Sample records for tailoring rna modular

  1. Modular arrangement of regulatory RNA elements.

    PubMed

    Roßmanith, Johanna; Narberhaus, Franz

    2017-03-04

    Due to their simple architecture and control mechanism, regulatory RNA modules are attractive building blocks in synthetic biology. This is especially true for riboswitches, which are natural ligand-binding regulators of gene expression. The discovery of various tandem riboswitches inspired the design of combined RNA modules with activities not yet found in nature. Riboswitches were placed in tandem or in combination with a ribozyme or temperature-responsive RNA thermometer resulting in new functionalities. Here, we compare natural examples of tandem riboswitches with recently designed artificial RNA regulators suggesting substantial modularity of regulatory RNA elements. Challenges associated with modular RNA design are discussed.

  2. Programmable formation of catalytic RNA triangles and squares by assembling modular RNA enzymes.

    PubMed

    Oi, Hiroki; Fujita, Daisuke; Suzuki, Yuki; Sugiyama, Hiroshi; Endo, Masayuki; Matsumura, Shigeyoshi; Ikawa, Yoshiya

    2017-05-01

    RNA is a biopolymer that is attractive for constructing nano-scale objects with complex structures. Three-dimensional (3D) structures of naturally occurring RNAs often have modular architectures. The 3D structure of a group I (GI) ribozyme from Tetrahymena has a typical modular architecture, which can be separated into two structural modules (ΔP5 and P5abc). The fully active ribozyme can be reconstructed by assembling the two separately prepared modules through highly specific and strong assembly between ΔP5 ribozyme and P5abc RNA. Such non-covalent assembly of the two modules allows the design of polygonal RNA nano-structures. Through rational redesign of the parent GI ribozyme, we constructed variant GI ribozymes as unit RNAs for polygonal-shaped (closed) oligomers with catalytic activity. Programmed trimerization and tetramerization of the unit RNAs afforded catalytically active nano-sized RNA triangles and squares, the structures of which were directly observed by atomic force microscopy (AFM). © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  3. Features of Modularly Assembled Compounds That Impart Bioactivity Against an RNA Target

    PubMed Central

    Rzuczek, Suzanne G.; Gao, Yu; Tang, Zhen-Zhi; Thornton, Charles A.; Kodadek, Thomas; Disney, Matthew D.

    2013-01-01

    Transcriptomes provide a myriad of potential RNAs that could be the targets of therapeutics or chemical genetic probes of function. Cell permeable small molecules, however, generally do not exploit these targets, owing to the difficulty in the design of high affinity, specific small molecules targeting RNA. As part of a general program to study RNA function using small molecules, we designed bioactive, modularly assembled small molecules that target the non-coding expanded RNA repeat that causes myotonic dystrophy type 1 (DM1), r(CUG)exp. Herein, we present a rigorous study to elucidate features in modularly assembled compounds that afford bioactivity. Different modular assembly scaffolds were investigated including polyamines, α-peptides, β-peptides, and peptide tertiary amides (PTAs). Based on activity as assessed by improvement of DM1-associated defects, stability against proteases, cellular permeability, and toxicity, we discovered that constrained backbones, namely PTAs, are optimal. Notably, we determined that r(CUG)exp is the target of the optimal PTA in cellular models and that the optimal PTA improves DM1-associated defects in a mouse model. Biophysical analyses were employed to investigate potential sources of bioactivity. These investigations show that modularly assembled compounds have increased residence times on their targets and faster on rates than the RNA-binding modules from which they were derived and faster on rates than the protein that binds r(CUG)exp, the inactivation of which gives rise to DM1-associated defects. These studies provide information about features of small molecules that are programmable for targeting RNA, allowing for the facile optimization of therapeutics or chemical probes against other cellular RNA targets. PMID:24032410

  4. Features of modularly assembled compounds that impart bioactivity against an RNA target.

    PubMed

    Rzuczek, Suzanne G; Gao, Yu; Tang, Zhen-Zhi; Thornton, Charles A; Kodadek, Thomas; Disney, Matthew D

    2013-10-18

    Transcriptomes provide a myriad of potential RNAs that could be the targets of therapeutics or chemical genetic probes of function. Cell-permeable small molecules, however, generally do not exploit these targets, owing to the difficulty in the design of high affinity, specific small molecules targeting RNA. As part of a general program to study RNA function using small molecules, we designed bioactive, modularly assembled small molecules that target the noncoding expanded RNA repeat that causes myotonic dystrophy type 1 (DM1), r(CUG)(exp). Herein, we present a rigorous study to elucidate features in modularly assembled compounds that afford bioactivity. Different modular assembly scaffolds were investigated, including polyamines, α-peptides, β-peptides, and peptide tertiary amides (PTAs). On the basis of activity as assessed by improvement of DM1-associated defects, stability against proteases, cellular permeability, and toxicity, we discovered that constrained backbones, namely, PTAs, are optimal. Notably, we determined that r(CUG)(exp) is the target of the optimal PTA in cellular models and that the optimal PTA improves DM1-associated defects in a mouse model. Biophysical analyses were employed to investigate potential sources of bioactivity. These investigations show that modularly assembled compounds have increased residence times on their targets and faster on rates than the RNA-binding modules from which they were derived. Moreover, they have faster on rates than the protein that binds r(CUG)(exp), the inactivation of which gives rise to DM1-associated defects. These studies provide information about features of small molecules that are programmable for targeting RNA, allowing for the facile optimization of therapeutics or chemical probes against other cellular RNA targets.

  5. RNA Graph Partitioning for the Discovery of RNA Modularity: A Novel Application of Graph Partition Algorithm to Biology

    PubMed Central

    Elmetwaly, Shereef; Schlick, Tamar

    2014-01-01

    Graph representations have been widely used to analyze and design various economic, social, military, political, and biological networks. In systems biology, networks of cells and organs are useful for understanding disease and medical treatments and, in structural biology, structures of molecules can be described, including RNA structures. In our RNA-As-Graphs (RAG) framework, we represent RNA structures as tree graphs by translating unpaired regions into vertices and helices into edges. Here we explore the modularity of RNA structures by applying graph partitioning known in graph theory to divide an RNA graph into subgraphs. To our knowledge, this is the first application of graph partitioning to biology, and the results suggest a systematic approach for modular design in general. The graph partitioning algorithms utilize mathematical properties of the Laplacian eigenvector (µ2) corresponding to the second eigenvalues (λ2) associated with the topology matrix defining the graph: λ2 describes the overall topology, and the sum of µ2′s components is zero. The three types of algorithms, termed median, sign, and gap cuts, divide a graph by determining nodes of cut by median, zero, and largest gap of µ2′s components, respectively. We apply these algorithms to 45 graphs corresponding to all solved RNA structures up through 11 vertices (∼220 nucleotides). While we observe that the median cut divides a graph into two similar-sized subgraphs, the sign and gap cuts partition a graph into two topologically-distinct subgraphs. We find that the gap cut produces the best biologically-relevant partitioning for RNA because it divides RNAs at less stable connections while maintaining junctions intact. The iterative gap cuts suggest basic modules and assembly protocols to design large RNA structures. Our graph substructuring thus suggests a systematic approach to explore the modularity of biological networks. In our applications to RNA structures, subgraphs also suggest

  6. Rational and Modular Design of Potent Ligands Targeting the RNA that Causes Myotonic Dystrophy 2

    PubMed Central

    Lee, Melissa M.; Pushechnikov, Alexei; Disney, Matthew D.

    2009-01-01

    Most ligands targeting RNA are identified through screening a therapeutic target for binding members of a ligand library. A potential alternative way to construct RNA binders is through rational design using information about the RNA motifs ligands prefer to bind. Herein, we describe such an approach to design modularly assembled ligands targeting the RNA that causes myotonic dystrophy type 2 (DM2), a currently untreatable disease. A previous study identified that 6′-N-5-hexynoate kanamycin A (1) prefers to bind 2×2 nucleotide, pyrimidine-rich RNA internal loops. Multiple copies of such loops were found in the RNA hairpin that causes DM2. The 1 ligand was then modularly displayed on a peptoid scaffold with varied number and spacing to target several internal loops simultaneously. Modularly assembled ligands were tested for binding to a series of RNAs and for inhibiting the formation of the toxic DM2 RNA-muscleblind protein (MBNL-1) interaction. The most potent ligand displays three 1 modules, each separated by four spacing submonomers, and inhibits the formation of the RNA-protein complex with an IC50 of 25 nM. This ligand is higher affinity and more specific for binding DM2 RNA than MBNL-1. It binds the DM2 RNA at least 20-times more tightly than related RNAs and 15-fold more tightly than MBNL-1. A related control peptoid displaying 6′-N-5-hexynoate neamine (2) is >100-fold less potent at inhibiting the RNA-protein interaction and binds to DM2 RNA >125-fold more weakly. Uptake studies into a mouse myoblast cell line also show that the most potent ligand is cell permeable. PMID:19348464

  7. Engineering modular ‘ON’ RNA switches using biological components

    PubMed Central

    Ceres, Pablo; Trausch, Jeremiah J.; Batey, Robert T.

    2013-01-01

    Riboswitches are cis-acting regulatory elements broadly distributed in bacterial mRNAs that control a wide range of critical metabolic activities. Expression is governed by two distinct domains within the mRNA leader: a sensory ‘aptamer domain’ and a regulatory ‘expression platform’. Riboswitches have also received considerable attention as important tools in synthetic biology because of their conceptually simple structure and the ability to obtain aptamers that bind almost any conceivable small molecule using in vitro selection (referred to as SELEX). In the design of artificial riboswitches, a significant hurdle has been to couple the two domains enabling their efficient communication. We previously demonstrated that biological transcriptional ‘OFF’ expression platforms are easily coupled to diverse aptamers, both biological and SELEX-derived, using simple design rules. Here, we present two modular transcriptional ‘ON’ riboswitch expression platforms that are also capable of hosting foreign aptamers. We demonstrate that these biological parts can be used to facilely generate artificial chimeric riboswitches capable of robustly regulating transcription both in vitro and in vivo. We expect that these modular expression platforms will be of great utility for various synthetic biological applications that use RNA-based biosensors. PMID:23999097

  8. Generation and development of RNA ligase ribozymes with modular architecture through "design and selection".

    PubMed

    Fujita, Yuki; Ishikawa, Junya; Furuta, Hiroyuki; Ikawa, Yoshiya

    2010-08-26

    In vitro selection with long random RNA libraries has been used as a powerful method to generate novel functional RNAs, although it often requires laborious structural analysis of isolated RNA molecules. Rational RNA design is an attractive alternative to avoid this laborious step, but rational design of catalytic modules is still a challenging task. A hybrid strategy of in vitro selection and rational design has been proposed. With this strategy termed "design and selection," new ribozymes can be generated through installation of catalytic modules onto RNA scaffolds with defined 3D structures. This approach, the concept of which was inspired by the modular architecture of naturally occurring ribozymes, allows prediction of the overall architectures of the resulting ribozymes, and the structural modularity of the resulting ribozymes allows modification of their structures and functions. In this review, we summarize the design, generation, properties, and engineering of four classes of ligase ribozyme generated by design and selection.

  9. Rational Modular RNA Engineering Based on In Vivo Profiling of Structural Accessibility.

    PubMed

    Leistra, Abigail N; Amador, Paul; Buvanendiran, Aishwarya; Moon-Walker, Alex; Contreras, Lydia M

    2017-12-15

    Bacterial small RNAs (sRNAs) have been established as powerful parts for controlling gene expression. However, development and application of engineered sRNAs has primarily focused on regulating novel synthetic targets. In this work, we demonstrate a rational modular RNA engineering approach that uses in vivo structural accessibility measurements to tune the regulatory activity of a multisubstrate sRNA for differential control of its native target network. Employing the CsrB global sRNA regulator as a model system, we use published in vivo structural accessibility data to infer the contribution of its local structures (substructures) to function and select a subset for engineering. We then modularly recombine the selected substructures, differentially representing those of presumed high or low functional contribution, to build a library of 21 CsrB variants. Using fluorescent translational reporter assays, we demonstrate that the CsrB variants achieve a 5-fold gradient of control of well-characterized Csr network targets. Interestingly, results suggest that less conserved local structures within long, multisubstrate sRNAs may represent better targets for rational engineering than their well-conserved counterparts. Lastly, mapping the impact of sRNA variants on a signature Csr network phenotype indicates the potential of this approach for tuning the activity of global sRNA regulators in the context of metabolic engineering applications.

  10. Specific and Modular Binding Code for Cytosine Recognition in Pumilio/FBF (PUF) RNA-binding Domains

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

    Dong, Shuyun; Wang, Yang; Cassidy-Amstutz, Caleb

    2011-10-28

    Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and themore » cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence.« less

  11. The modularity and dynamicity of miRNA-mRNA interactions in high-grade serous ovarian carcinomas and the prognostic implication.

    PubMed

    Zhang, Wensheng; Edwards, Andrea; Fan, Wei; Flemington, Erik K; Zhang, Kun

    2016-08-01

    Ovarian carcinoma is the fifth-leading cause of cancer death among women in the United States. Major reasons for this persistent mortality include the poor understanding of the underlying biology and a lack of reliable biomarkers. Previous studies have shown that aberrantly expressed MicroRNAs (miRNAs) are involved in carcinogenesis and tumor progression by post-transcriptionally regulating gene expression. However, the interference of miRNAs in tumorigenesis is quite complicated and far from being fully understood. In this work, by an integrative analysis of mRNA expression, miRNA expression and clinical data published by The Cancer Genome Atlas (TCGA), we studied the modularity and dynamicity of miRNA-mRNA interactions and the prognostic implications in high-grade serous ovarian carcinomas. With the top transcriptional correlations (Bonferroni-adjusted p-value<0.01) as inputs, we identified five miRNA-mRNA module pairs (MPs), each of which included one positive-connection (correlation) module and one negative-connection (correlation) module. The number of miRNAs or mRNAs in each module varied from 3 to 7 or from 2 to 873. Among the four major negative-connection modules, three fit well with the widely accepted miRNA-mediated post-transcriptional regulation theory. These modules were enriched with the genes relevant to cell cycle and immune response. Moreover, we proposed two novel algorithms to reveal the group or sample specific dynamic regulations between these two RNA classes. The obtained miRNA-mRNA dynamic network contains 3350 interactions captured across different cancer progression stages or tumor grades. We found that those dynamic interactions tended to concentrate on a few miRNAs (e.g. miRNA-936), and were more likely present on the miRNA-mRNA pairs outside the discovered modules. In addition, we also pinpointed a robust prognostic signature consisting of 56 modular protein-coding genes, whose co-expression patterns were predictive for the survival

  12. Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments.

    PubMed

    Lott, Steffen C; Wolfien, Markus; Riege, Konstantin; Bagnacani, Andrea; Wolkenhauer, Olaf; Hoffmann, Steve; Hess, Wolfgang R

    2017-11-10

    RNA-Sequencing (RNA-Seq) has become a widely used approach to study quantitative and qualitative aspects of transcriptome data. The variety of RNA-Seq protocols, experimental study designs and the characteristic properties of the organisms under investigation greatly affect downstream and comparative analyses. In this review, we aim to explain the impact of structured pre-selection, classification and integration of best-performing tools within modularized data analysis workflows and ready-to-use computing infrastructures towards experimental data analyses. We highlight examples for workflows and use cases that are presented for pro-, eukaryotic and mixed dual RNA-Seq (meta-transcriptomics) experiments. In addition, we are summarizing the expertise of the laboratories participating in the project consortium "Structured Analysis and Integration of RNA-Seq experiments" (de.STAIR) and its integration with the Galaxy-workbench of the RNA Bioinformatics Center (RBC). Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  13. Rational design of bioactive, modularly assembled aminoglycosides targeting the RNA that causes myotonic dystrophy type 1.

    PubMed

    Childs-Disney, Jessica L; Parkesh, Raman; Nakamori, Masayuki; Thornton, Charles A; Disney, Matthew D

    2012-12-21

    Myotonic dystrophy type 1 (DM1) is caused when an expanded r(CUG) repeat (r(CUG)(exp)) binds the RNA splicing regulator muscleblind-like 1 protein (MBNL1) as well as other proteins. Previously, we reported that modularly assembled small molecules displaying a 6'-N-5-hexynoate kanamycin A RNA-binding module (K) on a peptoid backbone potently inhibit the binding of MBNL1 to r(CUG)(exp). However, these parent compounds are not appreciably active in cell-based models of DM1. The lack of potency was traced to suboptimal cellular permeability and localization. To improve these properties, second-generation compounds that are conjugated to a d-Arg(9) molecular transporter were synthesized. These modified compounds enter cells in higher concentrations than the parent compounds and are efficacious in cell-based DM1 model systems at low micromolar concentrations. In particular, they improve three defects that are the hallmarks of DM1: a translational defect due to nuclear retention of transcripts containing r(CUG)(exp); pre-mRNA splicing defects due to inactivation of MBNL1; and the formation of nuclear foci. The best compound in cell-based studies was tested in a mouse model of DM1. Modest improvement of pre-mRNA splicing defects was observed. These studies suggest that a modular assembly approach can afford bioactive compounds that target RNA.

  14. Rational Design of Bioactive, Modularly Assembled Aminoglycosides Targeting the RNA that Causes Myotonic Dystrophy Type 1

    PubMed Central

    Childs-Disney, Jessica L.; Parkesh, Raman; Nakamori, Masayuki; Thornton, Charles A.; Disney, Matthew D.

    2012-01-01

    Myotonic dystrophy type 1 (DM1) is caused when an expanded r(CUG) repeat (r(CUG)exp) binds the RNA splicing regulator muscleblind-like 1 protein (MBNL1) as well as other proteins. Previously, we reported that modularly assembled small molecules displaying a 6′-N-5-hexynoate kanamycin A RNA-binding module (K) on a peptoid backbone potently inhibit the binding of MBNL1 to r(CUG)exp. However, these parent compounds are not appreciably active in cell-based models of DM1. The lack of potency was traced to suboptimal cellular permeability and localization. To improve these properties, second-generation compounds that are conjugated to a D-Arg9 molecular transporter were synthesized. These modified compounds enter cells in higher concentrations than the parent compounds and are efficacious in cell-based DM1 model systems at low micromolar concentrations. In particular, they improve three defects that are the hallmarks of DM1: a translational defect due to nuclear retention of transcripts containing r(CUG)exp; pre-mRNA splicing defects due to inactivation of MBNL1; and the formation of nuclear foci. The best compound in cell-based studies was tested in a mouse model of DM1. Modest improvement of pre-mRNA splicing defects was observed. These studies suggest that a modular assembly approach can afford bioactive compounds that target RNA. PMID:23130637

  15. Single-cell isolation by a modular single-cell pipette for RNA-sequencing.

    PubMed

    Zhang, Kai; Gao, Min; Chong, Zechen; Li, Ying; Han, Xin; Chen, Rui; Qin, Lidong

    2016-11-29

    Single-cell transcriptome sequencing highly requires a convenient and reliable method to rapidly isolate a live cell into a specific container such as a PCR tube. Here, we report a modular single-cell pipette (mSCP) consisting of three modular components, a SCP-Tip, an air-displacement pipette (ADP), and ADP-Tips, that can be easily assembled, disassembled, and reassembled. By assembling the SCP-Tip containing a hydrodynamic trap, the mSCP can isolate single cells from 5-10 cells per μL of cell suspension. The mSCP is compatible with microscopic identification of captured single cells to finally achieve 100% single-cell isolation efficiency. The isolated live single cells are in submicroliter volumes and well suitable for single-cell PCR analysis and RNA-sequencing. The mSCP possesses merits of convenience, rapidness, and high efficiency, making it a powerful tool to isolate single cells for transcriptome analysis.

  16. The dawn of the RNA World: Toward functional complexity through ligation of random RNA oligomers

    PubMed Central

    Briones, Carlos; Stich, Michael; Manrubia, Susanna C.

    2009-01-01

    A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered. PMID:19318464

  17. Modular Ligation Extension of Guide RNA Operons (LEGO) for Multiplexed dCas9 Regulation of Metabolic Pathways in Saccharomyces cerevisiae.

    PubMed

    Deaner, Matthew; Holzman, Allison; Alper, Hal S

    2018-04-16

    Metabolic engineering typically utilizes a suboptimal step-wise gene target optimization approach to parse a highly connected and regulated cellular metabolism. While the endonuclease-null CRISPR/Cas system has enabled gene expression perturbations without genetic modification, it has been mostly limited to small sets of gene targets in eukaryotes due to inefficient methods to assemble and express large sgRNA operons. In this work, we develop a TEF1p-tRNA expression system and demonstrate that the use of tRNAs as splicing elements flanking sgRNAs provides higher efficiency than both Pol III and ribozyme-based expression across a variety of single sgRNA and multiplexed contexts. Next, we devise and validate a scheme to allow modular construction of tRNA-sgRNA (TST) operons using an iterative Type IIs digestion/ligation extension approach, termed CRISPR-Ligation Extension of sgRNA Operons (LEGO). This approach enables facile construction of large TST operons. We demonstrate this utility by constructing a metabolic rewiring prototype for 2,3-butanediol production in 2 distinct yeast strain backgrounds. These results demonstrate that our approach can act as a surrogate for traditional genetic modification on a much shorter design-cycle timescale. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Modular transcriptional repertoire and MicroRNA target analyses characterize genomic dysregulation in the thymus of Down syndrome infants

    PubMed Central

    Moreira-Filho, Carlos Alberto; Bando, Silvia Yumi; Bertonha, Fernanda Bernardi; Silva, Filipi Nascimento; da Fontoura Costa, Luciano; Ferreira, Leandro Rodrigues; Furlanetto, Glaucio; Chacur, Paulo; Zerbini, Maria Claudia Nogueira; Carneiro-Sampaio, Magda

    2016-01-01

    Trisomy 21-driven transcriptional alterations in human thymus were characterized through gene coexpression network (GCN) and miRNA-target analyses. We used whole thymic tissue - obtained at heart surgery from Down syndrome (DS) and karyotipically normal subjects (CT) - and a network-based approach for GCN analysis that allows the identification of modular transcriptional repertoires (communities) and the interactions between all the system's constituents through community detection. Changes in the degree of connections observed for hierarchically important hubs/genes in CT and DS networks corresponded to community changes. Distinct communities of highly interconnected genes were topologically identified in these networks. The role of miRNAs in modulating the expression of highly connected genes in CT and DS was revealed through miRNA-target analysis. Trisomy 21 gene dysregulation in thymus may be depicted as the breakdown and altered reorganization of transcriptional modules. Leading networks acting in normal or disease states were identified. CT networks would depict the “canonical” way of thymus functioning. Conversely, DS networks represent a “non-canonical” way, i.e., thymic tissue adaptation under trisomy 21 genomic dysregulation. This adaptation is probably driven by epigenetic mechanisms acting at chromatin level and through the miRNA control of transcriptional programs involving the networks' high-hierarchy genes. PMID:26848775

  19. SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans.

    PubMed

    Kel, Ivan; Chang, Zisong; Galluccio, Nadia; Romeo, Margherita; Beretta, Stefano; Diomede, Luisa; Mezzelani, Alessandra; Milanesi, Luciano; Dieterich, Christoph; Merelli, Ivan

    2016-10-18

    The interpretation of genome-wide association study is difficult, as it is hard to understand how polymorphisms can affect gene regulation, in particular for trans-regulatory elements located far from their controlling gene. Using RNA or protein expression data as phenotypes, it is possible to correlate their variations with specific genotypes. This technique is usually referred to as expression Quantitative Trait Loci (eQTLs) analysis and only few packages exist for the integration of genotype patterns and expression profiles. In particular, tools are needed for the analysis of next-generation sequencing (NGS) data on a genome-wide scale, which is essential to identify eQTLs able to control a large number of genes (hotspots). Here we present SPIRE (Software for Polymorphism Identification Regulating Expression), a generic, modular and functionally highly flexible pipeline for eQTL processing. SPIRE integrates different univariate and multivariate approaches for eQTL analysis, paying particular attention to the scalability of the procedure in order to support cis- as well as trans-mapping, thus allowing the identification of hotspots in NGS data. In particular, we demonstrated how SPIRE can handle big association study datasets, reproducing published results and improving the identification of trans-eQTLs. Furthermore, we employed the pipeline to analyse novel data concerning the genotypes of two different C. elegans strains (N2 and Hawaii) and related miRNA expression data, obtained using RNA-Seq. A miRNA regulatory hotspot was identified in chromosome 1, overlapping the transcription factor grh-1, known to be involved in the early phases of embryonic development of C. elegans. In a follow-up qPCR experiment we were able to verify most of the predicted eQTLs, as well as to show, for a novel miRNA, a significant difference in the sequences of the two analysed strains of C. elegans. SPIRE is publicly available as open source software at , together with some example

  20. Design strategies to address the effect of hydrophobic epitope on stability and in vitro assembly of modular virus‐like particle

    PubMed Central

    Tekewe, Alemu; Connors, Natalie K.; Middelberg, Anton P. J.

