inhabiting environments such as thermal springs or hydrothermal vents. Recent studies have revealed a significant abundance of Archaea in moderate environments, for example, temperate sea water. Nevertheless, the composition and ecosystem function of these marine archaeal communities is largely unknown. To assess diversity and composition of active archaeal communities in the German Bight, seven marine water samples were taken and studied by RNA-based analysis of ribosomal 16S rRNA. For this purpose, total RNA was extracted from the samples and converted to cDNA. Archaeal community structures were investigated by pyrosequencing-based analysis of 16S rRNA amplicons generated from cDNA. To our knowledge, this is the first study combining next-generation sequencing and metatranscriptomics to study archaeal communities in marine habitats. The pyrosequencing-derived dataset comprised 62,045 archaeal 16S rRNA sequences. We identified Halobacteria as the predominant archaeal group across all samples with increased abundance in algal blooms. Thermoplasmatales (Euryarchaeota and the Marine Group I (Thaumarchaeota were identified in minor abundances. It is indicated that archaeal community patterns were influenced by environmental conditions.

  11. General classification of maturation reaction-norm shape from size-based processes

    DEFF Research Database (Denmark)

    Christensen, Asbjørn; Andersen, Ken Haste

    2011-01-01

    for growth and mortality is based on processes at the level of the individual, and is motivated by the energy budget of fish. MRN shape is a balance between opposing factors and depends on subtle details of size dependence of growth and mortality. MRNs with both positive and negative slopes are predicted...

  12. A Novel Technique for Shape Feature Extraction Using Content Based Image Retrieval

    Directory of Open Access Journals (Sweden)

    Dhanoa Jaspreet Singh

    2016-01-01

    Full Text Available With the advent of technology and multimedia information, digital images are increasing very quickly. Various techniques are being developed to retrieve/search digital information or data contained in the image. Traditional Text Based Image Retrieval System is not plentiful. Since it is time consuming as it require manual image annotation. Also, the image annotation differs with different peoples. An alternate to this is Content Based Image Retrieval (CBIR system. It retrieves/search for image using its contents rather the text, keywords etc. A lot of exploration has been compassed in the range of Content Based Image Retrieval (CBIR with various feature extraction techniques. Shape is a significant image feature as it reflects the human perception. Moreover, Shape is quite simple to use by the user to define object in an image as compared to other features such as Color, texture etc. Over and above, if applied alone, no descriptor will give fruitful results. Further, by combining it with an improved classifier, one can use the positive features of both the descriptor and classifier. So, a tryout will be made to establish an algorithm for accurate feature (Shape extraction in Content Based Image Retrieval (CBIR. The main objectives of this project are: (a To propose an algorithm for shape feature extraction using CBIR, (b To evaluate the performance of proposed algorithm and (c To compare the proposed algorithm with state of art techniques.

  13. Development of elastic properties of Cu-based shape memory alloys during martensitic transformation

    Czech Academy of Sciences Publication Activity Database

    Novák, Václav; Landa, Michal; Šittner, Petr

    2004-01-01

    Roč. 115, - (2004), s. 363 ISSN 1155-4339 Institutional research plan: CEZ:AV0Z1010914 Keywords : Cu-based shape memory alloy s * elastic properties * elastic constants * modelling Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.294, year: 2004

  14. A new bell-shaped function for idiotypic interactions based on cross-linking

    NARCIS (Netherlands)

    Boer, R.J. de; Boerlijst, M.C.; Sulzer, B.; Perelson, A.S.

    1996-01-01

    Most recent models of the immune network are based upon a phenomenological log bell-shaped interaction function. This function depends on a single parameter, the "field," which is the sum of all ligand concentrations weighted by their respective affinities. The typical behavior of these models is

  15. Theory of direct-interband-transition line shapes based on Mori's method

    International Nuclear Information System (INIS)

    Sam Nyung Yi; Jai Yon Ryu; Ok Hee Chung; Joung Young Sug; Sang Don Choi; Yeon Choon Chung

    1987-01-01

    A theory of direct interband optical transition in the electron-phonon system is introduced on the basis of the Kubo formalism and by using Mori's method of calculation. The line shape functions are introduced in two different ways and are compared with those obtained by Choi and Chung based on Argyres and Sigel's projection technique

  16. Descriptor Based Classification of Shapes in Terms of Style and Function

    DEFF Research Database (Denmark)

    Welnicka, Katarzyna; Bærentzen, Jakob Andreas; Aanæs, Henrik

    of a specific human being have some commonality that separate them from those of another person. Thus, one could argue that an individual represents a style. Style in the context of biological variation is something that we explore in the work presented here. Specifically, we investigate whether we can define...... of functions, since, as we discuss below, the function of the object (what it is) clearly also has a profound impact on shape. Thus, our work can be summed up as example based classification of digital 3D shapes in both style and function categories....

  17. Neutron–gamma discrimination based on bipolar trapezoidal pulse shaping using FPGAs in NE213

    International Nuclear Information System (INIS)

    Esmaeili-sani, Vahid; Moussavi-zarandi, Ali; Akbar-ashrafi, Nafiseh; Boghrati, Behzad; Afarideh, Hossein

    2012-01-01

    A technique employing neutron–gamma pulse shape discrimination (PSD) system that overcomes pile up limitations of previous methods to distinguish neutrons from gammas in scintillation detectors is described. The output signals of detectors were digitized and processed with a data acquisition system based on bipolar trapezoidal pulse shaping using Field programmable gate arrays (FPGA). FPGAs are capable of doing complex discrete signal processing algorithms with clock rates above 100 MHz. Their low cost, ease of use and selected dedicated hardware make them an ideal option for spectrometer systems.

  18. Neutron-gamma discrimination based on bipolar trapezoidal pulse shaping using FPGAs in NE213

    Energy Technology Data Exchange (ETDEWEB)

    Esmaeili-sani, Vahid, E-mail: vaheed_esmaeely80@yahoo.com [Department of Nuclear Engineering and Physics, Amirkabir University of Technology, P.O. Box 4155-4494, Tehran (Iran, Islamic Republic of); Moussavi-zarandi, Ali; Akbar-ashrafi, Nafiseh; Boghrati, Behzad; Afarideh, Hossein [Department of Nuclear Engineering and Physics, Amirkabir University of Technology, P.O. Box 4155-4494, Tehran (Iran, Islamic Republic of)

    2012-12-01

    A technique employing neutron-gamma pulse shape discrimination (PSD) system that overcomes pile up limitations of previous methods to distinguish neutrons from gammas in scintillation detectors is described. The output signals of detectors were digitized and processed with a data acquisition system based on bipolar trapezoidal pulse shaping using Field programmable gate arrays (FPGA). FPGAs are capable of doing complex discrete signal processing algorithms with clock rates above 100 MHz. Their low cost, ease of use and selected dedicated hardware make them an ideal option for spectrometer systems.

  19. A Dynamic Mesh-Based Approach to Model Melting and Shape of an ESR Electrode

    Science.gov (United States)

    Karimi-Sibaki, E.; Kharicha, A.; Bohacek, J.; Wu, M.; Ludwig, A.

    2015-10-01

    This paper presents a numerical method to investigate the shape of tip and melt rate of an electrode during electroslag remelting process. The interactions between flow, temperature, and electromagnetic fields are taken into account. A dynamic mesh-based approach is employed to model the dynamic formation of the shape of electrode tip. The effect of slag properties such as thermal and electrical conductivities on the melt rate and electrode immersion depth is discussed. The thermal conductivity of slag has a dominant influence on the heat transfer in the system, hence on melt rate of electrode. The melt rate decreases with increasing thermal conductivity of slag. The electrical conductivity of slag governs the electric current path that in turn influences flow and temperature fields. The melting of electrode is a quite unstable process due to the complex interaction between the melt rate, immersion depth, and shape of electrode tip. Therefore, a numerical adaptation of electrode position in the slag has been implemented in order to achieve steady state melting. In fact, the melt rate, immersion depth, and shape of electrode tip are interdependent parameters of process. The generated power in the system is found to be dependent on both immersion depth and shape of electrode tip. In other words, the same amount of power was generated for the systems where the shapes of tip and immersion depth were different. Furthermore, it was observed that the shape of electrode tip is very similar for the systems running with the same ratio of power generation to melt rate. Comparison between simulations and experimental results was made to verify the numerical model.

  20. Inference of Cell Mechanics in Heterogeneous Epithelial Tissue Based on Multivariate Clone Shape Quantification

    Science.gov (United States)

    Tsuboi, Alice; Umetsu, Daiki; Kuranaga, Erina; Fujimoto, Koichi

    2017-01-01

    Cell populations in multicellular organisms show genetic and non-genetic heterogeneity, even in undifferentiated tissues of multipotent cells during development and tumorigenesis. The heterogeneity causes difference of mechanical properties, such as, cell bond tension or adhesion, at the cell–cell interface, which determine the shape of clonal population boundaries via cell sorting or mixing. The boundary shape could alter the degree of cell–cell contacts and thus influence the physiological consequences of sorting or mixing at the boundary (e.g., tumor suppression or progression), suggesting that the cell mechanics could help clarify the physiology of heterogeneous tissues. While precise inference of mechanical tension loaded at each cell–cell contacts has been extensively developed, there has been little progress on how to distinguish the population-boundary geometry and identify the cause of geometry in heterogeneous tissues. We developed a pipeline by combining multivariate analysis of clone shape with tissue mechanical simulations. We examined clones with four different genotypes within Drosophila wing imaginal discs: wild-type, tartan (trn) overexpression, hibris (hbs) overexpression, and Eph RNAi. Although the clones were previously known to exhibit smoothed or convoluted morphologies, their mechanical properties were unknown. By applying a multivariate analysis to multiple criteria used to quantify the clone shapes based on individual cell shapes, we found the optimal criteria to distinguish not only among the four genotypes, but also non-genetic heterogeneity from genetic one. The efficient segregation of clone shape enabled us to quantitatively compare experimental data with tissue mechanical simulations. As a result, we identified the mechanical basis contributed to clone shape of distinct genotypes. The present pipeline will promote the understanding of the functions of mechanical interactions in heterogeneous tissue in a non-invasive manner. PMID

  1. A mRNA-Responsive G-Quadruplex-Based Drug Release System

    Directory of Open Access Journals (Sweden)

    Hidenobu Yaku

    2015-04-01

    Full Text Available G-quadruplex-based drug delivery carriers (GDDCs were designed to capture and release a telomerase inhibitor in response to a target mRNA. Hybridization between a loop on the GDDC structure and the mRNA should cause the G-quadruplex structure of the GDDC to unfold and release the bound inhibitor, anionic copper(II phthalocyanine (CuAPC. As a proof of concept, GDDCs were designed with a 10-30-mer loop, which can hybridize with a target sequence in epidermal growth factor receptor (EGFR mRNA. Structural analysis using circular dichroism (CD spectroscopy showed that the GDDCs form a (3 + 1 type G-quadruplex structure in 100 mM KCl and 10 mM MgCl2 in the absence of the target RNA. Visible absorbance titration experiments showed that the GDDCs bind to CuAPC with Ka values of 1.5 × 105 to 5.9 × 105 M−1 (Kd values of 6.7 to 1.7 μM at 25 °C, depending on the loop length. Fluorescence titration further showed that the G-quadruplex structure unfolds upon binding to the target RNA with Ka values above 1.0 × 108 M−1 (Kd values below 0.01 μM at 25 °C. These results suggest the carrier can sense and bind to the target RNA, which should result in release of the bound drug. Finally, visible absorbance titration experiments demonstrated that the GDDC release CuAPC in response to the target RNA.

  2. Construction of permanently inducible miRNA-based expression vectors using site-specific recombinases

    Directory of Open Access Journals (Sweden)

    Garwick-Coppens Sara E

    2011-11-01

    Full Text Available Abstract Background RNA interference (RNAi is a conserved gene silencing mechanism mediated by small inhibitory microRNAs (miRNAs. Promoter-driven miRNA expression vectors have emerged as important tools for delivering natural or artificially designed miRNAs to eukaryotic cells and organisms. Such systems can be used to query the normal or pathogenic functions of natural miRNAs or messenger RNAs, or to therapeutically silence disease genes. Results As with any molecular cloning procedure, building miRNA-based expression constructs requires a time investment and some molecular biology skills. To improve efficiency and accelerate the construction process, we developed a method to rapidly generate miRNA expression vectors using recombinases instead of more traditional cut-and-paste molecular cloning techniques. In addition to streamlining the construction process, our cloning strategy provides vectors with added versatility. In our system, miRNAs can be constitutively expressed from the U6 promoter, or inducibly expressed by Cre recombinase. We also engineered a built-in mechanism to destroy the vector with Flp recombinase, if desired. Finally, to further simplify the construction process, we developed a software package that automates the prediction and design of optimal miRNA sequences using our system. Conclusions We designed and tested a modular system to rapidly clone miRNA expression cassettes. Our strategy reduces the hands-on time required to successfully generate effective constructs, and can be implemented in labs with minimal molecular cloning expertise. This versatile system provides options that permit constitutive or inducible miRNA expression, depending upon the needs of the end user. As such, it has utility for basic or translational applications.

  3. Targeting miRNA-based medicines to cystic fibrosis airway epithelial cells using nanotechnology

    Directory of Open Access Journals (Sweden)

    McKiernan PJ

    2013-10-01

    Full Text Available Paul J McKiernan,2 Orla Cunninghamm,1,2 Catherine M Greenem,2 Sally-Ann Cryan1,31School of Pharmacy, Royal College of Surgeons in Ireland, 2Respiratory Research Division, Department of Medicine, Royal College of Surgeons in Ireland Education and Research Centre, Beaumont Hospital, 3Trinity Centre for Bioengineering, Trinity College Dublin, Dublin, IrelandAbstract: Cystic fibrosis (CF is an inherited disorder characterized by chronic airway inflammation. microRNAs (miRNAs are endogenous small RNAs which act on messenger (mRNA at a post transcriptional level, and there is a growing understanding that altered expression of miRNA is involved in the CF phenotype. Modulation of miRNA by replacement using miRNA mimics (premiRs presents a new therapeutic paradigm for CF, but effective and safe methods of delivery to the CF epithelium are limiting clinical translation. Herein, polymeric nanoparticles are investigated for delivery of miRNA mimics into CF airway epithelial cells, using miR-126 as a proof-of-concept premiR cargo to determine efficiency. Two polymers, polyethyleneimine (PEI and chitosan, were used to prepare miRNA nanomedicines, characterized for their size, surface (zeta potential, and RNA complexation efficiency, and screened for delivery and cytotoxicity in CFBE41o- (human F508del cystic fibrosis transmembrane conductance regulator bronchial epithelial cells using a novel high content analysis method. RNA extraction was carried out 24 hours post transfection, and miR-126 and TOM1 (target of Myb1 expression (a validated miR-126 target was assessed. Manufacture was optimized to produce small nanoparticles that effectively complexed miRNA. Using high content analysis, PEI-based nanoparticles were more effective than chitosan-based nanoparticles in facilitating uptake of miRNA into CFBE41o- cells and this was confirmed in miR-126 assays. PEI-premiR-126 nanoparticles at low nitrogen/phosphate (N/P ratios resulted in significant knockdown of

  4. Wilcoxon signed-rank-based technique for the pulse-shape analysis of HPGe detectors

    Science.gov (United States)

    Martín, S.; Quintana, B.; Barrientos, D.

    2016-07-01

    The characterization of the electric response of segmented-contact high-purity germanium detectors requires scanning systems capable of accurately associating each pulse with the position of the interaction that generated it. This process requires an algorithm sensitive to changes above the electronic noise in the pulse shapes produced at different positions, depending on the resolution of the Ge crystal. In this work, a pulse-shape comparison technique based on the Wilcoxon signed-rank test has been developed. It provides a method to distinguish pulses coming from different interaction points in the germanium crystal. Therefore, this technique is a necessary step for building a reliable pulse-shape database that can be used later for the determination of the position of interaction for γ-ray tracking spectrometry devices such as AGATA, GRETA or GERDA. The method was validated by comparison with a χ2 test using simulated and experimental pulses corresponding to a Broad Energy germanium detector (BEGe).

  5. Wilcoxon signed-rank-based technique for the pulse-shape analysis of HPGe detectors

    International Nuclear Information System (INIS)

    Martín, S.; Quintana, B.; Barrientos, D.

    2016-01-01

    The characterization of the electric response of segmented-contact high-purity germanium detectors requires scanning systems capable of accurately associating each pulse with the position of the interaction that generated it. This process requires an algorithm sensitive to changes above the electronic noise in the pulse shapes produced at different positions, depending on the resolution of the Ge crystal. In this work, a pulse-shape comparison technique based on the Wilcoxon signed-rank test has been developed. It provides a method to distinguish pulses coming from different interaction points in the germanium crystal. Therefore, this technique is a necessary step for building a reliable pulse-shape database that can be used later for the determination of the position of interaction for γ-ray tracking spectrometry devices such as AGATA, GRETA or GERDA. The method was validated by comparison with a χ"2 test using simulated and experimental pulses corresponding to a Broad Energy germanium detector (BEGe).

  6. Polymer-based candle-shaped microneedle electrodes for electroencephalography on hairy skin

    Science.gov (United States)

    Arai, Miyako; Kudo, Yuta; Miki, Norihisa

    2016-06-01

    In this paper, we report on the optimization of the shape of dry microneedle electrodes for electroencephalography (EEG) on hairy locations and compare the electrodes we developed with conventional wet electrodes. We propose the use of SU-8-based candle-shaped microneedle electrodes (CMEs), which have pillars of 1.0 mm height and 0.4 mm diameter with a gap of 0.43 mm between pillars. Microneedles are formed on the top of the pillars. The shape was determined by how well the pillars can avoid hairs and support the microneedles to penetrate through the stratum corneum. The skin-electrode contact impedances of the fabricated CMEs were found to be higher and less stable than those of conventional wet electrodes. However, the CMEs successfully acquired signals with qualities as good as those of conventional wet electrodes. Given the usability of the CMEs, which do not require skin preparation or gel, they are promising alternatives to conventional wet electrodes.

  7. Shape-memory effect of nanocomposites based on liquid-crystalline elastomers

    Science.gov (United States)

    Marotta, A.; Lama, G. C.; Gentile, G.; Cerruti, P.; Carfagna, C.; Ambrogi, V.

    2016-05-01

    In this work, nanocomposites based on liquid crystalline (LC) elastomers were prepared and characterized in their shape memory properties. For the synthesis of materials, p-bis(2,3-epoxypropoxy)-α-methylstilbene (DOMS) was used as mesogenic epoxy monomer, sebacic acid (SA) as curing agent and multi-walled carbon nanotubes (MWCNT) and graphene oxide (GO) as fillers. First, an effective compatibilization methodology was set up to improve the interfacial adhesion between the matrix and the carbonaceous nanofillers, thus obtaining homogeneous distribution and dispersion of the nanofillers within the polymer phase. Then, the obtained nanocomposite films were characterized in their morphological and thermal properties. In particular, the effect of the addition of the nanofillers on liquid crystalline behavior, as well as on shape-memory properties of the realized materials was investigated. It was found that both fillers were able to enhance the thermomechanical response of the LC elastomers, making them good candidates as shape memory materials.

  8. Shape models of asteroids based on lightcurve observations with BlueEye600 robotic observatory

    Science.gov (United States)

    Ďurech, Josef; Hanuš, Josef; Brož, Miroslav; Lehký, Martin; Behrend, Raoul; Antonini, Pierre; Charbonnel, Stephane; Crippa, Roberto; Dubreuil, Pierre; Farroni, Gino; Kober, Gilles; Lopez, Alain; Manzini, Federico; Oey, Julian; Poncy, Raymond; Rinner, Claudine; Roy, René

    2018-04-01

    We present physical models, i.e. convex shapes, directions of the rotation axis, and sidereal rotation periods, of 18 asteroids out of which 10 are new models and 8 are refined models based on much larger data sets than in previous work. The models were reconstructed by the lightcurve inversion method from archived publicly available lightcurves and our new observations with BlueEye600 robotic observatory. One of the new results is the shape model of asteroid (1663) van den Bos with the rotation period of 749 h, which makes it the slowest rotator with known shape. We describe our strategy for target selection that aims at fast production of new models using the enormous potential of already available photometry stored in public databases. We also briefly describe the control software and scheduler of the robotic observatory and we discuss the importance of building a database of asteroid models for studying asteroid physical properties in collisional families.

  9. Textual and shape-based feature extraction and neuro-fuzzy classifier for nuclear track recognition

    Science.gov (United States)

    Khayat, Omid; Afarideh, Hossein

    2013-04-01

    Track counting algorithms as one of the fundamental principles of nuclear science have been emphasized in the recent years. Accurate measurement of nuclear tracks on solid-state nuclear track detectors is the aim of track counting systems. Commonly track counting systems comprise a hardware system for the task of imaging and software for analysing the track images. In this paper, a track recognition algorithm based on 12 defined textual and shape-based features and a neuro-fuzzy classifier is proposed. Features are defined so as to discern the tracks from the background and small objects. Then, according to the defined features, tracks are detected using a trained neuro-fuzzy system. Features and the classifier are finally validated via 100 Alpha track images and 40 training samples. It is shown that principle textual and shape-based features concomitantly yield a high rate of track detection compared with the single-feature based methods.

  10. A Minimal Path Searching Approach for Active Shape Model (ASM)-based Segmentation of the Lung.

    Science.gov (United States)

    Guo, Shengwen; Fei, Baowei

    2009-03-27

    We are developing a minimal path searching method for active shape model (ASM)-based segmentation for detection of lung boundaries on digital radiographs. With the conventional ASM method, the position and shape parameters of the model points are iteratively refined and the target points are updated by the least Mahalanobis distance criterion. We propose an improved searching strategy that extends the searching points in a fan-shape region instead of along the normal direction. A minimal path (MP) deformable model is applied to drive the searching procedure. A statistical shape prior model is incorporated into the segmentation. In order to keep the smoothness of the shape, a smooth constraint is employed to the deformable model. To quantitatively assess the ASM-MP segmentation, we compare the automatic segmentation with manual segmentation for 72 lung digitized radiographs. The distance error between the ASM-MP and manual segmentation is 1.75 ± 0.33 pixels, while the error is 1.99 ± 0.45 pixels for the ASM. Our results demonstrate that our ASM-MP method can accurately segment the lung on digital radiographs.

  11. DNA origami-based shape IDs for single-molecule nanomechanical genotyping

    Science.gov (United States)

    Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

    2017-04-01

    Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ~10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level.

  12. An online detection system for aggregate sizes and shapes based on digital image processing

    Science.gov (United States)

    Yang, Jianhong; Chen, Sijia

    2017-02-01

    Traditional aggregate size measuring methods are time-consuming, taxing, and do not deliver online measurements. A new online detection system for determining aggregate size and shape based on a digital camera with a charge-coupled device, and subsequent digital image processing, have been developed to overcome these problems. The system captures images of aggregates while falling and flat lying. Using these data, the particle size and shape distribution can be obtained in real time. Here, we calibrate this method using standard globules. Our experiments show that the maximum particle size distribution error was only 3 wt%, while the maximum particle shape distribution error was only 2 wt% for data derived from falling aggregates, having good dispersion. In contrast, the data for flat-lying aggregates had a maximum particle size distribution error of 12 wt%, and a maximum particle shape distribution error of 10 wt%; their accuracy was clearly lower than for falling aggregates. However, they performed well for single-graded aggregates, and did not require a dispersion device. Our system is low-cost and easy to install. It can successfully achieve online detection of aggregate size and shape with good reliability, and it has great potential for aggregate quality assurance.

  13. A minimal path searching approach for active shape model (ASM)-based segmentation of the lung

    Science.gov (United States)

    Guo, Shengwen; Fei, Baowei

    2009-02-01

    We are developing a minimal path searching method for active shape model (ASM)-based segmentation for detection of lung boundaries on digital radiographs. With the conventional ASM method, the position and shape parameters of the model points are iteratively refined and the target points are updated by the least Mahalanobis distance criterion. We propose an improved searching strategy that extends the searching points in a fan-shape region instead of along the normal direction. A minimal path (MP) deformable model is applied to drive the searching procedure. A statistical shape prior model is incorporated into the segmentation. In order to keep the smoothness of the shape, a smooth constraint is employed to the deformable model. To quantitatively assess the ASM-MP segmentation, we compare the automatic segmentation with manual segmentation for 72 lung digitized radiographs. The distance error between the ASM-MP and manual segmentation is 1.75 +/- 0.33 pixels, while the error is 1.99 +/- 0.45 pixels for the ASM. Our results demonstrate that our ASM-MP method can accurately segment the lung on digital radiographs.

  14. Programmable thermal emissivity structures based on bioinspired self-shape materials

    Science.gov (United States)

    Athanasopoulos, N.; Siakavellas, N. J.

    2015-12-01

    Programmable thermal emissivity structures based on the bioinspired self-shape anisotropic materials were developed at macro-scale, and further studied theoretically at smaller scale. We study a novel concept, incorporating materials that are capable of transforming their shape via microstructural rearrangements under temperature stimuli, while avoiding the use of exotic shape memory materials or complex micro-mechanisms. Thus, programmed thermal emissivity behaviour of a surface is achievable. The self-shape structure reacts according to the temperature of the surrounding environment or the radiative heat flux. A surface which incorporates self-shape structures can be designed to quickly absorb radiative heat energy at low temperature levels, but is simultaneously capable of passively controlling its maximum temperature in order to prevent overheating. It resembles a “game” of colours, where two or more materials coexist with different values of thermal emissivity/ absorptivity/ reflectivity. The transformation of the structure conceals or reveals one of the materials, creating a surface with programmable - and therefore, variable- effective thermal emissivity. Variable thermal emissivity surfaces may be developed with a total hemispherical emissivity ratio (ɛEff_H/ɛEff_L) equal to 28.

  15. Influence of metal nanoparticle decorated CNTs on polyurethane based electro active shape memory nanocomposite actuators

    International Nuclear Information System (INIS)

    Raja, Mohan; Shanmugharaj, A.M.; Ryu, Sung Hun; Subha, J.

    2011-01-01

    Highlights: → Polyurethane based on pristine and metal (Ag and Cu) nanoparticle decorated CNTs nanocomposites are prepared through melt blending process. → The electrical, mechanical, dynamic mechanical, thermal conductivity and electro active shape memory properties of the PU nanocomposites were investigated. → The influence of metal nanoparticle decorated CNTs showed significant improvement in their all properties to compare to pristine CNTs. → Electro active shape memory studies of the PU/M-CNTs nanocomposites reveal extraordinary recoverability of its shape at lower applied dc voltages. - Abstract: Polymer nanocomposites based on thermoplastic polyurethane (PU) elastomer and metal nanoparticle (Ag and Cu) decorated multiwall carbon nanotubes (M-CNTs) were prepared through melt mixing process and investigated for its mechanical, dynamic mechanical and electro active shape memory properties. Structural characterization and morphological characterization of the PU nanocomposites were done using X-ray diffraction (XRD) and scanning electron microscopy (SEM). Morphological characterization revealed better dispersion of M-CNTs in the polyurethane, which is attributed to the improved interaction between the M-CNTs and polyurethane. Loading of the metal nanoparticle coated carbon nanotubes resulted in the significant improvement on the mechanical properties such as tensile strength of the PU composites in comparison to the pristine carbon nanotubes (P-CNTs). Dynamic mechanical analysis showed that the glass transition temperature (Tg) of the polyurethane increases slightly with increasing loading of both pristine and metal nanoparticle functionalized carbon nanotubes. The metal nanoparticles decorated carbon nanotubes also showed significant improvement in the thermal and electrical conductivity of the PU/M-CNTs nanocomposites. Shape memory studies of the PU/M-CNTs nanocomposites exhibit remarkable recoverability of its shape at lower applied dc voltages.

  16. SHERMAN - A shape-based thermophysical model II. Application to 8567 (1996 HW1)

    Science.gov (United States)

    Howell, E. S.; Magri, C.; Vervack, R. J.; Nolan, M. C.; Taylor, P. A.; Fernández, Y. R.; Hicks, M. D.; Somers, J. M.; Lawrence, K. J.; Rivkin, A. S.; Marshall, S. E.; Crowell, J. L.

    2018-03-01

    We apply a new shape-based thermophysical model, SHERMAN, to the near-Earth asteroid (NEA) 8567 (1996 HW1) to derive surface properties. We use the detailed shape model of Magri et al. (2011) for this contact binary NEA to analyze spectral observations (2-4.1 microns) obtained at the NASA IRTF on several different dates to find thermal parameters that match all the data. Visible and near-infrared (0.8-2.5 microns) spectral observations are also utilized in a self-consistent way. We find that an average visible albedo of 0.33, thermal inertia of 70 (SI units) and surface roughness of 50% closely match the observations. The shape and orientation of the asteroid is very important to constrain the thermal parameters to be consistent with all the observations. Multiple viewing geometries are equally important to achieve a robust solution for small, non-spherical NEAs. We separate the infrared beaming effects of shape, viewing geometry and surface roughness for this asteroid and show how their effects combine. We compare the diameter and albedo that would be derived from the thermal observations assuming a spherical shape with those from the shape-based model. We also discuss how observations from limited viewing geometries compare to the solution from multiple observations. The size that would be derived from the individual observation dates varies by 20% from the best-fit solution, and can be either larger or smaller. If the surface properties are not homogeneous, many solutions are possible, but the average properties derived here are very tightly constrained by the multiple observations, and give important insights into the nature of small NEAs.

  17. Novel extraction strategy of ribosomal RNA and genomic DNA from cheese for PCR-based investigations.

    Science.gov (United States)

    Bonaïti, Catherine; Parayre, Sandrine; Irlinger, Françoise

    2006-03-15

    Cheese microorganisms, such as bacteria and fungi, constitute a complex ecosystem that plays a central role in cheeses ripening. The molecular study of cheese microbial diversity and activity is essential but the extraction of high quality nucleic acid may be problematic: the cheese samples are characterised by a strong buffering capacity which negatively influenced the yield of the extracted rRNA. The objective of this study is to develop an effective method for the direct and simultaneous isolation of yeast and bacterial ribosomal RNA and genomic DNA from the same cheese samples. DNA isolation was based on a protocol used for nucleic acids isolation from anaerobic digestor, without preliminary washing step with the combined use of the action of chaotropic agent (acid guanidinium thiocyanate), detergents (SDS, N-lauroylsarcosine), chelating agent (EDTA) and a mechanical method (bead beating system). The DNA purification was carried out by two washing steps of phenol-chloroform. RNA was isolated successfully after the second acid extraction step by recovering it from the phenolic phase of the first acid extraction. The novel method yielded pure preparation of undegraded RNA accessible for reverse transcription-PCR. The extraction protocol of genomic DNA and rRNA was applicable to complex ecosystem of different cheese matrices.

  18. Emerging RNA-based drugs: siRNAs, microRNAs and derivates.

    Science.gov (United States)

    Pereira, Tiago Campos; Lopes-Cendes, Iscia

    2012-09-01

    An emerging new category of therapeutic agents based on ribonucleic acid has emerged and shown very promising in vitro, animal and pre-clinical results, known as small interfering RNAs (siRNAs), microRNAs mimics (miRNA mimics) and their derivates. siRNAs are small RNA molecules that promote potent and specific silencing of mutant, exogenous or aberrant genes through a mechanism known as RNA interference. These agents have called special attention to medicine since they have been used to experimentally treat a series of neurological conditions with distinct etiologies such as prion, viral, bacterial, fungal, genetic disorders and others. siRNAs have also been tested in other scenarios such as: control of anxiety, alcohol consumption, drug-receptor blockage and inhibition of pain signaling. Although in a much earlier stage, miRNAs mimics, anti-miRs and small activating RNAs (saRNAs) also promise novel therapeutic approaches to control gene expression. In this review we intend to introduce clinicians and medical researchers to the most recent advances in the world of siRNA- and miRNA-mediated gene control, its history, applications in cells, animals and humans, delivery methods (an yet unsolved hurdle), current status and possible applications in future clinical practice.

  19. Sequence-specific inhibition of Dicer measured with a force-based microarray for RNA ligands.

    Science.gov (United States)

    Limmer, Katja; Aschenbrenner, Daniela; Gaub, Hermann E

    2013-04-01

    Malfunction of protein translation causes many severe diseases, and suitable correction strategies may become the basis of effective therapies. One major regulatory element of protein translation is the nuclease Dicer that cuts double-stranded RNA independently of the sequence into pieces of 19-22 base pairs starting the RNA interference pathway and activating miRNAs. Inhibiting Dicer is not desirable owing to its multifunctional influence on the cell's gene regulation. Blocking specific RNA sequences by small-molecule binding, however, is a promising approach to affect the cell's condition in a controlled manner. A label-free assay for the screening of site-specific interference of small molecules with Dicer activity is thus needed. We used the Molecular Force Assay (MFA), recently developed in our lab, to measure the activity of Dicer. As a model system, we used an RNA sequence that forms an aptamer-binding site for paromomycin, a 615-dalton aminoglycoside. We show that Dicer activity is modulated as a function of concentration and incubation time: the addition of paromomycin leads to a decrease of Dicer activity according to the amount of ligand. The measured dissociation constant of paromomycin to its aptamer was found to agree well with literature values. The parallel format of the MFA allows a large-scale search and analysis for ligands for any RNA sequence.

  20. A plasmonic colorimetric strategy for visual miRNA detection based on hybridization chain reaction

    Science.gov (United States)

    Miao, Jie; Wang, Jingsheng; Guo, Jinyang; Gao, Huiguang; Han, Kun; Jiang, Chengmin; Miao, Peng

    2016-08-01

    In this work, a novel colorimetric strategy for miRNA analysis is proposed based on hybridization chain reaction (HCR)-mediated localized surface plasmon resonance (LSPR) variation of silver nanoparticles (AgNPs). miRNA in the sample to be tested is able to release HCR initiator from a solid interface to AgNPs colloid system by toehold exchange-mediated strand displacement, which then triggers the consumption of fuel strands with single-stranded tails for HCR. The final produced long nicked double-stranded DNA loses the ability to protect AgNPs from salt-induced aggregation. The stability variation of the colloid system can then be monitored by recording corresponding UV-vis spectrum and initial miRNA level is thus determined. This sensing system involves only four DNA strands which is quite simple. The practical utility is confirmed to be excellent by employing different biological samples.

  1. Yield impact for wafer shape misregistration-based binning for overlay APC diagnostic enhancement

    Science.gov (United States)

    Jayez, David; Jock, Kevin; Zhou, Yue; Govindarajulu, Venugopal; Zhang, Zhen; Anis, Fatima; Tijiwa-Birk, Felipe; Agarwal, Shivam

    2018-03-01

    The importance of traditionally acceptable sources of variation has started to become more critical as semiconductor technologies continue to push into smaller technology nodes. New metrology techniques are needed to pursue the process uniformity requirements needed for controllable lithography. Process control for lithography has the advantage of being able to adjust for cross-wafer variability, but this requires that all processes are close in matching between process tools/chambers for each process. When this is not the case, the cumulative line variability creates identifiable groups of wafers1 . This cumulative shape based effect is described as impacting overlay measurements and alignment by creating misregistration of the overlay marks. It is necessary to understand what requirements might go into developing a high volume manufacturing approach which leverages this grouping methodology, the key inputs and outputs, and what can be extracted from such an approach. It will be shown that this line variability can be quantified into a loss of electrical yield primarily at the edge of the wafer and proposes a methodology for root cause identification and improvement. This paper will cover the concept of wafer shape based grouping as a diagnostic tool for overlay control and containment, the challenges in implementing this in a manufacturing setting, and the limitations of this approach. This will be accomplished by showing that there are identifiable wafer shape based signatures. These shape based wafer signatures will be shown to be correlated to overlay misregistration, primarily at the edge. It will also be shown that by adjusting for this wafer shape signal, improvements can be made to both overlay as well as electrical yield. These improvements show an increase in edge yield, and a reduction in yield variability.