    2016-01-01

    Abstract Virus‐like particles (VLPs) and capsomere subunits have shown promising potential as safe and effective vaccine candidates. They can serve as platforms for the display of foreign epitopes on their surfaces in a modular architecture. Depending on the physicochemical properties of the antigenic modules, modularization may affect the expression, solubility and stability of capsomeres, and VLP assembly. In this study, three module designs of a rotavirus hydrophobic peptide (RV10) were synthesized using synthetic biology. Among the three synthetic modules, modularization of the murine polyomavirus VP1 with a single copy of RV10 flanked by long linkers and charged residues resulted in the expression of stable modular capsomeres. Further employing the approach of module titration of RV10 modules on each capsomere via Escherichia coli co‐expression of unmodified VP1 and modular VP1‐RV10 successfully translated purified modular capomeres into modular VLPs when assembled in vitro. Our results demonstrate that tailoring the physicochemical properties of modules to enhance modular capsomeres stability is achievable through synthetic biology designs. Combined with module titration strategy to avoid steric hindrance to intercapsomere interactions, this allows bioprocessing of bacterially produced in vitro assembled modular VLPs. PMID:27222486

  1. Design strategies to address the effect of hydrophobic epitope on stability and in vitro assembly of modular virus-like particle.

    PubMed

    Tekewe, Alemu; Connors, Natalie K; Middelberg, Anton P J; Lua, Linda H L

    2016-08-01

    Virus-like particles (VLPs) and capsomere subunits have shown promising potential as safe and effective vaccine candidates. They can serve as platforms for the display of foreign epitopes on their surfaces in a modular architecture. Depending on the physicochemical properties of the antigenic modules, modularization may affect the expression, solubility and stability of capsomeres, and VLP assembly. In this study, three module designs of a rotavirus hydrophobic peptide (RV10) were synthesized using synthetic biology. Among the three synthetic modules, modularization of the murine polyomavirus VP1 with a single copy of RV10 flanked by long linkers and charged residues resulted in the expression of stable modular capsomeres. Further employing the approach of module titration of RV10 modules on each capsomere via Escherichia coli co-expression of unmodified VP1 and modular VP1-RV10 successfully translated purified modular capomeres into modular VLPs when assembled in vitro. Our results demonstrate that tailoring the physicochemical properties of modules to enhance modular capsomeres stability is achievable through synthetic biology designs. Combined with module titration strategy to avoid steric hindrance to intercapsomere interactions, this allows bioprocessing of bacterially produced in vitro assembled modular VLPs. © 2016 The Protein Society.

  2. Messenger RNA (mRNA) nanoparticle tumour vaccination

    NASA Astrophysics Data System (ADS)

    Phua, Kyle K. L.; Nair, Smita K.; Leong, Kam W.

    2014-06-01

    Use of mRNA-based vaccines for tumour immunotherapy has gained increasing attention in recent years. A growing number of studies applying nanomedicine concepts to mRNA tumour vaccination show that the mRNA delivered in nanoparticle format can generate a more robust immune response. Advances in the past decade have deepened our understanding of gene delivery barriers, mRNA's biological stability and immunological properties, and support the notion for engineering innovations tailored towards a more efficient mRNA nanoparticle vaccine delivery system. In this review we will first examine the suitability of mRNA for engineering manipulations, followed by discussion of a model framework that highlights the barriers to a robust anti-tumour immunity mediated by mRNA encapsulated in nanoparticles. Finally, by consolidating existing literature on mRNA nanoparticle tumour vaccination within the context of this framework, we aim to identify bottlenecks that can be addressed by future nanoengineering research.

  3. A modular platform for targeted RNAi therapeutics

    NASA Astrophysics Data System (ADS)

    Kedmi, Ranit; Veiga, Nuphar; Ramishetti, Srinivas; Goldsmith, Meir; Rosenblum, Daniel; Dammes, Niels; Hazan-Halevy, Inbal; Nahary, Limor; Leviatan-Ben-Arye, Shani; Harlev, Michael; Behlke, Mark; Benhar, Itai; Lieberman, Judy; Peer, Dan

    2018-01-01

    Previous studies have identified relevant genes and signalling pathways that are hampered in human disorders as potential candidates for therapeutics. Developing nucleic acid-based tools to manipulate gene expression, such as short interfering RNAs1-3 (siRNAs), opens up opportunities for personalized medicine. Yet, although major progress has been made in developing siRNA targeted delivery carriers, mainly by utilizing monoclonal antibodies (mAbs) for targeting4-8, their clinical translation has not occurred. This is in part because of the massive development and production requirements and the high batch-to-batch variability of current technologies, which rely on chemical conjugation. Here we present a self-assembled modular platform that enables the construction of a theoretically unlimited repertoire of siRNA targeted carriers. The self-assembly of the platform is based on a membrane-anchored lipoprotein that is incorporated into siRNA-loaded lipid nanoparticles that interact with the antibody crystallizable fragment (Fc) domain. We show that a simple switch of eight different mAbs redirects the specific uptake of siRNAs by diverse leukocyte subsets in vivo. The therapeutic potential of the platform is demonstrated in an inflammatory bowel disease model by targeting colon macrophages to reduce inflammatory symptoms, and in a Mantle Cell Lymphoma xenograft model by targeting cancer cells to induce cell death and improve survival. This modular delivery platform represents a milestone in the development of precision medicine.

  4. A modular platform for targeted RNAi therapeutics.

    PubMed

    Kedmi, Ranit; Veiga, Nuphar; Ramishetti, Srinivas; Goldsmith, Meir; Rosenblum, Daniel; Dammes, Niels; Hazan-Halevy, Inbal; Nahary, Limor; Leviatan-Ben-Arye, Shani; Harlev, Michael; Behlke, Mark; Benhar, Itai; Lieberman, Judy; Peer, Dan

    2018-03-01

    Previous studies have identified relevant genes and signalling pathways that are hampered in human disorders as potential candidates for therapeutics. Developing nucleic acid-based tools to manipulate gene expression, such as short interfering RNAs 1-3 (siRNAs), opens up opportunities for personalized medicine. Yet, although major progress has been made in developing siRNA targeted delivery carriers, mainly by utilizing monoclonal antibodies (mAbs) for targeting 4-8 , their clinical translation has not occurred. This is in part because of the massive development and production requirements and the high batch-to-batch variability of current technologies, which rely on chemical conjugation. Here we present a self-assembled modular platform that enables the construction of a theoretically unlimited repertoire of siRNA targeted carriers. The self-assembly of the platform is based on a membrane-anchored lipoprotein that is incorporated into siRNA-loaded lipid nanoparticles that interact with the antibody crystallizable fragment (Fc) domain. We show that a simple switch of eight different mAbs redirects the specific uptake of siRNAs by diverse leukocyte subsets in vivo. The therapeutic potential of the platform is demonstrated in an inflammatory bowel disease model by targeting colon macrophages to reduce inflammatory symptoms, and in a Mantle Cell Lymphoma xenograft model by targeting cancer cells to induce cell death and improve survival. This modular delivery platform represents a milestone in the development of precision medicine.

  5. 5S rRNA-derived and tRNA-derived SINEs in fruit bats.

    PubMed

    Gogolevsky, Konstantin P; Vassetzky, Nikita S; Kramerov, Dmitri A

    2009-05-01

    Most short retroposons (SINEs) descend from cellular tRNA of 7SL RNA. Here, four new SINEs were found in megabats (Megachiroptera) but neither in microbats nor in other mammals. Two of them, MEG-RS and MEG-RL, descend from another cellular RNA, 5S rRNA; one (MEG-T2) is a tRNA-derived SINE; and MEG-TR is a hybrid tRNA/5S rRNA SINE. Insertion locus analysis suggests that these SINEs were active in the recent fruit bat evolution. Analysis of MEG-RS and MEG-RL in comparison with other few 5S rRNA-derived SINEs demonstrates that the internal RNA polymerase III promoter is their most invariant region, while the secondary structure is more variable. The mechanisms underlying the modular structure of these and other SINEs as well as their variation are discussed. The scenario of evolution of MEG SINEs is proposed.

  6. A modular positron camera for the study of industrial processes

    NASA Astrophysics Data System (ADS)

    Leadbeater, T. W.; Parker, D. J.

    2011-10-01

    Positron imaging techniques rely on the detection of the back-to-back annihilation photons arising from positron decay within the system under study. A standard technique, called positron emitting particle tracking (PEPT) [1], uses a number of these detected events to rapidly determine the position of a positron emitting tracer particle introduced into the system under study. Typical applications of PEPT are in the study of granular and multi-phase materials in the disciplines of engineering and the physical sciences. Using components from redundant medical PET scanners a modular positron camera has been developed. This camera consists of a number of small independent detector modules, which can be arranged in custom geometries tailored towards the application in question. The flexibility of the modular camera geometry allows for high photon detection efficiency within specific regions of interest, the ability to study large and bulky systems and the application of PEPT to difficult or remote processes as the camera is inherently transportable.

  7. Modular protein expression by RNA trans-splicing enables flexible expression of antibody formats in mammalian cells from a dual-host phage display vector.

    PubMed

    Shang, Yonglei; Tesar, Devin; Hötzel, Isidro

    2015-10-01

    A recently described dual-host phage display vector that allows expression of immunoglobulin G (IgG) in mammalian cells bypasses the need for subcloning of phage display clone inserts to mammalian vectors for IgG expression in large antibody discovery and optimization campaigns. However, antibody discovery and optimization campaigns usually need different antibody formats for screening, requiring reformatting of the clones in the dual-host phage display vector to an alternative vector. We developed a modular protein expression system mediated by RNA trans-splicing to enable the expression of different antibody formats from the same phage display vector. The heavy-chain region encoded by the phage display vector is directly and precisely fused to different downstream heavy-chain sequences encoded by complementing plasmids simply by joining exons in different pre-mRNAs by trans-splicing. The modular expression system can be used to efficiently express structurally correct IgG and Fab fragments or other antibody formats from the same phage display clone in mammalian cells without clone reformatting. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  8. Modular microfluidic systems using reversibly attached PDMS fluid control modules

    NASA Astrophysics Data System (ADS)

    Skafte-Pedersen, Peder; Sip, Christopher G.; Folch, Albert; Dufva, Martin

    2013-05-01

    The use of soft lithography-based poly(dimethylsiloxane) (PDMS) valve systems is the dominating approach for high-density microscale fluidic control. Integrated systems enable complex flow control and large-scale integration, but lack modularity. In contrast, modular systems are attractive alternatives to integration because they can be tailored for different applications piecewise and without redesigning every element of the system. We present a method for reversibly coupling hard materials to soft lithography defined systems through self-aligning O-ring features thereby enabling easy interfacing of complex-valve-based systems with simpler detachable units. Using this scheme, we demonstrate the seamless interfacing of a PDMS-based fluid control module with hard polymer chips. In our system, 32 self-aligning O-ring features protruding from the PDMS fluid control module form chip-to-control module interconnections which are sealed by tightening four screws. The interconnection method is robust and supports complex fluidic operations in the reversibly attached passive chip. In addition, we developed a double-sided molding method for fabricating PDMS devices with integrated through-holes. The versatile system facilitates a wide range of applications due to the modular approach, where application specific passive chips can be readily attached to the flow control module.

  9. Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging.

    PubMed

    Fang, Yun; Shu, Dan; Xiao, Feng; Guo, Peixuan; Qin, Peter Z

    2008-08-08

    The bacteriophage phi29 DNA packaging motor is a protein/RNA complex that can produce strong force to condense the linear-double-stranded DNA genome into a pre-formed protein capsid. The RNA component, called the packaging RNA (pRNA), utilizes magnesium-dependent inter-molecular base-pairing interactions to form ring-shaped complexes. The pRNA is a class of non-coding RNA, interacting with phi29 motor proteins to enable DNA packaging. Here, we report a two-piece chimeric pRNA construct that is fully competent in interacting with partner pRNA to form ring-shaped complexes, in packaging DNA via the motor, and in assembling infectious phi29 virions in vitro. This is the first example of a fully functional pRNA assembled using two non-covalently interacting fragments. The results support the notion of modular pRNA architecture in the phi29 packaging motor.

  10. Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging

    PubMed Central

    Fang, Yun; Shu, Dan; Xiao, Feng; Guo, Peixuan; Qin, Peter Z.

    2008-01-01

    The bacteriophage phi29 DNA packaging motor is a protein/RNA complex that can produce strong force to condense the linear-double stranded DNA genome into a pre-formed protein capsid. The RNA component, called the packaging RNA (pRNA), utilizes magnesium-dependent intermolecular base-pairing interactions to form ring-shaped complexes. The pRNA is a class of non-coding RNA, interacting with phi29 motor proteins to enable DNA packaging. Here, we report a 2-piece chimeric pRNA construct that is fully competent in interacting with partner pRNA to form ring-shaped complexes, in packaging DNA via the motor, and in assembling infectious phi29 virions in vitro. This is the first example of a fully functional pRNA assembled using two non-covalently interacting fragments. The results support the notion of modular pRNA architecture in the phi29 packaging motor. PMID:18514064

  11. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types

    PubMed Central

    Lever, Mark A.; Torti, Andrea; Eickenbusch, Philip; Michaud, Alexander B.; Šantl-Temkiv, Tina; Jørgensen, Bo Barker

    2015-01-01

    A method for the extraction of nucleic acids from a wide range of environmental samples was developed. This method consists of several modules, which can be individually modified to maximize yields in extractions of DNA and RNA or separations of DNA pools. Modules were designed based on elaborate tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world's oceans and the deepest borehole ever studied by scientific ocean drilling. Extraction yields of DNA and RNA are higher than with widely used commercial kits, indicating an advantage to optimizing extraction procedures to match specific sample characteristics. The ability to separate soluble extracellular DNA pools without cell lysis from intracellular and particle-complexed DNA pools may enable new insights into the cycling and preservation of DNA in environmental samples in the future. A general protocol is outlined, along with recommendations for optimizing this general protocol for specific sample types and research goals. PMID:26042110

  12. The relative efficiency of modular and non-modular networks of different size

    PubMed Central

    Tosh, Colin R.; McNally, Luke

    2015-01-01

    Most biological networks are modular but previous work with small model networks has indicated that modularity does not necessarily lead to increased functional efficiency. Most biological networks are large, however, and here we examine the relative functional efficiency of modular and non-modular neural networks at a range of sizes. We conduct a detailed analysis of efficiency in networks of two size classes: ‘small’ and ‘large’, and a less detailed analysis across a range of network sizes. The former analysis reveals that while the modular network is less efficient than one of the two non-modular networks considered when networks are small, it is usually equally or more efficient than both non-modular networks when networks are large. The latter analysis shows that in networks of small to intermediate size, modular networks are much more efficient that non-modular networks of the same (low) connective density. If connective density must be kept low to reduce energy needs for example, this could promote modularity. We have shown how relative functionality/performance scales with network size, but the precise nature of evolutionary relationship between network size and prevalence of modularity will depend on the costs of connectivity. PMID:25631996

  13. Tailored motivational message generation: A model and practical framework for real-time physical activity coaching.

    PubMed

    Op den Akker, Harm; Cabrita, Miriam; Op den Akker, Rieks; Jones, Valerie M; Hermens, Hermie J

    2015-06-01

    This paper presents a comprehensive and practical framework for automatic generation of real-time tailored messages in behavior change applications. Basic aspects of motivational messages are time, intention, content and presentation. Tailoring of messages to the individual user may involve all aspects of communication. A linear modular system is presented for generating such messages. It is explained how properties of user and context are taken into account in each of the modules of the system and how they affect the linguistic presentation of the generated messages. The model of motivational messages presented is based on an analysis of existing literature as well as the analysis of a corpus of motivational messages used in previous studies. The model extends existing 'ontology-based' approaches to message generation for real-time coaching systems found in the literature. Practical examples are given on how simple tailoring rules can be implemented throughout the various stages of the framework. Such examples can guide further research by clarifying what it means to use e.g. user targeting to tailor a message. As primary example we look at the issue of promoting daily physical activity. Future work is pointed out in applying the present model and framework, defining efficient ways of evaluating individual tailoring components, and improving effectiveness through the creation of accurate and complete user- and context models. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. RNA-SeQC: RNA-seq metrics for quality control and process optimization.

    PubMed

    DeLuca, David S; Levin, Joshua Z; Sivachenko, Andrey; Fennell, Timothy; Nazaire, Marc-Danie; Williams, Chris; Reich, Michael; Winckler, Wendy; Getz, Gad

    2012-06-01

    RNA-seq, the application of next-generation sequencing to RNA, provides transcriptome-wide characterization of cellular activity. Assessment of sequencing performance and library quality is critical to the interpretation of RNA-seq data, yet few tools exist to address this issue. We introduce RNA-SeQC, a program which provides key measures of data quality. These metrics include yield, alignment and duplication rates; GC bias, rRNA content, regions of alignment (exon, intron and intragenic), continuity of coverage, 3'/5' bias and count of detectable transcripts, among others. The software provides multi-sample evaluation of library construction protocols, input materials and other experimental parameters. The modularity of the software enables pipeline integration and the routine monitoring of key measures of data quality such as the number of alignable reads, duplication rates and rRNA contamination. RNA-SeQC allows investigators to make informed decisions about sample inclusion in downstream analysis. In summary, RNA-SeQC provides quality control measures critical to experiment design, process optimization and downstream computational analysis. See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.

  15. MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features.

    PubMed

    Xu, Juan; Li, Chuan-Xing; Li, Yong-Sheng; Lv, Jun-Ying; Ma, Ye; Shao, Ting-Ting; Xu, Liang-De; Wang, Ying-Ying; Du, Lei; Zhang, Yun-Peng; Jiang, Wei; Li, Chun-Quan; Xiao, Yun; Li, Xia

    2011-02-01

    Synergistic regulations among multiple microRNAs (miRNAs) are important to understand the mechanisms of complex post-transcriptional regulations in humans. Complex diseases are affected by several miRNAs rather than a single miRNA. So, it is a challenge to identify miRNA synergism and thereby further determine miRNA functions at a system-wide level and investigate disease miRNA features in the miRNA-miRNA synergistic network from a new view. Here, we constructed a miRNA-miRNA functional synergistic network (MFSN) via co-regulating functional modules that have three features: common targets of corresponding miRNA pairs, enriched in the same gene ontology category and close proximity in the protein interaction network. Predicted miRNA synergism is validated by significantly high co-expression of functional modules and significantly negative regulation to functional modules. We found that the MFSN exhibits a scale free, small world and modular architecture. Furthermore, the topological features of disease miRNAs in the MFSN are distinct from non-disease miRNAs. They have more synergism, indicating their higher complexity of functions and are the global central cores of the MFSN. In addition, miRNAs associated with the same disease are close to each other. The structure of the MFSN and the features of disease miRNAs are validated to be robust using different miRNA target data sets.

  16. Modular Fixturing System

    NASA Technical Reports Server (NTRS)

    Littell, Justin Anderson (Inventor); Street, Jon P. (Inventor)

    2017-01-01

    The modular fixturing system of the present invention is modular, reusable and capable of significant customization, both in terms of system radius and system height, allowing it to be arranged and rearranged in numerous unique configurations. The system includes multiple modular stanchions having stanchion shafts and stanchion feet that removably attach to apertures in a table. Angle brackets attached to the modular stanchions support shelves. These shelves in turn provide support to work pieces during fabrication processes such as welding.

  17. Modular synthetic inverters from zinc finger proteins and small RNAs

    DOE PAGES

    Hsia, Justin; Holtz, William J.; Maharbiz, Michel M.; ...

    2016-02-17

    Synthetic zinc finger proteins (ZFPs) can be created to target promoter DNA sequences, repressing transcription. The binding of small RNA (sRNA) to ZFP mRNA creates an ultrasensitive response to generate higher effective Hill coefficients. Here we combined three “off the shelf” ZFPs and three sRNAs to create new modular inverters in E. coli and quantify their behavior using induction fold. We found a general ordering of the effects of the ZFPs and sRNAs on induction fold that mostly held true when combining these parts. We then attempted to construct a ring oscillator using our new inverters. In conclusion, our chosenmore » parts performed insufficiently to create oscillations, but we include future directions for improvement upon our work presented here.« less

  18. Modular entanglement.

    PubMed

    Gualdi, Giulia; Giampaolo, Salvatore M; Illuminati, Fabrizio

    2011-02-04

    We introduce and discuss the concept of modular entanglement. This is the entanglement that is established between the end points of modular systems composed by sets of interacting moduli of arbitrarily fixed size. We show that end-to-end modular entanglement scales in the thermodynamic limit and rapidly saturates with the number of constituent moduli. We clarify the mechanisms underlying the onset of entanglement between distant and noninteracting quantum systems and its optimization for applications to quantum repeaters and entanglement distribution and sharing.

  19. Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics.

    PubMed

    Bisaria, Namita; Greenfeld, Max; Limouse, Charles; Mabuchi, Hideo; Herschlag, Daniel

    2017-09-12

    Decades of study of the architecture and function of structured RNAs have led to the perspective that RNA tertiary structure is modular, made of locally stable domains that retain their structure across RNAs. We formalize a hypothesis inspired by this modularity-that RNA folding thermodynamics and kinetics can be quantitatively predicted from separable energetic contributions of the individual components of a complex RNA. This reconstitution hypothesis considers RNA tertiary folding in terms of ΔG align , the probability of aligning tertiary contact partners, and ΔG tert , the favorable energetic contribution from the formation of tertiary contacts in an aligned state. This hypothesis predicts that changes in the alignment of tertiary contacts from different connecting helices and junctions (ΔG HJH ) or from changes in the electrostatic environment (ΔG +/- ) will not affect the energetic perturbation from a mutation in a tertiary contact (ΔΔG tert ). Consistent with these predictions, single-molecule FRET measurements of folding of model RNAs revealed constant ΔΔG tert values for mutations in a tertiary contact embedded in different structural contexts and under different electrostatic conditions. The kinetic effects of these mutations provide further support for modular behavior of RNA elements and suggest that tertiary mutations may be used to identify rate-limiting steps and dissect folding and assembly pathways for complex RNAs. Overall, our model and results are foundational for a predictive understanding of RNA folding that will allow manipulation of RNA folding thermodynamics and kinetics. Conversely, the approaches herein can identify cases where an independent, additive model cannot be applied and so require additional investigation.

  20. Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines.

    PubMed

    Porciani, David; Cardwell, Leah N; Tawiah, Kwaku D; Alam, Khalid K; Lange, Margaret J; Daniels, Mark A; Burke, Donald H

    2018-06-11

    Large RNAs and ribonucleoprotein complexes have powerful therapeutic potential, but effective cell-targeted delivery tools are limited. Aptamers that internalize into target cells can deliver siRNAs (<15 kDa, 19-21 nt/strand). We demonstrate a modular nanostructure for cellular delivery of large, functional RNA payloads (50-80 kDa, 175-250 nt) by aptamers that recognize multiple human B cell cancer lines and transferrin receptor-expressing cells. Fluorogenic RNA reporter payloads enable accelerated testing of platform designs and rapid evaluation of assembly and internalization. Modularity is demonstrated by swapping in different targeting and payload aptamers. Both modules internalize into leukemic B cell lines and remained colocalized within endosomes. Fluorescence from internalized RNA persists for ≥2 h, suggesting a sizable window for aptamer payloads to exert influence upon targeted cells. This demonstration of aptamer-mediated, cell-internalizing delivery of large RNAs with retention of functional structure raises the possibility of manipulating endosomes and cells by delivering large aptamers and regulatory RNAs.

  1. A modular and optimized single marker system for generating Trypanosoma brucei cell lines expressing T7 RNA polymerase and the tetracycline repressor.

    PubMed

    Poon, S K; Peacock, L; Gibson, W; Gull, K; Kelly, S

    2012-02-01

    Here, we present a simple modular extendable vector system for introducing the T7 RNA polymerase and tetracycline repressor genes into Trypanosoma brucei. This novel system exploits developments in our understanding of gene expression and genome organization to produce a streamlined plasmid optimized for high levels of expression of the introduced transgenes. We demonstrate the utility of this novel system in bloodstream and procyclic forms of Trypanosoma brucei, including the genome strain TREU927/4. We validate these cell lines using a variety of inducible experiments that recapture previously published lethal and non-lethal phenotypes. We further demonstrate the utility of the single marker (SmOx) TREU927/4 cell line for in vivo experiments in the tsetse fly and provide a set of plasmids that enable both whole-fly and salivary gland-specific inducible expression of transgenes.

  2. A modular and optimized single marker system for generating Trypanosoma brucei cell lines expressing T7 RNA polymerase and the tetracycline repressor

    PubMed Central

    Poon, S. K.; Peacock, L.; Gibson, W.; Gull, K.; Kelly, S.

    2012-01-01

    Here, we present a simple modular extendable vector system for introducing the T7 RNA polymerase and tetracycline repressor genes into Trypanosoma brucei. This novel system exploits developments in our understanding of gene expression and genome organization to produce a streamlined plasmid optimized for high levels of expression of the introduced transgenes. We demonstrate the utility of this novel system in bloodstream and procyclic forms of Trypanosoma brucei, including the genome strain TREU927/4. We validate these cell lines using a variety of inducible experiments that recapture previously published lethal and non-lethal phenotypes. We further demonstrate the utility of the single marker (SmOx) TREU927/4 cell line for in vivo experiments in the tsetse fly and provide a set of plasmids that enable both whole-fly and salivary gland-specific inducible expression of transgenes. PMID:22645659

  3. RNA self-assembly and RNA nanotechnology.

    PubMed

    Grabow, Wade W; Jaeger, Luc

    2014-06-17

    CONSPECTUS: Nanotechnology's central goal involves the direct control of matter at the molecular nanometer scale to build nanofactories, nanomachines, and other devices for potential applications including electronics, alternative fuels, and medicine. In this regard, the nascent use of nucleic acids as a material to coordinate the precise arrangements of specific molecules marked an important milestone in the relatively recent history of nanotechnology. While DNA served as the pioneer building material in nucleic acid nanotechnology, RNA continues to emerge as viable alternative material with its own distinct advantages for nanoconstruction. Several complementary assembly strategies have been used to build a diverse set of RNA nanostructures having unique structural attributes and the ability to self-assemble in a highly programmable and controlled manner. Of the different strategies, the architectonics approach uniquely endeavors to understand integrated structural RNA architectures through the arrangement of their characteristic structural building blocks. Viewed through this lens, it becomes apparent that nature routinely uses thermodynamically stable, recurrent modular motifs from natural RNA molecules to generate unique and more complex programmable structures. With the design principles found in natural structures, a number of synthetic RNAs have been constructed. The synthetic nanostructures constructed to date have provided, in addition to affording essential insights into RNA design, important platforms to characterize and validate the structural self-folding and assembly properties of RNA modules or building blocks. Furthermore, RNA nanoparticles have shown great promise for applications in nanomedicine and RNA-based therapeutics. Nevertheless, the synthetic RNA architectures achieved thus far consist largely of static, rigid particles that are still far from matching the structural and functional complexity of natural responsive structural elements such

  4. The architectonics of programmable RNA and DNA nanostructures.

    PubMed

    Jaeger, Luc; Chworos, Arkadiusz

    2006-08-01

    The past several years have witnessed the emergence of a new world of nucleic-acid-based architectures with highly predictable and programmable self-assembly properties. For almost two decades, DNA has been the primary material for nucleic acid nanoconstruction. More recently, the dramatic increase in RNA structural information led to the development of RNA architectonics, the scientific study of the principles of RNA architecture with the aim of constructing RNA nanostructures of any arbitrary size and shape. The remarkable modularity and the distinct but complementary nature of RNA and DNA nanomaterials are revealed by the various self-assembly strategies that aim to achieve control of the arrangement of matter at a nanoscale level.

  5. [Modular enteral nutrition in pediatrics].

    PubMed

    Murillo Sanchís, S; Prenafeta Ferré, M T; Sempere Luque, M D

    1991-01-01

    Modular Enteral Nutrition may be a substitute for Parenteral Nutrition in children with different pathologies. Study of 4 children with different pathologies selected from a group of 40 admitted to the Maternal-Childrens Hospital "Valle de Hebrón" in Barcelona, who received modular enteral nutrition. They were monitored on a daily basis by the Dietician Service. Modular enteral nutrition consists of modules of proteins, peptides, lipids, glucids and mineral salts-vitamins. 1.--Craneo-encephalic traumatisms with loss of consciousness, Feeding with a combination of parenteral nutrition and modular enteral nutrition for 7 days. In view of the tolerance and good results of the modular enteral nutrition, the parenteral nutrition was suspended and modular enteral nutrition alone used up to a total of 43 days. 2.--55% burns with 36 days of hyperproteic modular enteral nutrition together with normal feeding. A more rapid recovery was achieved with an increase in total proteins and albumin. 3.--Persistent diarrhoea with 31 days of modular enteral nutrition, 5 days on parenteral nutrition alone and 8 days on combined parenteral nutrition and modular enteral nutrition. In view of the tolerance and good results of the modular enteral nutrition, the parenteral nutrition was suspended. 4.--Mucoviscidosis with a total of 19 days on modular enteral nutrition, 12 of which were exclusively on modular enteral nutrition and 7 as a night supplement to normal feeding. We administered proteic intakes of up to 20% of the total calorific intake and in concentrations of up to 1.2 calories/ml of the final preparation, always with a good tolerance. Modular enteral nutrition can and should be used as a substitute for parenteral nutrition in children with different pathologies, thus preventing the complications inherent in parenteral nutrition.

  6. A modular optical sensor

    NASA Astrophysics Data System (ADS)

    Conklin, John Albert

    This dissertation presents the design of a modular, fiber-optic sensor and the results obtained from testing the modular sensor. The modular fiber-optic sensor is constructed in such manner that the sensor diaphragm can be replaced with different configurations to detect numerous physical phenomena. Additionally, different fiber-optic detection systems can be attached to the sensor. Initially, the modular sensor was developed to be used by university of students to investigate realistic optical sensors and detection systems to prepare for advance studies of micro-optical mechanical systems (MOMS). The design accomplishes this by doing two things. First, the design significantly lowers the costs associated with studying optical sensors by modularizing the sensor design. Second, the sensor broadens the number of physical phenomena that students can apply optical sensing techniques to in a fiber optics sensor course. The dissertation is divided into seven chapters covering the historical development of fiber-optic sensors, a theoretical overview of fiber-optic sensors, the design, fabrication, and the testing of the modular sensor developed in the course of this work. Chapter 1 discusses, in detail, how this dissertation is organized and states the purpose of the dissertation. Chapter 2 presents an historical overview of the development of optical fibers, optical pressure sensors, and fibers, optical pressure sensors, and optical microphones. Chapter 3 reviews the theory of multi-fiber optic detection systems, optical microphones, and pressure sensors. Chapter 4 presents the design details of the modular, optical sensor. Chapter 5 delves into how the modular sensor is fabricated and how the detection systems are constructed. Chapter 6 presents the data collected from the microphone and pressure sensor configurations of the modular sensor. Finally, Chapter 7 discusses the data collected and draws conclusions about the design based on the data collected. Chapter 7 also

  7. Portable modular detection system

    DOEpatents

    Brennan, James S [Rodeo, CA; Singh, Anup [Danville, CA; Throckmorton, Daniel J [Tracy, CA; Stamps, James F [Livermore, CA

    2009-10-13

    Disclosed herein are portable and modular detection devices and systems for detecting electromagnetic radiation, such as fluorescence, from an analyte which comprises at least one optical element removably attached to at least one alignment rail. Also disclosed are modular detection devices and systems having an integrated lock-in amplifier and spatial filter and assay methods using the portable and modular detection devices.

  8. MIDAS: A Modular DNA Assembly System for Synthetic Biology.

    PubMed

    van Dolleweerd, Craig J; Kessans, Sarah A; Van de Bittner, Kyle C; Bustamante, Leyla Y; Bundela, Rudranuj; Scott, Barry; Nicholson, Matthew J; Parker, Emily J

    2018-04-20

    A modular and hierarchical DNA assembly platform for synthetic biology based on Golden Gate (Type IIS restriction enzyme) cloning is described. This enabling technology, termed MIDAS (for Modular Idempotent DNA Assembly System), can be used to precisely assemble multiple DNA fragments in a single reaction using a standardized assembly design. It can be used to build genes from libraries of sequence-verified, reusable parts and to assemble multiple genes in a single vector, with full user control over gene order and orientation, as well as control of the direction of growth (polarity) of the multigene assembly, a feature that allows genes to be nested between other genes or genetic elements. We describe the detailed design and use of MIDAS, exemplified by the reconstruction, in the filamentous fungus Penicillium paxilli, of the metabolic pathway for production of paspaline and paxilline, key intermediates in the biosynthesis of a range of indole diterpenes-a class of secondary metabolites produced by several species of filamentous fungi. MIDAS was used to efficiently assemble a 25.2 kb plasmid from 21 different modules (seven genes, each composed of three basic parts). By using a parts library-based system for construction of complex assemblies, and a unique set of vectors, MIDAS can provide a flexible route to assembling tailored combinations of genes and other genetic elements, thereby supporting synthetic biology applications in a wide range of expression hosts.

  9. Why Go Modular? A Review of Modular A-Level Mathematics.

    ERIC Educational Resources Information Center

    Taverner, Sally; Wright, Martin

    1997-01-01

    Attitudes, academic intentions, and attainment of students gaining a grade in A-level (Advanced level) mathematics were compared for those who followed a modular course and those assessed at the end of two years of study. Overall, the final grades of those assessed modularly were half a grade higher. (JOW)

  10. RNA damage in biological conflicts and the diversity of responding RNA repair systems

    PubMed Central

    Burroughs, A. Maxwell; Aravind, L.

    2016-01-01

    RNA is targeted in biological conflicts by enzymatic toxins or effectors. A vast diversity of systems which repair or ‘heal’ this damage has only recently become apparent. Here, we summarize the known effectors, their modes of action, and RNA targets before surveying the diverse systems which counter this damage from a comparative genomics viewpoint. RNA-repair systems show a modular organization with extensive shuffling and displacement of the constituent domains; however, a general ‘syntax’ is strongly maintained whereby systems typically contain: a RNA ligase (either ATP-grasp or RtcB superfamilies), nucleotidyltransferases, enzymes modifying RNA-termini for ligation (phosphatases and kinases) or protection (methylases), and scaffold or cofactor proteins. We highlight poorly-understood or previously-uncharacterized repair systems and components, e.g. potential scaffolding cofactors (Rot/TROVE and SPFH/Band-7 modules) with their respective cognate non-coding RNAs (YRNAs and a novel tRNA-like molecule) and a novel nucleotidyltransferase associating with diverse ligases. These systems have been extensively disseminated by lateral transfer between distant prokaryotic and microbial eukaryotic lineages consistent with intense inter-organismal conflict. Components have also often been ‘institutionalized’ for non-conflict roles, e.g. in RNA-splicing and in RNAi systems (e.g. in kinetoplastids) which combine a distinct family of RNA-acting prim-pol domains with DICER-like proteins. PMID:27536007

  11. Quasispecies theory for evolution of modularity.

    PubMed

    Park, Jeong-Man; Niestemski, Liang Ren; Deem, Michael W

    2015-01-01

    Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here develop a quasispecies theory for the dynamics of modularity in populations of these systems. We show how the steady-state fitness in a randomly changing environment can be computed. We derive a fluctuation dissipation relation for the rate of change of modularity and use it to derive a relationship between rate of environmental changes and rate of growth of modularity. We also find a principle of least action for the evolved modularity at steady state. Finally, we compare our predictions to simulations of protein evolution and find them to be consistent.

  12. Modularization and Flexibilization.

    ERIC Educational Resources Information Center

    Van Meel, R. M.

    Publications in the fields of educational science, organization theory, and project management were analyzed to identify the possibilities that modularization offers to institutions of higher professional education and to obtain background information for use in developing a method for modularization in higher professional education. It was…

  13. Self-organized modularization in evolutionary algorithms.

    PubMed

    Dauscher, Peter; Uthmann, Thomas

    2005-01-01

    The principle of modularization has proven to be extremely successful in the field of technical applications and particularly for Software Engineering purposes. The question to be answered within the present article is whether mechanisms can also be identified within the framework of Evolutionary Computation that cause a modularization of solutions. We will concentrate on processes, where modularization results only from the typical evolutionary operators, i.e. selection and variation by recombination and mutation (and not, e.g., from special modularization operators). This is what we call Self-Organized Modularization. Based on a combination of two formalizations by Radcliffe and Altenberg, some quantitative measures of modularity are introduced. Particularly, we distinguish Built-in Modularity as an inherent property of a genotype and Effective Modularity, which depends on the rest of the population. These measures can easily be applied to a wide range of present Evolutionary Computation models. It will be shown, both theoretically and by simulation, that under certain conditions, Effective Modularity (as defined within this paper) can be a selection factor. This causes Self-Organized Modularization to take place. The experimental observations emphasize the importance of Effective Modularity in comparison with Built-in Modularity. Although the experimental results have been obtained using a minimalist toy model, they can lead to a number of consequences for existing models as well as for future approaches. Furthermore, the results suggest a complex self-amplification of highly modular equivalence classes in the case of respected relations. Since the well-known Holland schemata are just the equivalence classes of respected relations in most Simple Genetic Algorithms, this observation emphasizes the role of schemata as Building Blocks (in comparison with arbitrary subsets of the search space).

  14. Pharmacological Characterization of Chemically Synthesized Monomeric phi29 pRNA Nanoparticles for Systemic Delivery

    PubMed Central

    Abdelmawla, Sherine; Guo, Songchuan; Zhang, Limin; Pulukuri, Sai M; Patankar, Prithviraj; Conley, Patrick; Trebley, Joseph; Guo, Peixuan; Li, Qi-Xiang

    2011-01-01

    Previous studies have shown that the packaging RNA (pRNA) of bacteriophage phi29 DNA packaging motor folds into a compact structure, constituting a RNA nanoparticle that can be modularized with functional groups as a nanodelivery system. pRNA nanoparticles can also be self-assembled by the bipartite approach without altering folding property. The present study demonstrated that 2′-F-modified pRNA nanoparticles were readily manufactured through this scalable bipartite strategy, featuring total chemical synthesis and permitting diverse functional modularizations. The RNA nanoparticles were chemically and metabolically stable and demonstrated a favorable pharmacokinetic (PK) profile in mice (half-life (T1/2): 5–10 hours, clearance (Cl): <0.13 l/kg/hour, volume of distribution (Vd): 1.2 l/kg). It did not induce an interferon (IFN) response nor did it induce cytokine production in mice. Repeat intravenous administrations in mice up to 30 mg/kg did not result in any toxicity. Fluorescent folate-pRNA nanoparticles efficiently and specifically bound and internalized to folate receptor (FR)-bearing cancer cells in vitro. It also specifically and dose-dependently targeted to FR+ xenograft tumor in mice with minimal accumulation in normal tissues. This first comprehensive pharmacological study suggests that the pRNA nanoparticle had all the preferred pharmacological features to serve as an efficient nanodelivery platform for broad medical applications. PMID:21468004

  15. The Modular Organization of Protein Interactions in Escherichia coli

    PubMed Central

    Peregrín-Alvarez, José M.; Xiong, Xuejian; Su, Chong; Parkinson, John

    2009-01-01

    Escherichia coli serves as an excellent model for the study of fundamental cellular processes such as metabolism, signalling and gene expression. Understanding the function and organization of proteins within these processes is an important step towards a ‘systems’ view of E. coli. Integrating experimental and computational interaction data, we present a reliable network of 3,989 functional interactions between 1,941 E. coli proteins (∼45% of its proteome). These were combined with a recently generated set of 3,888 high-quality physical interactions between 918 proteins and clustered to reveal 316 discrete modules. In addition to known protein complexes (e.g., RNA and DNA polymerases), we identified modules that represent biochemical pathways (e.g., nitrate regulation and cell wall biosynthesis) as well as batteries of functionally and evolutionarily related processes. To aid the interpretation of modular relationships, several case examples are presented, including both well characterized and novel biochemical systems. Together these data provide a global view of the modular organization of the E. coli proteome and yield unique insights into structural and evolutionary relationships in bacterial networks. PMID:19798435

  16. A Modularized Counselor-Education Program.

    ERIC Educational Resources Information Center

    Miller, Thomas V.; Dimattia, Dominic J.

    1978-01-01

    Counselor-education programs may be enriched through the use of modularized learning experiences. This article notes several recent articles on competency-based counselor education, the concepts of simulation and modularization, and describes the process of developing a modularized master's program at the University of Bridgeport in Connecticut.…

  17. Robotic hand with modular extensions

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

    Salisbury, Curt Michael; Quigley, Morgan

    A robotic device is described herein. The robotic device includes a frame that comprises a plurality of receiving regions that are configured to receive a respective plurality of modular robotic extensions. The modular robotic extensions are removably attachable to the frame at the respective receiving regions by way of respective mechanical fuses. Each mechanical fuse is configured to trip when a respective modular robotic extension experiences a predefined load condition, such that the respective modular robotic extension detaches from the frame when the load condition is met.

  18. Systematic discovery of Xist RNA binding proteins

    PubMed Central

    Chu, Ci; Zhang, Qiangfeng Cliff; da Rocha, Simão Teixeira; Flynn, Ryan A.; Bharadwaj, Maheetha; Calabrese, J. Mauro; Magnuson, Terry; Heard, Edith; Chang, Howard Y.

    2015-01-01

    Summary Noncoding RNAs (ncRNAs) function with associated proteins to effect complex structural and regulatory outcomes. To reveal the composition and dynamics of specific noncoding RNA- protein complexes (RNPs) in vivo, we developed comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS). ChIRP-MS analysis of four ncRNAs captures key protein interactors, including a U1-specific link to the 3′ RNA processing machinery. Xist, an essential lncRNA for X-chromosome inactivation (XCI), interacts with 81 proteins from chromatin modification, nuclear matrix, and RNA remodeling pathways. The Xist RNA-protein particle assembles in two steps coupled with the transition from pluripotency to differentiation. Specific interactors include HnrnpK that participates in Xist-mediated gene silencing and histone modifications, but not Xist localization and Drosophila Split ends homolog Spen that interacts via the A-repeat domain of Xist and is required for gene silencing. Thus, Xist lncRNA engages with proteins in a modular and developmentally controlled manner to coordinate chromatin spreading and silencing. PMID:25843628

  19. Modular architecture of eukaryotic RNase P and RNase MRP revealed by electron microscopy

    PubMed Central

    Hipp, Katharina; Galani, Kyriaki; Batisse, Claire; Prinz, Simone; Böttcher, Bettina

    2012-01-01

    Ribonuclease P (RNase P) and RNase MRP are closely related ribonucleoprotein enzymes, which process RNA substrates including tRNA precursors for RNase P and 5.8 S rRNA precursors, as well as some mRNAs, for RNase MRP. The structures of RNase P and RNase MRP have not yet been solved, so it is unclear how the proteins contribute to the structure of the complexes and how substrate specificity is determined. Using electron microscopy and image processing we show that eukaryotic RNase P and RNase MRP have a modular architecture, where proteins stabilize the RNA fold and contribute to cavities, channels and chambers between the modules. Such features are located at strategic positions for substrate recognition by shape and coordination of the cleaved-off sequence. These are also the sites of greatest difference between RNase P and RNase MRP, highlighting the importance of the adaptation of this region to the different substrates. PMID:22167472

  20. Modular architecture of eukaryotic RNase P and RNase MRP revealed by electron microscopy.

    PubMed

    Hipp, Katharina; Galani, Kyriaki; Batisse, Claire; Prinz, Simone; Böttcher, Bettina

    2012-04-01

    Ribonuclease P (RNase P) and RNase MRP are closely related ribonucleoprotein enzymes, which process RNA substrates including tRNA precursors for RNase P and 5.8 S rRNA precursors, as well as some mRNAs, for RNase MRP. The structures of RNase P and RNase MRP have not yet been solved, so it is unclear how the proteins contribute to the structure of the complexes and how substrate specificity is determined. Using electron microscopy and image processing we show that eukaryotic RNase P and RNase MRP have a modular architecture, where proteins stabilize the RNA fold and contribute to cavities, channels and chambers between the modules. Such features are located at strategic positions for substrate recognition by shape and coordination of the cleaved-off sequence. These are also the sites of greatest difference between RNase P and RNase MRP, highlighting the importance of the adaptation of this region to the different substrates.

  1. Separate RNA-binding surfaces on the multifunctional La protein mediate distinguishable activities in tRNA maturation.

    PubMed

    Huang, Ying; Bayfield, Mark A; Intine, Robert V; Maraia, Richard J

    2006-07-01

    By sequence-specific binding to 3' UUU-OH, the La protein shields precursor (pre)-RNAs from 3' end digestion and is required to protect defective pre-transfer RNAs from decay. Although La is comprised of a La motif and an RNA-recognition motif (RRM), a recent structure indicates that the RRM beta-sheet surface is not involved in UUU-OH recognition, raising questions as to its function. Progressively defective suppressor tRNAs in Schizosaccharomyces pombe reveal differential sensitivities to La and Rrp6p, a 3' exonuclease component of pre-tRNA decay. 3' end protection is compromised by mutations to the La motif but not the RRM surface. The most defective pre-tRNAs require a second activity of La, in addition to 3' protection, that requires an intact RRM surface. The two activities of La in tRNA maturation map to its two conserved RNA-binding surfaces and suggest a modular model that has implications for its other ligands.