  2. New miRNA labeling method for bead-based quantification

    Directory of Open Access Journals (Sweden)

    Lanfranchi Gerolamo

    2010-06-01

    Full Text Available Abstract Background microRNAs (miRNAs are small single-stranded non-coding RNAs that act as crucial regulators of gene expression. Different methods have been developed for miRNA expression profiling in order to better understand gene regulation in normal and pathological conditions. miRNAs expression values obtained from large scale methodologies such as microarrays still need a validation step with alternative technologies. Results Here we have applied with an innovative approach, the Luminex® xMAP™ technology validate expression data of differentially expressed miRNAs obtained from high throughput arrays. We have developed a novel labeling system of small RNA molecules (below 200 nt, optimizing the sensitive cloning method for miRNAs, termed miRNA amplification profiling (mRAP. The Luminex expression patterns of three miRNAs (miR-23a, miR-27a and miR-199a in seven different cell lines have been validated by TaqMan miRNA assay. In all cases, bead-based meas were confirmed by the data obtained by TaqMan and microarray technologies. Conclusions We demonstrate that the measure of individual miRNA by the bead-based method is feasible, high speed, sensitive and low cost. The Luminex® xMAP™ technology also provides flexibility, since the central reaction can be scaled up with additional miRNA capturing beads, allowing validation of many differentially expressed miRNAs obtained from microarrays in a single experiment. We propose this technology as an alternative method to qRT-PCR for validating miRNAs expression data obtained with high-throughput technologies.

  3. Base substitutions at scissile bond sites are sufficient to alter RNA-binding and cleavage activity of RNase III.

    Science.gov (United States)

    Kim, Kyungsub; Sim, Se-Hoon; Jeon, Che Ok; Lee, Younghoon; Lee, Kangseok

    2011-02-01

    RNase III, a double-stranded RNA-specific endoribonuclease, degrades bdm mRNA via cleavage at specific sites. To better understand the mechanism of cleavage site selection by RNase III, we performed a genetic screen for sequences containing mutations at the bdm RNA cleavage sites that resulted in altered mRNA stability using a transcriptional bdm'-'cat fusion construct. While most of the isolated mutants showed the increased bdm'-'cat mRNA stability that resulted from the inability of RNase III to cleave the mutated sequences, one mutant sequence (wt-L) displayed in vivo RNA stability similar to that of the wild-type sequence. In vivo and in vitro analyses of the wt-L RNA substrate showed that it was cut only once on the RNA strand to the 5'-terminus by RNase III, while the binding constant of RNase III to this mutant substrate was moderately increased. A base substitution at the uncleaved RNase III cleavage site in wt-L mutant RNA found in another mutant lowered the RNA-binding affinity by 11-fold and abolished the hydrolysis of scissile bonds by RNase III. Our results show that base substitutions at sites forming the scissile bonds are sufficient to alter RNA cleavage as well as the binding activity of RNase III. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  4. Paper-Based MicroRNA Expression Profiling from Plasma and Circulating Tumor Cells.

    Science.gov (United States)

    Leong, Sai Mun; Tan, Karen Mei-Ling; Chua, Hui Wen; Huang, Mo-Chao; Cheong, Wai Chye; Li, Mo-Huang; Tucker, Steven; Koay, Evelyn Siew-Chuan

    2017-03-01

    Molecular characterization of circulating tumor cells (CTCs) holds great promise for monitoring metastatic progression and characterizing metastatic disease. However, leukocyte and red blood cell contamination of routinely isolated CTCs makes CTC-specific molecular characterization extremely challenging. Here we report the use of a paper-based medium for efficient extraction of microRNAs (miRNAs) from limited amounts of biological samples such as rare CTCs harvested from cancer patient blood. Specifically, we devised a workflow involving the use of Flinders Technology Associates (FTA) ® Elute Card with a digital PCR-inspired "partitioning" method to extract and purify miRNAs from plasma and CTCs. We demonstrated the sensitivity of this method to detect miRNA expression from as few as 3 cancer cells spiked into human blood. Using this method, background miRNA expression was excluded from contaminating blood cells, and CTC-specific miRNA expression profiles were derived from breast and colorectal cancer patients. Plasma separated out during purification of CTCs could likewise be processed using the same paper-based method for miRNA detection, thereby maximizing the amount of patient-specific information that can be derived from a single blood draw. Overall, this paper-based extraction method enables an efficient, cost-effective workflow for maximized recovery of small RNAs from limited biological samples for downstream molecular analyses. © 2016 American Association for Clinical Chemistry.

  5. Shape-based hand recognition approach using the morphological pattern spectrum

    Science.gov (United States)

    Ramirez-Cortes, Juan Manuel; Gomez-Gil, Pilar; Sanchez-Perez, Gabriel; Prieto-Castro, Cesar

    2009-01-01

    We propose the use of the morphological pattern spectrum, or pecstrum, as the base of a biometric shape-based hand recognition system. The system receives an image of the right hand of a subject in an unconstrained pose, which is captured with a commercial flatbed scanner. According to pecstrum property of invariance to translation and rotation, the system does not require the use of pegs for a fixed hand position, which simplifies the image acquisition process. This novel feature-extraction method is tested using a Euclidean distance classifier for identification and verification cases, obtaining 97% correct identification, and an equal error rate (EER) of 0.0285 (2.85%) for the verification mode. The obtained results indicate that the pattern spectrum represents a good feature-extraction alternative for low- and medium-level hand-shape-based biometric applications.

  6. Precise shape reconstruction by active pattern in total-internal-reflection-based tactile sensor.

    Science.gov (United States)

    Saga, Satoshi; Taira, Ryosuke; Deguchi, Koichiro

    2014-03-01

    We are developing a total-internal-reflection-based tactile sensor in which the shape is reconstructed using an optical reflection. This sensor consists of silicone rubber, an image pattern, and a camera. It reconstructs the shape of the sensor surface from an image of a pattern reflected at the inner sensor surface by total internal reflection. In this study, we propose precise real-time reconstruction by employing an optimization method. Furthermore, we propose to use active patterns. Deformation of the reflection image causes reconstruction errors. By controlling the image pattern, the sensor reconstructs the surface deformation more precisely. We implement the proposed optimization and active-pattern-based reconstruction methods in a reflection-based tactile sensor, and perform reconstruction experiments using the system. A precise deformation experiment confirms the linearity and precision of the reconstruction.

  7. Corrosion behaviour of Fe-Mn-Si based shape memory steels trained by cold rolling

    International Nuclear Information System (INIS)

    Soederberg, O.; Liu, X.W.; Ullakko, K.; Lindroos, V.K.

    1999-01-01

    Fe-Mn-Si based high nitrogen steels have been studied in recent years for potential industrial applications. These steels show good shape memory properties, high strength and excellent ductility. In the present study, the effects of training history on the corrosion properties of Fe-Mn-Si-Cr-Ni based high nitrogen steels were investigated. The corrosion behaviour of shape memory alloys was analyzed by implementing anodic polarisation measurements and immersion tests. The shape memory steels in annealed, deformed and recovered conditions were studied to examine the training effect on their corrosion behaviour. The features of the anodic polarisation curves indicated a general corrosion type of these steels. The experimental results showed that Cr and Mn had a marked influence on the corrosion behaviour of the steels, followed by Ni, N and V. It was also apparent that the deformation during the shape memory training by cold rolling decreased the corrosion stability, and the recovery heating reduced further their corrosion resistance. However, further studies are needed in order to better understand the corrosion behaviour of the investigated alloys. (orig.)

  8. Effect on injuries of assigning shoes based on foot shape in air force basic training.

    Science.gov (United States)

    Knapik, Joseph J; Brosch, Lorie C; Venuto, Margaret; Swedler, David I; Bullock, Steven H; Gaines, Lorraine S; Murphy, Ryan J; Tchandja, Juste; Jones, Bruce H

    2010-01-01

    This study examined whether assigning running shoes based on the shape of the bottom of the foot (plantar surface) influenced injury risk in Air Force Basic Military Training (BMT) and examined risk factors for injury in BMT. Data were collected from BMT recruits during 2007; analysis took place during 2008. After foot examinations, recruits were randomly consigned to either an experimental group (E, n=1042 men, 375 women) or a control group (C, n=913 men, 346 women). Experimental group recruits were assigned motion control, stability, or cushioned shoes for plantar shapes indicative of low, medium, or high arches, respectively. Control group recruits received a stability shoe regardless of plantar shape. Injuries during BMT were determined from outpatient visits provided from the Defense Medical Surveillance System. Other injury risk factors (fitness, smoking, physical activity, prior injury, menstrual history, and demographics) were obtained from a questionnaire, existing databases, or BMT units. Multivariate Cox regression controlling for other risk factors showed little difference in injury risk between the groups among men (hazard ratio [E/C]=1.11, 95% CI=0.89-1.38) or women (hazard ratio [E/C]=1.20, 95% CI= 0.90-1.60). Independent injury risk factors among both men and women included low aerobic fitness and cigarette smoking. This prospective study demonstrated that assigning running shoes based on the shape of the plantar surface had little influence on injury risk in BMT even after controlling for other injury risk factors. Published by Elsevier Inc.

  9. Shaping scientific attitude of biology education students through research-based teaching

    Science.gov (United States)

    Firdaus, Darmadi

    2017-08-01

    Scientific attitude is need of today's society for peaceful and meaningful living of every person in a multicultural world. A case study was conducted at the Faculty of Teacher Training and Education, University of Riau, Pekanbaru in order to describe the scientific attitude that shaped by research-based teaching (RBT). Eighteen students of English for Biology bilingual program were selected from 88 regular students as a subject of the study. RBT designed consists of 9 steps: 1) field observations, 2) developing research proposals, 3) research proposal seminar, 4) field data collecting, 5) data analyzing & ilustrating, 6) writing research papers, 7) preparing power point slides, 8) creating a scientific poster, 9) seminar & poster session. Data were collected by using check list observation instuments during 14 weeks (course sessions), then analyzed by using descriptive-quantitative method. The results showed that RBT were able to shape critical-mindedness, suspended judgement, respect for evidence, honesty, objectivity, and questioning attitude as well as tolerance of uncertainty. These attitudes which shaped were varies according to every steps of learning activities. It's seems that the preparation of scientific posters and research seminar quite good in shaping the critical-mindedness, suspended judgment, respect for evidence, honesty, objectivity, and questioning attitude, as well as tolerance of uncertainty. In conclusion, the application of research-based teaching through the English for Biology courses could shape the students scientific attitudes. However, the consistency of the appearance of a scientific attitude in every stage of Biology-based RBT learning process need more intensive and critical assessment.

  10. SPIDIA-RNA: second external quality assessment for the pre-analytical phase of blood samples used for RNA based analyses.

    Directory of Open Access Journals (Sweden)

    Francesca Malentacchi

    Full Text Available One purpose of the EC funded project, SPIDIA, is to develop evidence-based quality guidelines for the pre-analytical handling of blood samples for RNA molecular testing. To this end, two pan-European External Quality Assessments (EQAs were implemented. Here we report the results of the second SPIDIA-RNA EQA. This second study included modifications in the protocol related to the blood collection process, the shipping conditions and pre-analytical specimen handling for participants. Participating laboratories received two identical proficiency blood specimens collected in tubes with or without an RNA stabilizer. For pre-defined specimen storage times and temperatures, laboratories were asked to perform RNA extraction from whole blood according to their usual procedure and to return extracted RNA to the SPIDIA facility for further analysis. These RNA samples were evaluated for purity, yield, integrity, stability, presence of interfering substances, and gene expression levels for the validated markers of RNA stability: FOS, IL1B, IL8, GAPDH, FOSB and TNFRSF10c. Analysis of the gene expression results of FOS, IL8, FOSB, and TNFRSF10c, however, indicated that the levels of these transcripts were significantly affected by blood collection tube type and storage temperature. These results demonstrated that only blood collection tubes containing a cellular RNA stabilizer allowed reliable gene expression analysis within 48 h from blood collection for all the genes investigated. The results of these two EQAs have been proposed for use in the development of a Technical Specification by the European Committee for Standardization.

  11. Microstructure, mechanical and functional properties of NiTi-based shape memory ribbons

    International Nuclear Information System (INIS)

    Mehrabi, K.; Bruncko, M.; Kneissl, A.C.

    2012-01-01

    Highlights: ► Melt-spun samples exhibited martensite structure and shape memory effects immediately after processing at room temperature. ► Using a new etchant and interference contrast, it is possible to reveal the fine microstructures and grain boundaries. ► The martensite structure in NiTi is very fine, and nano-sized twin boundaries could be revealed using TEM only. ► Two-way effects have been successfully introduced by different thermomechanical training methods in NiTi, NiTiCu and NiTiW alloys, which can be used for several applications, e.g. microsensors and microactuators. - Abstract: The present work has been aimed to study the microstructures, functional properties and the influence of different thermomechanical training methods on the two-way shape memory effect in NiTi-based melt-spun ribbons. In order to get small-dimensioned shape memory alloys (SMAs) with good functional and mechanical properties, a rapid solidification technique was employed. Their fracture and elasticity characteristics have been determined, as well as shape memory properties by thermomechanical cycling. The ribbons were trained under tensile and bending deformation by thermal cycling through the phase transformation temperature range. The results displayed that all different training methods were effective in developing a two-way shape memory effect (TWSME). The influence of copper (5–25 at.% Cu) and tungsten (2 at.% W) on the microstructure, and the functional and mechanical behavior of NiTi thin ribbons was also investigated. All samples show a shape memory effect immediately after processing without further heat treatment. The melt-spun ribbons were trained under constant strain (bending and tensile deformation) by thermal cycling through the phase transformation temperature range. The addition of copper was effective to narrow the transformation hysteresis. The W addition has improved the TWSME stability of the NiTi alloys and mechanical properties. Results about

  12. A quantitative analysis of secondary RNA structure using domination based parameters on trees

    Directory of Open Access Journals (Sweden)

    Zou Yue

    2006-03-01

    Full Text Available Abstract Background It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants to be utilized to numerically identify secondary RNA motifs. The domination number of a graph is a graphical invariant that is sensitive to even a slight change in the structure of a tree. The invariants selected in this study are variations of the domination number of a graph. These graphical invariants are partitioned into two classes, and we define two parameters based on each of these classes. These parameters are calculated for all small order trees and a statistical analysis of the resulting data is conducted to determine if the values of these parameters can be utilized to identify which trees of orders seven and eight are RNA-like in structure. Results The statistical analysis shows that the domination based parameters correctly distinguish between the trees that represent native structures and those that are not likely candidates to represent RNA. Some of the trees previously identified as candidate structures are found to be "very" RNA like, while others are not, thereby refining the space of structures likely to be found as representing secondary RNA structure. Conclusion Search algorithms are available that mine nucleotide sequence databases. However, the number of motifs identified can be quite large, making a further search for similar motif computationally difficult. Much of the work in the bioinformatics arena is toward the development of better algorithms to address the computational problem. This work, on the other hand, uses mathematical descriptors to more clearly characterize the RNA motifs and thereby reduce the corresponding search space. These

  13. Matrix factorization-based data fusion for the prediction of lncRNA-disease associations.

    Science.gov (United States)

    Fu, Guangyuan; Wang, Jun; Domeniconi, Carlotta; Yu, Guoxian

    2018-05-01

    Long non-coding RNAs (lncRNAs) play crucial roles in complex disease diagnosis, prognosis, prevention and treatment, but only a small portion of lncRNA-disease associations have been experimentally verified. Various computational models have been proposed to identify lncRNA-disease associations by integrating heterogeneous data sources. However, existing models generally ignore the intrinsic structure of data sources or treat them as equally relevant, while they may not be. To accurately identify lncRNA-disease associations, we propose a Matrix Factorization based LncRNA-Disease Association prediction model (MFLDA in short). MFLDA decomposes data matrices of heterogeneous data sources into low-rank matrices via matrix tri-factorization to explore and exploit their intrinsic and shared structure. MFLDA can select and integrate the data sources by assigning different weights to them. An iterative solution is further introduced to simultaneously optimize the weights and low-rank matrices. Next, MFLDA uses the optimized low-rank matrices to reconstruct the lncRNA-disease association matrix and thus to identify potential associations. In 5-fold cross validation experiments to identify verified lncRNA-disease associations, MFLDA achieves an area under the receiver operating characteristic curve (AUC) of 0.7408, at least 3% higher than those given by state-of-the-art data fusion based computational models. An empirical study on identifying masked lncRNA-disease associations again shows that MFLDA can identify potential associations more accurately than competing models. A case study on identifying lncRNAs associated with breast, lung and stomach cancers show that 38 out of 45 (84%) associations predicted by MFLDA are supported by recent biomedical literature and further proves the capability of MFLDA in identifying novel lncRNA-disease associations. MFLDA is a general data fusion framework, and as such it can be adopted to predict associations between other biological

  14. Site-Specific Incorporation of Functional Components into RNA by an Unnatural Base Pair Transcription System

    Directory of Open Access Journals (Sweden)

    Rie Kawai

    2012-03-01

    Full Text Available Toward the expansion of the genetic alphabet, an unnatural base pair between 7-(2-thienylimidazo[4,5-b]pyridine (Ds and pyrrole-2-carbaldehyde (Pa functions as a third base pair in replication and transcription, and provides a useful tool for the site-specific, enzymatic incorporation of functional components into nucleic acids. We have synthesized several modified-Pa substrates, such as alkylamino-, biotin-, TAMRA-, FAM-, and digoxigenin-linked PaTPs, and examined their transcription by T7 RNA polymerase using Ds-containing DNA templates with various sequences. The Pa substrates modified with relatively small functional groups, such as alkylamino and biotin, were efficiently incorporated into RNA transcripts at the internal positions, except for those less than 10 bases from the 3′-terminus. We found that the efficient incorporation into a position close to the 3′-terminus of a transcript depended on the natural base contexts neighboring the unnatural base, and that pyrimidine-Ds-pyrimidine sequences in templates were generally favorable, relative to purine-Ds-purine sequences. The unnatural base pair transcription system provides a method for the site-specific functionalization of large RNA molecules.

  15. Improving the accuracy of ultrafast ligand-based screening: incorporating lipophilicity into ElectroShape as an extra dimension.

    Science.gov (United States)

    Armstrong, M Stuart; Finn, Paul W; Morris, Garrett M; Richards, W Graham

    2011-08-01

    In a previous paper, we presented the ElectroShape method, which we used to achieve successful ligand-based virtual screening. It extended classical shape-based methods by applying them to the four-dimensional shape of the molecule where partial charge was used as the fourth dimension to capture electrostatic information. This paper extends the approach by using atomic lipophilicity (alogP) as an additional molecular property and validates it using the improved release 2 of the Directory of Useful Decoys (DUD). When alogP replaced partial charge, the enrichment results were slightly below those of ElectroShape, though still far better than purely shape-based methods. However, when alogP was added as a complement to partial charge, the resulting five-dimensional enrichments shows a clear improvement in performance. This demonstrates the utility of extending the ElectroShape virtual screening method by adding other atom-based descriptors.

  16. Quantitative characterization and comparison of precipitate and grain shape in Nickel -base superalloys using moment invariants

    Science.gov (United States)

    Callahan, Patrick Gregory

    A fundamental objective of materials science and engineering is to understand the structure-property-processing-performance relationship. We need to know the true 3-D microstructure of a material to understand certain geometric properties of a material, and thus fulfill this objective. Focused ion beam (FIB) serial sectioning allows us to find the true 3-D microstructure of Ni-base superalloys. Once the true 3-D microstructure is obtained, an accurate quantitative description and characterization of precipitate and/or grain shapes is needed to understand the microstructure and describe it in an unbiased way. In this thesis, second order moment invariants, the shape quotient Q, a convexity measure relating the volume of an object to the volume of its convex hull, V/Vconv, and Gaussian curvature have been used to compare an experimentally observed polycrystalline IN100 microstructure to three synthetic microstructures. The three synthetic microstructures used different shape classes to produce starting grain shapes. The three shape classes are ellipsoids, superellipsoids, and the shapes generated when truncating a cube with an octahedron. The microstructures are compared using a distance measure, the Hellinger distance. The Hellinger distance is used to compare distributions of shape descriptors for the grains in each microstructure. The synthetic microstructure that has the smallest Hellinger distance, and so best matched the experimentally observed microstructure is the microstructure that used superellipsoids as a starting grain shape. While it has the smallest Hellinger distance, and is approaching realistic grain morphologies, the superellipsoidal microstructure is still not realistic. Second order moment invariants, Q, and V/V conv have also been used to characterize the γ' precipitate shapes from four experimental Ru-containing Ni-base superalloys with differences in alloying additions. The superalloys are designated UM-F9, UM-F18, UM-F19, and UM-F22. The

  17. Study design requirements for RNA sequencing-based breast cancer diagnostics.

    Science.gov (United States)

    Mer, Arvind Singh; Klevebring, Daniel; Grönberg, Henrik; Rantalainen, Mattias

    2016-02-01

    Sequencing-based molecular characterization of tumors provides information required for individualized cancer treatment. There are well-defined molecular subtypes of breast cancer that provide improved prognostication compared to routine biomarkers. However, molecular subtyping is not yet implemented in routine breast cancer care. Clinical translation is dependent on subtype prediction models providing high sensitivity and specificity. In this study we evaluate sample size and RNA-sequencing read requirements for breast cancer subtyping to facilitate rational design of translational studies. We applied subsampling to ascertain the effect of training sample size and the number of RNA sequencing reads on classification accuracy of molecular subtype and routine biomarker prediction models (unsupervised and supervised). Subtype classification accuracy improved with increasing sample size up to N = 750 (accuracy = 0.93), although with a modest improvement beyond N = 350 (accuracy = 0.92). Prediction of routine biomarkers achieved accuracy of 0.94 (ER) and 0.92 (Her2) at N = 200. Subtype classification improved with RNA-sequencing library size up to 5 million reads. Development of molecular subtyping models for cancer diagnostics requires well-designed studies. Sample size and the number of RNA sequencing reads directly influence accuracy of molecular subtyping. Results in this study provide key information for rational design of translational studies aiming to bring sequencing-based diagnostics to the clinic.

  18. BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.

    Science.gov (United States)

    Hoff, Katharina J; Lange, Simone; Lomsadze, Alexandre; Borodovsky, Mark; Stanke, Mario

    2016-03-01

    Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene finder that usually requires supervised training and uses information from RNA-Seq reads in the prediction step. Complementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for automatic gene prediction. We present BRAKER1, a pipeline for unsupervised RNA-Seq-based genome annotation that combines the advantages of GeneMark-ET and AUGUSTUS. As input, BRAKER1 requires a genome assembly file and a file in bam-format with spliced alignments of RNA-Seq reads to the genome. First, GeneMark-ET performs iterative training and generates initial gene structures. Second, AUGUSTUS uses predicted genes for training and then integrates RNA-Seq read information into final gene predictions. In our experiments, we observed that BRAKER1 was more accurate than MAKER2 when it is using RNA-Seq as sole source for training and prediction. BRAKER1 does not require pre-trained parameters or a separate expert-prepared training step. BRAKER1 is available for download at http://bioinf.uni-greifswald.de/bioinf/braker/ and http://exon.gatech.edu/GeneMark/ katharina.hoff@uni-greifswald.de or borodovsky@gatech.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda.

    Directory of Open Access Journals (Sweden)

    Shu Wu

    Full Text Available Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9 within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%; and could aid in species-level analyses, but with some limitations; 2 nearly-whole-length sequences and some partial regions (around V2, V4, and V9 of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%; 3 compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%; and 4 V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.

  20. Registration-based Bone Morphometry for Shape Analysis of the Bones of the Human Wrist

    Science.gov (United States)

    Joshi, Anand A.; Leahy, Richard M.; Badawi, Ramsey D.; Chaudhari, Abhijit J.

    2015-01-01

    We present a method that quantifies point-wise changes in surface morphology of the bones of the human wrist. The proposed method, referred to as Registration-based Bone Morphometry (RBM), consists of two steps: an atlas selection step and an atlas warping step. The atlas for individual wrist bones was selected based on the shortest l2 distance to the ensemble of wrist bones from a database of a healthy population of subjects. The selected atlas was then warped to the corresponding bones of individuals in the population using a non-linear registration method based on regularized l2 distance minimization. The displacement field thus calculated showed local differences in bone shape that then were used for the analysis of group differences. Our results indicate that RBM has potential to provide a standardized approach to shape analysis of bones of the human wrist. We demonstrate the performance of RBM for examining group differences in wrist bone shapes based on sex and between those of the right and left wrists in healthy individuals. We also present data to show the application of RBM for tracking bone erosion status in rheumatoid arthritis. PMID:26353369

  1. Spectroelectrochemical detection of microRNA-155 based on functional RNA immobilization onto ITO/GNP nanopattern.

    Science.gov (United States)

    Mohammadniaei, Mohsen; Yoon, Jinho; Lee, Taek; Choi, Jeong-Woo

    2018-05-20

    We fabricated a microRNA biosensor using the combination of surface enhanced Raman spectroscopy (SERS) and electrochemical (EC) techniques. For the first time, the weaknesses of each techniques for microRNA detection was compensated by the other ones to give rise to the specific and wide-range detection of miR-155. A single stranded 3' methylene blue (MB) and 5' thiol-modified RNA (MB-ssRNA-SH) was designed to detect the target miR-155 and immobilized onto the gold nanoparticle-modified ITO (ITO/GNP). Upon the invasion of target strand, the double-stranded RNA transformed rapidly to an upright structure resulting in a notable decrease in SERS and redox signals of the MB. For the first time, by combination of SERS and EC techniques in a single platform we extended the dynamic range of both techniques from 10 pM to 450 nM (SERS: 10 pM-5 nM and EC: 5 nM-450 nM). As well, the SERS technique improved the detection limit of the EC method from 100 pM to 100 fM, while the EC method covered single-mismatch detection which was the SERS deficiency. The fabricated single-step biosensor possessing a good capability of miRNA detection in human serum, could be employed throughout the broad ranges of biomedical and bioelectronics applications. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.

    Science.gov (United States)

    Behr, Jonas; Kahles, André; Zhong, Yi; Sreedharan, Vipin T; Drewe, Philipp; Rätsch, Gunnar

    2013-10-15

    High-throughput sequencing of mRNA (RNA-Seq) has led to tremendous improvements in the detection of expressed genes and reconstruction of RNA transcripts. However, the extensive dynamic range of gene expression, technical limitations and biases, as well as the observed complexity of the transcriptional landscape, pose profound computational challenges for transcriptome reconstruction. We present the novel framework MITIE (Mixed Integer Transcript IdEntification) for simultaneous transcript reconstruction and quantification. We define a likelihood function based on the negative binomial distribution, use a regularization approach to select a few transcripts collectively explaining the observed read data and show how to find the optimal solution using Mixed Integer Programming. MITIE can (i) take advantage of known transcripts, (ii) reconstruct and quantify transcripts simultaneously in multiple samples, and (iii) resolve the location of multi-mapping reads. It is designed for genome- and assembly-based transcriptome reconstruction. We present an extensive study based on realistic simulated RNA-Seq data. When compared with state-of-the-art approaches, MITIE proves to be significantly more sensitive and overall more accurate. Moreover, MITIE yields substantial performance gains when used with multiple samples. We applied our system to 38 Drosophila melanogaster modENCODE RNA-Seq libraries and estimated the sensitivity of reconstructing omitted transcript annotations and the specificity with respect to annotated transcripts. Our results corroborate that a well-motivated objective paired with appropriate optimization techniques lead to significant improvements over the state-of-the-art in transcriptome reconstruction. MITIE is implemented in C++ and is available from http://bioweb.me/mitie under the GPL license.

  3. Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.

    Science.gov (United States)

    Xu, Weijia; Ozer, Stuart; Gutell, Robin R

    2009-01-01

    With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure.

  4. 2-Dimension pulse shape discriminator for phoswich detector based on FPGA

    International Nuclear Information System (INIS)

    Ji Jianfeng; Liu Congzhan; Zhang Zhi

    2011-01-01

    It improves the data acquire system for the pulse signal based on digital front-rear pulse shape discrimination system. It adds pulse width information into the pulse's data package. Base on this, we divide the pulse event process into two process, on line coast process and offline accurate process: the online process sets a big threshold, just save the data of the event below this threshold; the offline process uses the acquired data, get the pulse amplitude and pulse width, and then according the spectrum's real shape, set the accurate threshold. this design resolves the problem that the detector's decay time change with the temperature; at the same time, it can correct the system's distortion when the input signal at small amplitude, improves the discrimination system's accuracy. (authors)

  5. Use of Image Based Modelling for Documentation of Intricately Shaped Objects

    Science.gov (United States)

    Marčiš, M.; Barták, P.; Valaška, D.; Fraštia, M.; Trhan, O.

    2016-06-01

    In the documentation of cultural heritage, we can encounter three dimensional shapes and structures which are complicated to measure. Such objects are for example spiral staircases, timber roof trusses, historical furniture or folk costume where it is nearly impossible to effectively use the traditional surveying or the terrestrial laser scanning due to the shape of the object, its dimensions and the crowded environment. The actual methods of digital photogrammetry can be very helpful in such cases with the emphasis on the automated processing of the extensive image data. The created high resolution 3D models and 2D orthophotos are very important for the documentation of architectural elements and they can serve as an ideal base for the vectorization and 2D drawing documentation. This contribution wants to describe the various usage of image based modelling in specific interior spaces and specific objects. The advantages and disadvantages of the photogrammetric measurement of such objects in comparison to other surveying methods are reviewed.

  6. Building and Programming a Smart Robotic System for Distinguishing Objects Based on their Shape and Colour

    Science.gov (United States)

    Sharari, T. M.

    2015-03-01

    This paper presents a robotic system designed for holding and placing objects based on their colour and shape. The presented robot is given a complete set of instructions of positions and orientation angles for each manipulation motion. The main feature in this paper is that the developed robot used a combination of vision and motion systems for holding and placing the work-objects, mounted on the flat work-plane, based on their shapes and colors. This combination improves the flexibility of manipulation which may help eliminate the use of some expensive manipulation tasks in a variety of industrial applications. The robotic system presented in this paper is designed as an educational robot that possesses the ability for holding-and-placing operations with limited load. To process the various instructions for holding and placing the work objects, a main control unit - Manipulation Control Unit (MCU) is used as well as a slave unit that performed the actual instructions from the MCU.

  7. Nonlinear control strategy based on using a shape-tunable neural controller

    Energy Technology Data Exchange (ETDEWEB)

    Chen, C.; Peng, S. [Feng Chia Univ, Taichung (Taiwan, Province of China). Department of chemical Engineering; Chang, W. [Feng Chia Univ, Taichung (Taiwan, Province of China). Department of Automatic Control

    1997-08-01

    In this paper, a nonlinear control strategy based on using a shape-tunable neural network is developed for adaptive control of nonlinear processes. Based on the steepest descent method, a learning algorithm that enables the neural controller to possess the ability of automatic controller output range adjustment is derived. The novel feature of automatic output range adjustment provides the neural controller more flexibility and capability, and therefore the scaling procedure, which is usually unavoidable for the conventional fixed-shape neural controllers, becomes unnecessary. The advantages and effectiveness of the proposed nonlinear control strategy are demonstrated through the challenge problem of controlling an open-loop unstable nonlinear continuous stirred tank reactor (CSTR). 14 refs., 11 figs.

  8. Ionization and fragmentation of DNA-RNA bases: a density functional theory study

    International Nuclear Information System (INIS)

    Sadr-Arani, Leila

    2014-01-01

    Ionizing radiation (IR) cross human tissue, deposit energy and dissipate fragmenting molecules. The resulting fragments may be highlighted by mass spectrometry. Despite the amount of information obtained experimentally by the interpretation of the mass spectrum, experience alone cannot answer all the questions of the mechanism of fragmentation of DNA/RNA bases and a theoretical study is a complement to this information. A theoretical study allows us to know the weakest bonds in the molecule during ionization and thus may help to provide mechanisms of dissociation and produced fragments. The purpose of this work, using the DFT with the PBE functional, is to study the ionization and fragmentation mechanisms of DNA/RNA bases (Uracil, Cytosine, Adenine and Guanine) and to identify the cations corresponding to each peak in mass spectra. For all RNA bases, the retro Diels-Alder reaction (elimination of HNCO or NCO*) is a major route for dissociating, with the exception of adenine for which there is no atom oxygen in its structure. Loss of NH 3 (NH 2 *) molecule is another common way to all bases that contain amine group. The possibility of the loss of hydrogen from the cations is also investigated, as well as the dissociation of dehydrogenated cations and protonated uracil. This work shows the interest of providing DFT calculation in the interpretation of mass spectra of DNA bases. (author)

  9. lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics.

    Science.gov (United States)

    Hu, Ruifeng; Sun, Xiaobo

    2016-08-01

    Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. We provided lncRNATargets, which is a web-based platform for lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together. lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/ .

  10. Spectrum shaping assessment of accelerator-based fusion neutron sources to be used in BNCT treatment

    Science.gov (United States)

    Cerullo, N.; Esposito, J.; Daquino, G. G.

    2004-01-01

    Monte Carlo modelling of an irradiation facility, for boron neutron capture therapy (BNCT) application, using a set of advanced type, accelerator based, 3H(d,n) 4He (D-T) fusion neutron source device is presented. Some general issues concerning the design of a proper irradiation beam shaping assembly, based on very hard energy neutron source spectrum, are reviewed. The facility here proposed, which represents an interesting solution compared to the much more investigated Li or Be based accelerator driven neutron source could fulfil all the medical and safety requirements to be used by an hospital environment.

  11. Lateral Penumbra Modelling Based Leaf End Shape Optimization for Multileaf Collimator in Radiotherapy

    Directory of Open Access Journals (Sweden)

    Dong Zhou

    2016-01-01

    Full Text Available Lateral penumbra of multileaf collimator plays an important role in radiotherapy treatment planning. Growing evidence has revealed that, for a single-focused multileaf collimator, lateral penumbra width is leaf position dependent and largely attributed to the leaf end shape. In our study, an analytical method for leaf end induced lateral penumbra modelling is formulated using Tangent Secant Theory. Compared with Monte Carlo simulation and ray tracing algorithm, our model serves well the purpose of cost-efficient penumbra evaluation. Leaf ends represented in parametric forms of circular arc, elliptical arc, Bézier curve, and B-spline are implemented. With biobjective function of penumbra mean and variance introduced, genetic algorithm is carried out for approximating the Pareto frontier. Results show that for circular arc leaf end objective function is convex and convergence to optimal solution is guaranteed using gradient based iterative method. It is found that optimal leaf end in the shape of Bézier curve achieves minimal standard deviation, while using B-spline minimum of penumbra mean is obtained. For treatment modalities in clinical application, optimized leaf ends are in close agreement with actual shapes. Taken together, the method that we propose can provide insight into leaf end shape design of multileaf collimator.