  2. Modular organization and hospital performance.

    PubMed

    Kuntz, Ludwig; Vera, Antonio

    2007-02-01

    The concept of modularization represents a modern form of organization, which contains the vertical disaggregation of the firm and the use of market mechanisms within hierarchies. The objective of this paper is to examine whether the use of modular structures has a positive effect on hospital performance. The empirical section makes use of multiple regression analyses and leads to the main result that modularization does not have a positive effect on hospital performance. However, the analysis also finds out positive efficiency effects of two central ideas of modularization, namely process orientation and internal market mechanisms.

  3. Product modular design incorporating preventive maintenance issues

    NASA Astrophysics Data System (ADS)

    Gao, Yicong; Feng, Yixiong; Tan, Jianrong

    2016-03-01

    Traditional modular design methods lead to product maintenance problems, because the module form of a system is created according to either the function requirements or the manufacturing considerations. For solving these problems, a new modular design method is proposed with the considerations of not only the traditional function related attributes, but also the maintenance related ones. First, modularity parameters and modularity scenarios for product modularity are defined. Then the reliability and economic assessment models of product modularity strategies are formulated with the introduction of the effective working age of modules. A mathematical model used to evaluate the difference among the modules of the product so that the optimal module of the product can be established. After that, a multi-objective optimization problem based on metrics for preventive maintenance interval different degrees and preventive maintenance economics is formulated for modular optimization. Multi-objective GA is utilized to rapidly approximate the Pareto set of optimal modularity strategy trade-offs between preventive maintenance cost and preventive maintenance interval difference degree. Finally, a coordinate CNC boring machine is adopted to depict the process of product modularity. In addition, two factorial design experiments based on the modularity parameters are constructed and analyzed. These experiments investigate the impacts of these parameters on the optimal modularity strategies and the structure of module. The research proposes a new modular design method, which may help to improve the maintainability of product in modular design.

  4. Regulatory RNA-assisted genome engineering in microorganisms.

    PubMed

    Si, Tong; HamediRad, Mohammad; Zhao, Huimin

    2015-12-01

    Regulatory RNAs are increasingly recognized and utilized as key modulators of gene expression in diverse organisms. Thanks to their modular and programmable nature, trans-acting regulatory RNAs are especially attractive in genome-scale applications. Here we discuss the recent examples in microbial genome engineering implementing various trans-acting RNA platforms, including sRNA, RNAi, asRNA and CRISRP-Cas. In particular, we focus on how the scalable and multiplex nature of trans-acting RNAs has been used to tackle the challenges in creating genome-wide and combinatorial diversity for functional genomics and metabolic engineering applications. Advances in computational design and context-dependent regulation are also discussed for their contribution in improving fine-tuning capabilities of trans-acting RNAs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors.

    PubMed

    Martella, Andrea; Matjusaitis, Mantas; Auxillos, Jamie; Pollard, Steven M; Cai, Yizhi

    2017-07-21

    Mammalian plasmid expression vectors are critical reagents underpinning many facets of research across biology, biomedical research, and the biotechnology industry. Traditional cloning methods often require laborious manual design and assembly of plasmids using tailored sequential cloning steps. This process can be protracted, complicated, expensive, and error-prone. New tools and strategies that facilitate the efficient design and production of bespoke vectors would help relieve a current bottleneck for researchers. To address this, we have developed an extensible mammalian modular assembly kit (EMMA). This enables rapid and efficient modular assembly of mammalian expression vectors in a one-tube, one-step golden-gate cloning reaction, using a standardized library of compatible genetic parts. The high modularity, flexibility, and extensibility of EMMA provide a simple method for the production of functionally diverse mammalian expression vectors. We demonstrate the value of this toolkit by constructing and validating a range of representative vectors, such as transient and stable expression vectors (transposon based vectors), targeting vectors, inducible systems, polycistronic expression cassettes, fusion proteins, and fluorescent reporters. The method also supports simple assembly combinatorial libraries and hierarchical assembly for production of larger multigenetic cargos. In summary, EMMA is compatible with automated production, and novel genetic parts can be easily incorporated, providing new opportunities for mammalian synthetic biology.

  6. Modular Design in Treaty Verification Equipment

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

    Macarthur, Duncan Whittemore; Benz, Jacob; Tolk, Keith

    2015-01-27

    It is widely believed that modular design is a good thing. However, there are often few explicit arguments, or even an agreed range of definitions, to back up this belief. In this paper, we examine the potential range of design modularity, the implications of various amounts of modularity, and the advantages and disadvantages of each level of modular construction. We conclude with a comparison of the advantages and disadvantages of each type, as well as discuss many caveats that should be observed to take advantage of the positive features of modularity and minimize the effects of the negative. The tradeoffsmore » described in this paper will be evaluated during the conceptual design to determine what amount of modularity should be included.« less

  7. Construction and analysis of lncRNA-lncRNA synergistic networks to reveal clinically relevant lncRNAs in cancer.

    PubMed

    Li, Yongsheng; Chen, Juan; Zhang, Jinwen; Wang, Zishan; Shao, Tingting; Jiang, Chunjie; Xu, Juan; Li, Xia

    2015-09-22

    Long non-coding RNAs (lncRNAs) play key roles in diverse biological processes. Moreover, the development and progression of cancer often involves the combined actions of several lncRNAs. Here we propose a multi-step method for constructing lncRNA-lncRNA functional synergistic networks (LFSNs) through co-regulation of functional modules having three features: common coexpressed genes of lncRNA pairs, enrichment in the same functional category and close proximity within protein interaction networks. Applied to three cancers, we constructed cancer-specific LFSNs and found that they exhibit a scale free and modular architecture. In addition, cancer-associated lncRNAs tend to be hubs and are enriched within modules. Although there is little synergistic pairing of lncRNAs across cancers, lncRNA pairs involved in the same cancer hallmarks by regulating same or different biological processes. Finally, we identify prognostic biomarkers within cancer lncRNA expression datasets using modules derived from LFSNs. In summary, this proof-of-principle study indicates synergistic lncRNA pairs can be identified through integrative analysis of genome-wide expression data sets and functional information.

  8. Modular interdependency in complex dynamical systems.

    PubMed

    Watson, Richard A; Pollack, Jordan B

    2005-01-01

    Herbert A. Simon's characterization of modularity in dynamical systems describes subsystems as having dynamics that are approximately independent of those of other subsystems (in the short term). This fits with the general intuition that modules must, by definition, be approximately independent. In the evolution of complex systems, such modularity may enable subsystems to be modified and adapted independently of other subsystems, whereas in a nonmodular system, modifications to one part of the system may result in deleterious side effects elsewhere in the system. But this notion of modularity and its effect on evolvability is not well quantified and is rather simplistic. In particular, modularity need not imply that intermodule dependences are weak or unimportant. In dynamical systems this is acknowledged by Simon's suggestion that, in the long term, the dynamical behaviors of subsystems do interact with one another, albeit in an "aggregate" manner--but this kind of intermodule interaction is omitted in models of modularity for evolvability. In this brief discussion we seek to unify notions of modularity in dynamical systems with notions of how modularity affects evolvability. This leads to a quantifiable measure of modularity and a different understanding of its effect on evolvability.

  9. Modular analysis of biological networks.

    PubMed

    Kaltenbach, Hans-Michael; Stelling, Jörg

    2012-01-01

    The analysis of complex biological networks has traditionally relied on decomposition into smaller, semi-autonomous units such as individual signaling pathways. With the increased scope of systems biology (models), rational approaches to modularization have become an important topic. With increasing acceptance of de facto modularity in biology, widely different definitions of what constitutes a module have sparked controversies. Here, we therefore review prominent classes of modular approaches based on formal network representations. Despite some promising research directions, several important theoretical challenges remain open on the way to formal, function-centered modular decompositions for dynamic biological networks.

  10. miRMaid: a unified programming interface for microRNA data resources

    PubMed Central

    2010-01-01

    Background MicroRNAs (miRNAs) are endogenous small RNAs that play a key role in post-transcriptional regulation of gene expression in animals and plants. The number of known miRNAs has increased rapidly over the years. The current release (version 14.0) of miRBase, the central online repository for miRNA annotation, comprises over 10.000 miRNA precursors from 115 different species. Furthermore, a large number of decentralized online resources are now available, each contributing with important miRNA annotation and information. Results We have developed a software framework, designated here as miRMaid, with the goal of integrating miRNA data resources in a uniform web service interface that can be accessed and queried by researchers and, most importantly, by computers. miRMaid is built around data from miRBase and is designed to follow the official miRBase data releases. It exposes miRBase data as inter-connected web services. Third-party miRNA data resources can be modularly integrated as miRMaid plugins or they can loosely couple with miRMaid as individual entities in the World Wide Web. miRMaid is available as a public web service but is also easily installed as a local application. The software framework is freely available under the LGPL open source license for academic and commercial use. Conclusion miRMaid is an intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources. Furthermore, miRMaid constitutes a basic framework for further programming in which microRNA-interested bioinformaticians can readily develop their own tools and data sources. PMID:20074352

  11. Modular invariant inflation

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

    Kobayashi, Tatsuo; Nitta, Daisuke; Urakawa, Yuko

    2016-08-08

    Modular invariance is a striking symmetry in string theory, which may keep stringy corrections under control. In this paper, we investigate a phenomenological consequence of the modular invariance, assuming that this symmetry is preserved as well as in a four dimensional (4D) low energy effective field theory. As a concrete setup, we consider a modulus field T whose contribution in the 4D effective field theory remains invariant under the modular transformation and study inflation drived by T. The modular invariance restricts a possible form of the scalar potenntial. As a result, large field models of inflation are hardly realized. Meanwhile,more » a small field model of inflation can be still accomodated in this restricted setup. The scalar potential traced during the slow-roll inflation mimics the hilltop potential V{sub ht}, but it also has a non-negligible deviation from V{sub ht}. Detecting the primordial gravitational waves predicted in this model is rather challenging. Yet, we argue that it may be still possible to falsify this model by combining the information in the reheating process which can be determined self-completely in this setup.« less

  12. Modular degradable dendrimers enable small RNAs to extend survival in an aggressive liver cancer model

    PubMed Central

    Zhou, Kejin; Nguyen, Liem H.; Miller, Jason B.; Yan, Yunfeng; Kos, Petra; Xiong, Hu; Li, Lin; Hao, Jing; Minnig, Jonathan T.; Siegwart, Daniel J.

    2016-01-01

    RNA-based cancer therapies are hindered by the lack of delivery vehicles that avoid cancer-induced organ dysfunction, which exacerbates carrier toxicity. We address this issue by reporting modular degradable dendrimers that achieve the required combination of high potency to tumors and low hepatotoxicity to provide a pronounced survival benefit in an aggressive genetic cancer model. More than 1,500 dendrimers were synthesized using sequential, orthogonal reactions where ester degradability was systematically integrated with chemically diversified cores, peripheries, and generations. A lead dendrimer, 5A2-SC8, provided a broad therapeutic window: identified as potent [EC50 < 0.02 mg/kg siRNA against FVII (siFVII)] in dose–response experiments, and well tolerated in separate toxicity studies in chronically ill mice bearing MYC-driven tumors (>75 mg/kg dendrimer repeated dosing). Delivery of let-7g microRNA (miRNA) mimic inhibited tumor growth and dramatically extended survival. Efficacy stemmed from a combination of a small RNA with the dendrimer’s own negligible toxicity, therefore illuminating an underappreciated complication in treating cancer with RNA-based drugs. PMID:26729861

  13. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

    PubMed Central

    Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

    2013-01-01

    The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

  14. Survey of Modular Military Vehicles: Benefits and Burdens

    DTIC Science & Technology

    2016-01-01

    Survey of Modular Military Vehicles: BENEFITS and BURDENS Jean M. Dasch and David J. Gorsich Modularity in military vehicle design is generally...considered a positive attribute that promotes adaptability, resilience, and cost savings. The benefits and burdens of modularity are considered by...Engineering Center, vehicles were considered based on horizontal modularity , vertical modularity , and distributed modularity . Examples were given for each

  15. Modular Power Standard for Space Explorations Missions

    NASA Technical Reports Server (NTRS)

    Oeftering, Richard C.; Gardner, Brent G.

    2016-01-01

    Future human space exploration will most likely be composed of assemblies of multiple modular spacecraft elements with interconnected electrical power systems. An electrical system composed of a standardized set modular building blocks provides significant development, integration, and operational cost advantages. The modular approach can also provide the flexibility to configure power systems to meet the mission needs. A primary goal of the Advanced Exploration Systems (AES) Modular Power System (AMPS) project is to establish a Modular Power Standard that is needed to realize these benefits. This paper is intended to give the space exploration community a "first look" at the evolving Modular Power Standard and invite their comments and technical contributions.

  16. Spacecraft Modularity for Serviceable Satellites

    NASA Technical Reports Server (NTRS)

    Rossetti, Dino; Keer, Beth; Panek, John; Reed, Benjamin; Cepollina, Frank; Ritter, Robert

    2015-01-01

    Satellite servicing has been a proven capability of NASA since the first servicing missions in the 1980s with astronauts on the space shuttle. This capability enabled the on-orbit assembly of the International Space Station (ISS) and saved the Hubble Space Telescope (HST) mission following the discovery of the flawed primary mirror. The effectiveness and scope of servicing opportunities, especially using robotic servicers, is a function of how cooperative a spacecraft is. In this paper, modularity will be presented as a critical design aspect for a spacecraft that is cooperative from a servicing perspective. Different features of modularity are discussed using examples from HST and the Multimission Modular Spacecraft (MMS) program from the 1980s and 1990s. The benefits of modularity will be presented including those directly related to servicing and those outside of servicing including reduced costs and increased flexibility. The new Reconfigurable Operational spacecraft for Science and Exploration (ROSE) concept is introduced as an affordable implementation of modularity that provides cost savings and flexibility. Key aspects of the ROSE architecture are discussed such as the module design and the distributed avionics architecture. The ROSE concept builds on the experience from MMS and due to its modularity, would be highly suitable as a future client for on-orbit servicing.

  17. Theory for the Emergence of Modularity in Complex Systems

    NASA Astrophysics Data System (ADS)

    Deem, Michael; Park, Jeong-Man

    2013-03-01

    Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here develop a theory for the dynamics of modularity in these systems. We find a principle of least action for the evolved modularity at long times. In addition, we find a fluctuation dissipation relation for the rate of change of modularity at short times. We discuss a number of biological and social systems that can be understood with this framework. The modularity of the protein-protein interaction network increases when yeast are exposed to heat shock, and the modularity of the protein-protein networks in both yeast and E. coli appears to have increased over evolutionary time. Food webs in low-energy, stressful environments are more modular than those in plentiful environments, arid ecologies are more modular during droughts, and foraging of sea otters is more modular when food is limiting. The modularity of social networks changes over time: stock brokers instant messaging networks are more modular under stressful market conditions, criminal networks are more modular under increased police pressure, and world trade network modularity has decreased

  18. Implementing Modular A Levels.

    ERIC Educational Resources Information Center

    Holding, Gordon

    This document, which is designed for curriculum managers at British further education (FE) colleges, presents basic information on the implementation and perceived benefits of the General Certificate of Education (GCE) modular A (Advanced) levels. The information was synthesized from a survey of 12 FE colleges that introduced the modular A levels…

  19. Computer-generated tailored feedback letters for smoking cessation: theoretical and empirical variability of tailoring.

    PubMed

    Schumann, Anja; John, Ulrich; Ulbricht, Sabina; Rüge, Jeannette; Bischof, Gallus; Meyer, Christian

    2008-11-01

    This study examines tailored feedback letters of a smoking cessation intervention that is conceptually based on the transtheoretical model, from a content-based perspective. Data of 2 population-based intervention studies, both randomized controlled trials, with total N=1044 were used. The procedure of the intervention, the tailoring principle for the feedback letters, and the content of the intervention materials are described in detail. Theoretical and empirical frequencies of unique feedback letters are presented. The intervention system was able to generate a total of 1040 unique letters with normative feedback only, and almost half a million unique letters with normative and ipsative feedback. Almost every single smoker in contemplation, preparation, action, and maintenance had an empirically unique combination of tailoring variables and received a unique letter. In contrast, many smokers in precontemplation shared a combination of tailoring variables and received identical letters. The transtheoretical model provides an enormous theoretical and empirical variability of tailoring. However, tailoring for a major subgroup of smokers, i.e. those who do not intend to quit, needs improvement. Conceptual ideas for additional tailoring variables are discussed.

  20. Modular bicompartmental knee arthroplasty : Indications, technique, prosthetic design, and results.

    PubMed

    Kanna, R

    2017-03-01

    The shifting demographics of patients with localized knee arthritis, including younger, more active patients, is a chief motivation for mounting interest in tissue preserving surgical substitutes for total knee arthroplasty (TKA). Unlinked, modular bi-compartmental knee arthroplasty (MBKA) is an emerging knee-resurfacing approach that provides a conservative alternative to TKA. Arthritis involving both patellofemoral and either medial or lateral tibiofemoral compartments, with no significant deformity or bone deficiency, preserved motion, and intact cruciate ligaments, can be effectively managed with MBKA. It is tailored to treat the pathologic areas of knees with bicompartmental arthritis with the benefit of improved function and tissue conservation. MBKA done in appropriate patients, using precise technique, with appropriate implants has shown to give good short and long term functional results. Long term results using modern MBKA implants are awaited and may further establish the durability and success of the procedure.

  1. VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis.

    PubMed

    Cornwell, MacIntosh; Vangala, Mahesh; Taing, Len; Herbert, Zachary; Köster, Johannes; Li, Bo; Sun, Hanfei; Li, Taiwen; Zhang, Jian; Qiu, Xintao; Pun, Matthew; Jeselsohn, Rinath; Brown, Myles; Liu, X Shirley; Long, Henry W

    2018-04-12

    RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses. VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion.

  2. RNA 3D Structural Motifs: Definition, Identification, Annotation, and Database Searching

    NASA Astrophysics Data System (ADS)

    Nasalean, Lorena; Stombaugh, Jesse; Zirbel, Craig L.; Leontis, Neocles B.

    Structured RNA molecules resemble proteins in the hierarchical organization of their global structures, folding and broad range of functions. Structured RNAs are composed of recurrent modular motifs that play specific functional roles. Some motifs direct the folding of the RNA or stabilize the folded structure through tertiary interactions. Others bind ligands or proteins or catalyze chemical reactions. Therefore, it is desirable, starting from the RNA sequence, to be able to predict the locations of recurrent motifs in RNA molecules. Conversely, the potential occurrence of one or more known 3D RNA motifs may indicate that a genomic sequence codes for a structured RNA molecule. To identify known RNA structural motifs in new RNA sequences, precise structure-based definitions are needed that specify the core nucleotides of each motif and their conserved interactions. By comparing instances of each recurrent motif and applying base pair isosteriCity relations, one can identify neutral mutations that preserve its structure and function in the contexts in which it occurs.

  3. Symmetric modular torsatron

    DOEpatents

    Rome, J.A.; Harris, J.H.

    1984-01-01

    A fusion reactor device is provided in which the magnetic fields for plasma confinement in a toroidal configuration is produced by a plurality of symmetrical modular coils arranged to form a symmetric modular torsatron referred to as a symmotron. Each of the identical modular coils is helically deformed and comprise one field period of the torsatron. Helical segments of each coil are connected by means of toroidally directed windbacks which may also provide part of the vertical field required for positioning the plasma. The stray fields of the windback segments may be compensated by toroidal coils. A variety of magnetic confinement flux surface configurations may be produced by proper modulation of the winding pitch of the helical segments of the coils, as in a conventional torsatron, winding the helix on a noncircular cross section and varying the poloidal and radial location of the windbacks and the compensating toroidal ring coils.

  4. Modular workcells: modern methods for laboratory automation.

    PubMed

    Felder, R A

    1998-12-01

    Laboratory automation is beginning to become an indispensable survival tool for laboratories facing difficult market competition. However, estimates suggest that only 8% of laboratories will be able to afford total laboratory automation systems. Therefore, automation vendors have developed alternative hardware configurations called 'modular automation', to fit the smaller laboratory. Modular automation consists of consolidated analyzers, integrated analyzers, modular workcells, and pre- and post-analytical automation. These terms will be defined in this paper. Using a modular automation model, the automated core laboratory will become a site where laboratory data is evaluated by trained professionals to provide diagnostic information to practising physicians. Modem software information management and process control tools will complement modular hardware. Proper standardization that will allow vendor-independent modular configurations will assure success of this revolutionary new technology.

  5. Modularity in robotic systems

    NASA Technical Reports Server (NTRS)

    Tesar, Delbert; Butler, Michael S.

    1989-01-01

    Most robotic systems today are designed one at a time, at a high cost of time and money. This wasteful approach has been necessary because the industry has not established a foundation for the continued evolution of intelligent machines. The next generation of robots will have to be generic, versatile machines capable of absorbing new technology rapidly and economically. This approach is demonstrated in the success of the personal computer, which can be upgraded or expanded with new software and hardware at virtually every level. Modularity is perceived as a major opportunity to reduce the 6 to 7 year design cycle time now required for new robotic manipulators, greatly increasing the breadth and speed of diffusion of robotic systems in manufacturing. Modularity and its crucial role in the next generation of intelligent machines are the focus of interest. The main advantages that modularity provides are examined; types of modules needed to create a generic robot are discussed. Structural modules designed by the robotics group at the University of Texas at Austin are examined to demonstrate the advantages of modular design.

  6. Modular High Voltage Power Supply

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

    Newell, Matthew R.

    The goal of this project is to develop a modular high voltage power supply that will meet the needs of safeguards applications and provide a modular plug and play supply for use with standard electronic racks.

  7. Rationally designed small molecules targeting the RNA that causes myotonic dystrophy type 1 are potently bioactive.

    PubMed

    Childs-Disney, Jessica L; Hoskins, Jason; Rzuczek, Suzanne G; Thornton, Charles A; Disney, Matthew D

    2012-05-18

    RNA is an important drug target, but it is difficult to design or discover small molecules that modulate RNA function. In the present study, we report that rationally designed, modularly assembled small molecules that bind the RNA that causes myotonic dystrophy type 1 (DM1) are potently bioactive in cell culture models. DM1 is caused when an expansion of r(CUG) repeats, or r(CUG)(exp), is present in the 3' untranslated region (UTR) of the dystrophia myotonica protein kinase (DMPK) mRNA. r(CUG)(exp) folds into a hairpin with regularly repeating 5'CUG/3'GUC motifs and sequesters muscleblind-like 1 protein (MBNL1). A variety of defects are associated with DM1, including (i) formation of nuclear foci, (ii) decreased translation of DMPK mRNA due to its nuclear retention, and (iii) pre-mRNA splicing defects due to inactivation of MBNL1, which controls the alternative splicing of various pre-mRNAs. Previously, modularly assembled ligands targeting r(CUG)(exp) were designed using information in an RNA motif-ligand database. These studies showed that a bis-benzimidazole (H) binds the 5'CUG/3'GUC motif in r(CUG)(exp.) Therefore, we designed multivalent ligands to bind simultaneously multiple copies of this motif in r(CUG)(exp). Herein, we report that the designed compounds improve DM1-associated defects including improvement of translational and pre-mRNA splicing defects and the disruption of nuclear foci. These studies may establish a foundation to exploit other RNA targets in genomic sequence.

  8. Modular properties of 6d (DELL) systems

    NASA Astrophysics Data System (ADS)

    Aminov, G.; Mironov, A.; Morozov, A.

    2017-11-01

    If super-Yang-Mills theory possesses the exact conformal invariance, there is an additional modular invariance under the change of the complex bare charge [InlineMediaObject not available: see fulltext.]. The low-energy Seiberg-Witten prepotential ℱ( a), however, is not explicitly invariant, because the flat moduli also change a - → a D = ∂ℱ/∂ a. In result, the prepotential is not a modular form and depends also on the anomalous Eisenstein series E 2. This dependence is usually described by the universal MNW modular anomaly equation. We demonstrate that, in the 6 d SU( N) theory with two independent modular parameters τ and \\widehat{τ} , the modular anomaly equation changes, because the modular transform of τ is accompanied by an ( N -dependent!) shift of \\widehat{τ} and vice versa. This is a new peculiarity of double-elliptic systems, which deserves further investigation.

  9. Tailored Testing Theory and Practice: A Basic Model, Normal Ogive Submodels, and Tailored Testing Algorithms

    DTIC Science & Technology

    1983-08-01

    ACCESSION NO «• TITLE (and Sublltle) TAILORED TESTING THEORY AND PRACTICE: A BASIC MODEL , NORMAL OGIVE SUBMODELS, AND TAILORED TESTING ALGORITHMS 7...single common-factor model , the author derives the two- and three-parametir normal ogfve il’^irTr^ functions as submodels. For both of these...PAOEfWiwi Dmia Bnfnd) NPRDC TR 83-32 AUGUST 1983 TAILORED TESTING THEORY AND PRACTICE: A BASIC MODEL , NORMAL OGIVE SUBMODELS, AND TAILORED TESTING

  10. Structural Integration of Sensors/Actuators by Laser Beam Melting for Tailored Smart Components

    NASA Astrophysics Data System (ADS)

    Töppel, Thomas; Lausch, Holger; Brand, Michael; Hensel, Eric; Arnold, Michael; Rotsch, Christian

    2018-03-01

    Laser beam melting (LBM), an additive laser powder bed fusion technology, enables the structural integration of temperature-sensitive sensors and actuators in complex monolithic metallic structures. The objective is to embed a functional component inside a metal part without losing its functionality by overheating. The first part of this paper addresses the development of a new process chain for bonded embedding of temperature-sensitive sensor/actuator systems by LBM. These systems are modularly built and coated by a multi-material/multi-layer thermal protection system of ceramic and metallic compounds. The characteristic of low global heat input in LBM is utilized for the functional embedding. In the second part, the specific functional design and optimization for tailored smart components with embedded functionalities are addressed. Numerical and experimental validated results are demonstrated on a smart femoral hip stem.

  11. Adaptive multi-resolution Modularity for detecting communities in networks

    NASA Astrophysics Data System (ADS)

    Chen, Shi; Wang, Zhi-Zhong; Bao, Mei-Hua; Tang, Liang; Zhou, Ji; Xiang, Ju; Li, Jian-Ming; Yi, Chen-He

    2018-02-01

    Community structure is a common topological property of complex networks, which attracted much attention from various fields. Optimizing quality functions for community structures is a kind of popular strategy for community detection, such as Modularity optimization. Here, we introduce a general definition of Modularity, by which several classical (multi-resolution) Modularity can be derived, and then propose a kind of adaptive (multi-resolution) Modularity that can combine the advantages of different Modularity. By applying the Modularity to various synthetic and real-world networks, we study the behaviors of the methods, showing the validity and advantages of the multi-resolution Modularity in community detection. The adaptive Modularity, as a kind of multi-resolution method, can naturally solve the first-type limit of Modularity and detect communities at different scales; it can quicken the disconnecting of communities and delay the breakup of communities in heterogeneous networks; and thus it is expected to generate the stable community structures in networks more effectively and have stronger tolerance against the second-type limit of Modularity.

  12. Modular thought in the circuit analysis

    NASA Astrophysics Data System (ADS)

    Wang, Feng

    2018-04-01

    Applied to solve the problem of modular thought, provides a whole for simplification's method, the complex problems have become of, and the study of circuit is similar to the above problems: the complex connection between components, make the whole circuit topic solution seems to be more complex, and actually components the connection between the have rules to follow, this article mainly tells the story of study on the application of the circuit modular thought. First of all, this paper introduces the definition of two-terminal network and the concept of two-terminal network equivalent conversion, then summarizes the common source resistance hybrid network modular approach, containing controlled source network modular processing method, lists the common module, typical examples analysis.

  13. Modular optical detector system

    DOEpatents

    Horn, Brent A [Livermore, CA; Renzi, Ronald F [Tracy, CA

    2006-02-14

    A modular optical detector system. The detector system is designed to detect the presence of molecules or molecular species by inducing fluorescence with exciting radiation and detecting the emitted fluorescence. Because the system is capable of accurately detecting and measuring picomolar concentrations it is ideally suited for use with microchemical analysis systems generally and capillary chromatographic systems in particular. By employing a modular design, the detector system provides both the ability to replace various elements of the detector system without requiring extensive realignment or recalibration of the components as well as minimal user interaction with the system. In addition, the modular concept provides for the use and addition of a wide variety of components, including optical elements (lenses and filters), light sources, and detection means, to fit particular needs.

  14. Elucidation of Sigma Factor-Associated Networks in Pseudomonas aeruginosa Reveals a Modular Architecture with Limited and Function-Specific Crosstalk

    PubMed Central

    Schulz, Sebastian; Eckweiler, Denitsa; Bielecka, Agata; Nicolai, Tanja; Franke, Raimo; Dötsch, Andreas; Hornischer, Klaus; Bruchmann, Sebastian; Düvel, Juliane; Häussler, Susanne

    2015-01-01

    Sigma factors are essential global regulators of transcription initiation in bacteria which confer promoter recognition specificity to the RNA polymerase core enzyme. They provide effective mechanisms for simultaneously regulating expression of large numbers of genes in response to challenging conditions, and their presence has been linked to bacterial virulence and pathogenicity. In this study, we constructed nine his-tagged sigma factor expressing and/or deletion mutant strains in the opportunistic pathogen Pseudomonas aeruginosa. To uncover the direct and indirect sigma factor regulons, we performed mRNA profiling, as well as chromatin immunoprecipitation coupled to high-throughput sequencing. We furthermore elucidated the de novo binding motif of each sigma factor, and validated the RNA- and ChIP-seq results by global motif searches in the proximity of transcriptional start sites (TSS). Our integrated approach revealed a highly modular network architecture which is composed of insulated functional sigma factor modules. Analysis of the interconnectivity of the various sigma factor networks uncovered a limited, but highly function-specific, crosstalk which orchestrates complex cellular processes. Our data indicate that the modular structure of sigma factor networks enables P. aeruginosa to function adequately in its environment and at the same time is exploited to build up higher-level functions by specific interconnections that are dominated by a participation of RpoN. PMID:25780925

  15. Westinghouse modular grinding process - improvement for follow on processes

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

    Fehrmann, Henning

    2013-07-01

    In nuclear power plants (NPP) ion exchange (IX) resins are used in several systems for water treatment. The resins can be in bead or powdered form. For waste treatment of spent IX resins, two methods are basically used: Direct immobilization (e.g. with cement, bitumen, polymer or High Integrity Container (HIC)); Thermal treatment (e.g. drying, oxidation or pyrolysis). Bead resins have some properties (e.g. particle size and density) that can have negative impacts on following waste treatment processes. Negative impacts could be: Floatation of bead resins in cementation process; Sedimentation in pipeline during transportation; Poor compaction properties for Hot Resin Supercompactionmore » (HRSC). Reducing the particle size of the bead resins can have beneficial effects enhancing further treatment processes and overcoming prior mentioned effects. Westinghouse Electric Company has developed a modular grinding process to crush/grind the bead resins. This modular process is designed for flexible use and enables a selective adjustment of particle size to tailor the grinding system to the customer needs. The system can be equipped with a crusher integrated in the process tank and if necessary a colloid mill. The crusher reduces the bead resins particle size and converts the bead resins to a pump able suspension with lower sedimentation properties. With the colloid mill the resins can be ground to a powder. Compared to existing grinding systems this equipment is designed to minimize radiation exposure of the worker during operation and maintenance. Using the crushed and/or ground bead resins has several beneficial effects like facilitating cementation process and recipe development, enhancing oxidation of resins, improving the Hot Resin Supercompaction volume reduction performance. (authors)« less

  16. Final Report: Self-Consolidating Concrete Construction for Modular Units

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

    Gentry, Russell; Kahn, Lawrence; Kurtis, Kimberly

    This report focuses on work completed on DE-NE0000667, Self-Consolidating Concrete for Modular Units, in connection with the Department of Energy Nuclear Energy Enabling Technologies (DOE-NEET) program. This project was completed in the School of Civil and Environmental Engineering at the Georgia Institute of Technology, with Westinghouse Corporation as the industrial partner. The primary objective of this project was to develop self-consolidating concrete (also termed “self-compacting concrete” or SCC) mixtures so that concrete placement can be made into steel plate composite (SC) modular structures without the need for continuous concrete placement. As part of the research, SCC mixtures were developed andmore » validated to ensure sufficient shear capacity across cold-joints, while minimizing shrinkage and temperature increase during curing to enhance concrete bonding with the steel plate construction found in modular units. The SCC mixtures developed were able to carry shearing forces across the cold-joint boundaries. This “self-roughening” was achieved by adding a tailored fraction of lightweight aggregate (LWA) to the concrete mix, some of which raised to the surface during curing, forming a rough surface on which subsequent concrete placements were made. The self-roughening behavior was validated through three sets of structural tests. Shear friction on small-scale specimens with cold joints was assessed using varying fractions of LWA and with varying amounts of external steel plate reinforcement. The results show that the shear friction coefficient, to be used with the provisions of ACI 318-14, Section 22.9, can be taken as 1.35. Mid-scale beam tests were completed to assess the cold-joint capacity in both in-plane and out-of-plane bending. The results showed that the self-roughened joints performed as well as monolithic joints. The final assessment was a full-scale test using a steel composite module supplied by Westinghouse and similar in

  17. Modularity-like objective function in annotated networks

    NASA Astrophysics Data System (ADS)

    Xie, Jia-Rong; Wang, Bing-Hong

    2017-12-01

    We ascertain the modularity-like objective function whose optimization is equivalent to the maximum likelihood in annotated networks. We demonstrate that the modularity-like objective function is a linear combination of modularity and conditional entropy. In contrast with statistical inference methods, in our method, the influence of the metadata is adjustable; when its influence is strong enough, the metadata can be recovered. Conversely, when it is weak, the detection may correspond to another partition. Between the two, there is a transition. This paper provides a concept for expanding the scope of modularity methods.

  18. On the classification of weakly integral modular categories

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

    Bruillard, Paul; Galindo, César; Ng, Siu-Hung

    In this paper we classify all modular categories of dimension 4m, where m is an odd square-free integer, and all rank 6 and rank 7 weakly integral modular categories. This completes the classification of weakly integral modular categories through rank 7. In particular, our results imply that all integral modular categories of rank at most 7 are pointed (that is, every simple object has dimension 1). All the non-integral (but weakly integral) modular categories of ranks 6 and 7 have dimension 4m, with m an odd square free integer, so their classification is an application of our main result. Themore » classification of rank 7 integral modular categories is facilitated by an analysis of the two group actions on modular categories: the Galois group of the field generated by the entries of the S-matrix and the group of invertible isomorphism classes of objects. We derive some valuable arithmetic consequences from these actions.« less

  19. A Formal Theory for Modular ERDF Ontologies

    NASA Astrophysics Data System (ADS)

    Analyti, Anastasia; Antoniou, Grigoris; Damásio, Carlos Viegas

    The success of the Semantic Web is impossible without any form of modularity, encapsulation, and access control. In an earlier paper, we extended RDF graphs with weak and strong negation, as well as derivation rules. The ERDF #n-stable model semantics of the extended RDF framework (ERDF) is defined, extending RDF(S) semantics. In this paper, we propose a framework for modular ERDF ontologies, called modular ERDF framework, which enables collaborative reasoning over a set of ERDF ontologies, while support for hidden knowledge is also provided. In particular, the modular ERDF stable model semantics of modular ERDF ontologies is defined, extending the ERDF #n-stable model semantics. Our proposed framework supports local semantics and different points of view, local closed-world and open-world assumptions, and scoped negation-as-failure. Several complexity results are provided.

  20. Tailor-welded blanks and their production

    NASA Astrophysics Data System (ADS)

    Yan, Qi

    2005-01-01

    Tailor welded blanks had been widely used in the automobile industry. A tailor welded blank consists of several flat sheets that were laser welded together before stamping. A combination of different materials, thickness, and coatings could be welded together to form a blank for stamping car body panels. As for the material for automobile industry, this technology was one of the development trend for automobile industry because of its weight reduction, safety improvement and economical use of materials. In this paper, the characters and production of tailor welded blanks in the market were discussed in detail. There had two major methods to produce tailor welded blanks. Laser welding would replace mesh seam welding for the production of tailor welded blanks in the future. The requirements on the edge preparation of unwelded blanks for tailor welded blanks were higher than the other steel processing technology. In order to produce the laser welded blank, there had the other process before the laser welding in the factory. In the world, there had three kinds of patterns for the large volume production of tailor welded blanks. In China, steel factory played the important role in the promotion of the application of tailor welded blanks. The competition for the supply of tailor welded blanks to the automobile industry would become fierce in the near future. As a result, the demand for the quality control on the production of tailor welded blanks would be the first priority concern for the factory.

  1. Modular health services: a single case study approach to the applicability of modularity to residential mental healthcare

    PubMed Central

    2014-01-01

    Background The Dutch mental healthcare sector has to decrease costs by reducing intramural capacity with one third by 2020 and treating more patients in outpatient care. This transition necessitates enabling patients to become as self-supporting as possible, by customising the residential care they receive to their needs for self-development. Theoretically, modularity might help mental healthcare institutions with this. Modularity entails the decomposition of a healthcare service in parts that can be mixed-and-matched in a variety of ways, and combined form a functional whole. It brings about easier and better configuration, increased transparency and more variety without increasing costs. Aim: this study aims to explore the applicability of the modularity concept to the residential care provided in Assisted Living Facilities (ALFs) of Dutch mental healthcare institutions. Methods A single case study is carried out at the centre for psychosis in Etten-Leur, part of the GGz Breburg IMPACT care group. The design enables in-depth analysis of a case in a specific context. This is considered appropriate since theory concerning healthcare modularity is in an early stage of development. The present study can be considered a pilot case. Data were gathered by means of interviews, observations and documentary analysis. Results At the centre for psychosis, the majority of the residential care can be decomposed in modules, which can be grouped in service bundles and sub-bundles; the service customisation process is sufficiently fit to apply modular thinking; and interfaces for most of the categories are present. Hence, the prerequisites for modular residential care offerings are already largely fulfilled. For not yet fulfilled aspects of these prerequisites, remedies are available. Conclusion The modularity concept seems applicable to the residential care offered by the ALF of the mental healthcare institution under study. For a successful implementation of modularity however

  2. Modular health services: a single case study approach to the applicability of modularity to residential mental healthcare.

    PubMed

    Soffers, Rutger; Meijboom, Bert; van Zaanen, Jos; van der Feltz-Cornelis, Christina

    2014-05-09

    The Dutch mental healthcare sector has to decrease costs by reducing intramural capacity with one third by 2020 and treating more patients in outpatient care. This transition necessitates enabling patients to become as self-supporting as possible, by customising the residential care they receive to their needs for self-development. Theoretically, modularity might help mental healthcare institutions with this. Modularity entails the decomposition of a healthcare service in parts that can be mixed-and-matched in a variety of ways, and combined form a functional whole. It brings about easier and better configuration, increased transparency and more variety without increasing costs. this study aims to explore the applicability of the modularity concept to the residential care provided in Assisted Living Facilities (ALFs) of Dutch mental healthcare institutions. A single case study is carried out at the centre for psychosis in Etten-Leur, part of the GGz Breburg IMPACT care group. The design enables in-depth analysis of a case in a specific context. This is considered appropriate since theory concerning healthcare modularity is in an early stage of development. The present study can be considered a pilot case. Data were gathered by means of interviews, observations and documentary analysis. At the centre for psychosis, the majority of the residential care can be decomposed in modules, which can be grouped in service bundles and sub-bundles; the service customisation process is sufficiently fit to apply modular thinking; and interfaces for most of the categories are present. Hence, the prerequisites for modular residential care offerings are already largely fulfilled. For not yet fulfilled aspects of these prerequisites, remedies are available. The modularity concept seems applicable to the residential care offered by the ALF of the mental healthcare institution under study. For a successful implementation of modularity however, some steps should be taken by the ALF

  3. Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

    PubMed Central

    Rutenberg-Schoenberg, Michael; Simon, Matthew D.

    2015-01-01

    The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. PMID:26646615

  4. Electronic properties of bimetallic metal–organic frameworks (MOFs): Tailoring the density of electronic states through MOF modularity

    DOE PAGES

    Dolgopolova, Ekaterina A.; Brandt, Amy J.; Ejegbavwo, Otega A.; ...

    2017-03-18

    The development of porous well-defined hybrid materials (e.g., metal-organic frameworks or MOFs) will add a new dimension to a wide number of applications ranging from supercapacitors and electrodes to 'smart' membranes and thermoelectrics. From this perspective, the understanding and tailoring of the electronic properties of MOFs are key fundamental challenges that could unlock the full potential of these materials. In this work, we focused on the fundamental insights responsible for the electronic properties of three distinct classes of bimetallic systems, M x-yM' y-MOFs, M xM' y- MOFs, and M x(ligand-M' y)-MOFs, in which the second metal (M') incorporation occurs throughmore » (i) metal (M) replacement in the framework nodes (type I), (ii) metal node extension (type II), and (iii) metal coordination to the organic ligand (type III), respectively. We employed microwave conductivity, X-ray photoelectron spectroscopy, diffuse reflectance spectroscopy, powder X-ray diffraction, inductively coupled plasma atomic emission spectroscopy, pressed-pellet conductivity, and theoretical modeling to shed light on the key factors responsible for the tunability of MOF electronic structures. Experimental prescreening of MOFs was performed based on changes in the density of electronic states near the Fermi edge, which was used as a starting point for further selection of suitable MOFs. As a result, we demonstrated that the tailoring of MOF electronic properties could be performed as a function of metal node engineering, framework topology, and/or the presence of unsaturated metal sites while preserving framework porosity and structural integrity. Finally, these studies unveil the possible pathways for transforming the electronic properties of MOFs from insulating to semiconducting, as well as provide a blueprint for the development of hybrid porous materials with desirable electronic structures.« less

  5. Modular Courses in British Higher Education: A Critical Assessment

    ERIC Educational Resources Information Center

    Church, Clive

    1975-01-01

    The trends towards modular course structures is examined. British conceptions of modularization are compared with American interpretations of modular instruction, the former shown to be concerned almost exclusively with content, the latter attempting more radical changes in students' learning behavior. Rationales for British modular schemes are…

  6. The Modular need for the Division Signal Battalion

    DTIC Science & Technology

    2017-06-09

    findings and analyzes them to expand on them. It is with these findings and subsequent analysis that the case studies shape the answer to the three...These case studies focus on the signal leadership development and how it occurred in the pre-modular force structure, during modularity, and the...the comparative case study research. The case studies focus on signal leader development in a pre-modular signal force, a modular signal force, and

  7. mESAdb: microRNA Expression and Sequence Analysis Database

    PubMed Central

    Kaya, Koray D.; Karakülah, Gökhan; Yakıcıer, Cengiz M.; Acar, Aybar C.; Konu, Özlen

    2011-01-01

    microRNA expression and sequence analysis database (http://konulab.fen.bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data. PMID:21177657

  8. mESAdb: microRNA expression and sequence analysis database.

    PubMed

    Kaya, Koray D; Karakülah, Gökhan; Yakicier, Cengiz M; Acar, Aybar C; Konu, Ozlen

    2011-01-01

    microRNA expression and sequence analysis database (http://konulab.fen.bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data.

  9. Modular avionics packaging standardization

    NASA Astrophysics Data System (ADS)

    Austin, M.; McNichols, J. K.

    The Modular Avionics Packaging (MAP) Program for packaging future military avionics systems with the objective of improving reliability, maintainability, and supportability, and reducing equipment life cycle costs is addressed. The basic MAP packaging concepts called the Standard Avionics Module, the Standard Enclosure, and the Integrated Rack are summarized, and the benefits of modular avionics packaging, including low risk design, technology independence with common functions, improved maintainability and life cycle costs are discussed. Progress made in MAP is briefly reviewed.

  10. RISE: a database of RNA interactome from sequencing experiments

    PubMed Central

    Gong, Jing; Shao, Di; Xu, Kui

    2018-01-01

    Abstract We present RISE (http://rise.zhanglab.net), a database of RNA Interactome from Sequencing Experiments. RNA-RNA interactions (RRIs) are essential for RNA regulation and function. RISE provides a comprehensive collection of RRIs that mainly come from recent transcriptome-wide sequencing-based experiments like PARIS, SPLASH, LIGR-seq, and MARIO, as well as targeted studies like RIA-seq, RAP-RNA and CLASH. It also includes interactions aggregated from other primary databases and publications. The RISE database currently contains 328,811 RNA-RNA interactions mainly in human, mouse and yeast. While most existing RNA databases mainly contain interactions of miRNA targeting, notably, more than half of the RRIs in RISE are among mRNA and long non-coding RNAs. We compared different RRI datasets in RISE and found limited overlaps in interactions resolved by different techniques and in different cell lines. It may suggest technology preference and also dynamic natures of RRIs. We also analyzed the basic features of the human and mouse RRI networks and found that they tend to be scale-free, small-world, hierarchical and modular. The analysis may nominate important RNAs or RRIs for further investigation. Finally, RISE provides a Circos plot and several table views for integrative visualization, with extensive molecular and functional annotations to facilitate exploration of biological functions for any RRI of interest. PMID:29040625

  11. Towards a Formal Basis for Modular Safety Cases

    NASA Technical Reports Server (NTRS)

    Denney, Ewen; Pai, Ganesh

    2015-01-01

    Safety assurance using argument-based safety cases is an accepted best-practice in many safety-critical sectors. Goal Structuring Notation (GSN), which is widely used for presenting safety arguments graphically, provides a notion of modular arguments to support the goal of incremental certification. Despite the efforts at standardization, GSN remains an informal notation whereas the GSN standard contains appreciable ambiguity especially concerning modular extensions. This, in turn, presents challenges when developing tools and methods to intelligently manipulate modular GSN arguments. This paper develops the elements of a theory of modular safety cases, leveraging our previous work on formalizing GSN arguments. Using example argument structures we highlight some ambiguities arising through the existing guidance, present the intuition underlying the theory, clarify syntax, and address modular arguments, contracts, well-formedness and well-scopedness of modules. Based on this theory, we have a preliminary implementation of modular arguments in our toolset, AdvoCATE.

  12. Modular standards for emerging avionics technologies

    NASA Astrophysics Data System (ADS)

    Radcliffe, B.; Boaz, J.

    The present investigation is concerned with modular standards for the integration of new avionics technologies into production aircraft, taking into account also major retrofit programs. It is pointed out that avionics systems are about to undergo drastic changes in the partitioning of functions and judicious sharing of resources. These changes have the potential to significantly improve reliability and maintainability, and to reduce costs. Attention is given to a definition of the modular avionics concept, the existing module program, the development approach, development progress on the modular avionics standard, and the future of avionics installation standards.

  13. Modular Apparatus and Method for Attaching Multiple Devices

    NASA Technical Reports Server (NTRS)

    Okojie, Robert S (Inventor)

    2015-01-01

    A modular apparatus for attaching sensors and electronics is disclosed. The modular apparatus includes a square recess including a plurality of cavities and a reference cavity such that a pressure sensor can be connected to the modular apparatus. The modular apparatus also includes at least one voltage input hole and at least one voltage output hole operably connected to each of the plurality of cavities such that voltage can be applied to the pressure sensor and received from the pressure sensor.