  12. Shape Distributions of Nonlinear Dynamical Systems for Video-Based Inference.

    Science.gov (United States)

    Venkataraman, Vinay; Turaga, Pavan

    2016-12-01

    This paper presents a shape-theoretic framework for dynamical analysis of nonlinear dynamical systems which appear frequently in several video-based inference tasks. Traditional approaches to dynamical modeling have included linear and nonlinear methods with their respective drawbacks. A novel approach we propose is the use of descriptors of the shape of the dynamical attractor as a feature representation of nature of dynamics. The proposed framework has two main advantages over traditional approaches: a) representation of the dynamical system is derived directly from the observational data, without any inherent assumptions, and b) the proposed features show stability under different time-series lengths where traditional dynamical invariants fail. We illustrate our idea using nonlinear dynamical models such as Lorenz and Rossler systems, where our feature representations (shape distribution) support our hypothesis that the local shape of the reconstructed phase space can be used as a discriminative feature. Our experimental analyses on these models also indicate that the proposed framework show stability for different time-series lengths, which is useful when the available number of samples are small/variable. The specific applications of interest in this paper are: 1) activity recognition using motion capture and RGBD sensors, 2) activity quality assessment for applications in stroke rehabilitation, and 3) dynamical scene classification. We provide experimental validation through action and gesture recognition experiments on motion capture and Kinect datasets. In all these scenarios, we show experimental evidence of the favorable properties of the proposed representation.

  13. The Design of Case Products’ Shape Form Information Database Based on NURBS Surface

    Science.gov (United States)

    Liu, Xing; Liu, Guo-zhong; Xu, Nuo-qi; Zhang, Wei-she

    2017-07-01

    In order to improve the computer design of product shape design,applying the Non-uniform Rational B-splines(NURBS) of curves and surfaces surface to the representation of the product shape helps designers to design the product effectively.On the basis of the typical product image contour extraction and using Pro/Engineer(Pro/E) to extract the geometric feature of scanning mold,in order to structure the information data base system of value point,control point and node vector parameter information,this paper put forward a unified expression method of using NURBS curves and surfaces to describe products’ geometric shape and using matrix laboratory(MATLAB) to simulate when products have the same or similar function.A case study of electric vehicle’s front cover illustrates the access process of geometric shape information of case product in this paper.This method can not only greatly reduce the capacity of information debate,but also improve the effectiveness of computer aided geometric innovation modeling.

  14. 3D deblending of simultaneous source data based on 3D multi-scale shaping operator

    Science.gov (United States)

    Zu, Shaohuan; Zhou, Hui; Mao, Weijian; Gong, Fei; Huang, Weilin

    2018-04-01

    We propose an iterative three-dimensional (3D) deblending scheme using 3D multi-scale shaping operator to separate 3D simultaneous source data. The proposed scheme is based on the property that signal is coherent, whereas interference is incoherent in some domains, e.g., common receiver domain and common midpoint domain. In two-dimensional (2D) blended record, the coherency difference of signal and interference is in only one spatial direction. Compared with 2D deblending, the 3D deblending can take more sparse constraints into consideration to obtain better performance, e.g., in 3D common receiver gather, the coherency difference is in two spatial directions. Furthermore, with different levels of coherency, signal and interference distribute in different scale curvelet domains. In both 2D and 3D blended records, most coherent signal locates in coarse scale curvelet domain, while most incoherent interference distributes in fine scale curvelet domain. The scale difference is larger in 3D deblending, thus, we apply the multi-scale shaping scheme to further improve the 3D deblending performance. We evaluate the performance of 3D and 2D deblending with the multi-scale and global shaping operators, respectively. One synthetic and one field data examples demonstrate the advantage of the 3D deblending with 3D multi-scale shaping operator.

  15. Polylactide-based polyurethane shape memory nanocomposites (Fe3O4/PLAUs) with fast magnetic responsiveness

    International Nuclear Information System (INIS)

    Gu, Shu-Ying; Jin, Sheng-Peng; Gao, Xie-Feng; Mu, Jian

    2016-01-01

    Polylactide-based polyurethane shape memory nanocomposites (Fe 3 O 4 /PLAUs) with fast magnetic responsiveness are presented. For the purpose of fast response and homogeneous dispersion of magnetic nanoparticles, oleic acid was used to improve the dispersibility of Fe 3 O 4 nanoparticles in a polymer matrix. A homogeneous distribution of Fe 3 O 4 nanoparticles in the polymer matrix was obtained for nanocomposites with low Fe 3 O 4 loading content. A small agglomeration was observed for nanocomposites with 6 wt% and 9 wt% loading content, leading to a small decline in the mechanical properties. PLAU and its nanocomposites have glass transition around 52 °C, which can be used as the triggering temperature. PLAU and its nanocomposites have shape fixity ratios above 99%, shape recovery ratios above 82% for the first cycle and shape recovery ratios above 91% for the second cycle. PLAU and its nanocomposites also exhibit a fast water bath or magnetic responsiveness. The magnetic recovery time decreases with an increase in the loading content of Fe 3 O 4 nanoparticles due to an improvement in heating performance for increased weight percentage of fillers. The nanocomposites have fast responses in an alternating magnetic field and have potential application in biomedical areas such as intravascular stent. (paper)

  16. Lateral Penumbra Modelling Based Leaf End Shape Optimization for Multileaf Collimator in Radiotherapy.

    Science.gov (United States)

    Zhou, Dong; Zhang, Hui; Ye, Peiqing

    2016-01-01

    Lateral penumbra of multileaf collimator plays an important role in radiotherapy treatment planning. Growing evidence has revealed that, for a single-focused multileaf collimator, lateral penumbra width is leaf position dependent and largely attributed to the leaf end shape. In our study, an analytical method for leaf end induced lateral penumbra modelling is formulated using Tangent Secant Theory. Compared with Monte Carlo simulation and ray tracing algorithm, our model serves well the purpose of cost-efficient penumbra evaluation. Leaf ends represented in parametric forms of circular arc, elliptical arc, Bézier curve, and B-spline are implemented. With biobjective function of penumbra mean and variance introduced, genetic algorithm is carried out for approximating the Pareto frontier. Results show that for circular arc leaf end objective function is convex and convergence to optimal solution is guaranteed using gradient based iterative method. It is found that optimal leaf end in the shape of Bézier curve achieves minimal standard deviation, while using B-spline minimum of penumbra mean is obtained. For treatment modalities in clinical application, optimized leaf ends are in close agreement with actual shapes. Taken together, the method that we propose can provide insight into leaf end shape design of multileaf collimator.

  17. Lateral Penumbra Modelling Based Leaf End Shape Optimization for Multileaf Collimator in Radiotherapy

    Science.gov (United States)

    Zhou, Dong; Zhang, Hui; Ye, Peiqing

    2016-01-01

    Lateral penumbra of multileaf collimator plays an important role in radiotherapy treatment planning. Growing evidence has revealed that, for a single-focused multileaf collimator, lateral penumbra width is leaf position dependent and largely attributed to the leaf end shape. In our study, an analytical method for leaf end induced lateral penumbra modelling is formulated using Tangent Secant Theory. Compared with Monte Carlo simulation and ray tracing algorithm, our model serves well the purpose of cost-efficient penumbra evaluation. Leaf ends represented in parametric forms of circular arc, elliptical arc, Bézier curve, and B-spline are implemented. With biobjective function of penumbra mean and variance introduced, genetic algorithm is carried out for approximating the Pareto frontier. Results show that for circular arc leaf end objective function is convex and convergence to optimal solution is guaranteed using gradient based iterative method. It is found that optimal leaf end in the shape of Bézier curve achieves minimal standard deviation, while using B-spline minimum of penumbra mean is obtained. For treatment modalities in clinical application, optimized leaf ends are in close agreement with actual shapes. Taken together, the method that we propose can provide insight into leaf end shape design of multileaf collimator. PMID:27110274

  18. Point defects behavior in beta Cu-based shape memory alloys

    International Nuclear Information System (INIS)

    Romero, R.; Somoza, A.

    1999-01-01

    A summary of positron annihilation spectroscopy data relating to the point defect behavior after quenching and to thermal equilibrium in β-phase Cu-based shape memory alloys Cu-Zn-Al and Cu-Al-Be is presented. Particular attention is given to the initial concentration of quenched-in vacancies as a function of the quenching temperature, migration of the retained point defects with aging temperature and time, and the vacancy formation and migration energies. (orig.)

  19. Set-Based Approach to Design under Uncertainty and Applications to Shaping a Hydrofoil

    Science.gov (United States)

    2016-01-01

    given requirements. This notion of set-based designwas pioneered by Toyota and adopted by the U.S. Navy [1]. It responds to most real-world design...in such a way that all desired shape variations are allowed both on the suction and pressure side. Figure 2 gives a schematic representation of the...of the hydrofoil. The control points of the pressure side have been changed in different ways to en- sure the overall hydrodynamic performance

  20. A nuclear radiation multi-parameter measurement system based on pulse-shape sampling

    International Nuclear Information System (INIS)

    Qiu Xiaolin; Fang Guoming; Xu Peng; Di Yuming

    2007-01-01

    In this paper, A nuclear radiation multi-parameter measurement system based on pulse-shape sampling is introduced, including the system's characteristics, composition, operating principle, experiment data and analysis. Compared with conventional nuclear measuring apparatus, it has some remarkable advantages such as the synchronous detection using multi-parameter measurement in the same measurement platform and the general analysis of signal data by user-defined program. (authors)

  1. Acoustic recognition of stress induced martensitic transformations in Cu-based shape memory alloys

    Czech Academy of Sciences Publication Activity Database

    Novák, Václav; Landa, Michal; Šittner, Petr

    2003-01-01

    Roč. 112, - (2003), s. 593-596 ISSN 1155-4339 R&D Projects: GA AV ČR IAA1048107; GA ČR GA106/01/0396 Institutional research plan: CEZ:AV0Z1010914 Keywords : shape memory alloys(SMA) * Cu-based SMA * Martensitic phase transformation * acoustic emission Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.319, year: 2003

  2. Treatment planning capability assessment of a beam shaping assembly for accelerator-based BNCT.

    Science.gov (United States)

    Herrera, M S; González, S J; Burlon, A A; Minsky, D M; Kreiner, A J

    2011-12-01

    Within the frame of an ongoing project to develop a folded Tandem-Electrostatic-Quadrupole accelerator facility for Accelerator-Based Boron Neutron Capture Therapy (AB-BNCT) a theoretical study was performed to assess the treatment planning capability of different configurations of an optimized beam shaping assembly for such a facility. In particular this study aims at evaluating treatment plans for a clinical case of Glioblastoma. Copyright © 2011 Elsevier Ltd. All rights reserved.

  3. Treatment planning capability assessment of a beam shaping assembly for accelerator-based BNCT

    International Nuclear Information System (INIS)

    Herrera, M.S.; González, S.J.; Burlon, A.A.; Minsky, D.M.; Kreiner, A.J.

    2011-01-01

    Within the frame of an ongoing project to develop a folded Tandem-Electrostatic-Quadrupole accelerator facility for Accelerator-Based Boron Neutron Capture Therapy (AB-BNCT) a theoretical study was performed to assess the treatment planning capability of different configurations of an optimized beam shaping assembly for such a facility. In particular this study aims at evaluating treatment plans for a clinical case of Glioblastoma.

  4. A PSF-Shape-Based Beamforming Strategy for Robust 2D Motion Estimation in Ultrafast Data

    OpenAIRE

    Anne E. C. M. Saris; Stein Fekkes; Maartje M. Nillesen; Hendrik H. G. Hansen; Chris L. de Korte

    2018-01-01

    This paper presents a framework for motion estimation in ultrafast ultrasound data. It describes a novel approach for determining the sampling grid for ultrafast data based on the system’s point-spread-function (PSF). As a consequence, the cross-correlation functions (CCF) used in the speckle tracking (ST) algorithm will have circular-shaped peaks, which can be interpolated using a 2D interpolation method to estimate subsample displacements. Carotid artery wall motion and parabolic blood flow...

  5. "Shape function + memory mechanism"-based hysteresis modeling of magnetorheological fluid actuators

    Science.gov (United States)

    Qian, Li-Jun; Chen, Peng; Cai, Fei-Long; Bai, Xian-Xu

    2018-03-01

    A hysteresis model based on "shape function + memory mechanism" is presented and its feasibility is verified through modeling the hysteresis behavior of a magnetorheological (MR) damper. A hysteresis phenomenon in resistor-capacitor (RC) circuit is first presented and analyzed. In the hysteresis model, the "memory mechanism" originating from the charging and discharging processes of the RC circuit is constructed by adopting a virtual displacement variable and updating laws for the reference points. The "shape function" is achieved and generalized from analytical solutions of the simple semi-linear Duhem model. Using the approach, the memory mechanism reveals the essence of specific Duhem model and the general shape function provides a direct and clear means to fit the hysteresis loop. In the frame of the structure of a "Restructured phenomenological model", the original hysteresis operator, i.e., the Bouc-Wen operator, is replaced with the new hysteresis operator. The comparative work with the Bouc-Wen operator based model demonstrates superior performances of high computational efficiency and comparable accuracy of the new hysteresis operator-based model.

  6. Scaling Mode Shapes in Output-Only Structure by a Mass-Change-Based Method

    Directory of Open Access Journals (Sweden)

    Liangliang Yu

    2017-01-01

    Full Text Available A mass-change-based method based on output-only data for the rescaling of mode shapes in operational modal analysis (OMA is introduced. The mass distribution matrix, which is defined as a diagonal matrix whose diagonal elements represent the ratios among the diagonal elements of the mass matrix, is calculated using the unscaled mode shapes. Based on the theory of null space, the mass distribution vector or mass distribution matrix is obtained. A small mass with calibrated weight is added to a certain location of the structure, and then the mass distribution vector of the modified structure is estimated. The mass matrix is identified according to the difference of the mass distribution vectors between the original and modified structures. Additionally, the universal set of modes is unnecessary when calculating the mass distribution matrix, indicating that modal truncation is allowed in the proposed method. The mass-scaled mode shapes estimated in OMA according to the proposed method are compared with those obtained by experimental modal analysis. A simulation is employed to validate the feasibility of the method. Finally, the method is tested on output-only data from an experiment on a five-storey structure, and the results confirm the effectiveness of the method.

  7. Integral force feedback control with input shaping: Application to piezo-based scanning systems in ECDLs

    Science.gov (United States)

    Zhang, Meng; Liu, Zhigang; Zhu, Yu; Bu, Mingfan; Hong, Jun

    2017-07-01

    In this paper, a hybrid control system is developed by integrating the closed-loop force feedback and input shaping method to overcome the problem of the hysteresis and dynamic behavior in piezo-based scanning systems and increase the scanning speed of tunable external cavity diode lasers. The flexible hinge and piezoelectric actuators are analyzed, and a dynamic model of the scanning systems is established. A force sensor and an integral controller are utilized in integral force feedback (IFF) to directly augment the damping of the piezoelectric scanning systems. Hysteresis has been effectively eliminated, but the mechanical resonance is still evident. Noticeable residual vibration occurred after the inflection points and then gradually disappeared. For the further control of mechanical resonance, based on the theory of minimum-acceleration trajectory planning, the time-domain input shaping method was developed. The turning sections of a scanning trajectory are replaced by smooth curves, while the linear sections are retained. The IFF method is combined with the input shaping method to control the non-linearity and mechanical resonance in high-speed piezo-based scanning systems. Experiments are conducted, and the results demonstrate the effectiveness of the proposed control approach.

  8. Online Learning for Classification of Alzheimer Disease based on Cortical Thickness and Hippocampal Shape Analysis.

    Science.gov (United States)

    Lee, Ga-Young; Kim, Jeonghun; Kim, Ju Han; Kim, Kiwoong; Seong, Joon-Kyung

    2014-01-01

    Mobile healthcare applications are becoming a growing trend. Also, the prevalence of dementia in modern society is showing a steady growing trend. Among degenerative brain diseases that cause dementia, Alzheimer disease (AD) is the most common. The purpose of this study was to identify AD patients using magnetic resonance imaging in the mobile environment. We propose an incremental classification for mobile healthcare systems. Our classification method is based on incremental learning for AD diagnosis and AD prediction using the cortical thickness data and hippocampus shape. We constructed a classifier based on principal component analysis and linear discriminant analysis. We performed initial learning and mobile subject classification. Initial learning is the group learning part in our server. Our smartphone agent implements the mobile classification and shows various results. With use of cortical thickness data analysis alone, the discrimination accuracy was 87.33% (sensitivity 96.49% and specificity 64.33%). When cortical thickness data and hippocampal shape were analyzed together, the achieved accuracy was 87.52% (sensitivity 96.79% and specificity 63.24%). In this paper, we presented a classification method based on online learning for AD diagnosis by employing both cortical thickness data and hippocampal shape analysis data. Our method was implemented on smartphone devices and discriminated AD patients for normal group.

  9. Integral force feedback control with input shaping: Application to piezo-based scanning systems in ECDLs.

    Science.gov (United States)

    Zhang, Meng; Liu, Zhigang; Zhu, Yu; Bu, Mingfan; Hong, Jun

    2017-07-01

    In this paper, a hybrid control system is developed by integrating the closed-loop force feedback and input shaping method to overcome the problem of the hysteresis and dynamic behavior in piezo-based scanning systems and increase the scanning speed of tunable external cavity diode lasers. The flexible hinge and piezoelectric actuators are analyzed, and a dynamic model of the scanning systems is established. A force sensor and an integral controller are utilized in integral force feedback (IFF) to directly augment the damping of the piezoelectric scanning systems. Hysteresis has been effectively eliminated, but the mechanical resonance is still evident. Noticeable residual vibration occurred after the inflection points and then gradually disappeared. For the further control of mechanical resonance, based on the theory of minimum-acceleration trajectory planning, the time-domain input shaping method was developed. The turning sections of a scanning trajectory are replaced by smooth curves, while the linear sections are retained. The IFF method is combined with the input shaping method to control the non-linearity and mechanical resonance in high-speed piezo-based scanning systems. Experiments are conducted, and the results demonstrate the effectiveness of the proposed control approach.

  10. [Characterization of Black and Dichothrix Cyanobacteria Based on the 16S Ribosomal RNA Gene Sequence

    Science.gov (United States)

    Ortega, Maya

    2010-01-01

    My project focuses on characterizing different cyanobacteria in thrombolitic mats found on the island of Highborn Cay, Bahamas. Thrombolites are interesting ecosystems because of the ability of bacteria in these mats to remove carbon dioxide from the atmosphere and mineralize it as calcium carbonate. In the future they may be used as models to develop carbon sequestration technologies, which could be used as part of regenerative life systems in space. These thrombolitic communities are also significant because of their similarities to early communities of life on Earth. I targeted two cyanobacteria in my research, Dichothrix spp. and whatever black is, since they are believed to be important to carbon sequestration in these thrombolitic mats. The goal of my summer research project was to molecularly identify these two cyanobacteria. DNA was isolated from each organism through mat dissections and DNA extractions. I ran Polymerase Chain Reactions (PCR) to amplify the 16S ribosomal RNA (rRNA) gene in each cyanobacteria. This specific gene is found in almost all bacteria and is highly conserved, meaning any changes in the sequence are most likely due to evolution. As a result, the 16S rRNA gene can be used for bacterial identification of different species based on the sequence of their 16S rRNA gene. Since the exact sequence of the Dichothrix gene was unknown, I designed different primers that flanked the gene based on the known sequences from other taxonomically similar cyanobacteria. Once the 16S rRNA gene was amplified, I cloned the gene into specialized Escherichia coli cells and sent the gene products for sequencing. Once the sequence is obtained, it will be added to a genetic database for future reference to and classification of other Dichothrix sp.

  11. Fine-grained parallelism accelerating for RNA secondary structure prediction with pseudoknots based on FPGA.

    Science.gov (United States)

    Xia, Fei; Jin, Guoqing

    2014-06-01

    PKNOTS is a most famous benchmark program and has been widely used to predict RNA secondary structure including pseudoknots. It adopts the standard four-dimensional (4D) dynamic programming (DP) method and is the basis of many variants and improved algorithms. Unfortunately, the O(N(6)) computing requirements and complicated data dependency greatly limits the usefulness of PKNOTS package with the explosion in gene database size. In this paper, we present a fine-grained parallel PKNOTS package and prototype system for accelerating RNA folding application based on FPGA chip. We adopted a series of storage optimization strategies to resolve the "Memory Wall" problem. We aggressively exploit parallel computing strategies to improve computational efficiency. We also propose several methods that collectively reduce the storage requirements for FPGA on-chip memory. To the best of our knowledge, our design is the first FPGA implementation for accelerating 4D DP problem for RNA folding application including pseudoknots. The experimental results show a factor of more than 50x average speedup over the PKNOTS-1.08 software running on a PC platform with Intel Core2 Q9400 Quad CPU for input RNA sequences. However, the power consumption of our FPGA accelerator is only about 50% of the general-purpose micro-processors.

  12. Rank-Based miRNA Signatures for Early Cancer Detection

    Directory of Open Access Journals (Sweden)

    Mario Lauria

    2014-01-01

    Full Text Available We describe a new signature definition and analysis method to be used as biomarker for early cancer detection. Our new approach is based on the construction of a reference map of transcriptional signatures of both healthy and cancer affected individuals using circulating miRNA from a large number of subjects. Once such a map is available, the diagnosis for a new patient can be performed by observing the relative position on the map of his/her transcriptional signature. To demonstrate its efficacy for this specific application we report the results of the application of our method to published datasets of circulating miRNA, and we quantify its performance compared to current state-of-the-art methods. A number of additional features make this method an ideal candidate for large-scale use, for example, as a mass screening tool for early cancer detection or for at-home diagnostics. Specifically, our method is minimally invasive (because it works well with circulating miRNA, it is robust with respect to lab-to-lab protocol variability and batch effects (it requires that only the relative ranking of expression value of miRNA in a profile be accurate not their absolute values, and it is scalable to a large number of subjects. Finally we discuss the need for HPC capability in a widespread application of our or similar methods.

  13. A DNA sequence obtained by replacement of the dopamine RNA aptamer bases is not an aptamer.

    Science.gov (United States)

    Álvarez-Martos, Isabel; Ferapontova, Elena E

    2017-08-05

    A unique specificity of the aptamer-ligand biorecognition and binding facilitates bioanalysis and biosensor development, contributing to discrimination of structurally related molecules, such as dopamine and other catecholamine neurotransmitters. The aptamer sequence capable of specific binding of dopamine is a 57 nucleotides long RNA sequence reported in 1997 (Biochemistry, 1997, 36, 9726). Later, it was suggested that the DNA homologue of the RNA aptamer retains the specificity of dopamine binding (Biochem. Biophys. Res. Commun., 2009, 388, 732). Here, we show that the DNA sequence obtained by the replacement of the RNA aptamer bases for their DNA analogues is not able of specific biorecognition of dopamine, in contrast to the original RNA aptamer sequence. This DNA sequence binds dopamine and structurally related catecholamine neurotransmitters non-specifically, as any DNA sequence, and, thus, is not an aptamer and cannot be used neither for in vivo nor in situ analysis of dopamine in the presence of structurally related neurotransmitters. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. High‐resolution stock discrimination of Atlantic herring (Clupea harengus) based on otolith shape, microstructure, and genetic markers

    DEFF Research Database (Denmark)

    Mosegaard, Henrik; Worsøe Clausen, Lotte; Bekkevold, Dorte

    2012-01-01

    between populations, which suggest genetic control as well. Thus otolith shape serves as a population marker, suitable for individual assignment. Here we use otolith morphological characteristics (otolith shape and larval otolith microstructure) combined with genetic markers to discriminate between...... otolith shape characteristics as separation parameters. Otolith shape was found to clearly discriminate between individuals at all ages from different spawning populations. The identified distances between populations based on otolith shape matched previously obtained genetic distances and were, when......One of the most rapidly developing applications of otolith research is shape analysis, often used for population discrimination as well as for species identification. Otolith shape is influenced by the environment through physiology, but also shows consistent and temporally stable differences...

  15. Development, characterization, and in vitro evaluation of phosphatidylcholine–sodium cholate-based nanoparticles for siRNA delivery to MCF-7 human breast cancer cells

    International Nuclear Information System (INIS)

    Pérez, Sebastián Ezequiel; Gándola, Yamila; Carlucci, Adriana Mónica; González, Lorena

    2015-01-01

    Phosphatidylcholine–sodium cholate (SC)-based nanoparticles were designed, characterized, and evaluated as plausible oligonucleotides delivery systems. For this purpose, formulation of the systems was optimized to obtain low cytotoxic vehicles with high siRNA-loading capacity and acceptable transfection ability. Mixtures of soybean phosphatidylcholine (SPC) and SC were prepared at different molar ratios with 2 % w/v total concentration; distilled water and two different buffers were used as dispersion medium. Nanoparticles below 150 nm were observed showing spherical shape which turned smaller in diameter as the SC molar proportion increased, accounting for small unilamellar vesicles when low proportions of SC were present in the formulation, but clear mixed micellar solutions at higher SC percentages. Macroscopic characteristics along with physico-chemical parameters values supported the presence of these types of structures. SYBR green displacement assays demonstrated an important oligonucleotide binding that increased as bile salt relative content got higher. Within the same molar ratio, nanoparticles showed the following binding efficiency order: pH 7.4 > pH 5.0 > distilled water. siRNA-loading capacity assays confirmed the higher siRNA binding by the mixed micelles containing higher SC proportion; moreover, the complexes formed were smaller as the SC:SPC ratio increased. Considering cytotoxicity and siRNA-loading capacity, 1:2 and 1:4 SPC:SC formulations were selected for further biological assays. Nanoparticles prepared in any of the three media were able to induce dsRNA uptake and efficiently transfect RNA for gene silencing, for the compositions prepared in buffer pH 5.0 being the most versatile

  16. Development, characterization, and in vitro evaluation of phosphatidylcholine–sodium cholate-based nanoparticles for siRNA delivery to MCF-7 human breast cancer cells

    Energy Technology Data Exchange (ETDEWEB)

    Pérez, Sebastián Ezequiel, E-mail: seperez@ffyb.uba.ar [University of Buenos Aires, Department of Pharmaceutical Technology, Faculty of Pharmacy and Biochemistry (Argentina); Gándola, Yamila [University of Buenos Aires, Institute and Department of Biological Chemistry, Faculty of Pharmacy and Biochemistry (Argentina); Carlucci, Adriana Mónica [University of Buenos Aires, Department of Pharmaceutical Technology, Faculty of Pharmacy and Biochemistry (Argentina); González, Lorena [University of Buenos Aires, Institute and Department of Biological Chemistry, Faculty of Pharmacy and Biochemistry (Argentina)

    2015-03-15

    Phosphatidylcholine–sodium cholate (SC)-based nanoparticles were designed, characterized, and evaluated as plausible oligonucleotides delivery systems. For this purpose, formulation of the systems was optimized to obtain low cytotoxic vehicles with high siRNA-loading capacity and acceptable transfection ability. Mixtures of soybean phosphatidylcholine (SPC) and SC were prepared at different molar ratios with 2 % w/v total concentration; distilled water and two different buffers were used as dispersion medium. Nanoparticles below 150 nm were observed showing spherical shape which turned smaller in diameter as the SC molar proportion increased, accounting for small unilamellar vesicles when low proportions of SC were present in the formulation, but clear mixed micellar solutions at higher SC percentages. Macroscopic characteristics along with physico-chemical parameters values supported the presence of these types of structures. SYBR green displacement assays demonstrated an important oligonucleotide binding that increased as bile salt relative content got higher. Within the same molar ratio, nanoparticles showed the following binding efficiency order: pH 7.4 > pH 5.0 > distilled water. siRNA-loading capacity assays confirmed the higher siRNA binding by the mixed micelles containing higher SC proportion; moreover, the complexes formed were smaller as the SC:SPC ratio increased. Considering cytotoxicity and siRNA-loading capacity, 1:2 and 1:4 SPC:SC formulations were selected for further biological assays. Nanoparticles prepared in any of the three media were able to induce dsRNA uptake and efficiently transfect RNA for gene silencing, for the compositions prepared in buffer pH 5.0 being the most versatile.

  17. Deep Correlated Holistic Metric Learning for Sketch-Based 3D Shape Retrieval.

    Science.gov (United States)

    Dai, Guoxian; Xie, Jin; Fang, Yi

    2018-07-01

    How to effectively retrieve desired 3D models with simple queries is a long-standing problem in computer vision community. The model-based approach is quite straightforward but nontrivial, since people could not always have the desired 3D query model available by side. Recently, large amounts of wide-screen electronic devices are prevail in our daily lives, which makes the sketch-based 3D shape retrieval a promising candidate due to its simpleness and efficiency. The main challenge of sketch-based approach is the huge modality gap between sketch and 3D shape. In this paper, we proposed a novel deep correlated holistic metric learning (DCHML) method to mitigate the discrepancy between sketch and 3D shape domains. The proposed DCHML trains two distinct deep neural networks (one for each domain) jointly, which learns two deep nonlinear transformations to map features from both domains into a new feature space. The proposed loss, including discriminative loss and correlation loss, aims to increase the discrimination of features within each domain as well as the correlation between different domains. In the new feature space, the discriminative loss minimizes the intra-class distance of the deep transformed features and maximizes the inter-class distance of the deep transformed features to a large margin within each domain, while the correlation loss focused on mitigating the distribution discrepancy across different domains. Different from existing deep metric learning methods only with loss at the output layer, our proposed DCHML is trained with loss at both hidden layer and output layer to further improve the performance by encouraging features in the hidden layer also with desired properties. Our proposed method is evaluated on three benchmarks, including 3D Shape Retrieval Contest 2013, 2014, and 2016 benchmarks, and the experimental results demonstrate the superiority of our proposed method over the state-of-the-art methods.

  18. The use of carrier RNA to enhance DNA extraction from microfluidic-based silica monoliths.

    Science.gov (United States)

    Shaw, Kirsty J; Thain, Lauren; Docker, Peter T; Dyer, Charlotte E; Greenman, John; Greenway, Gillian M; Haswell, Stephen J

    2009-10-12

    DNA extraction was carried out on silica-based monoliths within a microfluidic device. Solid-phase DNA extraction methodology was applied in which the DNA binds to silica in the presence of a chaotropic salt, such as guanidine hydrochloride, and is eluted in a low ionic strength solution, such as water. The addition of poly-A carrier RNA to the chaotropic salt solution resulted in a marked increase in the effective amount of DNA that could be recovered (25ng) compared to the absence of RNA (5ng) using the silica-based monolith. These findings confirm that techniques utilising nucleic acid carrier molecules can enhance DNA extraction methodologies in microfluidic applications.

  19. Associations between HIV-RNA-based indicators and virological and clinical outcomes

    DEFF Research Database (Denmark)

    Laut, Kamilla G; Shepherd, Leah C; Pedersen, Court

    2016-01-01

    OBJECTIVES: To evaluate and compare the performance of six HIV-RNA-based quality of care indicators for predicting short-term and long-term outcomes. DESIGN: Multinational cohort study. METHODS: We included EuroSIDA patients on antiretroviral therapy (ART) with at least three viral load measureme......OBJECTIVES: To evaluate and compare the performance of six HIV-RNA-based quality of care indicators for predicting short-term and long-term outcomes. DESIGN: Multinational cohort study. METHODS: We included EuroSIDA patients on antiretroviral therapy (ART) with at least three viral load...... measurements after baseline (the latest of 01/01/2001 or entry into EuroSIDA). Using multivariate Poisson regression, we modelled the association between short-term (resistance, triple-class failure) and long-term (all-cause mortality, any AIDS/non-AIDS clinical event) outcomes and the indicators: viraemia...

  20. Dissection of functional lncRNAs in Alzheimer's disease by construction and analysis of lncRNA-mRNA networks based on competitive endogenous RNAs.

    Science.gov (United States)

    Wang, Lian-Kun; Chen, Xiao-Feng; He, Dan-Dan; Li, You; Fu, Jin

    2017-04-08

    Alzheimer's disease (AD) is a neurodegenerative disorder that is the most common cause of dementia in the elderly, and intracellular neurofibrillary tangles (NFTs) are one of the pathological features of AD. Recent studies have suggested long noncoding RNAs (lncRNAs) play important roles in AD. Competing endogenous RNAs (ceRNAs) is a mechanism that has recently been proposed, in which lncRNAs compete for common miRNA-binding sites with mRNAs. However, the roles of lncRNAs and ceRNA in AD NFTs is limited. In this study, we constructed a global triple network based on ceRNA theory, then an AD NFT lncRNA-mRNA network (NFTLMN) was generated. By analyzing the NFTLMN, three lncRNAs (AP000265.1, KB-1460A1.5 and RP11-145M9.4), which are highly related with AD NFTs were identified. To further explore the cross-talk between mRNAs and lncRNAs, a clustering module analysis was performed on the NFTLMN and two AD NFT related modules were identified. Our study provides a better understanding of the molecular basis of AD NFTs and may offer novel treatment strategies for AD. Copyright © 2016. Published by Elsevier Inc.

  1. Structural imprints in vivo decode RNA regulatory mechanisms.

    Science.gov (United States)

    Spitale, Robert C; Flynn, Ryan A; Zhang, Qiangfeng Cliff; Crisalli, Pete; Lee, Byron; Jung, Jong-Wha; Kuchelmeister, Hannes Y; Batista, Pedro J; Torre, Eduardo A; Kool, Eric T; Chang, Howard Y

    2015-03-26

    Visualizing the physical basis for molecular behaviour inside living cells is a great challenge for biology. RNAs are central to biological regulation, and the ability of RNA to adopt specific structures intimately controls every step of the gene expression program. However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles include only two of the four nucleotides that make up RNA. Here we present a novel biochemical approach, in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE), which enables the first global view, to our knowledge, of RNA secondary structures in living cells for all four bases. icSHAPE of the mouse embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguish different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved from in vitro conditions, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA-binding proteins or RNA-modification sites that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N(6)-methyladenosine (m(6)A) modification genome wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.

  2. A shape-based quality evaluation and reconstruction method for electrical impedance tomography.

    Science.gov (United States)

    Antink, Christoph Hoog; Pikkemaat, Robert; Malmivuo, Jaakko; Leonhardt, Steffen

    2015-06-01

    Linear methods of reconstruction play an important role in medical electrical impedance tomography (EIT) and there is a wide variety of algorithms based on several assumptions. With the Graz consensus reconstruction algorithm for EIT (GREIT), a novel linear reconstruction algorithm as well as a standardized framework for evaluating and comparing methods of reconstruction were introduced that found widespread acceptance in the community. In this paper, we propose a two-sided extension of this concept by first introducing a novel method of evaluation. Instead of being based on point-shaped resistivity distributions, we use 2759 pairs of real lung shapes for evaluation that were automatically segmented from human CT data. Necessarily, the figures of merit defined in GREIT were adjusted. Second, a linear method of reconstruction that uses orthonormal eigenimages as training data and a tunable desired point spread function are proposed. Using our novel method of evaluation, this approach is compared to the classical point-shaped approach. Results show that most figures of merit improve with the use of eigenimages as training data. Moreover, the possibility of tuning the reconstruction by modifying the desired point spread function is shown. Finally, the reconstruction of real EIT data shows that higher contrasts and fewer artifacts can be achieved in ventilation- and perfusion-related images.

  3. CFD-based shape optimization of steam turbine blade cascade in transonic two phase flows

    International Nuclear Information System (INIS)

    Noori Rahim Abadi, S.M.A.; Ahmadpour, A.; Abadi, S.M.N.R.; Meyer, J.P.

    2017-01-01

    Highlights: • CFD-based shape optimization of a nozzle and a turbine blade regarding nucleating steam flow is performed. • Nucleation rate and droplet radius are the best suited objective functions for the optimization process. • Maximum 34% reduction in entropy generation rate is reported for turbine cascade. • A maximum 10% reduction in Baumann factor and a maximum 2.1% increase in efficiency is achieved for a turbine cascade. - Abstract: In this study CFD-based shape optimization of a 3D nozzle and a 2D turbine blade cascade is undertaken in the presence of non-equilibrium condensation within the considered flow channels. A two-fluid formulation is used for the simulation of unsteady, turbulent, supersonic and compressible flow of wet steam accounting for relevant phase interaction between nucleated liquid droplets and continuous vapor phase. An in-house CFD code is developed to solve the governing equations of the two phase flow and was validated against available experimental data. Optimization is carried out in respect to various objective functions. It is shown that nucleation rate and maximum droplet radius are the best suited target functions for reducing thermodynamic and aerodynamic losses caused by the spontaneous nucleation. The maximum increase of 2.1% in turbine blade efficiency is achieved through shape optimization process.

  4. Aircraft Segmentation in SAR Images Based on Improved Active Shape Model

    Science.gov (United States)

    Zhang, X.; Xiong, B.; Kuang, G.

    2018-04-01

    In SAR image interpretation, aircrafts are the important targets arousing much attention. However, it is far from easy to segment an aircraft from the background completely and precisely in SAR images. Because of the complex structure, different kinds of electromagnetic scattering take place on the aircraft surfaces. As a result, aircraft targets usually appear to be inhomogeneous and disconnected. It is a good idea to extract an aircraft target by the active shape model (ASM), since combination of the geometric information controls variations of the shape during the contour evolution. However, linear dimensionality reduction, used in classic ACM, makes the model rigid. It brings much trouble to segment different types of aircrafts. Aiming at this problem, an improved ACM based on ISOMAP is proposed in this paper. ISOMAP algorithm is used to extract the shape information of the training set and make the model flexible enough to deal with different aircrafts. The experiments based on real SAR data shows that the proposed method achieves obvious improvement in accuracy.

  5. A shape-based quality evaluation and reconstruction method for electrical impedance tomography

    International Nuclear Information System (INIS)

    Antink, Christoph Hoog; Pikkemaat, Robert; Leonhardt, Steffen; Malmivuo, Jaakko

    2015-01-01

    Linear methods of reconstruction play an important role in medical electrical impedance tomography (EIT) and there is a wide variety of algorithms based on several assumptions. With the Graz consensus reconstruction algorithm for EIT (GREIT), a novel linear reconstruction algorithm as well as a standardized framework for evaluating and comparing methods of reconstruction were introduced that found widespread acceptance in the community.In this paper, we propose a two-sided extension of this concept by first introducing a novel method of evaluation. Instead of being based on point-shaped resistivity distributions, we use 2759 pairs of real lung shapes for evaluation that were automatically segmented from human CT data. Necessarily, the figures of merit defined in GREIT were adjusted. Second, a linear method of reconstruction that uses orthonormal eigenimages as training data and a tunable desired point spread function are proposed.Using our novel method of evaluation, this approach is compared to the classical point-shaped approach. Results show that most figures of merit improve with the use of eigenimages as training data. Moreover, the possibility of tuning the reconstruction by modifying the desired point spread function is shown. Finally, the reconstruction of real EIT data shows that higher contrasts and fewer artifacts can be achieved in ventilation- and perfusion-related images. (paper)

  6. Modeling and flow analysis of piezoelectric based micropump with various shapes of microneedle

    Energy Technology Data Exchange (ETDEWEB)

    Haldkar, Rakesh Kumar; Gupta, Vijay Kumar; Sheorey, Tanuja [PDPM Indian Institute of Information Technology Design and Manufacturing Jabalpur, 482005 (India)

    2017-06-15

    Micropumps have been investigated as drug delivery and disease diagnostic devices. Many of these micropumps have been designed, considering primarily, available micro fabrication technologies rather than appropriate pump performance analysis. Piezoelectric and silicon based micro pumps are more popular as compared to other smart materials being explored. The microneedle is an integral part of these micropumps providing an interface between the drug reservoir and the patient’s body for extracting the blood for investigation. Blood collected in the pump chamber passes through the biosensor and gives the required investigation report. It is aimed to minimize the pain while the microneedle is inserted in the body without having any effect on the flow characteristics. Several factors affect the pain while inserting the needle, out of which shape and size of the microneedle are two important parameters. In this study we have investigated the effect of shape of the microneedle on the flow inside the micropump. A micropump design is based on the required flow at the biosensor point. All computations were carried out with water (Newtonian fluid) as the working fluid after carrying out a comparative analysis with human blood (non-Newtonian fluid). For the pentagonal shaped microneedle, the velocity at the top of the microneedle was minimum, which is beneficial in that fluid should remain in contact with the sensor for longer time.

  7. Modeling and flow analysis of piezoelectric based micropump with various shapes of microneedle

    International Nuclear Information System (INIS)

    Haldkar, Rakesh Kumar; Gupta, Vijay Kumar; Sheorey, Tanuja

    2017-01-01

    Micropumps have been investigated as drug delivery and disease diagnostic devices. Many of these micropumps have been designed, considering primarily, available micro fabrication technologies rather than appropriate pump performance analysis. Piezoelectric and silicon based micro pumps are more popular as compared to other smart materials being explored. The microneedle is an integral part of these micropumps providing an interface between the drug reservoir and the patient’s body for extracting the blood for investigation. Blood collected in the pump chamber passes through the biosensor and gives the required investigation report. It is aimed to minimize the pain while the microneedle is inserted in the body without having any effect on the flow characteristics. Several factors affect the pain while inserting the needle, out of which shape and size of the microneedle are two important parameters. In this study we have investigated the effect of shape of the microneedle on the flow inside the micropump. A micropump design is based on the required flow at the biosensor point. All computations were carried out with water (Newtonian fluid) as the working fluid after carrying out a comparative analysis with human blood (non-Newtonian fluid). For the pentagonal shaped microneedle, the velocity at the top of the microneedle was minimum, which is beneficial in that fluid should remain in contact with the sensor for longer time

  8. Intelligent structures based on the improved activation of shape memory polymers using Peltier cells

    International Nuclear Information System (INIS)

    Díaz Lantada, Andrés; Lafont Morgado, Pilar; Muñoz Sanz, José Luis; Muñoz García, Julio; Munoz-Guijosa, Juan Manuel; Echávarri Otero, Javier

    2010-01-01

    This study is focused on obtaining intelligent structures manufactured from shape memory polymers possessing the ability to change their geometry in successive or 'step-by-step' actions. This objective has been reached by changing the conventionally used shape memory activation systems (heating resistance, laser or induction heating). The solution set out consists in using Peltier cells as a heating system capable of heating (and activating) a specific zone of the device in the first activation, while the opposite zone keeps its original geometry. By carefully reversing the polarity of the electrical supply to the Peltier cell, in the second activation, the as yet unchanged zone is activated while the already changed zone in the first activation remains unaltered. We have described the criteria for the selection, calibration and design of this alternative heating (activation) system based on the thermoelectric effect, together with the development of different 'proof of concept' prototypes that have enabled us to validate the concepts put forward, as well as suggest future improvements for 'intelligent' shape memory polymer-based devices

  9. Beam shaping assembly optimization for (7)Li(p,n)(7)Be accelerator based BNCT.

    Science.gov (United States)

    Minsky, D M; Kreiner, A J

    2014-06-01

    Within the framework of accelerator-based BNCT, a project to develop a folded Tandem-ElectroStatic-Quadrupole accelerator is under way at the Atomic Energy Commission of Argentina. The proposed accelerator is conceived to deliver a proton beam of 30mA at about 2.5MeV. In this work we explore a Beam Shaping Assembly (BSA) design based on the (7)Li(p,n)(7)Be neutron production reaction to obtain neutron beams to treat deep seated tumors. © 2013 Elsevier Ltd. All rights reserved.

  10. Evolutionary patterns of RNA-based duplication in non-mammalian chordates.

    Directory of Open Access Journals (Sweden)

    Ming Chen

    Full Text Available The role of RNA-based duplication, or retroposition, in the evolution of new gene functions in mammals, plants, and Drosophila has been widely reported. However, little is known about RNA-based duplication in non-mammalian chordates. In this study, we screened ten non-mammalian chordate genomes for retrocopies and investigated their evolutionary patterns. We identified numerous retrocopies in these species. Examination of the age distribution of these retrocopies revealed no burst of young retrocopies in ancient chordate species. Upon comparing these non-mammalian chordate species to the mammalian species, we observed that a larger fraction of the non-mammalian retrocopies was under strong evolutionary constraints than mammalian retrocopies are, as evidenced by signals of purifying selection and expression profiles. For the Western clawed frog, Medaka, and Sea squirt, many retrogenes have evolved gonad and brain expression patterns, similar to what was observed in human. Testing of retrogene movement in the Medaka genome, where the nascent sex chrosomes have been well assembled, did not reveal any significant gene movement. Taken together, our analyses demonstrate that RNA-based duplication generates many functional genes and can make a significant contribution to the evolution of non-mammalian genomes.

  11. [Synthesis and characterization of polylactide-based thermosetting polyurethanes with shape memory properties].

    Science.gov (United States)

    Shi, Shuo; Gu, Lin; Yang, Yihu; Yu, Haibin; Chen, Rui; Xiao, Xianglian; Qiu, Jun

    2016-06-25

    A series of bio-based thermosetting polyurethanes (Bio-PUs) were synthesized by the crosslinking reaction of polylactide and its copolymers diols with hexamethylene diisocyanate (HDI) trimer. The obtained Bio-PUs were characterized by Fourier Transform Infrared Spectroscopy (FTIR), Differential Scanning Calorimetry (DSC), Thermal Gravimetric Analysis (TGA), universal tensile testing machine and cytotoxicity test. Results indicate that the PLA copolymer (P(LA-co-CL)) diols reduced the glass transition temperature (Tg) of Bio-PUs and improved their thermal stability, compared with PLA diols. The Bio-PUs synthesized from P (LA-co-CL) diols exhibit better mechanical performance and shape memory properties. Especially, Young modulus and elongation at break of the obtained Bio-PUs were 277.7 MPa and 230% respectively; the shape recovery time of the obtained Bio-PUs at body temperature was only 93 s. Furthermore, alamar blue assay results showed that the obtained Bio-PUs had no cell toxicity.

  12. Multi-resonant wideband energy harvester based on a folded asymmetric M-shaped cantilever

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Meng; Mao, Haiyang; Li, Zhigang; Liu, Ruiwen; Ming, Anjie [Key laboratory of Microelectronics Devices & Integrated Technology, Institute of Microelectronics, Chinese Academic of Sciences, Beijing 100029 (China); Ou, Yi; Ou, Wen [Key laboratory of Microelectronics Devices & Integrated Technology, Institute of Microelectronics, Chinese Academic of Sciences, Beijing 100029 (China); Smart Sensor Engineering Center, Jiangsu R& D Center for Internet of Things, Wuxi 214315 (China)

    2015-07-15

    This article reports a compact wideband piezoelectric vibration energy harvester consisting of three proof masses and an asymmetric M-shaped cantilever. The M-shaped beam comprises a main beam and two folded and dimension varied auxiliary beams interconnected through the proof mass at the end of the main cantilever. Such an arrangement constitutes a three degree-of-freedom vibrating body, which can tune the resonant frequencies of its first three orders close enough to obtain a utility wide bandwidth. The finite element simulation results and the experimental results are well matched. The operation bandwidth comprises three adjacent voltage peaks on account of the frequency interval shortening mechanism. The result shows that the proposed piezoelectric energy harvester could be efficient and adaptive in practical vibration circumstance based on multiple resonant modes.

  13. Tunable plasmon-induced transparency with graphene-based T-shaped array metasurfaces

    Science.gov (United States)

    Niu, Yuying; Wang, Jicheng; Hu, Zhengda; Zhang, Feng

    2018-06-01

    The frequency tunable Plasmonic induced transparency (PIT) effect is researched with a periodically patterned T-shaped graphene array in mid-infrared region. We adjust the geometrical parameters to obtain the optimized combination for the realization of the PIT response and use the coupled Lorentz oscillator model to analysis the physical mechanism. Due to the properties of graphene, the PIT effect can be easily and markedly enhanced with the increase of chemical potential and carrier mobility. The frequency of PIT effect is also insensitive with the angle of incident light. In addition, we also propose the π shaped structure to realizing the double-peak PIT effect. The results offer a flexible approach for the development of tunable graphene-based photonic devices.

  14. A Fixpoint-Based Calculus for Graph-Shaped Computational Fields

    DEFF Research Database (Denmark)

    Lluch Lafuente, Alberto; Loreti, Michele; Montanari, Ugo

    2015-01-01

    topology is represented by a graph-shaped field, namely a network with attributes on both nodes and arcs, where arcs represent interaction capabilities between nodes. We propose a calculus where computation is strictly synchronous and corresponds to sequential computations of fixpoints in the graph......-shaped field. Under some conditions, those fixpoints can be computed by synchronised iterations, where in each iteration the attributes of a node is updated based on the attributes of the neighbours in the previous iteration. Basic constructs are reminiscent of the semiring μ-calculus, a semiring......-valued generalisation of the modal μ-calculus, which provides a flexible mechanism to specify the neighbourhood range (according to path formulae) and the way attributes should be combined (through semiring operators). Additional control-How constructs allow one to conveniently structure the fixpoint computations. We...

  15. Spectral signature barcodes based on S-shaped Split Ring Resonators (S-SRRs

    Directory of Open Access Journals (Sweden)

    Herrojo Cristian

    2016-01-01

    Full Text Available In this paper, it is shown that S-shaped split ring resonators (S-SRRs are useful particles for the implementation of spectral signature (i.e., a class of radiofrequency barcodes based on coplanar waveguide (CPW transmission lines loaded with such resonant elements. By virtue of its S shape, these resonators are electrically small. Hence S-SRRs are of interest for the miniaturization of the barcodes, since multiple resonators, each tuned at a different frequency, are used for encoding purposes. In particular, a 10-bit barcode occupying 1 GHz spectral bandwidth centered at 2.5 GHz, with dimensions of 9 cm2, is presented in this paper.

  16. Engineering based assessment for a shape design of a pediatric ePTFE pulmonary conduit valve.

    Science.gov (United States)

    Tsuboko, Yusuke; Shiraishi, Yasuyuki; Yamada, Akihiro; Yambe, Tomoyuki; Miura, Hidekazu; Mura, Seitaro; Yamagishi, Masaaki

    2016-08-01

    The authors examined the hemodynamic characteristics of expanded polytetrafluoroethylene (ePTFE) pulmonary valved conduits quantitatively by our originally developed pediatric pulmonary mechanical circulatory system, in order to suggest the optimal shape design. The system consisted of pneumatically driven right atrium and ventricle model, a pulmonary valve chamber, and elastic pulmonary compliance model with peripheral vascular resistance units, a venous reservoir. We employed two different types of ePTFE valve and evaluated the relationship between the leaflets motion and hemodynamic characteristics by using a high-speed video camera. As a result, we successfully reproduced hemodynamic simulations in our pediatric pulmonary mock system. We confirmed that the presence of bulging sinuses in the pulmonary valved conduit reduced the transvalvular energy loss and increased the valve opening area during systolic period. Our engineering-based in vitro analysis could be useful for proposing a shape design optimization of sophisticated pediatric ePTFE pulmonary valve.

  17. Self-Assembly of Supramolecular Aggregates Based on Sector- and Cone-Shaped Dendrons and Bolaamphiphiles

    Science.gov (United States)

    Shcherbina, M. A.; Chvalun, S. N.

    2018-06-01

    Using a number of classes of such sector-shaped macromolecules as derivatives of 2,3,4- and 3,4,5- tri(dodecyloxy)benzenesulfonic acid and dendrimers based on gallic acid as an example, the main stages in the formation of supramolecular ensembles are considered: the formation of individual supramolecular aggregates due to the weak noncovalent interactions of mesogenic groups, and the subsequent ordering within these aggregates, which lowers the free energy of a system. Supramolecular aggregates are in turn organized into two- or three-dimensional supramolecular lattices. It is shown that the shape of the supramolecular aggregates and its change along with temperature are functions of the chemical structure of the mesogenic group (resulting in the controlled design of complex self-organizing systems with a given response to external stimuli).

  18. Optical-electronic shape recognition system based on synergetic associative memory

    Science.gov (United States)

    Gao, Jun; Bao, Jie; Chen, Dingguo; Yang, Youqing; Yang, Xuedong

    2001-04-01

    This paper presents a novel optical-electronic shape recognition system based on synergetic associative memory. Our shape recognition system is composed of two parts: the first one is feature extraction system; the second is synergetic pattern recognition system. Hough transform is proposed for feature extraction of unrecognized object, with the effects of reducing dimensions and filtering for object distortion and noise, synergetic neural network is proposed for realizing associative memory in order to eliminate spurious states. Then we adopt an approach of optical- electronic realization to our system that can satisfy the demands of real time, high speed and parallelism. In order to realize fast algorithm, we replace the dynamic evolution circuit with adjudge circuit according to the relationship between attention parameters and order parameters, then implement the recognition of some simple images and its validity is proved.

  19. Frequency-shaped and observer-based discrete-time sliding mode control

    CERN Document Server

    Mehta, Axaykumar

    2015-01-01

    It is well established that the sliding mode control strategy provides an effective and robust method of controlling the deterministic system due to its well-known invariance property to a class of bounded disturbance and parameter variations. Advances in microcomputer technologies have made digital control increasingly popular among the researchers worldwide. And that led to the study of discrete-time sliding mode control design and its implementation. This brief presents, a method for multi-rate frequency shaped sliding mode controller design based on switching and non-switching type of reaching law. In this approach, the frequency dependent compensator dynamics are introduced through a frequency-shaped sliding surface by assigning frequency dependent weighing matrices in a linear quadratic regulator (LQR) design procedure. In this way, the undesired high frequency dynamics or certain frequency disturbance can be eliminated. The states are implicitly obtained by measuring the output at a faster rate than th...

  20. Multi-resonant wideband energy harvester based on a folded asymmetric M-shaped cantilever

    International Nuclear Information System (INIS)

    Wu, Meng; Mao, Haiyang; Li, Zhigang; Liu, Ruiwen; Ming, Anjie; Ou, Yi; Ou, Wen

    2015-01-01

    This article reports a compact wideband piezoelectric vibration energy harvester consisting of three proof masses and an asymmetric M-shaped cantilever. The M-shaped beam comprises a main beam and two folded and dimension varied auxiliary beams interconnected through the proof mass at the end of the main cantilever. Such an arrangement constitutes a three degree-of-freedom vibrating body, which can tune the resonant frequencies of its first three orders close enough to obtain a utility wide bandwidth. The finite element simulation results and the experimental results are well matched. The operation bandwidth comprises three adjacent voltage peaks on account of the frequency interval shortening mechanism. The result shows that the proposed piezoelectric energy harvester could be efficient and adaptive in practical vibration circumstance based on multiple resonant modes

  1. GIMDA: Graphlet interaction-based MiRNA-disease association prediction.

    Science.gov (United States)

    Chen, Xing; Guan, Na-Na; Li, Jian-Qiang; Yan, Gui-Ying

    2018-03-01

    MicroRNAs (miRNAs) have been confirmed to be closely related to various human complex diseases by many experimental studies. It is necessary and valuable to develop powerful and effective computational models to predict potential associations between miRNAs and diseases. In this work, we presented a prediction model of Graphlet Interaction for MiRNA-Disease Association prediction (GIMDA) by integrating the disease semantic similarity, miRNA functional similarity, Gaussian interaction profile kernel similarity and the experimentally confirmed miRNA-disease associations. The related score of a miRNA to a disease was calculated by measuring the graphlet interactions between two miRNAs or two diseases. The novelty of GIMDA lies in that we used graphlet interaction to analyse the complex relationships between two nodes in a graph. The AUCs of GIMDA in global and local leave-one-out cross-validation (LOOCV) turned out to be 0.9006 and 0.8455, respectively. The average result of five-fold cross-validation reached to 0.8927 ± 0.0012. In case study for colon neoplasms, kidney neoplasms and prostate neoplasms based on the database of HMDD V2.0, 45, 45, 41 of the top 50 potential miRNAs predicted by GIMDA were validated by dbDEMC and miR2Disease. Additionally, in the case study of new diseases without any known associated miRNAs and the case study of predicting potential miRNA-disease associations using HMDD V1.0, there were also high percentages of top 50 miRNAs verified by the experimental literatures. © 2017 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  2. Whole vertebral bone segmentation method with a statistical intensity-shape model based approach

    Science.gov (United States)

    Hanaoka, Shouhei; Fritscher, Karl; Schuler, Benedikt; Masutani, Yoshitaka; Hayashi, Naoto; Ohtomo, Kuni; Schubert, Rainer

    2011-03-01

    An automatic segmentation algorithm for the vertebrae in human body CT images is presented. Especially we focused on constructing and utilizing 4 different statistical intensity-shape combined models for the cervical, upper / lower thoracic and lumbar vertebrae, respectively. For this purpose, two previously reported methods were combined: a deformable model-based initial segmentation method and a statistical shape-intensity model-based precise segmentation method. The former is used as a pre-processing to detect the position and orientation of each vertebra, which determines the initial condition for the latter precise segmentation method. The precise segmentation method needs prior knowledge on both the intensities and the shapes of the objects. After PCA analysis of such shape-intensity expressions obtained from training image sets, vertebrae were parametrically modeled as a linear combination of the principal component vectors. The segmentation of each target vertebra was performed as fitting of this parametric model to the target image by maximum a posteriori estimation, combined with the geodesic active contour method. In the experimental result by using 10 cases, the initial segmentation was successful in 6 cases and only partially failed in 4 cases (2 in the cervical area and 2 in the lumbo-sacral). In the precise segmentation, the mean error distances were 2.078, 1.416, 0.777, 0.939 mm for cervical, upper and lower thoracic, lumbar spines, respectively. In conclusion, our automatic segmentation algorithm for the vertebrae in human body CT images showed a fair performance for cervical, thoracic and lumbar vertebrae.

  3. Morpholino spin-labeling for base-pair sequencing of a 3'-terminal RNA stem by proton homonuclear Overhauser enhancements: yeast ribosomal 5S RNA

    International Nuclear Information System (INIS)

    Lee, K.M.; Marshall, A.G.

    1987-01-01

    Base-pair sequences for 5S and 5.8S RNAs are not readily extracted from proton homonuclear nuclear Overhauser enhancement (NOE) connectivity experiments alone, due to extensive peak overlap in the downfield (11-15 ppm) proton NMR spectrum. In this paper, we introduce a new method for base-pair proton peak assignment for ribosomal RNAs, based upon the distance-dependent broadening of the resonances of base-pair protons spatially proximal to a paramagnetic group. Introduction of a nitroxide spin-label covalently attached to the 3'-terminal ribose provides an unequivocal starting point for base-pair hydrogen-bond proton NMR assignment. Subsequent NOE connectivities then establish the base-pair sequence for the terminal stem of a 5S RNA. Periodate oxidation of yeast 5S RNA, followed by reaction with 4-amino-2,2,6,6-tetramethylpiperidinyl-1-oxy (TEMPO-NH2) and sodium borohydride reduction, produces yeast 5S RNA specifically labeled with a paramagnetic nitroxide group at the 3'-terminal ribose. Comparison of the 500-MHz 1H NMR spectra of native and 3'-terminal spin-labeled yeast 5S RNA serves to identify the terminal base pair (G1 . C120) and its adjacent base pair (G2 . U119) on the basis of their proximity to the 3'-terminal spin-label. From that starting point, we have then identified (G . C, A . U, or G . U) and sequenced eight of the nine base pairs in the terminal helix via primary and secondary NOE's

  4. mRNA-based vaccines synergize with radiation therapy to eradicate established tumors

    International Nuclear Information System (INIS)

    Fotin-Mleczek, Mariola; Zanzinger, Kai; Heidenreich, Regina; Lorenz, Christina; Kowalczyk, Aleksandra; Kallen, Karl-Josef; Huber, Stephan M

    2014-01-01

    The eradication of large, established tumors by active immunotherapy is a major challenge because of the numerous cancer evasion mechanisms that exist. This study aimed to establish a novel combination therapy consisting of messenger RNA (mRNA)-based cancer vaccines and radiation, which would facilitate the effective treatment of established tumors with aggressive growth kinetics. The combination of a tumor-specific mRNA-based vaccination with radiation was tested in two syngeneic tumor models, a highly immunogenic E.G7-OVA and a low immunogenic Lewis lung cancer (LLC). The molecular mechanism induced by the combination therapy was evaluated via gene expression arrays as well as flow cytometry analyses of tumor infiltrating cells. In both tumor models we demonstrated that a combination of mRNA-based immunotherapy with radiation results in a strong synergistic anti-tumor effect. This was manifested as either complete tumor eradication or delay in tumor growth. Gene expression analysis of mouse tumors revealed a variety of substantial changes at the tumor site following radiation. Genes associated with antigen presentation, infiltration of immune cells, adhesion, and activation of the innate immune system were upregulated. A combination of radiation and immunotherapy induced significant downregulation of tumor associated factors and upregulation of tumor suppressors. Moreover, combination therapy significantly increased CD4 + , CD8 + and NKT cell infiltration of mouse tumors. Our data provide a scientific rationale for combining immunotherapy with radiation and provide a basis for the development of more potent anti-cancer therapies. The online version of this article (doi:10.1186/1748-717X-9-180) contains supplementary material, which is available to authorized users

  5. Fluorescence-based codetection with protein markers reveals distinct cellular compartments for altered MicroRNA expression in solid tumors

    DEFF Research Database (Denmark)

    Sempere, Lorenzo F; Preis, Meir; Yezefski, Todd

    2010-01-01

    of altered miRNA expression in solid tumors, we developed a sensitive fluorescence-based in situ hybridization (ISH) method to visualize miRNA accumulation within individual cells in formalin-fixed, paraffin-embedded tissue specimens. This ISH method was implemented to be compatible with routine clinical...

  6. Whole Blood mRNA Expression-Based Prognosis of Metastatic Renal Cell Carcinoma.

    Science.gov (United States)

    Giridhar, Karthik V; Sosa, Carlos P; Hillman, David W; Sanhueza, Cristobal; Dalpiaz, Candace L; Costello, Brian A; Quevedo, Fernando J; Pitot, Henry C; Dronca, Roxana S; Ertz, Donna; Cheville, John C; Donkena, Krishna Vanaja; Kohli, Manish

    2017-11-03

    The Memorial Sloan Kettering Cancer Center (MSKCC) prognostic score is based on clinical parameters. We analyzed whole blood mRNA expression in metastatic clear cell renal cell carcinoma (mCCRCC) patients and compared it to the MSKCC score for predicting overall survival. In a discovery set of 19 patients with mRCC, we performed whole transcriptome RNA sequencing and selected eighteen candidate genes for further evaluation based on associations with overall survival and statistical significance. In an independent validation of set of 47 patients with mCCRCC, transcript expression of the 18 candidate genes were quantified using a customized NanoString probeset. Cox regression multivariate analysis confirmed that two of the candidate genes were significantly associated with overall survival. Higher expression of BAG1 [hazard ratio (HR) of 0.14, p < 0.0001, 95% confidence interval (CI) 0.04-0.36] and NOP56 (HR 0.13, p < 0.0001, 95% CI 0.05-0.34) were associated with better prognosis. A prognostic model incorporating expression of BAG1 and NOP56 into the MSKCC score improved prognostication significantly over a model using the MSKCC prognostic score only ( p < 0.0001). Prognostic value of using whole blood mRNA gene profiling in mCCRCC is feasible and should be prospectively confirmed in larger studies.

  7. Whole Blood mRNA Expression-Based Prognosis of Metastatic Renal Cell Carcinoma

    Directory of Open Access Journals (Sweden)

    Karthik V. Giridhar

    2017-11-01

    Full Text Available The Memorial Sloan Kettering Cancer Center (MSKCC prognostic score is based on clinical parameters. We analyzed whole blood mRNA expression in metastatic clear cell renal cell carcinoma (mCCRCC patients and compared it to the MSKCC score for predicting overall survival. In a discovery set of 19 patients with mRCC, we performed whole transcriptome RNA sequencing and selected eighteen candidate genes for further evaluation based on associations with overall survival and statistical significance. In an independent validation of set of 47 patients with mCCRCC, transcript expression of the 18 candidate genes were quantified using a customized NanoString probeset. Cox regression multivariate analysis confirmed that two of the candidate genes were significantly associated with overall survival. Higher expression of BAG1 [hazard ratio (HR of 0.14, p < 0.0001, 95% confidence interval (CI 0.04–0.36] and NOP56 (HR 0.13, p < 0.0001, 95% CI 0.05–0.34 were associated with better prognosis. A prognostic model incorporating expression of BAG1 and NOP56 into the MSKCC score improved prognostication significantly over a model using the MSKCC prognostic score only (p < 0.0001. Prognostic value of using whole blood mRNA gene profiling in mCCRCC is feasible and should be prospectively confirmed in larger studies.

  8. MicroRNA-based Therapy in Animal Models of Selected Gastrointestinal Cancers

    Directory of Open Access Journals (Sweden)

    Jana Merhautova

    2016-09-01

    Full Text Available Gastrointestinal cancer accounts for the 20 most frequent cancer diseases worldwide and there is a constant urge to bring new therapeutics with new mechanism of action into the clinical practice. Quantity of in vitro and in vivo evidences indicate, that exogenous change in pathologically imbalanced microRNAs (miRNAs is capable of transforming the cancer cell phenotype. This review analyzed preclinical miRNA-based therapy attempts in animal models of gastric, pancreatic, gallbladder, and colorectal cancer. From more than 400 original articles, 26 was found to assess the effect of miRNA mimics, precursors, expression vectors, or inhibitors administered locally or systemically being an approach with relatively high translational potential. We have focused on mapping available information on animal model used (animal strain, cell line, xenograft method, pharmacological aspects (oligonucleotide chemistry, delivery system, posology, route of administration and toxicology assessments. We also summarize findings in the field pharmacokinetics and toxicity of miRNA-based therapy.□

  9. Double-stranded RNA transcribed from vector-based oligodeoxynucleotide acts as transcription factor decoy

    International Nuclear Information System (INIS)

    Xiao, Xiao; Gang, Yi; Wang, Honghong; Wang, Jiayin; Zhao, Lina; Xu, Li; Liu, Zhiguo

    2015-01-01

    Highlights: • A shRNA vector based transcription factor decoy, VB-ODN, was designed. • VB-ODN for NF-κB inhibited cell viability in HEK293 cells. • VB-ODN inhibited expression of downstream genes of target transcription factors. • VB-ODN may enhance nuclear entry ratio for its feasibility of virus production. - Abstract: In this study, we designed a short hairpin RNA vector-based oligodeoxynucleotide (VB-ODN) carrying transcription factor (TF) consensus sequence which could function as a decoy to block TF activity. Specifically, VB-ODN for Nuclear factor-κB (NF-κB) could inhibit cell viability and decrease downstream gene expression in HEK293 cells without affecting expression of NF-κB itself. The specific binding between VB-ODN produced double-stranded RNA and NF-κB was evidenced by electrophoretic mobility shift assay. Moreover, similar VB-ODNs designed for three other TFs also inhibit their downstream gene expression but not that of themselves. Our study provides a new design of decoy for blocking TF activity

  10. Predicting microRNA-disease associations using label propagation based on linear neighborhood similarity.

    Science.gov (United States)

    Li, Guanghui; Luo, Jiawei; Xiao, Qiu; Liang, Cheng; Ding, Pingjian

    2018-05-12

    Interactions between microRNAs (miRNAs) and diseases can yield important information for uncovering novel prognostic markers. Since experimental determination of disease-miRNA associations is time-consuming and costly, attention has been given to designing efficient and robust computational techniques for identifying undiscovered interactions. In this study, we present a label propagation model with linear neighborhood similarity, called LPLNS, to predict unobserved miRNA-disease associations. Additionally, a preprocessing step is performed to derive new interaction likelihood profiles that will contribute to the prediction since new miRNAs and diseases lack known associations. Our results demonstrate that the LPLNS model based on the known disease-miRNA associations could achieve impressive performance with an AUC of 0.9034. Furthermore, we observed that the LPLNS model based on new interaction likelihood profiles could improve the performance to an AUC of 0.9127. This was better than other comparable methods. In addition, case studies also demonstrated our method's outstanding performance for inferring undiscovered interactions between miRNAs and diseases, especially for novel diseases. Copyright © 2018. Published by Elsevier Inc.

  11. Double-stranded RNA transcribed from vector-based oligodeoxynucleotide acts as transcription factor decoy

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Xiao [State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, Shaanxi Province (China); Gang, Yi [State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, Shaanxi Province (China); Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi’an 710038, Shaanxi Province (China); Wang, Honghong [No. 518 Hospital of Chinese People’s Liberation Army, Xi’an 710043, Shaanxi Province (China); Wang, Jiayin [The Genome Institute, Washington University in St. Louis, St. Louis, MO 63108 (United States); Zhao, Lina [Department of Radiation Oncology, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, Shaanxi Province (China); Xu, Li, E-mail: lxuhelen@163.com [State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, Shaanxi Province (China); Liu, Zhiguo, E-mail: liuzhiguo@fmmu.edu.cn [State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, Shaanxi Province (China)

    2015-02-06

    Highlights: • A shRNA vector based transcription factor decoy, VB-ODN, was designed. • VB-ODN for NF-κB inhibited cell viability in HEK293 cells. • VB-ODN inhibited expression of downstream genes of target transcription factors. • VB-ODN may enhance nuclear entry ratio for its feasibility of virus production. - Abstract: In this study, we designed a short hairpin RNA vector-based oligodeoxynucleotide (VB-ODN) carrying transcription factor (TF) consensus sequence which could function as a decoy to block TF activity. Specifically, VB-ODN for Nuclear factor-κB (NF-κB) could inhibit cell viability and decrease downstream gene expression in HEK293 cells without affecting expression of NF-κB itself. The specific binding between VB-ODN produced double-stranded RNA and NF-κB was evidenced by electrophoretic mobility shift assay. Moreover, similar VB-ODNs designed for three other TFs also inhibit their downstream gene expression but not that of themselves. Our study provides a new design of decoy for blocking TF activity.

  12. [TYPING OF LEPTOSPIRA SPP. STRAINS BASED ON 16S rRNA].

    Science.gov (United States)

    Ostankova, Yu V; Semenov, A V; Stoyanova, N A; Tokarevich, N K; Lyubimova, N E; Petrova, O A; Ananina, Yu V; Petrov, E M

    2016-01-01

    Comparative typing of Leptospira spp. strain collection based on analysis of 16S RNA fragment. 2 pairs of primers were used for PCR, that jointly flank 1423b.p. sized fragment. Sequences of Leptospira spp. strain 16S rRNA, presented in the international database, were used for phylogenetic analysis. A high similarity, including interspecies, of the 16S fragment in Leptospira spp. strains was shown independently of the source, serovar and serogroup. Heterogeneity of the primary matrix, spontaneous mutations of hotspots and erroneous nucleotide couplings, characteristic for 16S sequence of pathogenic Leptospira spp. strains, are discussed. Molecular-genetic characteristic of certain reference Leptospira spp. strains by 16S sequence is obtained. Results of the studies give evidence on expedience of introduction into clinical practice of identification of Leptospira spp. by 16S sequence directly from the clinical material, that would allow to significantly reduce identification time, dismiss complex type-specific sera and other labor-intensive methods.