  14. Modular Universal Scalable Ion-trap Quantum Computer

    DTIC Science & Technology

    2016-06-02

    SECURITY CLASSIFICATION OF: The main goal of the original MUSIQC proposal was to construct and demonstrate a modular and universally- expandable ion...Distribution Unlimited UU UU UU UU 02-06-2016 1-Aug-2010 31-Jan-2016 Final Report: Modular Universal Scalable Ion-trap Quantum Computer The views...P.O. Box 12211 Research Triangle Park, NC 27709-2211 Ion trap quantum computation, scalable modular architectures REPORT DOCUMENTATION PAGE 11

  15. Highly-Efficient and Modular Medium-Voltage Converters

    DTIC Science & Technology

    2015-09-28

    HVDC modular multilevel converter in decoupled double synchronous reference frame for voltage oscillation reduction," IEEE Trans. Ind...Electron., vol. 29, pp. 77-88, Jan 2014. [10] M. Guan and Z. Xu, "Modeling and control of a modular multilevel converter -based HVDC system under...34 Modular multilevel converter design for VSC HVDC applications," IEEE Journal of Emerging and Selected Topics in Power Electronics, vol. 3, pp.

  16. Cost effectiveness of computer tailored and non-tailored smoking cessation letters in general practice: randomised controlled trial

    PubMed Central

    Lennox, A Scott; Osman, Liesl M; Reiter, Ehud; Robertson, Roma; Friend, James; McCann, Ian; Skatun, Diane; Donnan, Peter T

    2001-01-01

    Objectives To develop and evaluate, in a primary care setting, a computerised system for generating tailored letters about smoking cessation. Design Randomised controlled trial. Setting Six general practices in Aberdeen, Scotland. Participants 2553 smokers aged 17 to 65. Interventions All participants received a questionnaire asking about their smoking. Participants subsequently received either a computer tailored or a non-tailored, standard letter on smoking cessation, or no letter. Main outcome measures Prevalence of validated abstinence at six months; change in intention to stop smoking in the next six months. Results The validated cessation rate at six months was 3.5% (30/857) (95% confidence interval 2.3% to 4.7%) for the tailored letter group, 4.4% (37/846) (3.0% to 5.8%) for the non-tailored letter group, and 2.6% (22/850) (1.5% to 3.7%) for the control (no letter) group. After adjustment for significant covariates, the cessation rate was 66% greater (−4% to 186%; P=0.07) in the non-tailored letter group than that in the no letter group. Among participants who smoked <20 cigarettes per day, the cessation rate in the non-tailored letter group was 87% greater (0% to 246%; P=0.05) than that in the no letter group. Among heavy smokers who did not quit, a 76% higher rate of positive shift in “stage of change” (intention to quit within a particular period of time) was seen compared with those who received no letter (11% to 180%; P=0.02). The increase in cost for each additional quitter in the non-tailored letter group compared with the no letter group was £89. Conclusions In a large general practice, a brief non-tailored letter effectively increased cessation rates among smokers. A tailored letter was not effective in increasing cessation rates but promoted shift in movement towards cessation (“stage of change”) in heavy smokers. As a pragmatic tool to encourage cessation of smoking, a mass mailing of non-tailored letters from general practices is more

  17. Generalized epidemic process on modular networks.

    PubMed

    Chung, Kihong; Baek, Yongjoo; Kim, Daniel; Ha, Meesoon; Jeong, Hawoong

    2014-05-01

    Social reinforcement and modular structure are two salient features observed in the spreading of behavior through social contacts. In order to investigate the interplay between these two features, we study the generalized epidemic process on modular networks with equal-sized finite communities and adjustable modularity. Using the analytical approach originally applied to clique-based random networks, we show that the system exhibits a bond-percolation type continuous phase transition for weak social reinforcement, whereas a discontinuous phase transition occurs for sufficiently strong social reinforcement. Our findings are numerically verified using the finite-size scaling analysis and the crossings of the bimodality coefficient.

  18. Modular support blocks for fluid lines

    NASA Technical Reports Server (NTRS)

    Dimino, J. M.; Deskin, R. D.

    1974-01-01

    Modular line block comprises matched modular elements machined to accept fluid lines of different diameters. Modules can support different fluid-line configurations. Top and bottom surfaces are machined to accept dovetail strip used for holding modules together. End modules have holes drilled through to accept fastening screws.

  19. Portable or Modular? There Is a Difference....

    ERIC Educational Resources Information Center

    Morton, Mike

    2002-01-01

    Describes differences between two types of school facilities: portable (prebuilt, temporary wood structure installed on site) and modular (method of construction for permanent buildings). Provides details of modular construction. (PKP)

  20. Future Concepts for Modular, Intelligent Aerospace Power Systems

    NASA Technical Reports Server (NTRS)

    Button, Robert M.; Soeder, James F.

    2004-01-01

    Nasa's resent commitment to Human and Robotic Space Exploration obviates the need for more affordable and sustainable systems and missions. Increased use of modularity and on-board intelligent technologies will enable these lofty goals. To support this new paradigm, an advanced technology program to develop modular, intelligent power management and distribution (PMAD) system technologies is presented. The many benefits to developing and including modular functionality in electrical power components and systems are shown to include lower costs and lower mass for highly reliable systems. The details of several modular technologies being developed by NASA are presented, broken down into hierarchical levels. Modularity at the device level, including the use of power electronic building blocks, is shown to provide benefits in lowering the development time and costs of new power electronic components.

  1. Implicit Contractive Mappings in Modular Metric and Fuzzy Metric Spaces

    PubMed Central

    Hussain, N.; Salimi, P.

    2014-01-01

    The notion of modular metric spaces being a natural generalization of classical modulars over linear spaces like Lebesgue, Orlicz, Musielak-Orlicz, Lorentz, Orlicz-Lorentz, and Calderon-Lozanovskii spaces was recently introduced. In this paper we investigate the existence of fixed points of generalized α-admissible modular contractive mappings in modular metric spaces. As applications, we derive some new fixed point theorems in partially ordered modular metric spaces, Suzuki type fixed point theorems in modular metric spaces and new fixed point theorems for integral contractions. In last section, we develop an important relation between fuzzy metric and modular metric and deduce certain new fixed point results in triangular fuzzy metric spaces. Moreover, some examples are provided here to illustrate the usability of the obtained results. PMID:25003157

  2. Criteria for software modularization

    NASA Technical Reports Server (NTRS)

    Card, David N.; Page, Gerald T.; Mcgarry, Frank E.

    1985-01-01

    A central issue in programming practice involves determining the appropriate size and information content of a software module. This study attempted to determine the effectiveness of two widely used criteria for software modularization, strength and size, in reducing fault rate and development cost. Data from 453 FORTRAN modules developed by professional programmers were analyzed. The results indicated that module strength is a good criterion with respect to fault rate, whereas arbitrary module size limitations inhibit programmer productivity. This analysis is a first step toward defining empirically based standards for software modularization.

  3. Modular biowaste monitoring system

    NASA Technical Reports Server (NTRS)

    Fogal, G. L.

    1975-01-01

    The objective of the Modular Biowaste Monitoring System Program was to generate and evaluate hardware for supporting shuttle life science experimental and diagnostic programs. An initial conceptual design effort established requirements and defined an overall modular system for the collection, measurement, sampling and storage of urine and feces biowastes. This conceptual design effort was followed by the design, fabrication and performance evaluation of a flight prototype model urine collection, volume measurement and sampling capability. No operational or performance deficiencies were uncovered as a result of the performance evaluation tests.

  4. Automatic Modeling and Simulation of Modular Robots

    NASA Astrophysics Data System (ADS)

    Jiang, C.; Wei, H.; Zhang, Y.

    2018-03-01

    The ability of reconfiguration makes modular robots have the ability of adaptable, low-cost, self-healing and fault-tolerant. It can also be applied to a variety of mission situations. In this manuscript, a robot platform which relied on the module library was designed, based on the screw theory and module theory. Then, the configuration design method of the modular robot was proposed. And the different configurations of modular robot system have been built, including industrial mechanical arms, the mobile platform, six-legged robot and 3D exoskeleton manipulator. Finally, the simulation and verification of one system among them have been made, using the analyses of screw kinematics and polynomial planning. The results of experiments demonstrate the feasibility and superiority of this modular system.

  5. Teleoperated Modular Robots for Lunar Operations

    NASA Technical Reports Server (NTRS)

    Globus, Al; Hornby, Greg; Larchev, Greg; Hancher, Matt; Cannon, Howard; Lohn, Jason

    2004-01-01

    Solar system exploration is currently carried out by special purpose robots exquisitely designed for the anticipated tasks. However, all contingencies for in situ resource utilization (ISRU), human habitat preparation, and exploration will be difficult to anticipate. Furthermore, developing the necessary special purpose mechanisms for deployment and other capabilities is difficult and error prone. For example, the Galileo high gain antenna never opened, severely restricting the quantity of data returned by the spacecraft. Also, deployment hardware is used only once. To address these problems, we are developing teleoperated modular robots for lunar missions, including operations in transit from Earth. Teleoperation of lunar systems from Earth involves a three second speed-of-light delay, but experiment suggests that interactive operations are feasible.' Modular robots typically consist of many identical modules that pass power and data between them and can be reconfigured for different tasks providing great flexibility, inherent redundancy and graceful degradation as modules fail. Our design features a number of different hub, link, and joint modules to simplify the individual modules, lower structure cost, and provide specialized capabilities. Modular robots are well suited for space applications because of their extreme flexibility, inherent redundancy, high-density packing, and opportunities for mass production. Simple structural modules can be manufactured from lunar regolith in situ using molds or directed solar sintering. Software to direct and control modular robots is difficult to develop. We have used genetic algorithms to evolve both the morphology and control system for walking modular robots3 We are currently using evolvable system technology to evolve controllers for modular robots in the ISS glove box. Development of lunar modular robots will require software and physical simulators, including regolith simulation, to enable design and test of robot

  6. Modular, Hierarchical Learning By Artificial Neural Networks

    NASA Technical Reports Server (NTRS)

    Baldi, Pierre F.; Toomarian, Nikzad

    1996-01-01

    Modular and hierarchical approach to supervised learning by artificial neural networks leads to neural networks more structured than neural networks in which all neurons fully interconnected. These networks utilize general feedforward flow of information and sparse recurrent connections to achieve dynamical effects. The modular organization, sparsity of modular units and connections, and fact that learning is much more circumscribed are all attractive features for designing neural-network hardware. Learning streamlined by imitating some aspects of biological neural networks.

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

    PubMed

    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.

  8. Employee Perceptions of Workplace Health Promotion Programs: Comparison of a Tailored, Semi-Tailored, and Standardized Approach.

    PubMed

    Street, Tamara D; Lacey, Sarah J

    2018-04-28

    In the design of workplace health promotion programs (WHPPs), employee perceptions represent an integral variable which is predicted to translate into rate of user engagement (i.e., participation) and program loyalty. This study evaluated employee perceptions of three workplace health programs promoting nutritional consumption and physical activity. Programs included: (1) an individually tailored consultation with an exercise physiologist and dietitian; (2) a semi-tailored 12-week SMS health message program; and (3) a standardized group workshop delivered by an expert. Participating employees from a transport company completed program evaluation surveys rating the overall program, affect, and utility of: consultations ( n = 19); SMS program ( n = 234); and workshops ( n = 86). Overall, participants’ affect and utility evaluations were positive for all programs, with the greatest satisfaction being reported in the tailored individual consultation and standardized group workshop conditions. Furthermore, mode of delivery and the physical presence of an expert health practitioner was more influential than the degree to which the information was tailored to the individual. Thus, the synergy in ratings between individually tailored consultations and standardized group workshops indicates that low-cost delivery health programs may be as appealing to employees as tailored, and comparatively high-cost, program options.

  9. Telepathology: design of a modular system.

    PubMed

    Brauchli, K; Christen, H; Meyer, P; Haroske, G; Meyer, W; Kunze, K D; Otto, R; Oberholzer, M

    2000-01-01

    Although telepathology systems have been developed for more than a decade, they are still not a widespread tool for routine diagnostic applications. Lacking interoperability, software that is not satisfying user needs as well as high costs have been identified as reasons. In this paper we would like to demonstrate that with a clear separation of the tasks required for a telepathology application, telepathology systems can be built in a modular way, where many modules can be implemented using standard software components. With such a modular design, systems can be easily adapted to changing user needs and new technological developments and it is easier to integrate modular systems into existing environments.

  10. Modular Certification

    NASA Technical Reports Server (NTRS)

    Rushby, John; Miner, Paul S. (Technical Monitor)

    2002-01-01

    Airplanes are certified as a whole: there is no established basis for separately certifying some components, particularly software-intensive ones, independently of their specific application in a given airplane. The absence of separate certification inhibits the development of modular components that could be largely "precertified" and used in several different contexts within a single airplane, or across many different airplanes. In this report, we examine the issues in modular certification of software components and propose an approach based on assume-guarantee reasoning. We extend the method from verification to certification by considering behavior in the presence of failures. This exposes the need for partitioning, and separation of assumptions and guarantees into normal and abnormal cases. We then identify three classes of property that must be verified within this framework: safe function, true guarantees, and controlled failure. We identify a particular assume-guarantee proof rule (due to McMillan) that is appropriate to the applications considered, and formally verify its soundness in PVS.

  11. Modular space station

    NASA Technical Reports Server (NTRS)

    1972-01-01

    The modular space station comprising small, shuttle-launched modules, and characterized by low initial cost and incremental manning, is described. The initial space station is designed to be delivered into orbit by three space shuttles and assembled in space. The three sections are the power/subsystems module, the crew/operations module, and the general purpose laboratory module. It provides for a crew of six. Subsequently duplicate/crew/operations and power/subsystems modules will be mated to the original modules, and provide for an additional six crewmen. A total of 17 research and applications modules is planned, three of which will be free-flying modules. Details are given on the program plan, modular characteristics, logistics, experiment support capability and requirements, operations analysis, design support analyses, and shuttle interfaces.

  12. Tailored program evaluation: Past, present, future.

    PubMed

    Suggs, L Suzanne; Cowdery, Joan E; Carroll, Jennifer B

    2006-11-01

    This paper discusses measurement issues related to the evaluation of computer-tailored health behavior change programs. As the first generation of commercially available tailored products is utilized in health promotion programming, programmers and researchers are becoming aware of the unique challenges that the evaluation of these programs presents. A project is presented that used an online tailored health behavior assessment (HBA) in a worksite setting. Process and outcome evaluation methods are described and include the challenges faced, and strategies proposed and implemented, for meeting them. Implications for future research in tailored program development, implementation, and evaluation are also discussed.

  13. Dynamics of modularity of neural activity in the brain during development

    NASA Astrophysics Data System (ADS)

    Deem, Michael; Chen, Man

    2014-03-01

    Theory suggests that more modular systems can have better response functions at short times. This theory suggests that greater cognitive performance may be achieved for more modular neural activity, and that modularity of neural activity may, therefore, likely increase with development in children. We study the relationship between age and modularity of brain neural activity in developing children. The value of modularity calculated from fMRI data is observed to increase during childhood development and peak in young adulthood. We interpret these results as evidence of selection for plasticity in the cognitive function of the human brain. We present a model to illustrate how modularity can provide greater cognitive performance at short times and enhance fast, low-level, automatic cognitive processes. Conversely, high-level, effortful, conscious cognitive processes may not benefit from modularity. We use quasispecies theory to predict how the average modularity evolves with age, given a fitness function extracted from the model. We suggest further experiments exploring the effect of modularity on cognitive performance and suggest that modularity may be a potential biomarker for injury, rehabilitation, or disease.

  14. Configurable double-sided modular jet impingement assemblies for electronics cooling

    DOEpatents

    Zhou, Feng; Dede, Ercan Mehmet

    2018-05-22

    A modular jet impingement assembly includes an inlet tube fluidly coupled to a fluid inlet, an outlet tube fluidly coupled to a fluid outlet, and a modular manifold having a first distribution recess extending into a first side of the modular manifold, a second distribution recess extending into a second side of the modular manifold, a plurality of inlet connection tubes positioned at an inlet end of the modular manifold, and a plurality of outlet connection tubes positioned at an outlet end of the modular manifold. A first manifold insert is removably positioned within the first distribution recess, a second manifold insert is removably positioned within the second distribution recess, and a first and second heat transfer plate each removably coupled to the modular manifold. The first and second heat transfer plates each comprise an impingement surface.

  15. Coding of Class I and II aminoacyl-tRNA synthetases

    PubMed Central

    Carter, Charles W.

    2018-01-01

    SUMMARY The aminoacyl-tRNA synthetases and their cognate transfer RNAs translate the universal genetic code. The twenty canonical amino acids are sufficiently diverse to create a selective advantage for dividing amino acid activation between two distinct, apparently unrelated superfamilies of synthetases, Class I amino acids being generally larger and less polar, Class II amino acids smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that the two Classes descended from opposite strands of the same ancestral gene. Parallel experimental deconstructions of Class I and II synthetases reveal parallel losses in catalytic proficiency at two novel modular levels—protozymes and Urzymes—associated with the evolution of catalytic activity. Bi-directional coding supports an important unification of the proteome; affords a genetic relatedness metric—middle base-pairing frequencies in sense/antisense alignments—that probes more deeply into the evolutionary history of translation than do single multiple sequence alignments; and has facilitated the analysis of hitherto unknown coding relationships in tRNA sequences. Reconstruction of native synthetases by modular thermodynamic cycles facilitated by domain engineering emphasizes the subtlety associated with achieving high specificity, shedding new light on allosteric relationships in contemporary synthetases. Synthetase Urzyme structural biology suggests that they are catalytically active molten globules, broadening the potential manifold of polypeptide catalysts accessible to primitive genetic coding and motivating revisions of the origins of catalysis. Finally, bi-directional genetic coding of some of the oldest genes in the proteome places major limitations on the likelihood that any RNA World preceded the origins of coded proteins. PMID:28828732

  16. Employee Perceptions of Workplace Health Promotion Programs: Comparison of a Tailored, Semi-Tailored, and Standardized Approach

    PubMed Central

    Street, Tamara D.; Lacey, Sarah J.

    2018-01-01

    In the design of workplace health promotion programs (WHPPs), employee perceptions represent an integral variable which is predicted to translate into rate of user engagement (i.e., participation) and program loyalty. This study evaluated employee perceptions of three workplace health programs promoting nutritional consumption and physical activity. Programs included: (1) an individually tailored consultation with an exercise physiologist and dietitian; (2) a semi-tailored 12-week SMS health message program; and (3) a standardized group workshop delivered by an expert. Participating employees from a transport company completed program evaluation surveys rating the overall program, affect, and utility of: consultations (n = 19); SMS program (n = 234); and workshops (n = 86). Overall, participants’ affect and utility evaluations were positive for all programs, with the greatest satisfaction being reported in the tailored individual consultation and standardized group workshop conditions. Furthermore, mode of delivery and the physical presence of an expert health practitioner was more influential than the degree to which the information was tailored to the individual. Thus, the synergy in ratings between individually tailored consultations and standardized group workshops indicates that low-cost delivery health programs may be as appealing to employees as tailored, and comparatively high-cost, program options. PMID:29710785

  17. Modularity Induced Gating and Delays in Neuronal Networks

    PubMed Central

    Shein-Idelson, Mark; Cohen, Gilad; Hanein, Yael

    2016-01-01

    Neural networks, despite their highly interconnected nature, exhibit distinctly localized and gated activation. Modularity, a distinctive feature of neural networks, has been recently proposed as an important parameter determining the manner by which networks support activity propagation. Here we use an engineered biological model, consisting of engineered rat cortical neurons, to study the role of modular topology in gating the activity between cell populations. We show that pairs of connected modules support conditional propagation (transmitting stronger bursts with higher probability), long delays and propagation asymmetry. Moreover, large modular networks manifest diverse patterns of both local and global activation. Blocking inhibition decreased activity diversity and replaced it with highly consistent transmission patterns. By independently controlling modularity and disinhibition, experimentally and in a model, we pose that modular topology is an important parameter affecting activation localization and is instrumental for population-level gating by disinhibition. PMID:27104350

  18. Modular femoral neck fracture after primary total hip arthroplasty.

    PubMed

    Sotereanos, Nicholas G; Sauber, Timothy J; Tupis, Todd T

    2013-01-01

    The use of modular femoral stems in primary total hip arthroplasty has increased considerably in recent years. These modular components offer the surgeon the ability to independently alter version, offset, and length of the femoral component of a hip arthroplasty. This increases the surgeon's ability to accurately recreate the relevant anatomy but increases the possibilities of corrosion and fracture. Multiple case reports have highlighted fractures of these modular components. We present a case of a fracture of a modular design that has had no previously reported modular neck fractures. The patient was informed that data concerning the case would be submitted, and he consented. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Spectral tailoring device

    DOEpatents

    Brager, H.R.; Schenter, R.E.; Carter, L.L.; Karnesky, R.A.

    1987-08-05

    A spectral tailoring device for altering the neutron energy spectra and flux of neutrons in a fast reactor thereby selectively to enhance or inhibit the transmutation rate of a target metrical to form a product isotope. Neutron moderators, neutron filters, neutron absorbers and neutron reflectors may be used as spectral tailoring devices. Depending on the intended use for the device, a member from each of these four classes of materials could be used singularly, or in combination, to provide a preferred neutron energy spectra and flux of the neutrons in the region of the target material. In one embodiment of the invention, an assembly is provided for enhancing the production of isotopes, such as cobalt 60 and gadolinium 153. In another embodiment of the invention, a spectral tailoring device is disposed adjacent a target material which comprises long lived or volatile fission products and the device is used to shift the neutron energy spectra and flux of neutrons in the region of the fission products to preferentially transmute them to produce a less volatile fission product inventory. 6 figs.

  20. The gravity duals of modular Hamiltonians

    DOE PAGES

    Jafferis, Daniel L.; Suh, S. Josephine

    2016-09-12

    In this study, we investigate modular Hamiltonians defined with respect to arbitrary spatial regions in quantum field theory states which have semi-classical gravity duals. We find prescriptions in the gravity dual for calculating the action of the modular Hamiltonian on its defining state, including its dual metric, and also on small excitations around the state. Curiously, use of the covariant holographic entanglement entropy formula leads us to the conclusion that the modular Hamiltonian, which in the quantum field theory acts only in the causal completion of the region, does not commute with bulk operators whose entire gauge-invariant description is space-likemore » to the causal completion of the region.« less

  1. The gravity duals of modular Hamiltonians

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

    Jafferis, Daniel L.; Suh, S. Josephine

    In this study, we investigate modular Hamiltonians defined with respect to arbitrary spatial regions in quantum field theory states which have semi-classical gravity duals. We find prescriptions in the gravity dual for calculating the action of the modular Hamiltonian on its defining state, including its dual metric, and also on small excitations around the state. Curiously, use of the covariant holographic entanglement entropy formula leads us to the conclusion that the modular Hamiltonian, which in the quantum field theory acts only in the causal completion of the region, does not commute with bulk operators whose entire gauge-invariant description is space-likemore » to the causal completion of the region.« less

  2. Brain modularity controls the critical behavior of spontaneous activity.

    PubMed

    Russo, R; Herrmann, H J; de Arcangelis, L

    2014-03-13

    The human brain exhibits a complex structure made of scale-free highly connected modules loosely interconnected by weaker links to form a small-world network. These features appear in healthy patients whereas neurological diseases often modify this structure. An important open question concerns the role of brain modularity in sustaining the critical behaviour of spontaneous activity. Here we analyse the neuronal activity of a model, successful in reproducing on non-modular networks the scaling behaviour observed in experimental data, on a modular network implementing the main statistical features measured in human brain. We show that on a modular network, regardless the strength of the synaptic connections or the modular size and number, activity is never fully scale-free. Neuronal avalanches can invade different modules which results in an activity depression, hindering further avalanche propagation. Critical behaviour is solely recovered if inter-module connections are added, modifying the modular into a more random structure.