  13. A compilation of Web-based research tools for miRNA analysis.

    Science.gov (United States)

    Shukla, Vaibhav; Varghese, Vinay Koshy; Kabekkodu, Shama Prasada; Mallya, Sandeep; Satyamoorthy, Kapaettu

    2017-09-01

    Since the discovery of microRNAs (miRNAs), a class of noncoding RNAs that regulate the gene expression posttranscriptionally in sequence-specific manner, there has been a release of number of tools useful for both basic and advanced applications. This is because of the significance of miRNAs in many pathophysiological conditions including cancer. Numerous bioinformatics tools that have been developed for miRNA analysis have their utility for detection, expression, function, target prediction and many other related features. This review provides a comprehensive assessment of web-based tools for the miRNA analysis that does not require prior knowledge of any computing languages. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  14. Ratiometric FRET-based detection of DNA and micro-RNA in solution

    International Nuclear Information System (INIS)

    Matveeva, Evgenia G.; Gryczynski, Zygmunt; Stewart, Donald R.; Gryczynski, Ignacy

    2009-01-01

    A ratiometric method for detecting DNA oligomers in bulk solution based on Foerster resonance energy transfer (FRET) is described. The two fluorescence signals (green and red), originating from Cy3 (donor, green) and Cy5 (acceptor, red) labels, are simultaneously detected from the pre-hybridized Cy3oligomerY:Cy5oligomerX system. The ratio of red to green intensities is sensitive to the presence of the single-stranded complimentary oligomer, which replaces single-stranded Cy3oligomerY in the donor:acceptor complex and perturbs the FRET. The detection scheme is generally applicable to the detection of DNA and RNA, and particularly micro-RNA. The proposed method is applicable to various double-stranded various lengths targets (manipulation of the sample preparation conditions, such as temperature, incubation time, denaturizing agent, may be needed).

  15. RNA aptamer-based electrochemical biosensor for selective and label-free analysis of dopamine

    DEFF Research Database (Denmark)

    Farjami, Elahe; Campos, Rui; Nielsen, Jesper Sejrup

    2013-01-01

    , including dopamine precursors and metabolites and other neurotransmitters (NT). Here we report an electrochemical RNA aptamer-based biosensor for analysis of dopamine in the presence of other NT. The biosensor exploits a specific binding of dopamine by the RNA aptamer, immobilized at a cysteamine......, norepinephrine, 3,4-dihydroxy-phenylalanine (l-DOPA), 3,4-dihydroxyphenylacetic acid (DOPAC), methyldopamine, and tyramine, which gave negligible signals under conditions of experiments (electroanalysis at 0.185 V vs Ag/AgCl). The interference from ascorbic and uric acids was eliminated by application...... as a general strategy not to restrict the conformational freedom and binding properties of surface-bound aptamers and, thus, be applicable for the development of other aptasensors...

  16. Smooth transition for CPG-based body shape control of a snake-like robot

    International Nuclear Information System (INIS)

    Nor, Norzalilah Mohamad; Ma, Shugen

    2014-01-01

    This paper presents a locomotion control based on central pattern generator (CPG) of a snake-like robot. The main point addressed in this paper is a method that produces a smooth transition of the body shape of a snake-like robot. Body shape transition is important for snake-like robot locomotion to adapt to different space widths and also for obstacle avoidance. By manipulating the phase difference of the CPG outputs instantly, it will results in a sharp point or discontinuity which lead to an unstable movement of the snake-like robot. To tackle the problem, we propose a way of controlling the body shape: by incorporating activation function in the phase oscillator CPG model. The simplicity of the method promises an easy implementation and simple control. Simulation results and torque analysis confirm the effectiveness of the proposed control method and thus, can be used as a locomotion control in various potential applications of a snake-like robot. (paper)

  17. Wilcoxon signed-rank-based technique for the pulse-shape analysis of HPGe detectors

    Energy Technology Data Exchange (ETDEWEB)

    Martín, S., E-mail: sergiomr@usal.es; Quintana, B.; Barrientos, D.

    2016-07-01

    The characterization of the electric response of segmented-contact high-purity germanium detectors requires scanning systems capable of accurately associating each pulse with the position of the interaction that generated it. This process requires an algorithm sensitive to changes above the electronic noise in the pulse shapes produced at different positions, depending on the resolution of the Ge crystal. In this work, a pulse-shape comparison technique based on the Wilcoxon signed-rank test has been developed. It provides a method to distinguish pulses coming from different interaction points in the germanium crystal. Therefore, this technique is a necessary step for building a reliable pulse-shape database that can be used later for the determination of the position of interaction for γ-ray tracking spectrometry devices such as AGATA, GRETA or GERDA. The method was validated by comparison with a χ{sup 2} test using simulated and experimental pulses corresponding to a Broad Energy germanium detector (BEGe).

  18. Nanofluidic channels of arbitrary shapes fabricated by tip-based nanofabrication

    International Nuclear Information System (INIS)

    Hu, Huan; Cunningham, Brian T; King, William P; Zhuo, Yue; Oruc, Muhammed E

    2014-01-01

    Nanofluidic channels have promising applications in biomolecule manipulation and sensing. While several different methods of fabrication have been demonstrated for nanofluidic channels, a rapid, low-cost fabrication method that can fabricate arbitrary shapes of nanofluidic channels is still in demand. Here, we report a tip-based nanofabrication (TBN) method for fabricating nanofluidic channels using a heated atomic force microscopy (AFM) tip. The heated AFM tip deposits polymer nanowires where needed to serve as etch mask to fabricate silicon molds through one step of etching. PDMS nanofluidic channels are easily fabricated through replicate molding using the silicon molds. Various shapes of nanofluidic channels with either straight or curvilinear features are demonstrated. The width of the nanofluidic channels is 500 nm, and is determined by the deposited polymer nanowire width. The height of the channel is 400 nm determined by the silicon etching time. Ion conductance measurement on one single curvy shaped nanofluidic channel exhibits the typical ion conductance saturation phenomenon as the ion concentration decreases. Moreover, fluorescence imaging of fluid flowing through a fabricated nanofluidic channel demonstrates the channel integrity. This TBN process is seamlessly compatible with existing nanofabrication processes and can be used to achieve new types of nanofluidic devices. (paper)

  19. Multifrequency Piezoelectric Energy Harvester Based on Polygon-Shaped Cantilever Array

    Directory of Open Access Journals (Sweden)

    Dalius Mažeika

    2018-01-01

    Full Text Available This paper focuses on numerical and experimental investigations of a novel design piezoelectric energy harvester. Investigated harvester is based on polygon-shaped cantilever array and employs multifrequency operating principle. It consists of eight cantilevers with irregular design of cross-sectional area. Cantilevers are connected to each other by specific angle to form polygon-shaped structure. Moreover, seven seismic masses with additional lever arms are added in order to create additional rotation moment. Numerical investigation showed that piezoelectric polygon-shaped energy harvester has five natural frequencies in the frequency range from 10 Hz to 240 Hz, where the first and the second bending modes of the cantilevers are dominating. Maximum output voltage density and energy density equal to 50.03 mV/mm3 and 604 μJ/mm3, respectively, were obtained during numerical simulation. Prototype of piezoelectric harvester was made and experimental investigation was performed. Experimental measurements of the electrical characteristics showed that maximum output voltage density, energy density, and output power are 37.5 mV/mm3, 815.16 μJ/mm3, and 65.24 μW, respectively.

  20. The Development of the Flat-Knitted Shaped Uppers based on Ergonomics

    Directory of Open Access Journals (Sweden)

    Lu Zhiwen

    2016-06-01

    Full Text Available To achieve the efficiency and specification of the flat-knitted uppers design, the basic patterns of uppers are made from shoe lasts based on the research on the characteristics of human’s feet and wearability requirements on uppers. The knitting technology for half-shaped and fully shaped uppers was formed after the shear deformation of basic pattern and combination with flat knitting technology. As regards to the functional requirements on key parts of uppers, the structures of flat-knitted shaped uppers were intensively analysed and studied, dividing them into two categories (functional structure and decorative structure, discussing the knitting methods and advantages of different structure, and finally experimentally proving that the planar pattern of flat knitted uppers can apply to the design of flat-knitted uppers and achieve the combination of functionality and artistry of sneakers after combining with structural changes, with a great significance on the achievement of the efficient production of uppers and the enhancement of its commercial value.

  1. A double base change in alternate base pairs induced by ultraviolet irradiation in a glycine transfer RNA gene

    International Nuclear Information System (INIS)

    Coleman, R.D.; Dunst, R.W.; Hill, C.W.; Pennsylvania State Univ., Hershey

    1980-01-01

    The glyUsusub(AGA) mutation affects Escherichia coli tRNAsup(Gly)sub(GGG), changing it to an AGA missense suppressor tRNA. Sequence studies have shown that the mutation involves a double base substitution at the first and third positions of the tRNA anticodon, the result being a change in the anticodon from CCC to UCU. A system has been developed to facilitate the detection of this novel mutation, and we have shown that ultraviolet irradiation and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) are effective in causing the double base change. A single observation of the mutation occuring spontaneously has been made also. The frequency of MNNG-induced glyUsusub(AGA) mutations is compatible with their being caused by two separate mutagenic events. The frequency of UV-induced glyUsusub(AGA) mutations, however, strongly suggests that the occurence of one base substitution strongly enhances the chance of finding the second substitution at the alternate position. In addition to the double change in the anticodon, the glyUsusub(AGA) tRNA differs from tRNAsup(gly)sub(GGG) in that it bears a modification of the A adjacent to the 3' position of the anticodon. Most likely, this modified base is N-[9-(β-D-ribofuranosyl)-purin-6-ylcarbamoyl] threonine. (orig.) 891 AJ/orig. 892 BRE [de

  2. Shape coexistence in 16O, 72Se, and 240Pu: a comprehensive view based on the dynamic deformation model

    International Nuclear Information System (INIS)

    Kumar, K.

    1980-01-01

    The dynamic deformation model has been improved and applied to calculate the potential energies of deformation and the collective spectra of 16 O, 72 Se, and 240 Pu. A comprehensive view based on the dynamics of five-dimensional quadrupole motion is provided for three seemingly different types of shape coexistence: spherical (Op - Oh) and deformed (2p - 2h) shapes in 16 O, spherical and deformed minima in the potential energy surface of 72 Se, ground-state shape and the fission-isomer shape of 240 Pu. 5 figures, 3 tables

  3. Shape tracking with occlusions via coarse-to-fine region-based sobolev descent

    KAUST Repository

    Yang, Yanchao; Sundaramoorthi, Ganesh

    2015-01-01

    We present a method to track the shape of an object from video. The method uses a joint shape and appearance model of the object, which is propagated to match shape and radiance in subsequent frames, determining object shape. Self-occlusions and dis

  4. Analysis of energy-based algorithms for RNA secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Hajiaghayi Monir

    2012-02-01

    Full Text Available Abstract Background RNA molecules play critical roles in the cells of organisms, including roles in gene regulation, catalysis, and synthesis of proteins. Since RNA function depends in large part on its folded structures, much effort has been invested in developing accurate methods for prediction of RNA secondary structure from the base sequence. Minimum free energy (MFE predictions are widely used, based on nearest neighbor thermodynamic parameters of Mathews, Turner et al. or those of Andronescu et al. Some recently proposed alternatives that leverage partition function calculations find the structure with maximum expected accuracy (MEA or pseudo-expected accuracy (pseudo-MEA methods. Advances in prediction methods are typically benchmarked using sensitivity, positive predictive value and their harmonic mean, namely F-measure, on datasets of known reference structures. Since such benchmarks document progress in improving accuracy of computational prediction methods, it is important to understand how measures of accuracy vary as a function of the reference datasets and whether advances in algorithms or thermodynamic parameters yield statistically significant improvements. Our work advances such understanding for the MFE and (pseudo-MEA-based methods, with respect to the latest datasets and energy parameters. Results We present three main findings. First, using the bootstrap percentile method, we show that the average F-measure accuracy of the MFE and (pseudo-MEA-based algorithms, as measured on our largest datasets with over 2000 RNAs from diverse families, is a reliable estimate (within a 2% range with high confidence of the accuracy of a population of RNA molecules represented by this set. However, average accuracy on smaller classes of RNAs such as a class of 89 Group I introns used previously in benchmarking algorithm accuracy is not reliable enough to draw meaningful conclusions about the relative merits of the MFE and MEA-based algorithms

  5. Lentiviral transgenic microRNA-based shRNA suppressed mouse cytochromosome P450 3A (CYP3A expression in a dose-dependent and inheritable manner.

    Directory of Open Access Journals (Sweden)

    Yong Wang

    Full Text Available Cytochomosome P450 enzymes (CYP are heme-containing monooxygenases responsible for oxidative metabolism of many exogenous and endogenous compounds including drugs. The species difference of CYP limits the extent to which data obtained from animals can be translated to humans in pharmacodynamics or pharmacokinetics studies. Transgenic expression of human CYP in animals lacking or with largely reduced endogenous CYP counterparts is recognized as an ideal strategy to correct CYP species difference. CYP3A is the most abundant CYP subfamily both in human and mammals. In this study, we designed a microRNA-based shRNA (miR-shRNA simultaneously targeting four members of mouse CYP3A subfamily (CYP3A11, CYP3A16, CYP3A41 and CYP3A44, and transgenic mice expressing the designed miR-shRNA were generated by lentiviral transgenesis. Results showed that the CYP3A expression level in transgenic mice was markedly reduced compared to that in wild type or unrelated miR-shRNA transgenic mice, and was inversely correlated to the miR-shRNA expression level. The CYP3A expression levels in transgenic offspring of different generations were also remarkably lower compared to those of controls, and moreover the inhibition rate of CYP3A expression remained comparable over generations. The ratio of the targeted CYP3A transcriptional levels was comparable between knockdown and control mice of the same gender as detected by RT-PCR DGGE analysis. These data suggested that transgenic miR-shRNA suppressed CYP3A expression in a dose-dependent and inheritable manner, and transcriptional levels of the targeted CYP3As were suppressed to a similar extent. The observed knockdown efficacy was further confirmed by enzymatic activity analysis, and data showed that CYP3A activities in transgenic mice were markedly reduced compared to those in wild-type or unrelated miR-shRNA transgenic controls (1.11±0.71 vs 5.85±1.74, 5.9±2.4; P<0.01. This work laid down a foundation to further knock

  6. Vector rectangular-shape laser based on reduced graphene oxide interacting with a long fiber taper.

    Science.gov (United States)

    Gao, Lei; Zhu, Tao; Huang, Wei; Zeng, Jing

    2014-10-01

    A vector dual-wavelength rectangular-shape laser (RSL) based on a long fiber taper deposited with reduced graphene oxide is proposed, where nonlinearity is enhanced due to a large evanescent-field-interacting length and strong field confinement of an 8 mm fiber taper with a waist diameter of 4 μm. Graphene flakes are deposited uniformly on the taper waist with light pressure effect, so this structure guarantees both excellent saturable absorption and high nonlinearity. The RSL with a repetition rate of 7.9 MHz shows fast polarization switching in two orthogonal polarization directions, and temporal and spectral characteristics are investigated.

  7. Artificial neural network based pulse-shape analysis for cryogenic detectors operated in CRESST-II

    Energy Technology Data Exchange (ETDEWEB)

    Zoeller, Andreas [Physik-Department and Excellence Cluster Universe, Technische Universitaet Muenchen, D-85747 Garching (Germany); Collaboration: CRESST-Collaboration

    2016-07-01

    In this talk we report on results of a pulse-shape analysis of cryogenic detectors based on artificial neural networks. To train the neural network a large amount of pulses with known properties are necessary. Therefore, a data-driven simulation used to generate these sets will be explained. The presented analysis shows an excellent discrimination performance even down to the energy threshold. The method is applied to several detectors, among them is the module with the lowest threshold (307eV) operated in CRESST-II phase 2. The performed blind analysis of this module confirms the substantially enhanced sensitivity for light dark matter published in 2015.

  8. A comparison of a track shape analysis-based automated slide scanner system with traditional methods

    International Nuclear Information System (INIS)

    Bator, G.; Csordas, A.; Horvath, D.; Somlai, J.; Kovacs, T.

    2015-01-01

    During recent years, CR-39 detector measurements have gained attention due to improvements in image processing methods. An assessment method based on the application of a high-resolution slide scanner and its quality checks is introduced, using commercially available software and hardware. Using the conventional (visual) comparing analysis for 563 detectors, the method was found suitable for high-precision and reliable track analysis. The accuracy of the measurements were not disturbed by any other pseudo-tracks (scratches or contamination) due to the signal shape of the analysis. (author)

  9. Optically Controlled Reconfigurable Antenna Array Based on E-Shaped Elements

    Directory of Open Access Journals (Sweden)

    Arismar Cerqueira Sodré Junior

    2014-01-01

    Full Text Available This work presents the development of optically controlled reconfigurable antenna arrays. They are based on two patch elements with E-shaped slots, a printed probe, and a photoconductive switch made from an intrinsic silicon die. Numerical simulations and experiments have been shown to be in agreement, and both demonstrate that the frequency response of the antenna arrays can be efficiently reconfigured over two different frequency ISM bands, namely, 2.4 and 5 GHz. A measured gain of 12.5 dBi has been obtained through the use of two radiating elements printed in a low-cost substrate and a dihedral corner reflector.

  10. Design of a beam shaping assembly for an accelerator-based BNCT system

    International Nuclear Information System (INIS)

    Stichelbaut, F.; Forton, E.; Jongen, Y.

    2006-01-01

    A complete BNCT system based on a high-intensity proton accelerator is developed by the IBA company. The neutron beam is produced via the 7 Li(p,n) 7 Be reaction using a solid lithium target. The neutron energy spectrum is tailored with a beam shaping assembly surrounding the target. This device is the object of an extensive R and D project and is fully designed with the Monte Carlo simulation code MCNPX. The emphasis is put on the treatment quality, notably the radiation dose at the skin level, and the achievable neutron flux. (author)

  11. Voxel-Based Neighborhood for Spatial Shape Pattern Classification of Lidar Point Clouds with Supervised Learning

    Directory of Open Access Journals (Sweden)

    Victoria Plaza-Leiva

    2017-03-01

    Full Text Available Improving the effectiveness of spatial shape features classification from 3D lidar data is very relevant because it is largely used as a fundamental step towards higher level scene understanding challenges of autonomous vehicles and terrestrial robots. In this sense, computing neighborhood for points in dense scans becomes a costly process for both training and classification. This paper proposes a new general framework for implementing and comparing different supervised learning classifiers with a simple voxel-based neighborhood computation where points in each non-overlapping voxel in a regular grid are assigned to the same class by considering features within a support region defined by the voxel itself. The contribution provides offline training and online classification procedures as well as five alternative feature vector definitions based on principal component analysis for scatter, tubular and planar shapes. Moreover, the feasibility of this approach is evaluated by implementing a neural network (NN method previously proposed by the authors as well as three other supervised learning classifiers found in scene processing methods: support vector machines (SVM, Gaussian processes (GP, and Gaussian mixture models (GMM. A comparative performance analysis is presented using real point clouds from both natural and urban environments and two different 3D rangefinders (a tilting Hokuyo UTM-30LX and a Riegl. Classification performance metrics and processing time measurements confirm the benefits of the NN classifier and the feasibility of voxel-based neighborhood.

  12. Voxel-Based Neighborhood for Spatial Shape Pattern Classification of Lidar Point Clouds with Supervised Learning.

    Science.gov (United States)

    Plaza-Leiva, Victoria; Gomez-Ruiz, Jose Antonio; Mandow, Anthony; García-Cerezo, Alfonso

    2017-03-15

    Improving the effectiveness of spatial shape features classification from 3D lidar data is very relevant because it is largely used as a fundamental step towards higher level scene understanding challenges of autonomous vehicles and terrestrial robots. In this sense, computing neighborhood for points in dense scans becomes a costly process for both training and classification. This paper proposes a new general framework for implementing and comparing different supervised learning classifiers with a simple voxel-based neighborhood computation where points in each non-overlapping voxel in a regular grid are assigned to the same class by considering features within a support region defined by the voxel itself. The contribution provides offline training and online classification procedures as well as five alternative feature vector definitions based on principal component analysis for scatter, tubular and planar shapes. Moreover, the feasibility of this approach is evaluated by implementing a neural network (NN) method previously proposed by the authors as well as three other supervised learning classifiers found in scene processing methods: support vector machines (SVM), Gaussian processes (GP), and Gaussian mixture models (GMM). A comparative performance analysis is presented using real point clouds from both natural and urban environments and two different 3D rangefinders (a tilting Hokuyo UTM-30LX and a Riegl). Classification performance metrics and processing time measurements confirm the benefits of the NN classifier and the feasibility of voxel-based neighborhood.

  13. Analytical Performances of Human Immunodeficiency Virus Type 1 RNA-Based Amplix® Real-Time PCR Platform for HIV-1 RNA Quantification

    Directory of Open Access Journals (Sweden)

    Christian Diamant Mossoro-Kpinde

    2016-01-01

    Full Text Available Objectives. We evaluated the performances of Amplix real-time PCR platform developed by Biosynex (Strasbourg, France, combining automated station extraction (Amplix station 16 Dx and real-time PCR (Amplix NG, for quantifying plasma HIV-1 RNA by lyophilized HIV-1 RNA-based Amplix reagents targeting gag and LTR, using samples from HIV-1-infected adults from Central African Republic. Results. Amplix real-time PCR assay showed low limit of detection (28 copies/mL, across wide dynamic range (1.4–10 log copies/mL, 100% sensitivity and 99% specificity, high reproducibility, and accuracy with mean bias < 5%. The assay showed excellent correlations and concordance of 95.3% with the reference HIV-1 RNA load assay (Roche, with mean absolute bias of +0.097 log copies/mL by Bland-Altman analysis. The assay was able to detect and quantify the most prevalent HIV-1 subtype strains and the majority of non-B subtypes, CRFs of HIV-1 group M, and HIV-1 groups N and O circulating in Central Africa. The Amplix assay showed 100% sensitivity and 99.6% specificity to diagnose virological failure in clinical samples from antiretroviral drug-experienced patients. Conclusions. The HIV-1 RNA-based Amplix real-time PCR platform constitutes sensitive and reliable system for clinical monitoring of HIV-1 RNA load in HIV-1-infected children and adults, particularly adapted to intermediate laboratory facilities in sub-Saharan Africa.

  14. Towards Antiviral shRNAs Based on the AgoshRNA Design.

    Directory of Open Access Journals (Sweden)

    Ying Poi Liu

    Full Text Available RNA interference (RNAi can be induced by intracellular expression of a short hairpin RNA (shRNA. Processing of the shRNA requires the RNaseIII-like Dicer enzyme to remove the loop and to release the biologically active small interfering RNA (siRNA. Dicer is also involved in microRNA (miRNA processing to liberate the mature miRNA duplex, but recent studies indicate that miR-451 is not processed by Dicer. Instead, this miRNA is processed by the Argonaute 2 (Ago2 protein, which also executes the subsequent cleavage of a complementary mRNA target. Interestingly, shRNAs that structurally resemble miR-451 can also be processed by Ago2 instead of Dicer. The key determinant of these "AgoshRNA" molecules is a relatively short basepaired stem, which avoids Dicer recognition and consequently allows alternative processing by Ago2. AgoshRNA processing yields a single active RNA strand, whereas standard shRNAs produce a duplex with guide and passenger strands and the latter may cause adverse off-target effects. In this study, we converted previously tested active anti-HIV-1 shRNA molecules into AgoshRNA. We tested several designs that could potentially improve AgoshRNA activity, including extension of the complementarity between the guide strand and the mRNA target and reduction of the thermodynamic stability of the hairpins. We demonstrate that active AgoshRNAs can be generated. However, the RNAi activity is reduced compared to the matching shRNAs. Despite reduced RNAi activity, comparison of an active AgoshRNA and the matching shRNA in a sensitive cell toxicity assay revealed that the AgoshRNA is much less toxic.

  15. AUTOMATIC SHAPE-BASED TARGET EXTRACTION FOR CLOSE-RANGE PHOTOGRAMMETRY

    Directory of Open Access Journals (Sweden)

    X. Guo

    2016-06-01

    Full Text Available In order to perform precise identification and location of artificial coded targets in natural scenes, a novel design of circle-based coded target and the corresponding coarse-fine extraction algorithm are presented. The designed target separates the target box and coding box totally and owns an advantage of rotation invariance. Based on the original target, templates are prepared by three geometric transformations and are used as the input of shape-based template matching. Finally, region growing and parity check methods are used to extract the coded targets as final results. No human involvement is required except for the preparation of templates and adjustment of thresholds in the beginning, which is conducive to the automation of close-range photogrammetry. The experimental results show that the proposed recognition method for the designed coded target is robust and accurate.

  16. Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm

    Directory of Open Access Journals (Sweden)

    Wu Chi-Yeh

    2010-01-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are short non-coding RNA molecules, which play an important role in post-transcriptional regulation of gene expression. There have been many efforts to discover miRNA precursors (pre-miRNAs over the years. Recently, ab initio approaches have attracted more attention because they do not depend on homology information and provide broader applications than comparative approaches. Kernel based classifiers such as support vector machine (SVM are extensively adopted in these ab initio approaches due to the prediction performance they achieved. On the other hand, logic based classifiers such as decision tree, of which the constructed model is interpretable, have attracted less attention. Results This article reports the design of a predictor of pre-miRNAs with a novel kernel based classifier named the generalized Gaussian density estimator (G2DE based classifier. The G2DE is a kernel based algorithm designed to provide interpretability by utilizing a few but representative kernels for constructing the classification model. The performance of the proposed predictor has been evaluated with 692 human pre-miRNAs and has been compared with two kernel based and two logic based classifiers. The experimental results show that the proposed predictor is capable of achieving prediction performance comparable to those delivered by the prevailing kernel based classification algorithms, while providing the user with an overall picture of the distribution of the data set. Conclusion Software predictors that identify pre-miRNAs in genomic sequences have been exploited by biologists to facilitate molecular biology research in recent years. The G2DE employed in this study can deliver prediction accuracy comparable with the state-of-the-art kernel based machine learning algorithms. Furthermore, biologists can obtain valuable insights about the different characteristics of the sequences of pre-miRNAs with the models generated by the G

  17. Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies.

    Science.gov (United States)

    Zhao, Shanrong; Prenger, Kurt; Smith, Lance

    2013-01-01

    RNA-Seq is becoming a promising replacement to microarrays in transcriptome profiling and differential gene expression study. Technical improvements have decreased sequencing costs and, as a result, the size and number of RNA-Seq datasets have increased rapidly. However, the increasing volume of data from large-scale RNA-Seq studies poses a practical challenge for data analysis in a local environment. To meet this challenge, we developed Stormbow, a cloud-based software package, to process large volumes of RNA-Seq data in parallel. The performance of Stormbow has been tested by practically applying it to analyse 178 RNA-Seq samples in the cloud. In our test, it took 6 to 8 hours to process an RNA-Seq sample with 100 million reads, and the average cost was $3.50 per sample. Utilizing Amazon Web Services as the infrastructure for Stormbow allows us to easily scale up to handle large datasets with on-demand computational resources. Stormbow is a scalable, cost effective, and open-source based tool for large-scale RNA-Seq data analysis. Stormbow can be freely downloaded and can be used out of box to process Illumina RNA-Seq datasets.

  18. Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format.

    Science.gov (United States)

    Salvo-Chirnside, Eliane; Kane, Steven; Kerr, Lorraine E

    2011-12-02

    The increasing popularity of systems-based approaches to plant research has resulted in a demand for high throughput (HTP) methods to be developed. RNA extraction from multiple samples in an experiment is a significant bottleneck in performing systems-level genomic studies. Therefore we have established a high throughput method of RNA extraction from Arabidopsis thaliana to facilitate gene expression studies in this widely used plant model. We present optimised manual and automated protocols for the extraction of total RNA from 9-day-old Arabidopsis seedlings in a 96 well plate format using silica membrane-based methodology. Consistent and reproducible yields of high quality RNA are isolated averaging 8.9 μg total RNA per sample (~20 mg plant tissue). The purified RNA is suitable for subsequent qPCR analysis of the expression of over 500 genes in triplicate from each sample. Using the automated procedure, 192 samples (2 × 96 well plates) can easily be fully processed (samples homogenised, RNA purified and quantified) in less than half a day. Additionally we demonstrate that plant samples can be stored in RNAlater at -20°C (but not 4°C) for 10 months prior to extraction with no significant effect on RNA yield or quality. Additionally, disrupted samples can be stored in the lysis buffer at -20°C for at least 6 months prior to completion of the extraction procedure providing a flexible sampling and storage scheme to facilitate complex time series experiments.

  19. Development of GAGG depth-of-interaction (DOI) block detectors based on pulse shape analysis

    International Nuclear Information System (INIS)

    Yamamoto, Seiichi; Kobayashi, Takahiro; Yeol Yeom, Jung; Morishita, Yuki; Sato, Hiroki; Endo, Takanori; Usuki, Yoshiyuki; Kamada, Kei; Yoshikawa, Akira

    2014-01-01

    A depth-of-interaction (DOI) detector is required for developing a high resolution and high sensitivity PET system. Ce-doped Gd 3 Al 2 Ga 3 O 12 (GAGG fast: GAGG-F) is a promising scintillator for PET applications with high light output, no natural radioisotope and suitable light emission wavelength for semiconductor based photodetectors. However, no DOI detector based on pulse shape analysis with GAGG-F has been developed to date, due to the lack of appropriate scintillators of pairing. Recently a new variation of this scintillator with different Al/Ga ratios—Ce-doped Gd 3 Al 2.6 Ga 2.4 O 12 (GAGG slow: GAGG-S), which has slower decay time was developed. The combination of GAGG-F and GAGG-S may allow us to realize high resolution DOI detectors based on pulse shape analysis. We developed and tested two GAGG phoswich DOI block detectors comprised of pixelated GAGG-F and GAGG-S scintillation crystals. One phoswich block detector comprised of 2×2×5 mm pixel that were assembled into a 5×5 matrix. The DOI block was optically coupled to a silicon photomultiplier (Si-PM) array (Hamamatsu MPPC S11064-050P) with a 2-mm thick light guide. The other phoswich block detector comprised of 0.5×0.5×5 mm (GAGG-F) and 0.5×0.5×6 mm 3 (GAGG-S) pixels that were assembled into a 20×20 matrix. The DOI block was also optically coupled to the same Si-PM array with a 2-mm thick light guide. In the block detector of 2-mm crystal pixels (5×5 matrix), the 2-dimensional histogram revealed excellent separation with an average energy resolution of 14.1% for 662-keV gamma photons. The pulse shape spectrum displayed good separation with a peak-to-valley ratio of 8.7. In the block detector that used 0.5-mm crystal pixels (20×20 matrix), the 2-dimensional histogram also showed good separation with energy resolution of 27.5% for the 662-keV gamma photons. The pulse shape spectrum displayed good separation with a peak-to-valley ratio of 6.5. These results indicate that phoswich DOI

  20. Bio-based hyperbranched thermosetting polyurethane/triethanolamine functionalized multi-walled carbon nanotube nanocomposites as shape memory materials.

    Science.gov (United States)

    Kalita, Hemjyoti; Karak, Niranjan

    2014-07-01

    Here, bio-based shape memory polymers have generated immense interest in recent times. Here, Bio-based hyperbranched polyurethane/triethanolamine functionalized multi-walled carbon nanotube (TEA-f-MWCNT) nanocomposites were prepared by in-situ pre-polymerization technique. The Fourier transform infrared spectroscopy and the transmission electron microscopic studies showed the strong interfacial adhesion and the homogeneous distribution of TEA-f-MWCNT in the polyurethane matrix. The prepared epoxy cured thermosetting nanocomposites exhibited enhanced tensile strength (6.5-34.5 MPa), scratch hardness (3.0-7.5 kg) and thermal stability (241-288 degrees C). The nanocomposites showed excellent shape fixity and shape recovery. The shape recovery time decreases (24-10 s) with the increase of TEA-f-MWCNT content in the nanocomposites. Thus the studied nanocomposites have potential to be used as advanced shape memory materials.

  1. An albumin-mediated cholesterol design-based strategy for tuning siRNA pharmacokinetics and gene silencing.

    Science.gov (United States)

    Bienk, Konrad; Hvam, Michael Lykke; Pakula, Malgorzata Maria; Dagnæs-Hansen, Frederik; Wengel, Jesper; Malle, Birgitte Mølholm; Kragh-Hansen, Ulrich; Cameron, Jason; Bukrinski, Jens Thostrup; Howard, Kenneth A

    2016-06-28

    Major challenges for the clinical translation of small interfering RNA (siRNA) include overcoming the poor plasma half-life, site-specific delivery and modulation of gene silencing. In this work, we exploit the intrinsic transport properties of human serum albumin to tune the blood circulatory half-life, hepatic accumulation and gene silencing; based on the number of siRNA cholesteryl modifications. We demonstrate by a gel shift assay a strong and specific affinity of recombinant human serum albumin (rHSA) towards cholesteryl-modified siRNA (Kd>1×10(-7)M) dependent on number of modifications. The rHSA/siRNA complex exhibited reduced nuclease degradation and reduced induction of TNF-α production by human peripheral blood mononuclear cells. The increased solubility of heavily cholesteryl modified siRNA in the presence of rHSA facilitated duplex annealing and consequent interaction that allowed in vivo studies using multiple cholesteryl modifications. A structural-activity-based screen of in vitro EGFP-silencing was used to select optimal siRNA designs containing cholesteryl modifications within the sense strand that were used for in vivo studies. We demonstrate plasma half-life extension in NMRI mice from t1/2 12min (naked) to t1/2 45min (single cholesteryl) and t1/2 71min (double cholesteryl) using fluorescent live bioimaging. The biodistribution showed increased accumulation in the liver for the double cholesteryl modified siRNA that correlated with an increase in hepatic Factor VII gene silencing of 28% (rHSA/siRNA) compared to 4% (naked siRNA) 6days post-injection. This work presents a novel albumin-mediated cholesteryl design-based strategy for tuning pharmacokinetics and systemic gene silencing. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. USE OF IMAGE BASED MODELLING FOR DOCUMENTATION OF INTRICATELY SHAPED OBJECTS

    Directory of Open Access Journals (Sweden)

    M. Marčiš

    2016-06-01

    Full Text Available In the documentation of cultural heritage, we can encounter three dimensional shapes and structures which are complicated to measure. Such objects are for example spiral staircases, timber roof trusses, historical furniture or folk costume where it is nearly impossible to effectively use the traditional surveying or the terrestrial laser scanning due to the shape of the object, its dimensions and the crowded environment. The actual methods of digital photogrammetry can be very helpful in such cases with the emphasis on the automated processing of the extensive image data. The created high resolution 3D models and 2D orthophotos are very important for the documentation of architectural elements and they can serve as an ideal base for the vectorization and 2D drawing documentation. This contribution wants to describe the various usage of image based modelling in specific interior spaces and specific objects. The advantages and disadvantages of the photogrammetric measurement of such objects in comparison to other surveying methods are reviewed.

  3. Dual-band plasmonic resonator based on Jerusalem cross-shaped nanoapertures

    Science.gov (United States)

    Cetin, Arif E.; Kaya, Sabri; Mertiri, Alket; Aslan, Ekin; Erramilli, Shyamsunder; Altug, Hatice; Turkmen, Mustafa

    2015-06-01

    In this paper, we both experimentally and numerically introduce a dual-resonant metamaterial based on subwavelength Jerusalem cross-shaped apertures. We numerically investigate the physical origin of the dual-resonant behavior, originating from the constituting aperture elements, through finite difference time domain calculations. Our numerical calculations show that at the dual-resonances, the aperture system supports large and easily accessible local electromagnetic fields. In order to experimentally realize the aperture system, we utilize a high-precision and lift-off free fabrication method based on electron-beam lithography. We also introduce a fine-tuning mechanism for controlling the dual-resonant spectral response through geometrical device parameters. Finally, we show the aperture system's highly advantageous far- and near-field characteristics through numerical calculations on refractive index sensitivity. The quantitative analyses on the availability of the local fields supported by the aperture system are employed to explain the grounds behind the sensitivity of each spectral feature within the dual-resonant behavior. Possessing dual-resonances with large and accessible electromagnetic fields, Jerusalem cross-shaped apertures can be highly advantageous for wide range of applications demanding multiple spectral features with strong nearfield characteristics.

  4. [A novel method based on Y-shaped cotton-polyester thread microfluidic channel].

    Science.gov (United States)

    Wang, Lu; Shi, Yan-ru; Yan, Hong-tao

    2014-08-01

    A novel method based on Y-shaped microfluidic channel was firstly proposed in this study. The microfluidic channel was made of two cotton-polyester threads based on the capillary effect of cotton-polyester threads for the determination solutions. A special device was developed to fix the Y-shaped microfluidic channel by ourselves, through which the length and the tilt angle of the channel can be adjusted as requested. The spectrophotometry was compared with Scan-Adobe Photoshop software processing method. The former had a lower detection limit while the latter showed advantages in both convenience and fast operations and lower amount of samples. The proposed method was applied to the determination of nitrite. The linear ranges and detection limits are 1.0-70 micromol x L(-1), 0.66 micromol x L(-1) (spectrophotometry) and 50-450 micromol x L(-1), 45.10 micromol x L(-1) (Scan-Adobe Photoshop software processing method) respectively. This method has been successfully used to the determination of nitrite in soil samples and moat water with recoveries between 96.7% and 104%. It was proved that the proposed method was a low-cost, rapid and convenient analytical method with extensive application prospect.

  5. Surface inspection system for industrial components based on shape from shading minimization approach

    Science.gov (United States)

    Kotan, Muhammed; Öz, Cemil

    2017-12-01

    An inspection system using estimated three-dimensional (3-D) surface characteristics information to detect and classify the faults to increase the quality control on the frequently used industrial components is proposed. Shape from shading (SFS) is one of the basic and classic 3-D shape recovery problems in computer vision. In our application, we developed a system using Frankot and Chellappa SFS method based on the minimization of the selected basis function. First, the specialized image acquisition system captured the images of the component. To eliminate noise, wavelet transform is applied to the taken images. Then, estimated gradients were used to obtain depth and surface profiles. Depth information was used to determine and classify the surface defects. Also, a comparison made with some linearization-based SFS algorithms was discussed. The developed system was applied to real products and the results indicated that using SFS approaches is useful and various types of defects can easily be detected in a short period of time.

  6. QFT Based Robust Positioning Control of the PMSM Using Automatic Loop Shaping with Teaching Learning Optimization

    Directory of Open Access Journals (Sweden)

    Nitish Katal

    2016-01-01

    Full Text Available Automation of the robust control system synthesis for uncertain systems is of great practical interest. In this paper, the loop shaping step for synthesizing quantitative feedback theory (QFT based controller for a two-phase permanent magnet stepper motor (PMSM has been automated using teaching learning-based optimization (TLBO algorithm. The QFT controller design problem has been posed as an optimization problem and TLBO algorithm has been used to minimize the proposed cost function. This facilitates designing low-order fixed-structure controller, eliminates the need of manual loop shaping step on the Nichols charts, and prevents the overdesign of the controller. A performance comparison of the designed controller has been made with the classical PID tuning method of Ziegler-Nichols and QFT controller tuned using other optimization algorithms. The simulation results show that the designed QFT controller using TLBO offers robust stability, disturbance rejection, and proper reference tracking over a range of PMSM’s parametric uncertainties as compared to the classical design techniques.

  7. Shape-Memory Effect and Pseudoelasticity in Fe-Mn-Based Alloys

    Science.gov (United States)

    La Roca, P.; Baruj, A.; Sade, M.

    2017-03-01

    Several Fe-based alloys are being considered as potential candidates for applications which require shape-memory behavior or superelastic properties. The possibility of using fabrication methods which are well known in the steel industry is very attractive and encourages a large amount of research in the field. In the present article, Fe-Mn-based alloys are mainly addressed. On the one hand, attention is paid to the shape-memory effect where the alloys contain (a) a maximum amount of Mn up to around 30 wt%, (b) several possible substitutional elements like Si, Cr, Ni, Co, and Nb and (c) some possible interstitial elements like C. On the other hand, superelastic alloys are analyzed, mainly the Fe-Mn-Al-Ni system discovered a few years ago. The most noticeable properties resulting from the martensitic transformations which are responsible for the mentioned properties, i.e., the fcc-hcp in the first case and the bcc-fcc in the latter are discussed. Selected potential applications are also analyzed.

  8. Cu-based shape memory alloys with enhanced thermal stability and mechanical properties

    International Nuclear Information System (INIS)

    Chung, C.Y.; Lam, C.W.H.

    1999-01-01

    Cu-based shape memory alloys were developed in the 1960s. They show excellent thermoelastic martensitic transformation. However the problems in mechanical properties and thermal instability have inhibited them from becoming promising engineering alloys. A new Cu-Zn-Al-Mn-Zr Cu-based shape memory alloy has been developed. With the addition of Mn and Zr, the martensitic transformation behaviour and the grain size ca be better controlled. The new alloys demonstrates good mechanical properties with ultimate tensile strenght and ductility, being 460 MPa and 9%, respectively. Experimental results revealed that the alloy has better thermal stability, i.e. martensite stabilisation is less serious. In ordinary Cu-Zn-Al alloys, martensite stabilisation usually occurs at room temperature. The new alloy shows better thermal stability even at elevated temperature (∝150 C, >A f =80 C). A limited small amount of martensite stabilisation was observed upon ageing of the direct quenched samples as well as the step quenched samples. This implies that the thermal stability of the new alloy is less dependent on the quenching procedure. Furthermore, such minor martensite stabilisation can be removed by subsequent suitable parent phase ageing. The new alloy is ideal for engineering applications because of its better thermal stability and better mechanical properties. (orig.)

  9. Broadband reflective multi-polarization converter based on single-layer double-L-shaped metasurface

    Science.gov (United States)

    Mao, Chenyang; Yang, Yang; He, Xiaoxiang; Zheng, Jingming; Zhou, Chun

    2017-12-01

    In this paper, a broadband reflective multi-polarization converter based on single-layer double-L-shaped metasurface is proposed. The proposed metasurface can effectively convert linear-polarized (TE/TM) incident wave into the reflected wave with three different polarizations within the frequency bands of 5.5-22.75 GHz. Based on the electric and magnetic resonant features of the double-L-shaped structure, the proposed metasurface can convert linearly polarized waves into cross-polarized waves at three resonant frequency bands. Furthermore, the incident linearly polarized waves can be effectively converted into left/right handed circular-polarized (LHCP and RHCP) waves at other four non-resonance frequency bands. Thus, the proposed metasurface can be regarded as a seven-band multi-polarization converter. The prototype of the proposed polarization converter is analyzed and measured. Both simulated and measured results show the 3-dB axis ratio bandwidth of circular polarization bands and the high polarization conversion efficiency of cross-polarization bands when the incident wave changes from 0° to 30° at both TE and TM modes.

  10. A Method of Road Extraction from High-resolution Remote Sensing Images Based on Shape Features

    Directory of Open Access Journals (Sweden)

    LEI Xiaoqi

    2016-02-01

    Full Text Available Road extraction from high-resolution remote sensing image is an important and difficult task.Since remote sensing images include complicated information,the methods that extract roads by spectral,texture and linear features have certain limitations.Also,many methods need human-intervention to get the road seeds(semi-automatic extraction,which have the great human-dependence and low efficiency.The road-extraction method,which uses the image segmentation based on principle of local gray consistency and integration shape features,is proposed in this paper.Firstly,the image is segmented,and then the linear and curve roads are obtained by using several object shape features,so the method that just only extract linear roads are rectified.Secondly,the step of road extraction is carried out based on the region growth,the road seeds are automatic selected and the road network is extracted.Finally,the extracted roads are regulated by combining the edge information.In experiments,the images that including the better gray uniform of road and the worse illuminated of road surface were chosen,and the results prove that the method of this study is promising.

  11. A PSF-Shape-Based Beamforming Strategy for Robust 2D Motion Estimation in Ultrafast Data

    Directory of Open Access Journals (Sweden)

    Anne E. C. M. Saris

    2018-03-01

    Full Text Available This paper presents a framework for motion estimation in ultrafast ultrasound data. It describes a novel approach for determining the sampling grid for ultrafast data based on the system’s point-spread-function (PSF. As a consequence, the cross-correlation functions (CCF used in the speckle tracking (ST algorithm will have circular-shaped peaks, which can be interpolated using a 2D interpolation method to estimate subsample displacements. Carotid artery wall motion and parabolic blood flow simulations together with rotating disk experiments using a Verasonics Vantage 256 are used for performance evaluation. Zero-degree plane wave data were acquired using an ATL L5-12 (fc = 9 MHz transducer for a range of pulse repetition frequencies (PRFs, resulting in 0–600 µm inter-frame displacements. The proposed methodology was compared to data beamformed on a conventionally spaced grid, combined with the commonly used 1D parabolic interpolation. The PSF-shape-based beamforming grid combined with 2D cubic interpolation showed the most accurate and stable performance with respect to the full range of inter-frame displacements, both for the assessment of blood flow and vessel wall dynamics. The proposed methodology can be used as a protocolled way to beamform ultrafast data and obtain accurate estimates of tissue motion.

  12. Spliceosomal small nuclear RNAs of Tetrahymena thermophila and some possible snRNA-snRNA base-pairing interactions

    DEFF Research Database (Denmark)

    Orum, H; Nielsen, Henrik; Engberg, J

    1991-01-01

    We have identified and characterized the full set of spliceosomal small nuclear RNAs (snRNAs; U1, U2, U4, U5 and U6) from the ciliated protozoan Tetrahymena thermophila. With the exception of U4 snRNA, the sizes of the T. thermophila snRNAs are closely similar to their metazoan homologues. The T....... thermophila snRNAs all have unique 5' ends, which start with an adenine residue. In contrast, with the exception of U6, their 3' ends show some size heterogeneity. The primary sequences of the T. thermophila snRNAs contain the sequence motifs shown, or proposed, to be of functional importance in other...

  13. Water Extraction in High Resolution Remote Sensing Image Based on Hierarchical Spectrum and Shape Features

    International Nuclear Information System (INIS)

    Li, Bangyu; Zhang, Hui; Xu, Fanjiang

    2014-01-01

    This paper addresses the problem of water extraction from high resolution remote sensing images (including R, G, B, and NIR channels), which draws considerable attention in recent years. Previous work on water extraction mainly faced two difficulties. 1) It is difficult to obtain accurate position of water boundary because of using low resolution images. 2) Like all other image based object classification problems, the phenomena of ''different objects same image'' or ''different images same object'' affects the water extraction. Shadow of elevated objects (e.g. buildings, bridges, towers and trees) scattered in the remote sensing image is a typical noise objects for water extraction. In many cases, it is difficult to discriminate between water and shadow in a remote sensing image, especially in the urban region. We propose a water extraction method with two hierarchies: the statistical feature of spectral characteristic based on image segmentation and the shape feature based on shadow removing. In the first hierarchy, the Statistical Region Merging (SRM) algorithm is adopted for image segmentation. The SRM includes two key steps: one is sorting adjacent regions according to a pre-ascertained sort function, and the other one is merging adjacent regions based on a pre-ascertained merging predicate. The sort step is done one time during the whole processing without considering changes caused by merging which may cause imprecise results. Therefore, we modify the SRM with dynamic sort processing, which conducts sorting step repetitively when there is large adjacent region changes after doing merging. To achieve robust segmentation, we apply the merging region with six features (four remote sensing image bands, Normalized Difference Water Index (NDWI), and Normalized Saturation-value Difference Index (NSVDI)). All these features contribute to segment image into region of object. NDWI and NSVDI are discriminate between water and

  14. Injury Reduction Effectiveness of Prescribing Running Shoes Based on Foot Shape in Air Force Basic Military Training

    National Research Council Canada - National Science Library

    Knapik, Joseph J; Brosch, Lorie C; Venuto, Margaret; Swedler, David I; Bullock, Steven H; Gaines, Lorraine S; Murphy, Ryan J; Canada, Sara E; Hoedebecke, Edward L; Tobler, Steven K

    2008-01-01

    In response to a request from the Military Training Task Force of the Defense Safety Oversight Council this study examined whether prescribing running shoes based on the shape of the plantar surface...

  15. Classification and energetics of the base-phosphate interactions in RNA

    Czech Academy of Sciences Publication Activity Database

    Zirbel, C.L.; Šponer, Judit E.; Šponer, Jiří; Stombaugh, J.; Leontis, N.B.

    2009-01-01

    Roč. 37, č. 15 (2009), s. 4898-4918 ISSN 0305-1048 R&D Projects: GA AV ČR(CZ) IAA400550701; GA AV ČR(CZ) IAA400040802; GA AV ČR(CZ) 1QS500040581; GA MŠk(CZ) LC06030 Grant - others:GA ČR(CZ) GA203/09/1476 Program:GA Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : RNA * base * phosphate Subject RIV: BO - Biophysics Impact factor: 7.479, year: 2009

  16. Substrate-Based Noble-Metal Nanomaterials: Shape Engineering and Applications

    Science.gov (United States)

    Hajfathalian, Maryam

    Nanostructures have potential for use in state-of-the-art applications such as sensing, imaging, therapeutics, drug delivery, and electronics. The ability to fabricate and engineer these nanoscale materials is essential for the continued development of such devices. Because the morphological features of nanomaterials play a key role in determining chemical and physical properties, there is great interest in developing and improving methods capable of controlling their size, shape, and composition. While noble nanoparticles have opened the door to promising applications in fields such as imaging, cancer targeting, photothermal treatment, drug delivery, catalysis and sensing, the synthetic processes required to form these nanoparticles on surfaces are not well-developed. Herein is a detailed account on efforts for adapting established solution-based seed-mediated synthetic protocols to structure in a substrate-based platform. These syntheses start by (i) defining heteroepitaxially oriented nanostructured seeds at site-specific locations using lithographic or directed-assembly techniques, and then (ii) transforming the seeds using either a solution or vapor phase processing route to activate kinetically- or thermodynamically-driven growth modes, to arrive at nanocrystals with complex and useful geometries. The first series of investigations highlight synthesis-routes based on heterogeneous nucleation, where templates serve as nucleation sites for metal atoms arriving in the vapor phase. In the first research direction, the vapor-phase heterogeneous nucleation of Ag on Au was carried out at high temperatures, where the Ag vapor was sourced from a sublimating foil onto adjacent Au templates. This process transformed both the composition and morphology of the initial Au Wulff-shaped nanocrystals to a homogeneous AuAg nanoprism. In the second case, the vapor-phase heterogeneous nucleation of Cu atoms on Au nanocrystal templates was investigated by placing a Cu foil next

  17. 3D base: a geometrical data base system for the analysis and visualisation of 3D-shapes obtained from parallel serial sections including three different geometrical representations

    NARCIS (Netherlands)

    Verbeek, F. J.; de Groot, M. M.; Huijsmans, D. P.; Lamers, W. H.; Young, I. T.

    1993-01-01

    In this paper we discuss a geometrical data base that includes three different geometrical representations of one and the same reconstructed 3D shape: the contour-pile, the voxel enumeration, and the triangulation of a surface. The data base is tailored for 3D shapes obtained from plan-parallel

  18. Design and analysis of a MEMS-based bifurcate-shape piezoelectric energy harvester

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Yuan; Gan, Ruyi, E-mail: 2471390146@qq.com; Wan, Shalang; Xu, Ruilin; Zhou, Hanxing [Chongqing Municipal Level Key Laboratory of Photoelectronic Information Sensing and Transmitting Technology, Chongqing University of Posts and Telecommunications, 400065, Chongqing, Chongqing Municipality (China)

    2016-04-15

    This paper presents a novel piezoelectric energy harvester, which is a MEMS-based device. This piezoelectric energy harvester uses a bifurcate-shape. The derivation of the mathematical modeling is based on the Euler-Bernoulli beam theory, and the main mechanical and electrical parameters of this energy harvester are analyzed and simulated. The experiment result shows that the maximum output voltage can achieve 3.3 V under an acceleration of 1 g at 292.11 Hz of frequency, and the output power can be up to 0.155 mW under the load of 0.4 MΩ. The power density is calculated as 496.79 μWmm{sup −3}. Besides that, it is demonstrated efficiently at output power and voltage and adaptively in practical vibration circumstance. This energy harvester could be used for low-power electronic devices.

  19. Design and analysis of a MEMS-based bifurcate-shape piezoelectric energy harvester

    Directory of Open Access Journals (Sweden)

    Yuan Luo

    2016-04-01

    Full Text Available This paper presents a novel piezoelectric energy harvester, which is a MEMS-based device. This piezoelectric energy harvester uses a bifurcate-shape. The derivation of the mathematical modeling is based on the Euler-Bernoulli beam theory, and the main mechanical and electrical parameters of this energy harvester are analyzed and simulated. The experiment result shows that the maximum output voltage can achieve 3.3V under an acceleration of 1g at 292.11Hz of frequency, and the output power can be up to 0.155mW under the load of 0.4MΩ. The power density is calculated as 496.79μWmm−3. Besides that, it is demonstrated efficiently at output power and voltage and adaptively in practical vibration circumstance. This energy harvester could be used for low-power electronic devices.

  20. Shape memory alloy-based small crawling robots inspired by C. elegans

    Energy Technology Data Exchange (ETDEWEB)

    Yuk, Hyunwoo; Kim, Daeyeon; Shin, Jennifer H [Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon (Korea, Republic of); Lee, Honggu; Jo, Sungho, E-mail: shjo@kaist.ac.kr, E-mail: j_shin@kaist.ac.kr [Department of Computer Science, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon (Korea, Republic of)

    2011-12-15

    Inspired by its simple musculature, actuation and motion mechanisms, we have developed a small crawling robot that closely mimics the model organism of our choice: Caenorhabditis elegans. A thermal shape memory alloy (SMA) was selected as an actuator due to the similarities of its properties to C. elegans muscles. Based on the anatomy of C. elegans, a 12-unit robot was designed to generate a sinusoidal undulating motion. Each body unit consisting of a pair of SMA actuators is serially connected by rigid links with an embedded motion control circuit. A simple binary operation-based motion control mechanism was implemented using a microcontroller. The assembled robot can execute C. elegans-like motion with a 0.17 Hz undulation frequency. Its motion is comparable to that of a real worm.

  1. Coupled stress-strain and electrical resistivity measurements on copper based shape memory single crystals

    Directory of Open Access Journals (Sweden)

    Gonzalez Cezar Henrique

    2004-01-01

    Full Text Available Recently, electrical resistivity (ER measurements have been done during some thermomechanical tests in copper based shape memory alloys (SMA's. In this work, single crystals of Cu-based SMA's have been studied at different temperatures to analyse the relationship between stress (s and ER changes as a function of the strain (e. A good consistency between ER change values is observed in different experiments: thermal martensitic transformation, stress induced martensitic transformation and stress induced reorientation of martensite variants. During stress induced martensitic transformation (superelastic behaviour and stress induced reorientation of martensite variants, a linear relationship is obtained between ER and strain as well as the absence of hys teresis. In conclusion, the present results show a direct evidence of martensite electrical resistivity anisotropy.

  2. Human disease MiRNA inference by combining target information based on heterogeneous manifolds.

    Science.gov (United States)

    Ding, Pingjian; Luo, Jiawei; Liang, Cheng; Xiao, Qiu; Cao, Buwen

    2018-04-01

    The emergence of network medicine has provided great insight into the identification of disease-related molecules, which could help with the development of personalized medicine. However, the state-of-the-art methods could neither simultaneously consider target information and the known miRNA-disease associations nor effectively explore novel gene-disease associations as a by-product during the process of inferring disease-related miRNAs. Computational methods incorporating multiple sources of information offer more opportunities to infer disease-related molecules, including miRNAs and genes in heterogeneous networks at a system level. In this study, we developed a novel algorithm, named inference of Disease-related MiRNAs based on Heterogeneous Manifold (DMHM), to accurately and efficiently identify miRNA-disease associations by integrating multi-omics data. Graph-based regularization was utilized to obtain a smooth function on the data manifold, which constitutes the main principle of DMHM. The novelty of this framework lies in the relatedness between diseases and miRNAs, which are measured via heterogeneous manifolds on heterogeneous networks integrating target information. To demonstrate the effectiveness of DMHM, we conducted comprehensive experiments based on HMDD datasets and compared DMHM with six state-of-the-art methods. Experimental results indicated that DMHM significantly outperformed the other six methods under fivefold cross validation and de novo prediction tests. Case studies have further confirmed the practical usefulness of DMHM. Copyright © 2018 Elsevier Inc. All rights reserved.

  3. Tuning iteration space slicing based tiled multi-core code implementing Nussinov's RNA folding.

    Science.gov (United States)

    Palkowski, Marek; Bielecki, Wlodzimierz

    2018-01-15

    RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology. Fortunately, RNA secondary structure approaches, such as Nussinov's recurrence, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. This allows us to apply powerful polyhedral compilation techniques based on the transitive closure of dependence graphs to generate parallel tiled code implementing Nussinov's RNA folding. Such techniques are within the iteration space slicing framework - the transitive dependences are applied to the statement instances of interest to produce valid tiles. The main problem at generating parallel tiled code is defining a proper tile size and tile dimension which impact parallelism degree and code locality. To choose the best tile size and tile dimension, we first construct parallel parametric tiled code (parameters are variables defining tile size). With this purpose, we first generate two nonparametric tiled codes with different fixed tile sizes but with the same code structure and then derive a general affine model, which describes all integer factors available in expressions of those codes. Using this model and known integer factors present in the mentioned expressions (they define the left-hand side of the model), we find unknown integers in this model for each integer factor available in the same fixed tiled code position and replace in this code expressions, including integer factors, with those including parameters. Then we use this parallel parametric tiled code to implement the well-known tile size selection (TSS) technique, which allows us to discover in a given search space the best tile size and tile dimension maximizing target code performance. For a given search space, the presented approach allows us to choose the best tile size and tile dimension in

  4. Controlling the Size and Shape of the Elastin-Like Polypeptide based Micelles

    Science.gov (United States)

    Streletzky, Kiril; Shuman, Hannah; Maraschky, Adam; Holland, Nolan

    Elastin-like polypeptide (ELP) trimer constructs make reliable environmentally responsive micellar systems because they exhibit a controllable transition from being water-soluble at low temperatures to aggregating at high temperatures. It has been shown that depending on the specific details of the ELP design (length of the ELP chain, pH and salt concentration) micelles can vary in size and shape between spherical micelles with diameter 30-100 nm to elongated particles with an aspect ratio of about 10. This makes ELP trimers a convenient platform for developing potential drug delivery and bio-sensing applications as well as for understanding micelle formation in ELP systems. Since at a given salt concentration, the headgroup area for each foldon should be constant, the size of the micelles is expected to be proportional to the volume of the linear ELP available per foldon headgroup. Therefore, adding linear ELPs to a system of ELP-foldon should result in changes of the micelle volume allowing to control micelle size and possibly shape. The effects of addition of linear ELPs on size, shape, and molecular weight of micelles at different salt concentrations were studied by a combination of Dynamic Light Scattering and Static Light Scattering. The initial results on 50 µM ELP-foldon samples (at low salt) show that Rh of mixed micelles increases more than 5-fold as the amount of linear ELP raised from 0 to 50 µM. It was also found that a given mixture of linear and trimer constructs has two temperature-based transitions and therefore displays three predominant size regimes.

  5. Fourier-based quantification of renal glomeruli size using Hough transform and shape descriptors.

    Science.gov (United States)

    Najafian, Sohrab; Beigzadeh, Borhan; Riahi, Mohammad; Khadir Chamazkoti, Fatemeh; Pouramir, Mahdi

    2017-11-01

    Analysis of glomeruli geometry is important in histopathological evaluation of renal microscopic images. Due to the shape and size disparity of even glomeruli of same kidney, automatic detection of these renal objects is not an easy task. Although manual measurements are time consuming and at times are not very accurate, it is commonly used in medical centers. In this paper, a new method based on Fourier transform following usage of some shape descriptors is proposed to detect these objects and their geometrical parameters. Reaching the goal, a database of 400 regions are selected randomly. 200 regions of which are part of glomeruli and the other 200 regions are not belong to renal corpuscles. ROC curve is used to decide which descriptor could classify two groups better. f_measure, which is a combination of both tpr (true positive rate) and fpr (false positive rate), is also proposed to select optimal threshold for descriptors. Combination of three parameters (solidity, eccentricity, and also mean squared error of fitted ellipse) provided better result in terms of f_measure to distinguish desired regions. Then, Fourier transform of outer edges is calculated to form a complete curve out of separated region(s). The generality of proposed model is verified by use of cross validation method, which resulted tpr of 94%, and fpr of 5%. Calculation of glomerulus' and Bowman's space with use of the algorithm are also compared with a non-automatic measurement done by a renal pathologist, and errors of 5.9%, 5.4%, and 6.26% are resulted in calculation of Capsule area, Bowman space, and glomeruli area, respectively. Having tested different glomeruli with various shapes, the experimental consequences show robustness and reliability of our method. Therefore, it could be used to illustrate renal diseases and glomerular disorders by measuring the morphological changes accurately and expeditiously. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. A Regions of Confidence Based Approach to Enhance Segmentation with Shape Priors.

    Science.gov (United States)

    Appia, Vikram V; Ganapathy, Balaji; Abufadel, Amer; Yezzi, Anthony; Faber, Tracy

    2010-01-18

    We propose an improved region based segmentation model with shape priors that uses labels of confidence/interest to exclude the influence of certain regions in the image that may not provide useful information for segmentation. These could be regions in the image which are expected to have weak, missing or corrupt edges or they could be regions in the image which the user is not interested in segmenting, but are part of the object being segmented. In the training datasets, along with the manual segmentations we also generate an auxiliary map indicating these regions of low confidence/interest. Since, all the training images are acquired under similar conditions, we can train our algorithm to estimate these regions as well. Based on this training we will generate a map which indicates the regions in the image that are likely to contain no useful information for segmentation. We then use a parametric model to represent the segmenting curve as a combination of shape priors obtained by representing the training data as a collection of signed distance functions. We evolve an objective energy functional to evolve the global parameters that are used to represent the curve. We vary the influence each pixel has on the evolution of these parameters based on the confidence/interest label. When we use these labels to indicate the regions with low confidence; the regions containing accurate edges will have a dominant role in the evolution of the curve and the segmentation in the low confidence regions will be approximated based on the training data. Since our model evolves global parameters, it improves the segmentation even in the regions with accurate edges. This is because we eliminate the influence of the low confidence regions which may mislead the final segmentation. Similarly when we use the labels to indicate the regions which are not of importance, we will get a better segmentation of the object in the regions we are interested in.

  7. Thermo-mechanical properties of polystyrene-based shape memory nanocomposites

    NARCIS (Netherlands)

    Xu, B.; Fu, Y.Q.; Ahmad, M.; Luo, J.K.; Huang, W.M.; Kraft, A.; Reuben, R.; Pei, Y.T.; Chen, Zhenguo; Hosson, J.Th.M. De

    2010-01-01

    Shape memory nanocomposites were fabricated using chemically cross-linked polystyrene (PS) copolymer as a matrix and different nanofillers (including alumina, silica and clay) as the reinforcing agents. Their thermo-mechanical properties and shape memory effects were characterized. Experimental

  8. Prostate segmentation in MRI using a convolutional neural network architecture and training strategy based on statistical shape models.

    Science.gov (United States)

    Karimi, Davood; Samei, Golnoosh; Kesch, Claudia; Nir, Guy; Salcudean, Septimiu E

    2018-05-15

    Most of the existing convolutional neural network (CNN)-based medical image segmentation methods are based on methods that have originally been developed for segmentation of natural images. Therefore, they largely ignore the differences between the two domains, such as the smaller degree of variability in the shape and appearance of the target volume and the smaller amounts of training data in medical applications. We propose a CNN-based method for prostate segmentation in MRI that employs statistical shape models to address these issues. Our CNN predicts the location of the prostate center and the parameters of the shape model, which determine the position of prostate surface keypoints. To train such a large model for segmentation of 3D images using small data (1) we adopt a stage-wise training strategy by first training the network to predict the prostate center and subsequently adding modules for predicting the parameters of the shape model and prostate rotation, (2) we propose a data augmentation method whereby the training images and their prostate surface keypoints are deformed according to the displacements computed based on the shape model, and (3) we employ various regularization techniques. Our proposed method achieves a Dice score of 0.88, which is obtained by using both elastic-net and spectral dropout for regularization. Compared with a standard CNN-based method, our method shows significantly better segmentation performance on the prostate base and apex. Our experiments also show that data augmentation using the shape model significantly improves the segmentation results. Prior knowledge about the shape of the target organ can improve the performance of CNN-based segmentation methods, especially where image features are not sufficient for a precise segmentation. Statistical shape models can also be employed to synthesize additional training data that can ease the training of large CNNs.

  9. New Atrophic Acne Scar Classification: Reliability of Assessments Based on Size, Shape, and Number.

    Science.gov (United States)

    Kang, Sewon; Lozada, Vicente Torres; Bettoli, Vincenzo; Tan, Jerry; Rueda, Maria Jose; Layton, Alison; Petit, Lauren; Dréno, Brigitte

    2016-06-01

    Post-acne atrophic scarring is a major concern for which standardized outcome measures are needed. Traditionally, this type of scar has been classified based on shape; but survey of practicing dermatologists has shown that atrophic scar morphology has not been well enough defined to allow good agreement in clinical classification. Reliance on clinical assessment is still needed at the current time, since objective tools are not yet available in routine practice. Evaluate classification for atrophic acne scars by shape, size, and facial location and establish reliability in assessments. We conducted a non-interventional study with dermatologists performing live clinical assessments of atrophic acne scars. To objectively compare identification of lesions, individual lesions were marked on a high-resolution photo of the patient that was displayed on a computer during the clinical evaluation. The Jacob clinical classification system was used to define three primary shapes of scars 1) icepick, 2) boxcar, and 3) rolling. To determine agreement for classification by size, independent technicians assessed the investigators' markings on digital images. Identical localization of scars was denoted if the maximal distance between their centers was ≤ 60 pixels (approximately 3 mm). Raters assessed scars on the same patients twice (morning/afternoon). Aggregate models of rater assessments were created and analyzed for agreement. Raters counted a mean scar count per subject ranging from 15.75 to 40.25 scars. Approximately 50% of scars were identified by all raters and ~75% of scars were identified by at least 2 of 3 raters (weak agreement, Kappa pairwise agreement 0.30). Agreement between consecutive counts was moderate, with Kappa index ranging from 0.26 to 0.47 (after exclusion of one outlier investigator who had significantly higher counts than all others). Shape classifications of icepick, boxcar, and rolling differed significantly between raters and even for same raters at

  10. Reversible Modulation of DNA-Based Hydrogel Shapes by Internal Stress Interactions.

    Science.gov (United States)

    Hu, Yuwei; Kahn, Jason S; Guo, Weiwei; Huang, Fujian; Fadeev, Michael; Harries, Daniel; Willner, Itamar

    2016-12-14

    We present the assembly of asymmetric two-layer hybrid DNA-based hydrogels revealing stimuli-triggered reversibly modulated shape transitions. Asymmetric, linear hydrogels that include layer-selective switchable stimuli-responsive elements that control the hydrogel stiffness are designed. Trigger-induced stress in one of the layers results in the bending of the linear hybrid structure, thereby minimizing the elastic free energy of the systems. The removal of the stress by a counter-trigger restores the original linear bilayer hydrogel. The stiffness of the DNA hydrogel layers is controlled by thermal, pH (i-motif), K + ion/crown ether (G-quadruplexes), chemical (pH-doped polyaniline), or biocatalytic (glucose oxidase/urease) triggers. A theoretical model relating the experimental bending radius of curvatures of the hydrogels with the Young's moduli and geometrical parameters of the hydrogels is provided. Promising applications of shape-regulated stimuli-responsive asymmetric hydrogels include their use as valves, actuators, sensors, and drug delivery devices.

  11. Pulse width modulation-based temperature tracking for feedback control of a shape memory alloy actuator.

    Science.gov (United States)

    Ayvali, Elif; Desai, Jaydev P

    2014-04-01

    This work presents a temperature-feedback approach to control the radius of curvature of an arc-shaped shape memory alloy (SMA) wire. The nonlinear properties of the SMA such as phase transformation and its dependence on temperature and stress make SMA actuators difficult to control. Tracking a desired trajectory is more challenging than controlling just the position of the SMA actuator since the desired path is continuously changing. Consequently, tracking the desired strain directly or tracking the parameters such as temperature and electrical resistance that are related to strain with a model is a challenging task. Temperature-feedback is an attractive approach when direct measurement of strain is not practical. Pulse width modulation (PWM) is an effective method for SMA actuation and it can be used along with a compensator to control the temperature of the SMA. Using the constitutive model of the SMA, the desired temperature profile can be obtained for a given strain trajectory. A PWM-based nonlinear PID controller with a feed-forward heat transfer model is proposed to use temperature-feedback for tracking a desired temperature trajectory. The proposed controller is used during the heating phase of the SMA actuator. The controller proves to be effective in tracking step-wise and continuous trajectories.

  12. Shape-Tailorable Graphene-Based Ultra-High-Rate Supercapacitor for Wearable Electronics.

    Science.gov (United States)

    Xie, Binghe; Yang, Cheng; Zhang, Zhexu; Zou, Peichao; Lin, Ziyin; Shi, Gaoquan; Yang, Quanhong; Kang, Feiyu; Wong, Ching-Ping

    2015-06-23

    With the bloom of wearable electronics, it is becoming necessary to develop energy storage units, e.g., supercapacitors that can be arbitrarily tailored at the device level. Although gel electrolytes have been applied in supercapacitors for decades, no report has studied the shape-tailorable capability of a supercapacitor, for instance, where the device still works after being cut. Here we report a tailorable gel-based supercapacitor with symmetric electrodes prepared by combining electrochemically reduced graphene oxide deposited on a nickel nanocone array current collector with a unique packaging method. This supercapacitor with good flexibility and consistency showed excellent rate performance, cycling stability, and mechanical properties. As a demonstration, these tailorable supercapacitors connected in series can be used to drive small gadgets, e.g., a light-emitting diode (LED) and a minimotor propeller. As simple as it is (electrochemical deposition, stencil printing, etc.), this technique can be used in wearable electronics and miniaturized device applications that require arbitrarily shaped energy storage units.