  3. Modular assembly of optical nanocircuits.

    PubMed

    Shi, Jinwei; Monticone, Francesco; Elias, Sarah; Wu, Yanwen; Ratchford, Daniel; Li, Xiaoqin; Alù, Andrea

    2014-05-29

    A key element enabling the microelectronic technology advances of the past decades has been the conceptualization of complex circuits with versatile functionalities as being composed of the proper combination of basic 'lumped' circuit elements (for example, inductors and capacitors). In contrast, modern nanophotonic systems are still far from a similar level of sophistication, partially because of the lack of modularization of their response in terms of basic building blocks. Here we demonstrate the design, assembly and characterization of relatively complex photonic nanocircuits by accurately positioning a number of metallic and dielectric nanoparticles acting as modular lumped elements. The nanoparticle clusters produce the desired spectral response described by simple circuit rules and are shown to be dynamically reconfigurable by modifying the direction or polarization of impinging signals. Our work represents an important step towards extending the powerful modular design tools of electronic circuits into nanophotonic systems.

  4. Modular assembly of optical nanocircuits

    NASA Astrophysics Data System (ADS)

    Shi, Jinwei; Monticone, Francesco; Elias, Sarah; Wu, Yanwen; Ratchford, Daniel; Li, Xiaoqin; Alù, Andrea

    2014-05-01

    A key element enabling the microelectronic technology advances of the past decades has been the conceptualization of complex circuits with versatile functionalities as being composed of the proper combination of basic ‘lumped’ circuit elements (for example, inductors and capacitors). In contrast, modern nanophotonic systems are still far from a similar level of sophistication, partially because of the lack of modularization of their response in terms of basic building blocks. Here we demonstrate the design, assembly and characterization of relatively complex photonic nanocircuits by accurately positioning a number of metallic and dielectric nanoparticles acting as modular lumped elements. The nanoparticle clusters produce the desired spectral response described by simple circuit rules and are shown to be dynamically reconfigurable by modifying the direction or polarization of impinging signals. Our work represents an important step towards extending the powerful modular design tools of electronic circuits into nanophotonic systems.

  5. A thioacidolysis method tailored for higher‐throughput quantitative analysis of lignin monomers

    PubMed Central

    Foster, Cliff; Happs, Renee M.; Doeppke, Crissa; Meunier, Kristoffer; Gehan, Jackson; Yue, Fengxia; Lu, Fachuang; Davis, Mark F.

    2016-01-01

    Abstract Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β‐O‐4 linkages. Current thioacidolysis methods are low‐throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non‐chlorinated organic solvent and is tailored for higher‐throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1–2 mg of biomass per assay and has been quantified using fast‐GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, including standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day‐to‐day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. The method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses. PMID:27534715

  6. A thioacidolysis method tailored for higher-throughput quantitative analysis of lignin monomers

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

    Harman-Ware, Anne E.; Foster, Cliff; Happs, Renee M.

    Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β-O-4 linkages. Current thioacidolysis methods are low-throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non-chlorinated organic solvent and is tailored for higher-throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1-2 mg of biomass per assay and has been quantified using fast-GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, includingmore » standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day-to-day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. As a result, the method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses.« less

  7. A thioacidolysis method tailored for higher-throughput quantitative analysis of lignin monomers

    DOE PAGES

    Harman-Ware, Anne E.; Foster, Cliff; Happs, Renee M.; ...

    2016-09-14

    Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β-O-4 linkages. Current thioacidolysis methods are low-throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non-chlorinated organic solvent and is tailored for higher-throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1-2 mg of biomass per assay and has been quantified using fast-GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, includingmore » standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day-to-day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. As a result, the method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses.« less

  8. Individual differences and time-varying features of modular brain architecture.

    PubMed

    Liao, Xuhong; Cao, Miao; Xia, Mingrui; He, Yong

    2017-05-15

    Recent studies have suggested that human brain functional networks are topologically organized into functionally specialized but inter-connected modules to facilitate efficient information processing and highly flexible cognitive function. However, these studies have mainly focused on group-level network modularity analyses using "static" functional connectivity approaches. How these extraordinary modular brain structures vary across individuals and spontaneously reconfigure over time remain largely unknown. Here, we employed multiband resting-state functional MRI data (N=105) from the Human Connectome Project and a graph-based modularity analysis to systematically investigate individual variability and dynamic properties in modular brain networks. We showed that the modular structures of brain networks dramatically vary across individuals, with higher modular variability primarily in the association cortex (e.g., fronto-parietal and attention systems) and lower variability in the primary systems. Moreover, brain regions spontaneously changed their module affiliations on a temporal scale of seconds, which cannot be simply attributable to head motion and sampling error. Interestingly, the spatial pattern of intra-subject dynamic modular variability largely overlapped with that of inter-subject modular variability, both of which were highly reproducible across repeated scanning sessions. Finally, the regions with remarkable individual/temporal modular variability were closely associated with network connectors and the number of cognitive components, suggesting a potential contribution to information integration and flexible cognitive function. Collectively, our findings highlight individual modular variability and the notable dynamic characteristics in large-scale brain networks, which enhance our understanding of the neural substrates underlying individual differences in a variety of cognition and behaviors. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. A Modular Laser Graphics Projection System

    NASA Astrophysics Data System (ADS)

    Newswanger, Craig D.

    1984-05-01

    WED Enterprises has designed and built a modular projection system for the presentation of animated laser shows. This system was designed specifically for use in Disney theme shows. Its modular design allows it to be adapted to many show situations with simple hardware and software adjustments. The primary goals were superior animation, long life, low maintenance and stand alone operation.

  10. Full characterization of modular values for finite-dimensional systems

    NASA Astrophysics Data System (ADS)

    Ho, Le Bin; Imoto, Nobuyuki

    2016-06-01

    Kedem and Vaidman obtained a relationship between the spin-operator modular value and its weak value for specific coupling strengths [14]. Here we give a general expression for the modular value in the n-dimensional Hilbert space using the weak values up to (n - 1)th order of an arbitrary observable for any coupling strength, assuming non-degenerated eigenvalues. For two-dimensional case, it shows a linear relationship between the weak value and the modular value. We also relate the modular value of the sum of observables to the weak value of their product.

  11. Modular survivable satellite support

    NASA Astrophysics Data System (ADS)

    Wagner, R. E.

    The development of a highly mobile, survivable satellite system from the Transportable Mobile Ground Station (T/MGS) is proposed. The addition of advanced capabilities to the T/MGS such as telemetry processing equipment, and the flexibility of a modularly designed system are examined. The need to increase survivability and mobility while reducing life cycle costs is discussed. A modular survivable satellite support system which consists of a 40-foot van, a diesel tractor, and a multimedia communications subsystem is described. The use of planar and phased arrays to improve transportability and new materials and structural designs to enhance hardness are discussed. Diagrams of the system are provided.

  12. 46 CFR 181.450 - Independent modular smoke detecting units.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 7 2013-10-01 2013-10-01 false Independent modular smoke detecting units. 181.450... Independent modular smoke detecting units. (a) An independent modular smoke detecting unit must: (1) Meet UL 217 (incorporated by reference, see 46 CFR 175.600) and be listed as a “Single Station Smoke detector...

  13. 46 CFR 181.450 - Independent modular smoke detecting units.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 7 2012-10-01 2012-10-01 false Independent modular smoke detecting units. 181.450... Independent modular smoke detecting units. (a) An independent modular smoke detecting unit must: (1) Meet UL 217 (incorporated by reference, see 46 CFR 175.600) and be listed as a “Single Station Smoke detector...

  14. 46 CFR 181.450 - Independent modular smoke detecting units.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 7 2011-10-01 2011-10-01 false Independent modular smoke detecting units. 181.450... Independent modular smoke detecting units. (a) An independent modular smoke detecting unit must: (1) Meet UL 217 (incorporated by reference, see 46 CFR 175.600) and be listed as a “Single Station Smoke detector...

  15. 46 CFR 181.450 - Independent modular smoke detecting units.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Independent modular smoke detecting units. 181.450... Independent modular smoke detecting units. (a) An independent modular smoke detecting unit must: (1) Meet UL 217 (incorporated by reference, see 46 CFR 175.600) and be listed as a “Single Station Smoke detector...

  16. 46 CFR 181.450 - Independent modular smoke detecting units.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 7 2014-10-01 2014-10-01 false Independent modular smoke detecting units. 181.450... Independent modular smoke detecting units. (a) An independent modular smoke detecting unit must: (1) Meet UL 217 (incorporated by reference, see 46 CFR 175.600) and be listed as a “Single Station Smoke detector...

  17. Convergent evolution of modularity in metabolic networks through different community structures.

    PubMed

    Zhou, Wanding; Nakhleh, Luay

    2012-09-14

    It has been reported that the modularity of metabolic networks of bacteria is closely related to the variability of their living habitats. However, given the dependency of the modularity score on the community structure, it remains unknown whether organisms achieve certain modularity via similar or different community structures. In this work, we studied the relationship between similarities in modularity scores and similarities in community structures of the metabolic networks of 1021 species. Both similarities are then compared against the genetic distances. We revisited the association between modularity and variability of the microbial living environments and extended the analysis to other aspects of their life style such as temperature and oxygen requirements. We also tested both topological and biological intuition of the community structures identified and investigated the extent of their conservation with respect to the taxonomy. We find that similar modularities are realized by different community structures. We find that such convergent evolution of modularity is closely associated with the number of (distinct) enzymes in the organism's metabolome, a consequence of different life styles of the species. We find that the order of modularity is the same as the order of the number of the enzymes under the classification based on the temperature preference but not on the oxygen requirement. Besides, inspection of modularity-based communities reveals that these communities are graph-theoretically meaningful yet not reflective of specific biological functions. From an evolutionary perspective, we find that the community structures are conserved only at the level of kingdoms. Our results call for more investigation into the interplay between evolution and modularity: how evolution shapes modularity, and how modularity affects evolution (mainly in terms of fitness and evolvability). Further, our results call for exploring new measures of modularity and network

  18. Convergent evolution of modularity in metabolic networks through different community structures

    PubMed Central

    2012-01-01

    Background It has been reported that the modularity of metabolic networks of bacteria is closely related to the variability of their living habitats. However, given the dependency of the modularity score on the community structure, it remains unknown whether organisms achieve certain modularity via similar or different community structures. Results In this work, we studied the relationship between similarities in modularity scores and similarities in community structures of the metabolic networks of 1021 species. Both similarities are then compared against the genetic distances. We revisited the association between modularity and variability of the microbial living environments and extended the analysis to other aspects of their life style such as temperature and oxygen requirements. We also tested both topological and biological intuition of the community structures identified and investigated the extent of their conservation with respect to the taxomony. Conclusions We find that similar modularities are realized by different community structures. We find that such convergent evolution of modularity is closely associated with the number of (distinct) enzymes in the organism’s metabolome, a consequence of different life styles of the species. We find that the order of modularity is the same as the order of the number of the enzymes under the classification based on the temperature preference but not on the oxygen requirement. Besides, inspection of modularity-based communities reveals that these communities are graph-theoretically meaningful yet not reflective of specific biological functions. From an evolutionary perspective, we find that the community structures are conserved only at the level of kingdoms. Our results call for more investigation into the interplay between evolution and modularity: how evolution shapes modularity, and how modularity affects evolution (mainly in terms of fitness and evolvability). Further, our results call for exploring new

  19. Modular structural elements in the replication origin region of Tetrahymena rDNA.

    PubMed Central

    Du, C; Sanzgiri, R P; Shaiu, W L; Choi, J K; Hou, Z; Benbow, R M; Dobbs, D L

    1995-01-01

    Computer analyses of the DNA replication origin region in the amplified rRNA genes of Tetrahymena thermophila identified a potential initiation zone in the 5'NTS [Dobbs, Shaiu and Benbow (1994), Nucleic Acids Res. 22, 2479-2489]. This region consists of a putative DNA unwinding element (DUE) aligned with predicted bent DNA segments, nuclear matrix or scaffold associated region (MAR/SAR) consensus sequences, and other common modular sequence elements previously shown to be clustered in eukaryotic chromosomal origin regions. In this study, two mung bean nuclease-hypersensitive sites in super-coiled plasmid DNA were localized within the major DUE-like element predicted by thermodynamic analyses. Three restriction fragments of the 5'NTS region predicted to contain bent DNA segments exhibited anomalous migration characteristic of bent DNA during electrophoresis on polyacrylamide gels. Restriction fragments containing the 5'NTS region bound Tetrahymena nuclear matrices in an in vitro binding assay, consistent with an association of the replication origin region with the nuclear matrix in vivo. The direct demonstration in a protozoan origin region of elements previously identified in Drosophila, chick and mammalian origin regions suggests that clusters of modular structural elements may be a conserved feature of eukaryotic chromosomal origins of replication. Images PMID:7784181

  20. Modular multiplication in GF(p) for public-key cryptography

    NASA Astrophysics Data System (ADS)

    Olszyna, Jakub

    Modular multiplication forms the basis of modular exponentiation which is the core operation of the RSA cryptosystem. It is also present in many other cryptographic algorithms including those based on ECC and HECC. Hence, an efficient implementation of PKC relies on efficient implementation of modular multiplication. The paper presents a survey of most common algorithms for modular multiplication along with hardware architectures especially suitable for cryptographic applications in energy constrained environments. The motivation for studying low-power and areaefficient modular multiplication algorithms comes from enabling public-key security for ultra-low power devices that can perform under constrained environments like wireless sensor networks. Serial architectures for GF(p) are analyzed and presented. Finally proposed architectures are verified and compared according to the amount of power dissipated throughout the operation.

  1. Z-Score-Based Modularity for Community Detection in Networks

    PubMed Central

    Miyauchi, Atsushi; Kawase, Yasushi

    2016-01-01

    Identifying community structure in networks is an issue of particular interest in network science. The modularity introduced by Newman and Girvan is the most popular quality function for community detection in networks. In this study, we identify a problem in the concept of modularity and suggest a solution to overcome this problem. Specifically, we obtain a new quality function for community detection. We refer to the function as Z-modularity because it measures the Z-score of a given partition with respect to the fraction of the number of edges within communities. Our theoretical analysis shows that Z-modularity mitigates the resolution limit of the original modularity in certain cases. Computational experiments using both artificial networks and well-known real-world networks demonstrate the validity and reliability of the proposed quality function. PMID:26808270

  2. Modular Rocket Engine Control Software (MRECS)

    NASA Technical Reports Server (NTRS)

    Tarrant, Charlie; Crook, Jerry

    1997-01-01

    The Modular Rocket Engine Control Software (MRECS) Program is a technology demonstration effort designed to advance the state-of-the-art in launch vehicle propulsion systems. Its emphasis is on developing and demonstrating a modular software architecture for a generic, advanced engine control system that will result in lower software maintenance (operations) costs. It effectively accommodates software requirements changes that occur due to hardware. technology upgrades and engine development testing. Ground rules directed by MSFC were to optimize modularity and implement the software in the Ada programming language. MRECS system software and the software development environment utilize Commercial-Off-the-Shelf (COTS) products. This paper presents the objectives and benefits of the program. The software architecture, design, and development environment are described. MRECS tasks are defined and timing relationships given. Major accomplishment are listed. MRECS offers benefits to a wide variety of advanced technology programs in the areas of modular software, architecture, reuse software, and reduced software reverification time related to software changes. Currently, the program is focused on supporting MSFC in accomplishing a Space Shuttle Main Engine (SSME) hot-fire test at Stennis Space Center and the Low Cost Boost Technology (LCBT) Program.

  3. Modular Knowledge Representation and Reasoning in the Semantic Web

    NASA Astrophysics Data System (ADS)

    Serafini, Luciano; Homola, Martin

    Construction of modular ontologies by combining different modules is becoming a necessity in ontology engineering in order to cope with the increasing complexity of the ontologies and the domains they represent. The modular ontology approach takes inspiration from software engineering, where modularization is a widely acknowledged feature. Distributed reasoning is the other side of the coin of modular ontologies: given an ontology comprising of a set of modules, it is desired to perform reasoning by combination of multiple reasoning processes performed locally on each of the modules. In the last ten years, a number of approaches for combining logics has been developed in order to formalize modular ontologies. In this chapter, we survey and compare the main formalisms for modular ontologies and distributed reasoning in the Semantic Web. We select four formalisms build on formal logical grounds of Description Logics: Distributed Description Logics, ℰ-connections, Package-based Description Logics and Integrated Distributed Description Logics. We concentrate on expressivity and distinctive modeling features of each framework. We also discuss reasoning capabilities of each framework.

  4. Development of modularity in the neural activity of childrenʼs brains

    NASA Astrophysics Data System (ADS)

    Chen, Man; Deem, Michael W.

    2015-02-01

    We study how modularity of the human brain changes as children develop into adults. Theory suggests that modularity can enhance the response function of a networked system subject to changing external stimuli. Thus, greater cognitive performance might be achieved for more modular neural activity, and modularity might likely increase as children develop. The value of modularity calculated from functional magnetic resonance imaging (fMRI) data is observed to increase during childhood development and peak in young adulthood. Head motion is deconvolved from the fMRI data, and it is shown that the dependence of modularity on age is independent of the magnitude of head motion. A model is presented to illustrate how modularity can provide greater cognitive performance at short times, i.e. task switching. A fitness function is extracted from the model. Quasispecies theory is used to predict how the average modularity evolves with age, illustrating the increase of modularity during development from children to adults that arises from selection for rapid cognitive function in young adults. Experiments exploring the effect of modularity on cognitive performance are suggested. Modularity may be a potential biomarker for injury, rehabilitation, or disease.

  5. Curriculum Development through YTS Modular Credit Accumulation.

    ERIC Educational Resources Information Center

    Further Education Unit, London (England).

    This document reports the evaluation of the collaborately developed Modular Training Framework (MainFrame), a British curriculum development project, built around a commitment to a competency-based, modular credit accumulation program. The collaborators were three local education authorities (LEAs), those of Bedfordshire, Haringey, and Sheffield,…

  6. Aeroelastic Tailoring via Tow Steered Composites

    NASA Technical Reports Server (NTRS)

    Stanford, Bret K.; Jutte, Christine V.

    2014-01-01

    The use of tow steered composites, where fibers follow prescribed curvilinear paths within a laminate, can improve upon existing capabilities related to aeroelastic tailoring of wing structures, though this tailoring method has received relatively little attention in the literature. This paper demonstrates the technique for both a simple cantilevered plate in low-speed flow, as well as the wing box of a full-scale high aspect ratio transport configuration. Static aeroelastic stresses and dynamic flutter boundaries are obtained for both cases. The impact of various tailoring choices upon the aeroelastic performance is quantified: curvilinear fiber steering versus straight fiber steering, certifiable versus noncertifiable stacking sequences, a single uniform laminate per wing skin versus multiple laminates, and identical upper and lower wing skins structures versus individual tailoring.

  7. RAG-3D: A search tool for RNA 3D substructures

    DOE PAGES

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; ...

    2015-08-24

    In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

  8. RAG-3D: a search tool for RNA 3D substructures

    PubMed Central

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-01-01

    To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

  9. RAG-3D: A search tool for RNA 3D substructures

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

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef

    In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

  10. Determination of Key Residues for Catalysis and RNA Cleavage Specificity

    PubMed Central

    Barbas, Ana; Matos, Rute G.; Amblar, Mónica; López-Viñas, Eduardo; Gomez-Puertas, Paulino; Arraiano, Cecília M.

    2009-01-01

    RNase II is the prototype of a ubiquitous family of enzymes that are crucial for RNA metabolism. In Escherichia coli this protein is a single-stranded-specific 3′-exoribonuclease with a modular organization of four functional domains. In eukaryotes, the RNase II homologue Rrp44 (also known as Dis3) is the catalytic subunit of the exosome, an exoribonuclease complex essential for RNA processing and decay. In this work we have performed a functional characterization of several highly conserved residues located in the RNase II catalytic domain to address their precise role in the RNase II activity. We have constructed a number of RNase II mutants and compared their activity and RNA binding to the wild type using different single- or double-stranded substrates. The results presented in this study substantially improve the RNase II model for RNA degradation. We have identified the residues that are responsible for the discrimination of cleavage of RNA versus DNA. We also show that the Arg-500 residue present in the RNase II active site is crucial for activity but not for RNA binding. The most prominent finding presented is the extraordinary catalysis observed in the E542A mutant that turns RNase II into a “super-enzyme.” PMID:19458082

  11. Hierarchical functional modularity in the resting-state human brain.

    PubMed

    Ferrarini, Luca; Veer, Ilya M; Baerends, Evelinda; van Tol, Marie-José; Renken, Remco J; van der Wee, Nic J A; Veltman, Dirk J; Aleman, André; Zitman, Frans G; Penninx, Brenda W J H; van Buchem, Mark A; Reiber, Johan H C; Rombouts, Serge A R B; Milles, Julien

    2009-07-01

    Functional magnetic resonance imaging (fMRI) studies have shown that anatomically distinct brain regions are functionally connected during the resting state. Basic topological properties in the brain functional connectivity (BFC) map have highlighted the BFC's small-world topology. Modularity, a more advanced topological property, has been hypothesized to be evolutionary advantageous, contributing to adaptive aspects of anatomical and functional brain connectivity. However, current definitions of modularity for complex networks focus on nonoverlapping clusters, and are seriously limited by disregarding inclusive relationships. Therefore, BFC's modularity has been mainly qualitatively investigated. Here, we introduce a new definition of modularity, based on a recently improved clustering measurement, which overcomes limitations of previous definitions, and apply it to the study of BFC in resting state fMRI of 53 healthy subjects. Results show hierarchical functional modularity in the brain. Copyright 2009 Wiley-Liss, Inc

  12. OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

    PubMed

    Huang, Jingshan; Gutierrez, Fernando; Strachan, Harrison J; Dou, Dejing; Huang, Weili; Smith, Barry; Blake, Judith A; Eilbeck, Karen; Natale, Darren A; Lin, Yu; Wu, Bin; Silva, Nisansa de; Wang, Xiaowei; Liu, Zixing; Borchert, Glen M; Tan, Ming; Ruttenberg, Alan

    2016-01-01

    As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The realization of miRNA functions depends largely on how miRNAs regulate specific target genes. It is therefore critical to identify, analyze, and cross-reference miRNA-target interactions to better explore and delineate miRNA functions. Semantic technologies can help in this regard. We previously developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), whose goal was to serve as a foundation for semantic annotation, data integration, and semantic search in the miRNA field. In this paper we describe our continuing effort to develop the OMIT, and demonstrate its use within a semantic search system, OmniSearch, designed to facilitate knowledge capture of miRNA-target interaction data. Important changes in the current version OMIT are summarized as: (1) following a modularized ontology design (with 2559 terms imported from the NCRO ontology); (2) encoding all 1884 human miRNAs (vs. 300 in previous versions); and (3) setting up a GitHub project site along with an issue tracker for more effective community collaboration on the ontology development. The OMIT ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/omit.owl. The OmniSearch system is also free and open to all users, accessible at: http://omnisearch.soc.southalabama.edu/index.php/Software.