  13. Fast protein tertiary structure retrieval based on global surface shape similarity.

    Science.gov (United States)

    Sael, Lee; Li, Bin; La, David; Fang, Yi; Ramani, Karthik; Rustamov, Raif; Kihara, Daisuke

    2008-09-01

    Characterization and identification of similar tertiary structure of proteins provides rich information for investigating function and evolution. The importance of structure similarity searches is increasing as structure databases continue to expand, partly due to the structural genomics projects. A crucial drawback of conventional protein structure comparison methods, which compare structures by their main-chain orientation or the spatial arrangement of secondary structure, is that a database search is too slow to be done in real-time. Here we introduce a global surface shape representation by three-dimensional (3D) Zernike descriptors, which represent a protein structure compactly as a series expansion of 3D functions. With this simplified representation, the search speed against a few thousand structures takes less than a minute. To investigate the agreement between surface representation defined by 3D Zernike descriptor and conventional main-chain based representation, a benchmark was performed against a protein classification generated by the combinatorial extension algorithm. Despite the different representation, 3D Zernike descriptor retrieved proteins of the same conformation defined by combinatorial extension in 89.6% of the cases within the top five closest structures. The real-time protein structure search by 3D Zernike descriptor will open up new possibility of large-scale global and local protein surface shape comparison. 2008 Wiley-Liss, Inc.

  14. Shape Memory Properties and Enzymatic Degradability of Poly(ε-caprolactone)-Based Polyurethane Urea Containing Phenylalanine-Derived Chain Extender.

    Science.gov (United States)

    Wang, Rong; Zhang, Fanjun; Lin, Weiwei; Liu, Wenkai; Li, Jiehua; Luo, Feng; Wang, Yaning; Tan, Hong

    2018-04-24

    Biodegradable shape memory polymers are promising biomaterials for minimally invasive surgical procedures. Herein, a series of linear biodegradable shape memory poly(ε-caprolactone) (PCL)-based polyurethane ureas (PUUs) containing a novel phenylalanine-derived chain extender is synthesized. The phenylalanine-derived chain extender, phenylalanine-hexamethylenediamine-phenylalanine (PHP), contains two chymotrypsin cleaving sites to enhance the enzymatic degradation of PUUs. The degradation rate, the crystallinity, and mechanical properties of PUUs are tailored by the content of PHP. Meanwhile, semicrystalline PCL is not only hydrolytically degradable but also vital for shape memory. Good shape memory ability under body temperature is achieved for PUUs due to the strong interactions in hard segments for permanent crosslinking and the crystallization-melt transition of PCL to switch temporary shape. The PUUs would have a great potential in application as implanting stent. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Quantitative evaluation of changes in eyeball shape in emmetropization and myopic changes based on elliptic fourier descriptors.

    Science.gov (United States)

    Ishii, Kotaro; Iwata, Hiroyoshi; Oshika, Tetsuro

    2011-11-04

    To evaluate changes in eyeball shape in emmetropization and myopic changes using magnetic resonance imaging (MRI) and elliptic Fourier descriptors (EFDs). The subjects were 105 patients (age range, 1 month-19 years) who underwent head MRI. The refractive error was determined in 30 patients, and eyeball shape was expressed numerically by principal components analysis of standardized EFDs. In the first principal component (PC1; the oblate-to-prolate change), the proportion of variance/total variance in the development of the eyeball shape was 76%. In all subjects, PC1 showed a significant correlation with age (Pearson r = -0.314; P = 0.001), axial length (AL, r = -0.378; P eyeball shape from oblate to prolate was clarified by quantitative analysis based on EFDs. The results showed clear differences between age groups with regard to changes in the shape of the eyeball, the correlation between these changes, and refractive status changes.

  16. Impaired capacity of cerebellar patients to perceive and learn two-dimensional shapes based on kinesthetic cues.

    Science.gov (United States)

    Shimansky, Y; Saling, M; Wunderlich, D A; Bracha, V; Stelmach, G E; Bloedel, J R

    1997-01-01

    This study addresses the issue of the role of the cerebellum in the processing of sensory information by determining the capability of cerebellar patients to acquire and use kinesthetic cues received via the active or passive tracing of an irregular shape while blindfolded. Patients with cerebellar lesions and age-matched healthy controls were tested on four tasks: (1) learning to discriminate a reference shape from three others through the repeated tracing of the reference template; (2) reproducing the reference shape from memory by drawing blindfolded; (3) performing the same task with vision; and (4) visually recognizing the reference shape. The cues used to acquire and then to recognize the reference shape were generated under four conditions: (1) "active kinesthesia," in which cues were acquired by the blindfolded subject while actively tracing a reference template; (2) "passive kinesthesia," in which the tracing was performed while the hand was guided passively through the template; (3) "sequential vision," in which the shape was visualized by the serial exposure of small segments of its outline; and (4) "full vision," in which the entire shape was visualized. The sequential vision condition was employed to emulate the sequential way in which kinesthetic information is acquired while tracing the reference shape. The results demonstrate a substantial impairment of cerebellar patients in their capability to perceive two-dimensional irregular shapes based only on kinesthetic cues. There also is evidence that this deficit in part relates to a reduced capacity to integrate temporal sequences of sensory cues into a complete image useful for shape discrimination tasks or for reproducing the shape through drawing. Consequently, the cerebellum has an important role in this type of sensory information processing even when it is not directly associated with the execution of movements.

  17. Tadpole-Shaped POSS-Based Copolymers and the Aggregation Behavior at Air/Water Interface

    Directory of Open Access Journals (Sweden)

    Lin Zhu

    2018-01-01

    Full Text Available The aggregation behavior of three tadpole-shaped Polyhedral oligomeric silsesquioxane (POSS based block copolymers using different blocks poly(methyl methacrylate (PMMA and poly(trifluoroethyl methacrylate (PTFEMA with different block sequence and ratio (POSS-PTFEMA161-b-PMMA236, POSS-PMMA277-b-PTFEMA130, and POSS-PMMA466-b-PTFEMA172 was investigated on the air-water interface. The interfacial rheology of three block copolymers was studied by surface pressure isotherm, compression modulus measurements, and compression and expansion hysteresis analysis on the Langmuir trough. The block sequence and ratio play a great role in self-assembly behavior at the interface. Based on surface pressure isotherm analysis, a thin film with low elasticity was achieved for the POSS-PTFEMA161-b-PMMA236. Moreover, for the block copolymer with same segment sequence (POSS-PMMA2-b-PTFEMA, the thin film compression capability is increased with increasing the PMMA ratio. The morphology of the deposited LB thin film was illustrated by atomic force microscopy (AFM and X-ray photoelectron spectroscopy (XPS. We observed that a thin film was composed by crater-shaped quasi-2D micelles for POSS-PTFEMA-b-PMMA, while it was proved that only flaky texture was observed for both POSS-PMMA277-b-PTFEMA130 and POSS-PMMA466-b-PTFEMA172. The thickness and area of flaky aggregates were greatly related to PMMA ratio. The different interface self-assembly structure evolution was proposed based on the interfacial rheology and thin film morphology studies.

  18. Sorting live stem cells based on Sox2 mRNA expression.

    Directory of Open Access Journals (Sweden)

    Hans M Larsson

    Full Text Available While cell sorting usually relies on cell-surface protein markers, molecular beacons (MBs offer the potential to sort cells based on the presence of any expressed mRNA and in principle could be extremely useful to sort rare cell populations from primary isolates. We show here how stem cells can be purified from mixed cell populations by sorting based on MBs. Specifically, we designed molecular beacons targeting Sox2, a well-known stem cell marker for murine embryonic (mES and neural stem cells (NSC. One of our designed molecular beacons displayed an increase in fluorescence compared to a nonspecific molecular beacon both in vitro and in vivo when tested in mES and NSCs. We sorted Sox2-MB(+SSEA1(+ cells from a mixed population of 4-day retinoic acid-treated mES cells and effectively isolated live undifferentiated stem cells. Additionally, Sox2-MB(+ cells isolated from primary mouse brains were sorted and generated neurospheres with higher efficiency than Sox2-MB(- cells. These results demonstrate the utility of MBs for stem cell sorting in an mRNA-specific manner.

  19. Model-based design of RNA hybridization networks implemented in living cells.

    Science.gov (United States)

    Rodrigo, Guillermo; Prakash, Satya; Shen, Shensi; Majer, Eszter; Daròs, José-Antonio; Jaramillo, Alfonso

    2017-09-19

    Synthetic gene circuits allow the behavior of living cells to be reprogrammed, and non-coding small RNAs (sRNAs) are increasingly being used as programmable regulators of gene expression. However, sRNAs (natural or synthetic) are generally used to regulate single target genes, while complex dynamic behaviors would require networks of sRNAs regulating each other. Here, we report a strategy for implementing such networks that exploits hybridization reactions carried out exclusively by multifaceted sRNAs that are both targets of and triggers for other sRNAs. These networks are ultimately coupled to the control of gene expression. We relied on a thermodynamic model of the different stable conformational states underlying this system at the nucleotide level. To test our model, we designed five different RNA hybridization networks with a linear architecture, and we implemented them in Escherichia coli. We validated the network architecture at the molecular level by native polyacrylamide gel electrophoresis, as well as the network function at the bacterial population and single-cell levels with a fluorescent reporter. Our results suggest that it is possible to engineer complex cellular programs based on RNA from first principles. Because these networks are mainly based on physical interactions, our designs could be expanded to other organisms as portable regulatory resources or to implement biological computations. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Direct RNA-based detection of CTX-M β-lactamases in human blood samples.

    Science.gov (United States)

    Stein, Claudia; Makarewicz, Oliwia; Pfeifer, Yvonne; Brandt, Christian; Pletz, Mathias W

    2015-05-01

    Bloodstream infections with ESBL-producers are associated with increased mortality, which is due to delayed appropriate treatment resulting in clinical failure. Current routine diagnostics for detection of bloodstream infections consists of blood culture followed by species identification and susceptibility testing. In attempts to improve and accelerate diagnostic procedures, PCR-based methods have been developed. These methods focus on species identification covering only a limited number of ESBL coding genes. Therefore, they fail to cover the steadily further evolving genetic diversity of clinically relevant β-lactamases. We have recently designed a fast and novel RNA targeting method to detect and specify CTX-M alleles from bacterial cultures, based on an amplification-pyrosequencing approach. We further developed this assay towards a diagnostic tool for clinical use and evaluated its sensitivity and specificity when applied directly to human blood samples. An optimized protocol for mRNA isolation allows detection of specific CTX-M groups from as little as 100 CFU/mL blood via reverse transcription, amplification, and pyrosequencing directly from human EDTA blood samples as well as from pre-incubated human blood cultures with a turnaround time for test results of <7 h. Copyright © 2015 Elsevier GmbH. All rights reserved.

  1. RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.

    Science.gov (United States)

    Orenstein, Yaron; Wang, Yuhao; Berger, Bonnie

    2016-06-15

    Protein-RNA interactions, which play vital roles in many processes, are mediated through both RNA sequence and structure. CLIP-based methods, which measure protein-RNA binding in vivo, suffer from experimental noise and systematic biases, whereas in vitro experiments capture a clearer signal of protein RNA-binding. Among them, RNAcompete provides binding affinities of a specific protein to more than 240 000 unstructured RNA probes in one experiment. The computational challenge is to infer RNA structure- and sequence-based binding models from these data. The state-of-the-art in sequence models, Deepbind, does not model structural preferences. RNAcontext models both sequence and structure preferences, but is outperformed by GraphProt. Unfortunately, GraphProt cannot detect structural preferences from RNAcompete data due to the unstructured nature of the data, as noted by its developers, nor can it be tractably run on the full RNACompete dataset. We develop RCK, an efficient, scalable algorithm that infers both sequence and structure preferences based on a new k-mer based model. Remarkably, even though RNAcompete data is designed to be unstructured, RCK can still learn structural preferences from it. RCK significantly outperforms both RNAcontext and Deepbind in in vitro binding prediction for 244 RNAcompete experiments. Moreover, RCK is also faster and uses less memory, which enables scalability. While currently on par with existing methods in in vivo binding prediction on a small scale test, we demonstrate that RCK will increasingly benefit from experimentally measured RNA structure profiles as compared to computationally predicted ones. By running RCK on the entire RNAcompete dataset, we generate and provide as a resource a set of protein-RNA structure-based models on an unprecedented scale. Software and models are freely available at http://rck.csail.mit.edu/ bab@mit.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by

  2. p53 shapes genome-wide and cell type-specific changes in microRNA expression during the human DNA damage response.

    Science.gov (United States)

    Hattori, Hiroyoshi; Janky, Rekin's; Nietfeld, Wilfried; Aerts, Stein; Madan Babu, M; Venkitaraman, Ashok R

    2014-01-01

    The human DNA damage response (DDR) triggers profound changes in gene expression, whose nature and regulation remain uncertain. Although certain micro-(mi)RNA species including miR34, miR-18, miR-16 and miR-143 have been implicated in the DDR, there is as yet no comprehensive description of genome-wide changes in the expression of miRNAs triggered by DNA breakage in human cells. We have used next-generation sequencing (NGS), combined with rigorous integrative computational analyses, to describe genome-wide changes in the expression of miRNAs during the human DDR. The changes affect 150 of 1523 miRNAs known in miRBase v18 from 4-24 h after the induction of DNA breakage, in cell-type dependent patterns. The regulatory regions of the most-highly regulated miRNA species are enriched in conserved binding sites for p53. Indeed, genome-wide changes in miRNA expression during the DDR are markedly altered in TP53-/- cells compared to otherwise isogenic controls. The expression levels of certain damage-induced, p53-regulated miRNAs in cancer samples correlate with patient survival. Our work reveals genome-wide and cell type-specific alterations in miRNA expression during the human DDR, which are regulated by the tumor suppressor protein p53. These findings provide a genomic resource to identify new molecules and mechanisms involved in the DDR, and to examine their role in tumor suppression and the clinical outcome of cancer patients.

  3. The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli

    Science.gov (United States)

    Beisel, Chase L.; Storz, Gisela

    2011-01-01

    SUMMARY Bacteria selectively consume some carbon sources over others through a regulatory mechanism termed catabolite repression. Here, we show that the base pairing RNA Spot 42 plays a broad role in catabolite repression in Escherichia coli by directly repressing genes involved in central and secondary metabolism, redox balancing, and the consumption of diverse non-preferred carbon sources. Many of the genes repressed by Spot 42 are transcriptionally activated by the global regulator CRP. Since CRP represses Spot 42, these regulators participate in a specific regulatory circuit called a multi-output feedforward loop. We found that this loop can reduce leaky expression of target genes in the presence of glucose and can maintain repression of target genes under changing nutrient conditions. Our results suggest that base pairing RNAs in feedforward loops can help shape the steady-state levels and dynamics of gene expression. PMID:21292161

  4. Modified Polyadenylation-Based RT-qPCR Increases Selectivity of Amplification of 3′-MicroRNA Isoforms

    Directory of Open Access Journals (Sweden)

    Charlotte Nejad

    2018-01-01

    Full Text Available MicroRNA (miRNA detection by reverse transcription (RT quantitative real-time PCR (RT-qPCR is the most popular method currently used to measure miRNA expression. Although the majority of miRNA families are constituted of several 3′-end length variants (“isomiRs”, little attention has been paid to their differential detection by RT-qPCR. However, recent evidence indicates that 3′-end miRNA isoforms can exhibit 3′-length specific regulatory functions, underlining the need to develop strategies to differentiate 3′-isomiRs by RT-qPCR approaches. We demonstrate here that polyadenylation-based RT-qPCR strategies targeted to 20–21 nt isoforms amplify entire miRNA families, but that primers targeted to >22 nt isoforms were specific to >21 nt isoforms. Based on this observation, we developed a simple method to increase selectivity of polyadenylation-based RT-qPCR assays toward shorter isoforms, and demonstrate its capacity to help distinguish short RNAs from longer ones, using synthetic RNAs and biological samples with altered isomiR stoichiometry. Our approach can be adapted to many polyadenylation-based RT-qPCR technologies already exiting, providing a convenient way to distinguish long and short 3′-isomiRs.

  5. An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes.

    Science.gov (United States)

    Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Masaki, Shunpei; Nakayama, Hiroshi; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

    2009-11-01

    We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a approximately 21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes.

  6. A LEVEL SET BASED SHAPE OPTIMIZATION METHOD FOR AN ELLIPTIC OBSTACLE PROBLEM

    KAUST Repository

    Burger, Martin

    2011-04-01

    In this paper, we construct a level set method for an elliptic obstacle problem, which can be reformulated as a shape optimization problem. We provide a detailed shape sensitivity analysis for this reformulation and a stability result for the shape Hessian at the optimal shape. Using the shape sensitivities, we construct a geometric gradient flow, which can be realized in the context of level set methods. We prove the convergence of the gradient flow to an optimal shape and provide a complete analysis of the level set method in terms of viscosity solutions. To our knowledge this is the first complete analysis of a level set method for a nonlocal shape optimization problem. Finally, we discuss the implementation of the methods and illustrate its behavior through several computational experiments. © 2011 World Scientific Publishing Company.

  7. Theragnosis-based combined cancer therapy using doxorubicin-conjugated microRNA-221 molecular beacon.

    Science.gov (United States)

    Lee, Jonghwan; Choi, Kyung-Ju; Moon, Sung Ung; Kim, Soonhag

    2016-01-01

    Recently, microRNA (miRNA or miR) has emerged as a new cancer biomarker because of its high expression level in various cancer types and its role in the control of tumor suppressor genes. In cancer studies, molecular imaging and treatment based on target cancer markers have been combined to facilitate simultaneous cancer diagnosis and therapy. In this study, for combined therapy with diagnosis of cancer, we developed a doxorubicin-conjugated miR-221 molecular beacon (miR-221 DOXO MB) in a single platform composed of three different nucleotides: miR-221 binding sequence, black hole quencher 1 (BHQ1), and doxorubicin binding site. Imaging of endogenous miR-221 was achieved by specific hybridization between miR-221 and the miR-221 binding site in miR-221 DOXO MB. The presence of miR-221 triggered detachment of the quencher oligo and subsequent activation of a fluorescent signal of miR-221 DOXO MB. Simultaneous cancer therapy in C6 astrocytoma cells and nude mice was achieved by inhibition of miRNA-221 function that downregulates tumor suppressor genes. The detection of miR-221 expression and inhibition of miR-221 function by miR-221 DOXO MB provide the feasibility as a cancer theragnostic probe. Furthermore, a cytotoxic effect was induced by unloading of doxorubicin intercalated into miR-221 DOXO MB inside cells. Loss of miR-221 function and cytotoxicity induced by the miR-221 DOXO MB provides combined therapeutic efficacy against cancers. This method could be used as a new theragnostic probe with enhanced therapy to detect and inhibit many cancer-related miRNAs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Energy-based fatigue model for shape memory alloys including thermomechanical coupling

    Science.gov (United States)

    Zhang, Yahui; Zhu, Jihong; Moumni, Ziad; Van Herpen, Alain; Zhang, Weihong

    2016-03-01

    This paper is aimed at developing a low cycle fatigue criterion for pseudoelastic shape memory alloys to take into account thermomechanical coupling. To this end, fatigue tests are carried out at different loading rates under strain control at room temperature using NiTi wires. Temperature distribution on the specimen is measured using a high speed thermal camera. Specimens are tested to failure and fatigue lifetimes of specimens are measured. Test results show that the fatigue lifetime is greatly influenced by the loading rate: as the strain rate increases, the fatigue lifetime decreases. Furthermore, it is shown that the fatigue cracks initiate when the stored energy inside the material reaches a critical value. An energy-based fatigue criterion is thus proposed as a function of the irreversible hysteresis energy of the stabilized cycle and the loading rate. Fatigue life is calculated using the proposed model. The experimental and computational results compare well.

  9. Energy-based fatigue model for shape memory alloys including thermomechanical coupling

    International Nuclear Information System (INIS)

    Zhang, Yahui; Zhu, Jihong; Moumni, Ziad; Zhang, Weihong; Van Herpen, Alain

    2016-01-01

    This paper is aimed at developing a low cycle fatigue criterion for pseudoelastic shape memory alloys to take into account thermomechanical coupling. To this end, fatigue tests are carried out at different loading rates under strain control at room temperature using NiTi wires. Temperature distribution on the specimen is measured using a high speed thermal camera. Specimens are tested to failure and fatigue lifetimes of specimens are measured. Test results show that the fatigue lifetime is greatly influenced by the loading rate: as the strain rate increases, the fatigue lifetime decreases. Furthermore, it is shown that the fatigue cracks initiate when the stored energy inside the material reaches a critical value. An energy-based fatigue criterion is thus proposed as a function of the irreversible hysteresis energy of the stabilized cycle and the loading rate. Fatigue life is calculated using the proposed model. The experimental and computational results compare well. (paper)

  10. Evaluation of LSF based SOFC Cathodes using Cone-shaped Electrodes

    DEFF Research Database (Denmark)

    Kammer Hansen, Kent; Mogensen, Mogens Bjerg

    2008-01-01

    Seven La1-xSrxFeO3-delta (x = 0, 0.05, 0.15, 0.25, 0.35, 0.50, 0.70) based perovskites were synthesized using the glycine-nitrate method. The La1-xSrxFeO3-delta compounds were characterized with powder X-ray diffraction and electrochemical impedance spectroscopy on cone-shaped electrodes using a Ce......(III) is the catalytic active specie towards the electrochemical reduction of oxygen in a solid oxide fuel cell on La1-xSrxFeO3-delta compounds. The results also show that oxide ion vacancies in the perovskite structure are important for the electrochemical reduction of oxygen. However, the effect of ordering of oxide...

  11. Angular shaping of fluorescence from synthetic opal-based photonic crystal.

    Science.gov (United States)

    Boiko, Vitalii; Dovbeshko, Galyna; Dolgov, Leonid; Kiisk, Valter; Sildos, Ilmo; Loot, Ardi; Gorelik, Vladimir

    2015-01-01

    Spectral, angular, and temporal distributions of fluorescence as well as specular reflection were investigated for silica-based artificial opals. Periodic arrangement of nanosized silica globules in the opal causes a specific dip in the defect-related fluorescence spectra and a peak in the reflectance spectrum. The spectral position of the dip coincides with the photonic stop band. The latter is dependent on the size of silica globules and the angle of observation. The spectral shape and intensity of defect-related fluorescence can be controlled by variation of detection angle. Fluorescence intensity increases up to two times at the edges of the spectral dip. Partial photobleaching of fluorescence was observed. Photonic origin of the observed effects is discussed.

  12. 3D shape measurement of moving object with FFT-based spatial matching

    Science.gov (United States)

    Guo, Qinghua; Ruan, Yuxi; Xi, Jiangtao; Song, Limei; Zhu, Xinjun; Yu, Yanguang; Tong, Jun

    2018-03-01

    This work presents a new technique for 3D shape measurement of moving object in translational motion, which finds applications in online inspection, quality control, etc. A low-complexity 1D fast Fourier transform (FFT)-based spatial matching approach is devised to obtain accurate object displacement estimates, and it is combined with single shot fringe pattern prolometry (FPP) techniques to achieve high measurement performance with multiple captured images through coherent combining. The proposed technique overcomes some limitations of existing ones. Specifically, the placement of marks on object surface and synchronization between projector and camera are not needed, the velocity of the moving object is not required to be constant, and there is no restriction on the movement trajectory. Both simulation and experimental results demonstrate the effectiveness of the proposed technique.

  13. Identification by shape-based virtual screening and evaluation of new tyrosinase inhibitors

    Directory of Open Access Journals (Sweden)

    Qi Li

    2018-01-01

    Full Text Available Targeting tyrosinase is considered to be an effective way to control the production of melanin. Tyrosinase inhibitor is anticipated to provide new therapy to prevent skin pigmentation, melanoma and neurodegenerative diseases. Herein, we report our results in identifying new tyrosinase inhibitors. The shape-based virtual screening was performed to discover new tyrosinase inhibitors. Thirteen potential hits derived from virtual screening were tested by biological determinations. Compound 5186-0429 exhibited the most potent inhibitory activity. It dose-dependently inhibited the activity of tyrosinase, with the IC50 values 6.2 ± 2.0 µM and 10.3 ± 5.4 µM on tyrosine and L-Dopa formation, respectively. The kinetic study of 5186-0429 demonstrated that this compound acted as a competitive inhibitor. We believe the discoveries here could serve as a good starting point for further design of potent tyrosinase inhibitor.

  14. Blind Separation of Two Users Based on User Delays and Optimal Pulse-Shape Design

    Directory of Open Access Journals (Sweden)

    Poor HVincent

    2010-01-01

    Full Text Available A wireless network is considered, in which two spatially distributed users transmit narrow-band signals simultaneously over the same channel using the same power. User separation is achieved by oversampling the received signal and formulating a virtual multiple-input multiple-output (MIMO system based on the resulting polyphase components. Because of oversampling, high correlations can occur between the columns of the virtual MIMO system matrix which can be detrimental to user separation. A novel pulse-shape waveform design is proposed that results in low correlation between the columns of the system matrix, while it exploits all available bandwidth as dictated by a spectral mask. It is also shown that the use of successive interference cancelation in combination with blind source separation further improves the separation performance.

  15. An informatics approach to transformation temperatures of NiTi-based shape memory alloys

    International Nuclear Information System (INIS)

    Xue, Dezhen; Xue, Deqing; Yuan, Ruihao; Zhou, Yumei; Balachandran, Prasanna V.; Ding, Xiangdong; Sun, Jun; Lookman, Turab

    2017-01-01

    The martensitic transformation serves as the basis for applications of shape memory alloys (SMAs). The ability to make rapid and accurate predictions of the transformation temperature of SMAs is therefore of much practical importance. In this study, we demonstrate that a statistical learning approach using three features or material descriptors related to the chemical bonding and atomic radii of the elements in the alloys, provides a means to predict transformation temperatures. Together with an adaptive design framework, we show that iteratively learning and improving the statistical model can accelerate the search for SMAs with targeted transformation temperatures. The possible mechanisms underlying the dependence of the transformation temperature on these features is discussed based on a Landau-type phenomenological model.

  16. Feature Matching for SAR and Optical Images Based on Gaussian-Gamma-shaped Edge Strength Map

    Directory of Open Access Journals (Sweden)

    CHEN Min

    2016-03-01

    Full Text Available A matching method for SAR and optical images, robust to pixel noise and nonlinear grayscale differences, is presented. Firstly, a rough correction to eliminate rotation and scale change between images is performed. Secondly, features robust to speckle noise of SAR image are detected by improving the original phase congruency based method. Then, feature descriptors are constructed on the Gaussian-Gamma-shaped edge strength map according to the histogram of oriented gradient pattern. Finally, descriptor similarity and geometrical relationship are combined to constrain the matching processing.The experimental results demonstrate that the proposed method provides significant improvement in correct matches number and image registration accuracy compared with other traditional methods.

  17. Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing.

    Science.gov (United States)

    Urbarova, Ilona; Patel, Hardip; Forêt, Sylvain; Karlsen, Bård Ove; Jørgensen, Tor Erik; Hall-Spencer, Jason M; Johansen, Steinar D

    2018-02-01

    Cnidarians harbor a variety of small regulatory RNAs that include microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), but detailed information is limited. Here, we report the identification and expression of novel miRNAs and putative piRNAs, as well as their genomic loci, in the symbiotic sea anemone Anemonia viridis. We generated a draft assembly of the A. viridis genome with putative size of 313 Mb that appeared to be composed of about 36% repeats, including known transposable elements. We detected approximately equal fractions of DNA transposons and retrotransposons. Deep sequencing of small RNA libraries constructed from A. viridis adults sampled at a natural CO2 gradient off Vulcano Island, Italy, identified 70 distinct miRNAs. Eight were homologous to previously reported miRNAs in cnidarians, whereas 62 appeared novel. Nine miRNAs were recognized as differentially expressed along the natural seawater pH gradient. We found a highly abundant and diverse population of piRNAs, with a substantial fraction showing ping-pong signatures. We identified nearly 22% putative piRNAs potentially targeting transposable elements within the A. viridis genome. The A. viridis genome appeared similar in size to that of other hexacorals with a very high divergence of transposable elements resembling that of the sea anemone genus Exaiptasia. The genome encodes and expresses a high number of small regulatory RNAs, which include novel miRNAs and piRNAs. Differentially expressed small RNAs along the seawater pH gradient indicated regulatory gene responses to environmental stressors. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Interactive dose shaping - efficient strategies for CPU-based real-time treatment planning

    International Nuclear Information System (INIS)

    Ziegenhein, P; Kamerling, C P; Oelfke, U

    2014-01-01

    Conventional intensity modulated radiation therapy (IMRT) treatment planning is based on the traditional concept of iterative optimization using an objective function specified by dose volume histogram constraints for pre-segmented VOIs. This indirect approach suffers from unavoidable shortcomings: i) The control of local dose features is limited to segmented VOIs. ii) Any objective function is a mathematical measure of the plan quality, i.e., is not able to define the clinically optimal treatment plan. iii) Adapting an existing plan to changed patient anatomy as detected by IGRT procedures is difficult. To overcome these shortcomings, we introduce the method of Interactive Dose Shaping (IDS) as a new paradigm for IMRT treatment planning. IDS allows for a direct and interactive manipulation of local dose features in real-time. The key element driving the IDS process is a two-step Dose Modification and Recovery (DMR) strategy: A local dose modification is initiated by the user which translates into modified fluence patterns. This also affects existing desired dose features elsewhere which is compensated by a heuristic recovery process. The IDS paradigm was implemented together with a CPU-based ultra-fast dose calculation and a 3D GUI for dose manipulation and visualization. A local dose feature can be implemented via the DMR strategy within 1-2 seconds. By imposing a series of local dose features, equal plan qualities could be achieved compared to conventional planning for prostate and head and neck cases within 1-2 minutes. The idea of Interactive Dose Shaping for treatment planning has been introduced and first applications of this concept have been realized.

  19. Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format

    OpenAIRE

    Salvo-Chirnside, Eliane; Kane, Steven; Kerr, Lorraine E

    2011-01-01

    Abstract The increasing popularity of systems-based approaches to plant research has resulted in a demand for high throughput (HTP) methods to be developed. RNA extraction from multiple samples in an experiment is a significant bottleneck in performing systems-level genomic studies. Therefore we have established a high throughput method of RNA extraction from Arabidopsis thaliana to facilitate gene expression studies in this widely used plant model. We present optimised manual and automated p...

  20. Micropore Geometry Manipulation by Macroscopic Deformation Based on Shape Memory Effect in Porous PLLA Membrane and its Enhanced Separation Performance.

    Science.gov (United States)

    Zhao, Jingxin; Yang, Qiucheng; Wang, Tao; Wang, Lian; You, Jichun; Li, Yongjin

    2017-12-20

    An effective strategy to tailor the microporous structures has been developed based on the shape memory effect in porous poly(l-lactic acid) membranes in which tiny crystals and amorphous matrix play the roles of shape-fixed phase and reversible-phase, respectively. Our results indicate that not only PLLA membranes but micropores exhibit shape memory properties. The proportional deformations on two scales have been achieved by uniaxial or biaxial tension, providing a facile way to manipulate continuously the size and the orientation degree of pores on microscale. The enhanced separation performance has been validated by taking polystyrene colloids with varying diameters as an example.

  1. RNA-based ovarian cancer research from 'a gene to systems biomedicine' perspective.

    Science.gov (United States)

    Gov, Esra; Kori, Medi; Arga, Kazim Yalcin

    2017-08-01

    Ovarian cancer remains the leading cause of death from a gynecologic malignancy, and treatment of this disease is harder than any other type of female reproductive cancer. Improvements in the diagnosis and development of novel and effective treatment strategies for complex pathophysiologies, such as ovarian cancer, require a better understanding of disease emergence and mechanisms of progression through systems medicine approaches. RNA-level analyses generate new information that can help in understanding the mechanisms behind disease pathogenesis, to identify new biomarkers and therapeutic targets and in new drug discovery. Whole RNA sequencing and coding and non-coding RNA expression array datasets have shed light on the mechanisms underlying disease progression and have identified mRNAs, miRNAs, and lncRNAs involved in ovarian cancer progression. In addition, the results from these analyses indicate that various signalling pathways and biological processes are associated with ovarian cancer. Here, we present a comprehensive literature review on RNA-based ovarian cancer research and highlight the benefits of integrative approaches within the systems biomedicine concept for future ovarian cancer research. We invite the ovarian cancer and systems biomedicine research fields to join forces to achieve the interdisciplinary caliber and rigor required to find real-life solutions to common, devastating, and complex diseases such as ovarian cancer. CAF: cancer-associated fibroblasts; COG: Cluster of Orthologous Groups; DEA: disease enrichment analysis; EOC: epithelial ovarian carcinoma; ESCC: oesophageal squamous cell carcinoma; GSI: gamma secretase inhibitor; GO: Gene Ontology; GSEA: gene set enrichment analyzes; HAS: Hungarian Academy of Sciences; lncRNAs: long non-coding RNAs; MAPK/ERK: mitogen-activated protein kinase/extracellular signal-regulated kinases; NGS: next-generation sequencing; ncRNAs: non-coding RNAs; OvC: ovarian cancer; PI3K

  2. RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

    Science.gov (United States)

    Drory Retwitzer, Matan; Polishchuk, Maya; Churkin, Elena; Kifer, Ilona; Yakhini, Zohar; Barash, Danny

    2015-01-01

    Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular—no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence. Here, we introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods. RNAPattMatch service is available at http://www.cs.bgu.ac.il/rnapattmatch. A standalone version of the search tool is also available to download at the site. PMID:25940619

  3. Nuclear factor 90 uses an ADAR2-like binding mode to recognize specific bases in dsRNA.

    Science.gov (United States)

    Jayachandran, Uma; Grey, Heather; Cook, Atlanta G

    2016-02-29

    Nuclear factors 90 and 45 (NF90 and NF45) form a protein complex involved in the post-transcriptional control of many genes in vertebrates. NF90 is a member of the dsRNA binding domain (dsRBD) family of proteins. RNA binding partners identified so far include elements in 3' untranslated regions of specific mRNAs and several non-coding RNAs. In NF90, a tandem pair of dsRBDs separated by a natively unstructured segment confers dsRNA binding activity. We determined a crystal structure of the tandem dsRBDs of NF90 in complex with a synthetic dsRNA. This complex shows surprising similarity to the tandem dsRBDs from an adenosine-to-inosine editing enzyme, ADAR2 in complex with a substrate RNA. Residues involved in unusual base-specific recognition in the minor groove of dsRNA are conserved between NF90 and ADAR2. These data suggest that, like ADAR2, underlying sequences in dsRNA may influence how NF90 recognizes its target RNAs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Confirming the RNAi-mediated mechanism of action of siRNA-based cancer therapeutics in mice.

    Science.gov (United States)

    Judge, Adam D; Robbins, Marjorie; Tavakoli, Iran; Levi, Jasna; Hu, Lina; Fronda, Anna; Ambegia, Ellen; McClintock, Kevin; MacLachlan, Ian

    2009-03-01

    siRNAs that specifically silence the expression of cancer-related genes offer a therapeutic approach in oncology. However, it remains critical to determine the true mechanism of their therapeutic effects. Here, we describe the preclinical development of chemically modified siRNA targeting the essential cell-cycle proteins polo-like kinase 1 (PLK1) and kinesin spindle protein (KSP) in mice. siRNA formulated in stable nucleic acid lipid particles (SNALP) displayed potent antitumor efficacy in both hepatic and subcutaneous tumor models. This was correlated with target gene silencing following a single intravenous administration that was sufficient to cause extensive mitotic disruption and tumor cell apoptosis. Our siRNA formulations induced no measurable immune response, minimizing the potential for nonspecific effects. Additionally, RNAi-specific mRNA cleavage products were found in tumor cells, and their presence correlated with the duration of target mRNA silencing. Histological biomarkers confirmed that RNAi-mediated gene silencing effectively inhibited the target's biological activity. This report supports an RNAi-mediated mechanism of action for siRNA antitumor effects, suggesting a new methodology for targeting other key genes in cancer development with siRNA-based therapeutics.

  5. In-vivo quantification of primary microRNA processing by Drosha with a luciferase based system

    International Nuclear Information System (INIS)

    Allegra, Danilo; Mertens, Daniel

    2011-01-01

    Research highlights: → Posttranscriptional regulation of miRNA processing is difficult to quantify. → Our in-vivo processing assay can quantify Drosha cleavage in live cells. → It is based on luciferase reporters fused with pri-miRNAs. → The assay validates the processing defect caused by a mutation in pri-16-1. → It is a sensitive method to quantify pri-miRNA cleavage by Drosha in live cells. -- Abstract: The RNAse III Drosha is responsible for the first step of microRNA maturation, the cleavage of primary miRNA to produce the precursor miRNA. Processing by Drosha is finely regulated and influences the amount of mature microRNA in a cell. We describe in the present work a method to quantify Drosha processing activity in-vivo, which is applicable to any microRNA. With respect to other methods for measuring Drosha activity, our system is faster and scalable, can be used with any cellular system and does not require cell sorting or use of radioactive isotopes. This system is useful to study regulation of Drosha activity in physiological and pathological conditions.

  6. REMap: Operon map of M. tuberculosis based on RNA sequence data.

    Science.gov (United States)

    Pelly, Shaaretha; Winglee, Kathryn; Xia, Fang Fang; Stevens, Rick L; Bishai, William R; Lamichhane, Gyanu

    2016-07-01

    A map of the transcriptional organization of genes of an organism is a basic tool that is necessary to understand and facilitate a more accurate genetic manipulation of the organism. Operon maps are largely generated by computational prediction programs that rely on gene conservation and genome architecture and may not be physiologically relevant. With the widespread use of RNA sequencing (RNAseq), the prediction of operons based on actual transcriptome sequencing rather than computational genomics alone is much needed. Here, we report a validated operon map of Mycobacterium tuberculosis, developed using RNAseq data from both the exponential and stationary phases of growth. At least 58.4% of M. tuberculosis genes are organized into 749 operons. Our prediction algorithm, REMap (RNA Expression Mapping of operons), considers the many cases of transcription coverage of intergenic regions, and avoids dependencies on functional annotation and arbitrary assumptions about gene structure. As a result, we demonstrate that REMap is able to more accurately predict operons, especially those that contain long intergenic regions or functionally unrelated genes, than previous operon prediction programs. The REMap algorithm is publicly available as a user-friendly tool that can be readily modified to predict operons in other bacteria. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. ''Some features of γ-ε martensitic transformation and shape memory effect in Fe-Mn-Si based alloys''

    International Nuclear Information System (INIS)

    Gulyaev, A.A.

    1995-01-01

    In the present paper several important aspects concerning the shape memory behavior of the ε-martensite in the cost-saving Fe-Mn-Si-based alloys and its application are reported. Some kinetic features of the γ-ε martensitic transformation are discussed. The effects of the composition, volume change induced by the transformation, strength of austenite, temperature of pre strain on the shape memory effect have been investigated. (orig.)

  8. Injury Reduction Effectiveness of Prescribing Running Shoes Based on Foot Shape in Air Force Basic Military Training

    Science.gov (United States)

    2008-08-01

    resulted in excessive pronation, creating a torsional force that repeatedly overstretched the plantar fascia leading to the fasciitis. However, the...Defense Safety Oversight Council, this study examined whether prescribing running shoes based on the shape of the plantar surface influenced injury risk...prescribed motion control, stability, or cushioned shoes for plantar shapes indicative of low, medium, or high arches, respectively. A control group (C, n

  9. A New Spectral Shape-Based Record Selection Approach Using Np and Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Edén Bojórquez

    2013-01-01

    Full Text Available With the aim to improve code-based real records selection criteria, an approach inspired in a parameter proxy of spectral shape, named Np, is analyzed. The procedure is based on several objectives aimed to minimize the record-to-record variability of the ground motions selected for seismic structural assessment. In order to select the best ground motion set of records to be used as an input for nonlinear dynamic analysis, an optimization approach is applied using genetic algorithms focuse on finding the set of records more compatible with a target spectrum and target Np values. The results of the new Np-based approach suggest that the real accelerograms obtained with this procedure, reduce the scatter of the response spectra as compared with the traditional approach; furthermore, the mean spectrum of the set of records is very similar to the target seismic design spectrum in the range of interest periods, and at the same time, similar Np values are obtained for the selected records and the target spectrum.

  10. An innovative seismic bracing system based on a superelastic shape memory alloy ring

    International Nuclear Information System (INIS)

    Gao, Nan; Jeon, Jong-Su; DesRoches, Reginald; Hodgson, Darel E

    2016-01-01

    Shape memory alloys (SMAs) have great potential in seismic applications because of their remarkable superelasticity. Seismic bracing systems based on SMAs can mitigate the damage caused by earthquakes. The current study investigates a bracing system based on an SMA ring which is capable of both re-centering and energy dissipation. This lateral force resisting system is a cross-braced system consisting of an SMA ring and four tension-only cable assemblies, which can be applied to both new construction and seismic retrofit. The performance of this bracing system is examined through a quasi-static cyclic loading test and finite element (FE) analysis. This paper describes the experimental design in detail, discusses the experimental results, compares the performance with other bracing systems based on SMAs, and presents an Abaqus FE model calibrated on the basis of experimental results to simulate the superelastic behavior of the SMA ring. The experimental results indicate that the seismic performance of this system is promising in terms of damping and re-centering. The FE model can be used in the simulation of building structures using the proposed bracing system. (paper)

  11. Efficient delivery of Notch1 siRNA to SKOV3 cells by cationic cholesterol derivative-based liposome

    Directory of Open Access Journals (Sweden)

    Zhao Y

    2016-10-01

    Full Text Available Yun-Chun Zhao,1 Li Zhang,2 Shi-Sen Feng,3 Lu Hong,3 Hai-Li Zheng,3 Li-Li Chen,4 Xiao-Ling Zheng,1 Yi-Qing Ye,1 Meng-Dan Zhao,1 Wen-Xi Wang,3 Cai-Hong Zheng1 1Pharmacy Department, Women’s Hospital, 2Pharmacy Department, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, People’s Republic of China; 3Department of Pharmaceutic Preparation, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 4Department of Gynecologic Oncology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, People’s Republic of China Abstract: A novel cationic cholesterol derivative-based small interfering RNA (siRNA interference strategy was suggested to inhibit Notch1 activation in SKOV3 cells for the gene therapy of ovarian cancer. The cationic cholesterol derivative, N-(cholesterylhemisuccinoyl-amino-3-propyl-N, N-dimethylamine (DMAPA-chems liposome, was incubated with siRNA at different nitrogen-to-phosphate ratios to form stabilized, near-spherical siRNA/DMAPA-chems nanoparticles with sizes of 100–200 nm and zeta potentials of 40–50 mV. The siRNA/DMAPA-chems nanoparticles protected siRNA from nuclease degradation in 25% fetal bovine serum. The nanoparticles exhibited high cell uptake and Notch1 gene knockdown efficiency in SKOV3 cells at an nitrogen-to-phosphate ratio of 100 and an siRNA concentration of 50 nM. They also inhibited the growth and promoted the apoptosis of SKOV3 cells. These results may provide the potential for using cationic cholesterol derivatives as efficient nonviral siRNA carriers for the suppression of Notch1 activation in ovarian cancer cells. Keywords: siRNA, cationic cholesterol derivative, Notch1, ovarian cancer cells

  12. Polyethylenimine-based polyplex delivery of self-replicating RNA vaccines.

    Science.gov (United States)

    Démoulins, Thomas; Milona, Panagiota; Englezou, Pavlos C; Ebensen, Thomas; Schulze, Kai; Suter, Rolf; Pichon, Chantal; Midoux, Patrick; Guzmán, Carlos A; Ruggli, Nicolas; McCullough, Kenneth C

    2016-04-01

    Self-amplifying replicon RNA (RepRNA) are large molecules (12-14 kb); their self-replication amplifies mRNA template numbers, affording several rounds of antigen production, effectively increasing vaccine antigen payloads. Their sensitivity to RNase-sensitivity and inefficient uptake by dendritic cells (DCs) - absolute requirements for vaccine design - were tackled by condensing RepRNA into synthetic, nanoparticulate, polyethylenimine (PEI)-polyplex delivery vehicles. Polyplex-delivery formulations for small RNA molecules cannot be transferred to RepRNA due to its greater size and complexity; the N:P charge ratio and impact of RepRNA folding would influence polyplex condensation, post-delivery decompaction and the cytosolic release essential for RepRNA translation. Polyplex-formulations proved successful for delivery of RepRNA encoding influenza virus hemagglutinin and nucleocapsid to DCs. Cytosolic translocation was facilitated, leading to RepRNA translation. This efficacy was confirmed in vivo, inducing both humoral and cellular immune responses. Accordingly, this paper describes the first PEI-polyplexes providing efficient delivery of the complex and large, self-amplifying RepRNA vaccines. The use of self-amplifying replicon RNA (RepRNA) to increase vaccine antigen payloads can potentially be useful in effective vaccine design. Nonetheless, its use is limited by the degradation during the uptake process. Here, the authors attempted to solve this problem by packaging RepRNA using polyethylenimine (PEI)-polyplex delivery vehicles. The efficacy was confirmed in vivo by the appropriate humoral and cellular immune responses. This novel delivery method may prove to be very useful for future vaccine design. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Stability of non-Watson-Crick G-A/A-G base pair in synthetic DNA and RNA oligonucleotides.

    Science.gov (United States)

    Ito, Yuko; Sone, Yumiko; Mizutani, Takaharu

    2004-03-01

    A non-Watson-Crick G-A/A-G base pair is found in SECIS (selenocysteine-insertion sequence) element in the 3'-untranslated region of Se-protein mRNAs and in the functional site of the hammerhead ribozyme. We studied the stability of G-A/A-G base pair (bold) in 17mer GT(U)GACGGAAACCGGAAC synthetic DNA and RNA oligonucleotides by thermal melting experiments and gel electrophoresis. The measured Tm value of DNA oligonucleotide having G-A/A-G pair showed an intermediate value (58 degrees C) between that of Watson-Crick G-C/C-G base pair (75 degrees C) and that of G-G/A-A of non-base-pair (40 degrees C). Similar thermal melting patterns were obtained with RNA oligonucleotides. This result indicates that the secondary structure of oligonucleotide having G-A/A-G base pair is looser than that of the G-C type Watson-Crick base pair. In the comparison between RNA and DNA having G-A/A-G base pair, the Tm value of the RNA oligonucleotide was 11 degrees C lower than that of DNA, indicating that DNA has a more rigid structure than RNA. The stained pattern of oligonucleotide on polyacrylamide gel clarified that the mobility of the DNA oligonucleotide G-A/A-G base pair changed according to the urea concentration from the rigid state (near the mobility of G-C/C-G oligonucleotide) in the absence of urea to the random state (near the mobility of G-G/A-A oligonucleotide) in 7 M urea. However, the RNA oligonucleotide with G-A/A-G pair moved at an intermediate mobility between that of oligonucleotide with G-C/C-G and of the oligonucleotide with G-G/A-A, and the mobility pattern did not depend on urea concentration. Thus, DNA and RNA oligonucleotides with the G-A/A-G base pair showed a pattern indicating an intermediate structure between the rigid Watson-Crick base pair and the random structure of non-base pair. RNA with G-A/A-G base pair has the intermediate structure not influenced by urea concentration. Finally, this study indicated that the intermediate rigidity imparted by Non

  14. Visualization of RNA structure models within the Integrative Genomics Viewer.

    Science.gov (United States)

    Busan, Steven; Weeks, Kevin M

    2017-07-01

    Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist. We have developed a module within the widely used and well supported open-source Integrative Genomics Viewer (IGV) that allows visualization of SHAPE and other chemical probing data, including raw reactivities, data-driven structural entropies, and data-constrained base-pair secondary structure models, in context with linear genomic data tracks. We illustrate the usefulness of visualizing RNA structure in the IGV by exploring structure models for a large viral RNA genome, comparing bacterial mRNA structure in cells with its structure under cell- and protein-free conditions, and comparing a noncoding RNA structure modeled using SHAPE data with a base-pairing model inferred through sequence covariation analysis. © 2017 Busan and Weeks; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  15. Strengthening of Fe-Mn-Si based shape memory alloys by grain size refinement

    International Nuclear Information System (INIS)

    Sato, A.; Masuya, T.; Kumai, S.; Inoue, A.

    2000-01-01

    Degree of the shape memory effect was measured either by bending, tensile and compression tests in the temperature range 77∝300 K. The yield stress increased substantially by the grain size refinement, yet maintaining a good shape memory effect. In addition to usual mentioned slow strain rate tests (about 10 -3 s -1 ), shape deformation was given at high strain rate (10 3 s -1 ) by hammering, in order to induce fine structure. It is also found that the shape memory effect under an opposing force was improved by the high-speed deformation. (orig.)

  16. Shape tracking with occlusions via coarse-to-fine region-based sobolev descent

    KAUST Repository

    Yang, Yanchao

    2015-05-01

    We present a method to track the shape of an object from video. The method uses a joint shape and appearance model of the object, which is propagated to match shape and radiance in subsequent frames, determining object shape. Self-occlusions and dis-occlusions of the object from camera and object motion pose difficulties to joint shape and appearance models in tracking. They are unable to adapt to new shape and appearance information, leading to inaccurate shape detection. In this work, we model self-occlusions and dis-occlusions in a joint shape and appearance tracking framework. Self-occlusions and the warp to propagate the model are coupled, thus we formulate a joint optimization problem. We derive a coarse-to-fine optimization method, advantageous in tracking, that initially perturbs the model by coarse perturbations before transitioning to finer-scale perturbations seamlessly. This coarse-to-fine behavior is automatically induced by gradient descent on a novel infinite-dimensional Riemannian manifold that we introduce. The manifold consists of planar parameterized regions, and the metric that we introduce is a novel Sobolev metric. Experiments on video exhibiting occlusions/dis-occlusions, complex radiance and background show that occlusion/dis-occlusion modeling leads to superior shape accuracy. © 2014 IEEE.

  17. Shape-memory properties of magnetically active triple-shape nanocomposites based on a grafted polymer network with two crystallizable switching segments

    Directory of Open Access Journals (Sweden)

    A. Lendlein

    2012-01-01

    Full Text Available Thermo-sensitive shape-memory polymers (SMP, which are capable of memorizing two or more different shapes, have generated significant research and technological interest. A triple-shape effect (TSE of SMP can be activated e.g. by increasing the environmental temperature (Tenv, whereby two switching temperatures (Tsw have to be exceeded to enable the subsequent shape changes from shape (A to shape (B and finally the original shape (C. In this work, we explored the thermally and magnetically initiated shape-memory properties of triple-shape nanocomposites with various compositions and particle contents using different shape-memory creation procedures (SMCP. The nanocomposites were prepared by the incorporation of magnetite nanoparticles into a multiphase polymer network matrix with grafted polymer network architecture containing crystallizable poly(ethylene glycol (PEG side chains and poly(ε-caprolactone (PCL crosslinks named CLEGC. Excellent triple-shape properties were achieved for nanocomposites with high PEG weight fraction when two-step programming procedures were applied. In contrast, single-step programming resulted in dual-shape properties for all investigated materials as here the temporary shape (A was predominantly fixed by PCL crystallites.

  18. Integrating chemical footprinting data into RNA secondary structure prediction.

    Directory of Open Access Journals (Sweden)

    Kourosh Zarringhalam

    Full Text Available Chemical and enzymatic footprinting experiments, such as shape (selective 2'-hydroxyl acylation analyzed by primer extension, yield important information about RNA secondary structure. Indeed, since the [Formula: see text]-hydroxyl is reactive at flexible (loop regions, but unreactive at base-paired regions, shape yields quantitative data about which RNA nucleotides are base-paired. Recently, low error rates in secondary structure prediction have been reported for three RNAs of moderate size, by including base stacking pseudo-energy terms derived from shape data into the computation of minimum free energy secondary structure. Here, we describe a novel method, RNAsc (RNA soft constraints, which includes pseudo-energy terms for each nucleotide position, rather than only for base stacking positions. We prove that RNAsc is self-consistent, in the sense that the nucleotide-specific probabilities of being unpaired in the low energy Boltzmann ensemble always become more closely correlated with the input shape data after application of RNAsc. From this mathematical perspective, the secondary structure predicted by RNAsc should be 'correct', in as much as the shape data is 'correct'. We benchmark RNAsc against the previously mentioned method for eight RNAs, for which both shape data and native structures are known, to find the same accuracy in 7 out of 8 cases, and an improvement of 25% in one case. Furthermore, we present what appears to be the first direct comparison of shape data and in-line probing data, by comparing yeast asp-tRNA shape data from the literature with data from in-line probing experiments we have recently performed. With respect to several criteria, we find that shape data appear to be more robust than in-line probing data, at least in the case of asp-tRNA.

  19. New 3-D coordination polymers based on semi-rigid V-shape tetracarboxylates

    International Nuclear Information System (INIS)

    Huang, Jing-Jing; Xu, Wei; Wang, Yan-Ning; Yu, Jie-Hui; Zhang, Ping; Xu, Ji-Qing

    2015-01-01

    Under the hydrothermal conditions, the reactions of transition-metal salts, tetracarboxylic acids and N,N′-donor ligands yielded three new coordination polymers as [Cu 4 (fph) 2 (bpe) 3 (H 2 O) 2 ]·2H 2 O (fph=4,4′-(hexafluoroisopropylidene)diphthalate, bpe=1,2-bis(pyridyl)ethylene) 1, [Co 2 (fph)(bpa) 2 (H 2 O) 2 ]·3H 2 O (bpa=1,2-bis(pyridyl)ethylane) 2, and [Ni(H 2 O)(H 2 oph)(bpa)] (oph=4,4′-oxydiphthalate) 3. X-ray single-crystal diffraction analysis revealed that the title three compounds all possess the three-dimensional (3-D) network structures. For compound 1, the fph molecules first link the Cu 2+ ions into a two-dimensional (2-D) wave-like layer with a (4,4) topology. The bpe molecules act as the second linkers, extending the 2-D layers into a 3-D network. For compound 2, the fph molecules still serve as the first connectors, linking the Co 2+ ions into a one-dimensional (1-D) tube-like chain. Then the bpa molecules propagate the chains into a 3-D (4,4,4)-connected network. In the formation of the 3-D network of compound 3, the oph molecule does not play a role. The bpa molecules as well as the water molecules act as a mixed bridge. Only a kind of 4-connected metal node is observed in compound 3. The magnetic properties of compounds 1–3 were investigated and all exhibit the predominant antiferromegnetic magnetic behaviors. - Graphical abstract: Structures of three semi-rigid V-shape tetracarboxylate-based coordination polymers were reported, and their magnetic properties were investigated. - Highlights: • Structures of three tetracarboxylate-based coordination polymers were reported. • Role of organic bases in metal–tetracarboxylate compounds was discussed. • Characters of V-shape and semi-rigidity for tetracarboxylate play a key role in crystal growth. • Their magnetic properties were investigated

  20. New 3-D coordination polymers based on semi-rigid V-shape tetracarboxylates

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Jing-Jing; Xu, Wei; Wang, Yan-Ning [College of Chemistry, Jilin University, Jiefang Road 2519, Changchun 130023, Jilin (China); State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Qianjin Road 2699, Changchun 130012, Jilin (China); Yu, Jie-Hui, E-mail: jhyu@jlu.edu.cn [College of Chemistry, Jilin University, Jiefang Road 2519, Changchun 130023, Jilin (China); State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Qianjin Road 2699, Changchun 130012, Jilin (China); Zhang, Ping, E-mail: zhangping@jlu.edu.cn [College of Chemistry, Jilin University, Jiefang Road 2519, Changchun 130023, Jilin (China); Xu, Ji-Qing [College of Chemistry, Jilin University, Jiefang Road 2519, Changchun 130023, Jilin (China); State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Qianjin Road 2699, Changchun 130012, Jilin (China)

    2015-03-15

    Under the hydrothermal conditions, the reactions of transition-metal salts, tetracarboxylic acids and N,N′-donor ligands yielded three new coordination polymers as [Cu{sub 4}(fph){sub 2}(bpe){sub 3}(H{sub 2}O){sub 2}]·2H{sub 2}O (fph=4,4′-(hexafluoroisopropylidene)diphthalate, bpe=1,2-bis(pyridyl)ethylene) 1, [Co{sub 2}(fph)(bpa){sub 2}(H{sub 2}O){sub 2}]·3H{sub 2}O (bpa=1,2-bis(pyridyl)ethylane) 2, and [Ni(H{sub 2}O)(H{sub 2}oph)(bpa)] (oph=4,4′-oxydiphthalate) 3. X-ray single-crystal diffraction analysis revealed that the title three compounds all possess the three-dimensional (3-D) network structures. For compound 1, the fph molecules first link the Cu{sup 2+} ions into a two-dimensional (2-D) wave-like layer with a (4,4) topology. The bpe molecules act as the second linkers, extending the 2-D layers into a 3-D network. For compound 2, the fph molecules still serve as the first connectors, linking the Co{sup 2+} ions into a one-dimensional (1-D) tube-like chain. Then the bpa molecules propagate the chains into a 3-D (4,4,4)-connected network. In the formation of the 3-D network of compound 3, the oph molecule does not play a role. The bpa molecules as well as the water molecules act as a mixed bridge. Only a kind of 4-connected metal node is observed in compound 3. The magnetic properties of compounds 1–3 were investigated and all exhibit the predominant antiferromegnetic magnetic behaviors. - Graphical abstract: Structures of three semi-rigid V-shape tetracarboxylate-based coordination polymers were reported, and their magnetic properties were investigated. - Highlights: • Structures of three tetracarboxylate-based coordination polymers were reported. • Role of organic bases in metal–tetracarboxylate compounds was discussed. • Characters of V-shape and semi-rigidity for tetracarboxylate play a key role in crystal growth. • Their magnetic properties were investigated.

  1. Biofluid-based microRNA Biomarkers for Parkinsons Disease: an Overview and Update

    Directory of Open Access Journals (Sweden)

    Sapana Shinde

    2015-02-01

    Full Text Available Parkinson's disease (PD is a highly debilitating motor disorder and is the second most common neurodegenerative disease after Alzheimer's disease. Its current method of diagnosis mainly relies on subjective clinical rating scales in the presence of clinical motor features. Early detection of PD is a known challenge as neuronal cell death may range from 50% to 80% when a patient is first diagnosed with PD. Therefore, there is an urgent need to identify and develop biomarkers for early detection of this progressive disease. This mini review focuses on the recent developments of biofluid-based microRNAs (miRNAs as molecular biomarkers for PD. A comprehensive list of miRNA biomarkers found in blood, plasma, serum, and cerebral spinal fluid is presented. Challenges and future perspectives of using these PD-related molecular biomarkers in a “real-world” clinical setting are also discussed.

  2. MKRMDA: multiple kernel learning-based Kronecker regularized least squares for MiRNA-disease association prediction.

    Science.gov (United States)

    Chen, Xing; Niu, Ya-Wei; Wang, Guang-Hui; Yan, Gui-Ying

    2017-12-12

    Recently, as the research of microRNA (miRNA) continues, there are plenty of experimental evidences indicating that miRNA could be associated with various human complex diseases development and progression. Hence, it is necessary and urgent to pay more attentions to the relevant study of predicting diseases associated miRNAs, which may be helpful for effective prevention, diagnosis and treatment of human diseases. Especially, constructing computational methods to predict potential miRNA-disease associations is worthy of more studies because of the feasibility and effectivity. In this work, we developed a novel computational model of multiple kernels learning-based Kronecker regularized least squares for MiRNA-disease association prediction (MKRMDA), which could reveal potential miRNA-disease associations by automatically optimizing the combination of multiple kernels for disease and miRNA. MKRMDA obtained AUCs of 0.9040 and 0.8446 in global and local leave-one-out cross validation, respectively. Meanwhile, MKRMDA achieved average AUCs of 0.8894 ± 0.0015 in fivefold cross validation. Furthermore, we conducted three different kinds of case studies on some important human cancers for further performance evaluation. In the case studies of colonic cancer, esophageal cancer and lymphoma based on known miRNA-disease associations in HMDDv2.0 database, 76, 94 and 88% of the corresponding top 50 predicted miRNAs were confirmed by experimental reports, respectively. In another two kinds of case studies for new diseases without any known associated miRNAs and diseases only with known associations in HMDDv1.0 database, the verified ratios of two different cancers were 88 and 94%, respectively. All the results mentioned above adequately showed the reliable prediction ability of MKRMDA. We anticipated that MKRMDA could serve to facilitate further developments in the field and the follow-up investigations by biomedical researchers.

  3. Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format

    Directory of Open Access Journals (Sweden)

    Salvo-Chirnside Eliane

    2011-12-01

    Full Text Available Abstract The increasing popularity of systems-based approaches to plant research has resulted in a demand for high throughput (HTP methods to be developed. RNA extraction from multiple samples in an experiment is a significant bottleneck in performing systems-level genomic studies. Therefore we have established a high throughput method of RNA extraction from Arabidopsis thaliana to facilitate gene expression studies in this widely used plant model. We present optimised manual and automated protocols for the extraction of total RNA from 9-day-old Arabidopsis seedlings in a 96 well plate format using silica membrane-based methodology. Consistent and reproducible yields of high quality RNA are isolated averaging 8.9 μg total RNA per sample (~20 mg plant tissue. The purified RNA is suitable for subsequent qPCR analysis of the expression of over 500 genes in triplicate from each sample. Using the automated procedure, 192 samples (2 × 96 well plates can easily be fully processed (samples homogenised, RNA purified and quantified in less than half a day. Additionally we demonstrate that plant samples can be stored in RNAlater at -20°C (but not 4°C for 10 months prior to extraction with no significant effect on RNA yield or quality. Additionally, disrupted samples can be stored in the lysis buffer at -20°C for at least 6 months prior to completion of the extraction procedure providing a flexible sampling and storage scheme to facilitate complex time series experiments.

  4. MicroRNA prediction using a fixed-order Markov model based on the secondary structure pattern.

    Directory of Open Access Journals (Sweden)

    Wei Shen

    Full Text Available Predicting miRNAs is an arduous task, due to the diversity of the precursors and complexity of enzyme processes. Although several prediction approaches have reached impressive performances, few of them could achieve a full-function recognition of mature miRNA directly from the candidate hairpins across species. Therefore, researchers continue to seek a more powerful model close to biological recognition to miRNA structure. In this report, we describe a novel miRNA prediction algorithm, known as FOMmiR, using a fixed-order Markov model based on the secondary structural pattern. For a training dataset containing 809 human pre-miRNAs and 6441 human pseudo-miRNA hairpins, the model's parameters were defined and evaluated. The results showed that FOMmiR reached 91% accuracy on the human dataset through 5-fold cross-validation. Moreover, for the independent test datasets, the FOMmiR presented an outstanding prediction in human and other species including vertebrates, Drosophila, worms and viruses, even plants, in contrast to the well-known algorithms and models. Especially, the FOMmiR was not only able to distinguish the miRNA precursors from the hairpins, but also locate the position and strand of the mature miRNA. Therefore, this study provides a new generation of miRNA prediction algorithm, which successfully realizes a full-function recognition of the mature miRNAs directly from the hairpin sequences. And it presents a new understanding of the biological recognition based on the strongest signal's location detected by FOMmiR, which might be closely associated with the enzyme cleavage mechanism during the miRNA maturation.

  5. An automated procedure for covariation-based detection of RNA structure

    International Nuclear Information System (INIS)

    Winker, S.; Overbeek, R.; Woese, C.R.; Olsen, G.J.; Pfluger, N.

    1989-12-01

    This paper summarizes our investigations into the computational detection of secondary and tertiary structure of ribosomal RNA. We have developed a new automated procedure that not only identifies potential bondings of secondary and tertiary structure, but also provides the covariation evidence that supports the proposed bondings, and any counter-evidence that can be detected in the known sequences. A small number of previously unknown bondings have been detected in individual RNA molecules (16S rRNA and 7S RNA) through the use of our automated procedure. Currently, we are systematically studying mitochondrial rRNA. Our goal is to detect tertiary structure within 16S rRNA and quaternary structure between 16S and 23S rRNA. Our ultimate hope is that automated covariation analysis will contribute significantly to a refined picture of ribosome structure. Our colleagues in biology have begun experiments to test certain hypotheses suggested by an examination of our program's output. These experiments involve sequencing key portions of the 23S ribosomal RNA for species in which the known 16S ribosomal RNA exhibits variation (from the dominant pattern) at the site of a proposed bonding. The hope is that the 23S ribosomal RNA of these species will exhibit corresponding complementary variation or generalized covariation. 24 refs

  6. An automated procedure for covariation-based detection of RNA structure

    Energy Technology Data Exchange (ETDEWEB)

    Winker, S.; Overbeek, R.; Woese, C.R.; Olsen, G.J.; Pfluger, N.

    1989-12-01

    This paper summarizes our investigations into the computational detection of secondary and tertiary structure of ribosomal RNA. We have developed a new automated procedure that not only identifies potential bondings of secondary and tertiary structure, but also provides the covariation evidence that supports the proposed bondings, and any counter-evidence that can be detected in the known sequences. A small number of previously unknown bondings have been detected in individual RNA molecules (16S rRNA and 7S RNA) through the use of our automated procedure. Currently, we are systematically studying mitochondrial rRNA. Our goal is to detect tertiary structure within 16S rRNA and quaternary structure between 16S and 23S rRNA. Our ultimate hope is that automated covariation analysis will contribute significantly to a refined picture of ribosome structure. Our colleagues in biology have begun experiments to test certain hypotheses suggested by an examination of our program's output. These experiments involve sequencing key portions of the 23S ribosomal RNA for species in which the known 16S ribosomal RNA exhibits variation (from the dominant pattern) at the site of a proposed bonding. The hope is that the 23S ribosomal RNA of these species will exhibit corresponding complementary variation or generalized covariation. 24 refs.

  7. Nanoscale characterization of martensite structures in copper based shape memory alloys

    Energy Technology Data Exchange (ETDEWEB)

    Adiguzel, O, E-mail: oadiguzel@firat.edu.t [Firat University Department of Physics, 23169 Elazig (Turkey)

    2010-11-01

    Martensitic transformations are first order displacive transitions and occur in the materials on cooling from high temperature. Shape memory effect is an unusual property exhibited by certain alloy systems, and leads to martensitic transition. Copper-based alloys exhibit this property in beta phase field which possess simple bcc- structures, austenite structure at high-temperatures. As temperature is lowered the austenite undergoes martensitic transition following two ordering reactions, and structural changes in nanoscale govern this transition. Atomic movements are also confined to interatomic lengths in sub-{mu}m or angstrom scale in martensitic transformation. The formation of the layered structures in copper based alloys consists of shears and shear mechanism. Martensitic transformations occur in a few steps with the cooperative movement of atoms less than interatomic distances by means of lattice invariant shears on a {l_brace}110{r_brace} - type plane of austenite matrix which is basal plane or stacking plane of martensite. The lattice invariant shears occurs, in two opposite directions, <110> -type directions on the {l_brace}110{r_brace}-type plane. These shears gives rise to the formation of layered structure.

  8. Hourglass-ShapeNetwork Based Semantic Segmentation for High Resolution Aerial Imagery

    Directory of Open Access Journals (Sweden)

    Yu Liu

    2017-05-01

    Full Text Available A new convolution neural network (CNN architecture for semantic segmentation of high resolution aerial imagery is proposed in this paper. The proposed architecture follows an hourglass-shaped network (HSN design being structured into encoding and decoding stages. By taking advantage of recent advances in CNN designs, we use the composed inception module to replace common convolutional layers, providing the network with multi-scale receptive areas with rich context. Additionally, in order to reduce spatial ambiguities in the up-sampling stage, skip connections with residual units are also employed to feed forward encoding-stage information directly to the decoder. Moreover, overlap inference is employed to alleviate boundary effects occurring when high resolution images are inferred from small-sized patches. Finally, we also propose a post-processing method based on weighted belief propagation to visually enhance the classification results. Extensive experiments based on the Vaihingen and Potsdam datasets demonstrate that the proposed architectures outperform three reference state-of-the-art network designs both numerically and visually.

  9. Size, shape, and topology optimization of planar and space trusses using mutation-based improved metaheuristics

    Directory of Open Access Journals (Sweden)

    Ghanshyam G. Tejani

    2018-04-01

    Full Text Available In this study, simultaneous size, shape, and topology optimization of planar and space trusses are investigated. Moreover, the trusses are subjected to constraints for element stresses, nodal displacements, and kinematic stability conditions. Truss Topology Optimization (TTO removes the superfluous elements and nodes from the ground structure. In this method, the difficulties arise due to unacceptable and singular topologies; therefore, the Grubler’s criterion and the positive definiteness are used to handle such issue. Moreover, the TTO is challenging due to its search space, which is implicit, non-convex, non-linear, and often leading to divergence. Therefore, mutation-based metaheuristics are proposed to investigate them. This study compares the performance of four improved metaheuristics (viz. Improved Teaching–Learning-Based Optimization (ITLBO, Improved Heat Transfer Search (IHTS, Improved Water Wave Optimization (IWWO, and Improved Passing Vehicle Search (IPVS and four basic metaheuristics (viz. TLBO, HTS, WWO, and PVS in order to solve structural optimization problems. Keywords: Structural optimization, Mutation operator, Improved metaheuristics, Modified algorithms, Truss topology optimization

  10. A python-based docking program utilizing a receptor bound ligand shape: PythDock.

    Science.gov (United States)

    Chung, Jae Yoon; Cho, Seung Joo; Hah, Jung-Mi

    2011-09-01

    PythDock is a heuristic docking program that uses Python programming language with a simple scoring function and a population based search engine. The scoring function considers electrostatic and dispersion/repulsion terms. The search engine utilizes a particle swarm optimization algorithm. A grid potential map is generated using the shape information of a bound ligand within the active site. Therefore, the searching area is more relevant to the ligand binding. To evaluate the docking performance of PythDock, two well-known docking programs (AutoDock and DOCK) were also used with the same data. The accuracy of docked results were measured by the difference of the ligand structure between x-ray structure, and do