  13. Grape RNA-Seq analysis pipeline environment

    PubMed Central

    Knowles, David G.; Röder, Maik; Merkel, Angelika; Guigó, Roderic

    2013-01-01

    Motivation: The avalanche of data arriving since the development of NGS technologies have prompted the need for developing fast, accurate and easily automated bioinformatic tools capable of dealing with massive datasets. Among the most productive applications of NGS technologies is the sequencing of cellular RNA, known as RNA-Seq. Although RNA-Seq provides similar or superior dynamic range than microarrays at similar or lower cost, the lack of standard and user-friendly pipelines is a bottleneck preventing RNA-Seq from becoming the standard for transcriptome analysis. Results: In this work we present a pipeline for processing and analyzing RNA-Seq data, that we have named Grape (Grape RNA-Seq Analysis Pipeline Environment). Grape supports raw sequencing reads produced by a variety of technologies, either in FASTA or FASTQ format, or as prealigned reads in SAM/BAM format. A minimal Grape configuration consists of the file location of the raw sequencing reads, the genome of the species and the corresponding gene and transcript annotation. Grape first runs a set of quality control steps, and then aligns the reads to the genome, a step that is omitted for prealigned read formats. Grape next estimates gene and transcript expression levels, calculates exon inclusion levels and identifies novel transcripts. Grape can be run on a single computer or in parallel on a computer cluster. It is distributed with specific mapping and quantification tools, but given its modular design, any tool supporting popular data interchange formats can be integrated. Availability: Grape can be obtained from the Bioinformatics and Genomics website at: http://big.crg.cat/services/grape. Contact: david.gonzalez@crg.eu or roderic.guigo@crg.eu PMID:23329413

  14. Rationalizing context-dependent performance of dynamic RNA regulatory devices.

    PubMed

    Kent, Ross; Halliwell, Samantha; Young, Kate; Swainston, Neil; Dixon, Neil

    2018-06-21

    The ability of RNA to sense, regulate and store information is an attractive attribute for a variety of functional applications including the development of regulatory control devices for synthetic biology. RNA folding and function is known to be highly context sensitive, which limits the modularity and reuse of RNA regulatory devices to control different heterologous sequences and genes. We explored the cause and effect of sequence context sensitivity for translational ON riboswitches located in the 5' UTR, by constructing and screening a library of N-terminal synonymous codon variants. By altering the N-terminal codon usage we were able to obtain RNA devices with a broad range of functional performance properties (ON, OFF, fold-change). Linear regression and calculated metrics were used to rationalize the major determining features leading to optimal riboswitch performance, and to identify multiple interactions between the explanatory metrics. Finally, partial least squared (PLS) analysis was employed in order to understand the metrics and their respective effect on performance. This PLS model was shown to provide good explanation of our library. This study provides a novel multi-variant analysis framework by which to rationalize the codon context performance of allosteric RNA-devices. The framework will also serve as a platform for future riboswitch context engineering endeavors.

  15. Neonates need tailored drug formulations.

    PubMed

    Allegaert, Karel

    2013-02-08

    Drugs are very strong tools used to improve outcome in neonates. Despite this fact and in contrast to tailored perfusion equipment, incubators or ventilators for neonates, we still commonly use drug formulations initially developed for adults. We would like to make the point that drug formulations given to neonates need to be tailored for this age group. Besides the obvious need to search for active compounds that take the pathophysiology of the newborn into account, this includes the dosage and formulation. The dosage or concentration should facilitate the administration of low amounts and be flexible since clearance is lower in neonates with additional extensive between-individual variability. Formulations need to be tailored for dosage variability in the low ranges and also to the clinical characteristics of neonates. A specific focus of interest during neonatal drug development therefore is a need to quantify and limit excipient exposure based on the available knowledge of their safety or toxicity. Until such tailored vials and formulations become available, compounding practices for drug formulations in neonates should be evaluated to guarantee the correct dosing, product stability and safety.

  16. Manufactured Housing--The Modular Home in Texas.

    ERIC Educational Resources Information Center

    Sindt, Roger P.

    This report deals principally with modular homes (permanently sited structures) although it also presents some recent information on mobile homes. In 1976, modular home construction companies were surveyed in Texas and across the United States to assess the extent of their construction activity and market penetration and to gather some insight…

  17. Data handling for the modular observatory

    NASA Technical Reports Server (NTRS)

    Taber, J. E.

    1975-01-01

    The current paper summarizes work undertaken at TRW for the EOS satellite and related missions, and it presents conclusions that lead to a flexible and low-cost overall system implementation. It shows how the usual communication and data handling functions must be altered to meet the modularization ground rules, and it demonstrates the modularization that is possible in the handling of wideband payload data both on board and on the ground.

  18. Oasis: online analysis of small RNA deep sequencing data.

    PubMed

    Capece, Vincenzo; Garcia Vizcaino, Julio C; Vidal, Ramon; Rahman, Raza-Ur; Pena Centeno, Tonatiuh; Shomroni, Orr; Suberviola, Irantzu; Fischer, Andre; Bonn, Stefan

    2015-07-01

    Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis' exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. Oasis generates downloadable interactive web reports for easy visualization, exploration and analysis of data on a local system. Finally, Oasis' modular workflow enables for the rapid (re-) analysis of data. Oasis is implemented in Python, R, Java, PHP, C++ and JavaScript. It is freely available at http://oasis.dzne.de. stefan.bonn@dzne.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  19. Physicochemically Tunable Polyfunctionalized RNA Square Architecture with Fluorogenic and Ribozymatic Properties

    PubMed Central

    2015-01-01

    Recent advances in RNA nanotechnology allow the rational design of various nanoarchitectures. Previous methods utilized conserved angles from natural RNA motifs to form geometries with specific sizes. However, the feasibility of producing RNA architecture with variable sizes using native motifs featuring fixed sizes and angles is limited. It would be advantageous to display RNA nanoparticles of diverse shape and size derived from a given primary sequence. Here, we report an approach to construct RNA nanoparticles with tunable size and stability. Multifunctional RNA squares with a 90° angle were constructed by tuning the 60° angle of the three-way junction (3WJ) motif from the packaging RNA (pRNA) of the bacteriophage phi29 DNA packaging motor. The physicochemical properties and size of the RNA square were also easily tuned by modulating the “core” strand and adjusting the length of the sides of the square via predictable design. Squares of 5, 10, and 20 nm were constructed, each showing diverse thermodynamic and chemical stabilities. Four “arms” extending from the corners of the square were used to incorporate siRNA, ribozyme, and fluorogenic RNA motifs. Unique intramolecular contact using the pre-existing intricacy of the 3WJ avoids relatively weaker intermolecular interactions via kissing loops or sticky ends. Utilizing the 3WJ motif, we have employed a modular design technique to construct variable-size RNA squares with controllable properties and functionalities for diverse and versatile applications with engineering, pharmaceutical, and medical potential. This technique for simple design to finely tune physicochemical properties adds a new angle to RNA nanotechnology. PMID:24971772

  20. Modular biometric system

    NASA Astrophysics Data System (ADS)

    Hsu, Charles; Viazanko, Michael; O'Looney, Jimmy; Szu, Harold

    2009-04-01

    Modularity Biometric System (MBS) is an approach to support AiTR of the cooperated and/or non-cooperated standoff biometric in an area persistent surveillance. Advanced active and passive EOIR and RF sensor suite is not considered here. Neither will we consider the ROC, PD vs. FAR, versus the standoff POT in this paper. Our goal is to catch the "most wanted (MW)" two dozens, separately furthermore ad hoc woman MW class from man MW class, given their archrivals sparse front face data basis, by means of various new instantaneous input called probing faces. We present an advanced algorithm: mini-Max classifier, a sparse sample realization of Cramer-Rao Fisher bound of the Maximum Likelihood classifier that minimize the dispersions among the same woman classes and maximize the separation among different man-woman classes, based on the simple feature space of MIT Petland eigen-faces. The original aspect consists of a modular structured design approach at the system-level with multi-level architectures, multiple computing paradigms, and adaptable/evolvable techniques to allow for achieving a scalable structure in terms of biometric algorithms, identification quality, sensors, database complexity, database integration, and component heterogenity. MBS consist of a number of biometric technologies including fingerprints, vein maps, voice and face recognitions with innovative DSP algorithm, and their hardware implementations such as using Field Programmable Gate arrays (FPGAs). Biometric technologies and the composed modularity biometric system are significant for governmental agencies, enterprises, banks and all other organizations to protect people or control access to critical resources.

  1. Advanced Modular Power Approach to Affordable, Supportable Space Systems

    NASA Technical Reports Server (NTRS)

    Oeftering, Richard C.; Kimnach, Greg L.; Fincannon, James; Mckissock,, Barbara I.; Loyselle, Patricia L.; Wong, Edmond

    2013-01-01

    Recent studies of missions to the Moon, Mars and Near Earth Asteroids (NEA) indicate that these missions often involve several distinct separately launched vehicles that must ultimately be integrated together in-flight and operate as one unit. Therefore, it is important to see these vehicles as elements of a larger segmented spacecraft rather than separate spacecraft flying in formation. The evolution of large multi-vehicle exploration architecture creates the need (and opportunity) to establish a global power architecture that is common across all vehicles. The Advanced Exploration Systems (AES) Modular Power System (AMPS) project managed by NASA Glenn Research Center (GRC) is aimed at establishing the modular power system architecture that will enable power systems to be built from a common set of modular building blocks. The project is developing, demonstrating and evaluating key modular power technologies that are expected to minimize non-recurring development costs, reduce recurring integration costs, as well as, mission operational and support costs. Further, modular power is expected to enhance mission flexibility, vehicle reliability, scalability and overall mission supportability. The AMPS project not only supports multi-vehicle architectures but should enable multi-mission capability as well. The AMPS technology development involves near term demonstrations involving developmental prototype vehicles and field demonstrations. These operational demonstrations not only serve as a means of evaluating modular technology but also provide feedback to developers that assure that they progress toward truly flexible and operationally supportable modular power architecture.

  2. Discovering cancer vulnerabilities using high-throughput micro-RNA screening.

    PubMed

    Nikolic, Iva; Elsworth, Benjamin; Dodson, Eoin; Wu, Sunny Z; Gould, Cathryn M; Mestdagh, Pieter; Marshall, Glenn M; Horvath, Lisa G; Simpson, Kaylene J; Swarbrick, Alexander

    2017-12-15

    Micro-RNAs (miRNAs) are potent regulators of gene expression and cellular phenotype. Each miRNA has the potential to target hundreds of transcripts within the cell thus controlling fundamental cellular processes such as survival and proliferation. Here, we exploit this important feature of miRNA networks to discover vulnerabilities in cancer phenotype, and map miRNA-target relationships across different cancer types. More specifically, we report the results of a functional genomics screen of 1280 miRNA mimics and inhibitors in eight cancer cell lines, and its presentation in a sophisticated interactive data portal. This resource represents the most comprehensive survey of miRNA function in oncology, incorporating breast cancer, prostate cancer and neuroblastoma. A user-friendly web portal couples this experimental data with multiple tools for miRNA target prediction, pathway enrichment analysis and visualization. In addition, the database integrates publicly available gene expression and perturbation data enabling tailored and context-specific analysis of miRNA function in a particular disease. As a proof-of-principle, we use the database and its innovative features to uncover novel determinants of the neuroblastoma malignant phenotype. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Optimal Network Modularity for Information Diffusion

    NASA Astrophysics Data System (ADS)

    Nematzadeh, Azadeh; Ferrara, Emilio; Flammini, Alessandro; Ahn, Yong-Yeol

    2014-08-01

    We investigate the impact of community structure on information diffusion with the linear threshold model. Our results demonstrate that modular structure may have counterintuitive effects on information diffusion when social reinforcement is present. We show that strong communities can facilitate global diffusion by enhancing local, intracommunity spreading. Using both analytic approaches and numerical simulations, we demonstrate the existence of an optimal network modularity, where global diffusion requires the minimal number of early adopters.

  4. New Aminoacyl-tRNA Synthetase-like Protein in Insecta with an Essential Mitochondrial Function*♦

    PubMed Central

    Guitart, Tanit; Leon Bernardo, Teresa; Sagalés, Jessica; Stratmann, Thomas; Bernués, Jordi; Ribas de Pouplana, Lluís

    2010-01-01

    Aminoacyl-tRNA synthetases (ARS) are modular enzymes that aminoacylate transfer RNAs (tRNA) for their use by the ribosome during protein synthesis. ARS are essential and universal components of the genetic code that were almost completely established before the appearance of the last common ancestor of all living species. This long evolutionary history explains the growing number of functions being discovered for ARS, and for ARS homologues, beyond their canonical role in gene translation. Here we present a previously uncharacterized paralogue of seryl-tRNA synthetase named SLIMP (seryl-tRNA synthetase-like insect mitochondrial protein). SLIMP is the result of a duplication of a mitochondrial seryl-tRNA synthetase (SRS) gene that took place in early metazoans and was fixed in Insecta. Here we show that SLIMP is localized in the mitochondria, where it carries out an essential function that is unrelated to the aminoacylation of tRNA. The knockdown of SLIMP by RNA interference (RNAi) causes a decrease in respiration capacity and an increase in mitochondrial mass in the form of aberrant mitochondria. PMID:20870726

  5. PRADA: pipeline for RNA sequencing data analysis.

    PubMed

    Torres-García, Wandaliz; Zheng, Siyuan; Sivachenko, Andrey; Vegesna, Rahulsimham; Wang, Qianghu; Yao, Rong; Berger, Michael F; Weinstein, John N; Getz, Gad; Verhaak, Roel G W

    2014-08-01

    Technological advances in high-throughput sequencing necessitate improved computational tools for processing and analyzing large-scale datasets in a systematic automated manner. For that purpose, we have developed PRADA (Pipeline for RNA-Sequencing Data Analysis), a flexible, modular and highly scalable software platform that provides many different types of information available by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, quality metrics, detection of unsupervised and supervised fusion transcripts, detection of intragenic fusion variants, homology scores and fusion frame classification. PRADA uses a dual-mapping strategy that increases sensitivity and refines the analytical endpoints. PRADA has been used extensively and successfully in the glioblastoma and renal clear cell projects of The Cancer Genome Atlas program.  http://sourceforge.net/projects/prada/  gadgetz@broadinstitute.org or rverhaak@mdanderson.org  Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. Local modular Hamiltonians from the quantum null energy condition

    NASA Astrophysics Data System (ADS)

    Koeller, Jason; Leichenauer, Stefan; Levine, Adam; Shahbazi-Moghaddam, Arvin

    2018-03-01

    The vacuum modular Hamiltonian K of the Rindler wedge in any relativistic quantum field theory is given by the boost generator. Here we investigate the modular Hamiltonian for more general half-spaces which are bounded by an arbitrary smooth cut of a null plane. We derive a formula for the second derivative of the modular Hamiltonian with respect to the coordinates of the cut which schematically reads K''=Tv v . This formula can be integrated twice to obtain a simple expression for the modular Hamiltonian. The result naturally generalizes the standard expression for the Rindler modular Hamiltonian to this larger class of regions. Our primary assumptions are the quantum null energy condition—an inequality between the second derivative of the von Neumann entropy of a region and the stress tensor—and its saturation in the vacuum for these regions. We discuss the validity of these assumptions in free theories and holographic theories to all orders in 1 /N .

  7. Standardized Modular Power Interfaces for Future Space Explorations Missions

    NASA Technical Reports Server (NTRS)

    Oeftering, Richard

    2015-01-01

    Earlier studies show that future human explorations missions are composed of multi-vehicle assemblies with interconnected electric power systems. Some vehicles are often intended to serve as flexible multi-purpose or multi-mission platforms. This drives the need for power architectures that can be reconfigured to support this level of flexibility. Power system developmental costs can be reduced, program wide, by utilizing a common set of modular building blocks. Further, there are mission operational and logistics cost benefits of using a common set of modular spares. These benefits are the goals of the Advanced Exploration Systems (AES) Modular Power System (AMPS) project. A common set of modular blocks requires a substantial level of standardization in terms of the Electrical, Data System, and Mechanical interfaces. The AMPS project is developing a set of proposed interface standards that will provide useful guidance for modular hardware developers but not needlessly constrain technology options, or limit future growth in capability. In 2015 the AMPS project focused on standardizing the interfaces between the elements of spacecraft power distribution and energy storage. The development of the modular power standard starts with establishing mission assumptions and ground rules to define design application space. The standards are defined in terms of AMPS objectives including Commonality, Reliability-Availability, Flexibility-Configurability and Supportability-Reusability. The proposed standards are aimed at assembly and sub-assembly level building blocks. AMPS plans to adopt existing standards for spacecraft command and data, software, network interfaces, and electrical power interfaces where applicable. Other standards including structural encapsulation, heat transfer, and fluid transfer, are governed by launch and spacecraft environments and bound by practical limitations of weight and volume. Developing these mechanical interface standards is more difficult but

  8. Modular, Reconfigurable, High-Energy Technology Development

    NASA Technical Reports Server (NTRS)

    Carrington, Connie; Howell, Joe

    2006-01-01

    The Modular, Reconfigurable High-Energy (MRHE) Technology Demonstrator project was to have been a series of ground-based demonstrations to mature critical technologies needed for in-space assembly of a highpower high-voltage modular spacecraft in low Earth orbit, enabling the development of future modular solar-powered exploration cargo-transport vehicles and infrastructure. MRHE was a project in the High Energy Space Systems (HESS) Program, within NASA's Exploration Systems Research and Technology (ESR&T) Program. NASA participants included Marshall Space Flight Center (MSFC), the Jet Propulsion Laboratory (JPL), and Glenn Research Center (GRC). Contractor participants were the Boeing Phantom Works in Huntsville, AL, Lockheed Martin Advanced Technology Center in Palo Alto, CA, ENTECH, Inc. in Keller, TX, and the University of AL Huntsville (UAH). MRHE's technical objectives were to mature: (a) lightweight, efficient, high-voltage, radiation-resistant solar power generation (SPG) technologies; (b) innovative, lightweight, efficient thermal management systems; (c) efficient, 100kW-class, high-voltage power delivery systems from an SPG to an electric thruster system; (d) autonomous rendezvous and docking technology for in-space assembly of modular, reconfigurable spacecraft; (e) robotic assembly of modular space systems; and (f) modular, reconfigurable distributed avionics technologies. Maturation of these technologies was to be implemented through a series of increasingly-inclusive laboratory demonstrations that would have integrated and demonstrated two systems-of-systems: (a) the autonomous rendezvous and docking of modular spacecraft with deployable structures, robotic assembly, reconfiguration both during assembly and (b) the development and integration of an advanced thermal heat pipe and a high-voltage power delivery system with a representative lightweight high-voltage SPG array. In addition, an integrated simulation testbed would have been developed

  9. Automatically producing tailored web materials for public administration

    NASA Astrophysics Data System (ADS)

    Colineau, Nathalie; Paris, Cécile; Vander Linden, Keith

    2013-06-01

    Public administration organizations commonly produce citizen-focused, informational materials describing public programs and the conditions under which citizens or citizen groups are eligible for these programs. The organizations write these materials for generic audiences because of the excessive human resource costs that would be required to produce personalized materials for everyone. Unfortunately, generic materials tend to be longer and harder to understand than materials tailored for particular citizens. Our work explores the feasibility and effectiveness of automatically producing tailored materials. We have developed an adaptive hypermedia application system that automatically produces tailored informational materials and have evaluated it in a series of studies. The studies demonstrate that: (1) subjects prefer tailored materials over generic materials, even if the tailoring requires answering a set of demographic questions first; (2) tailored materials are more effective at supporting subjects in their task of learning about public programs; and (3) the time required to specify the demographic information on which the tailoring is based does not significantly slow down the subjects in their information seeking task.

  10. Analysis of Advanced Modular Power Systems (AMPS) for Deep Space Exploration

    NASA Technical Reports Server (NTRS)

    Oeftering, Richard; Soeder, James F.; Beach, Ray

    2014-01-01

    The Advanced Modular Power Systems (AMPS) project is developing a modular approach to spacecraft power systems for exploration beyond Earth orbit. AMPS is intended to meet the need of reducing the cost of design development, test and integration and also reducing the operational logistics cost of supporting exploration missions. AMPS seeks to establish modular power building blocks with standardized electrical, mechanical, thermal and data interfaces that can be applied across multiple exploration vehicles. The presentation discusses the results of a cost analysis that compares the cost of the modular approach against a traditional non-modular approach.

  11. The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis.

    PubMed

    Mohorianu, Irina; Stocks, Matthew Benedict; Applegate, Christopher Steven; Folkes, Leighton; Moulton, Vincent

    2017-01-01

    RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations. The processing of the resulting big data sets facilitated the computational analysis of the sRNA patterns of variation within biological samples such as time point experiments, tissue series or various treatments. Rapid technological advances enable larger experiments, often with biological replicates leading to a vast amount of raw data. As a result, in this fast-evolving field, the existing methods for sequence characterization and prediction of interaction (regulatory) networks periodically require adapting or in extreme cases, a complete redesign to cope with the data deluge. In addition, the presence of numerous tools focused only on particular steps of HTS analysis hinders the systematic parsing of the results and their interpretation.The UEA small RNA Workbench (v1-4), described in this chapter, provides a user-friendly, modular, interactive analysis in the form of a suite of computational tools designed to process and mine sRNA datasets for interesting characteristics that can be linked back to the observed phenotypes. First, we show how to preprocess the raw sequencing output and prepare it for downstream analysis. Then we review some quality checks that can be used as a first indication of sources of variability between samples. Next we show how the Workbench can provide a comparison of the effects of different normalization approaches on the distributions of expression, enhanced methods for the identification of differentially expressed

  12. Modularization of Courses.

    ERIC Educational Resources Information Center

    Eastern Arizona Coll., Thatcher.

    Eastern Arizona College has developed a modularized system of instruction for five vocational and vocationally related courses--Introduction to Business, Business Mathematics, English, Drafting, and Electronics. Each course is divided into independent segments of instruction and students have open-entry and exit options. This document reviews the…

  13. Functional modularity in lake-dwelling characin fishes of Mexico

    PubMed Central

    Bautista, Amando; Herder, Fabian; Doadrio, Ignacio

    2017-01-01

    Modular evolution promotes evolutionary change, allowing independent variation across morphological units. Recent studies have shown that under contrasting ecological pressures, patterns of modularity could be related to divergent evolution. The main goal of the present study was to evaluate the presence of modular evolution in two sister lacustrine species, Astyanax aeneus and A. caballeroi, which are differentiated by their trophic habits. Two different datasets were analyzed: (1) skull X-rays from 73 specimens (35 A. aeneus and 38 A. caballeroi) to characterize skull variation patterns, considering both species and sex effects. For this dataset, three different modularity hypotheses were tested, previously supported in other lacustrine divergent species; (2) a complete body shape dataset was also tested for four modularity hypotheses, which included a total of 196 individuals (110 Astyanax aeneus and 86 A. caballeroi). Skull shape showed significant differences among species and sex (P < 0.001), where Astyanax caballeroi species showed an upwardly projected mandible and larger preorbital region. For the skull dataset, the modularity hypothesis ranked first included three partitioning modules. While for the complete body dataset the best ranked hypothesis included two modules (head vs the rest of the body), being significant only for A. caballeroi. PMID:28951817

  14. Functional modularity in lake-dwelling characin fishes of Mexico.

    PubMed

    Ornelas-García, Claudia Patricia; Bautista, Amando; Herder, Fabian; Doadrio, Ignacio

    2017-01-01

    Modular evolution promotes evolutionary change, allowing independent variation across morphological units. Recent studies have shown that under contrasting ecological pressures, patterns of modularity could be related to divergent evolution. The main goal of the present study was to evaluate the presence of modular evolution in two sister lacustrine species, Astyanax aeneus and A. caballeroi , which are differentiated by their trophic habits. Two different datasets were analyzed: (1) skull X-rays from 73 specimens (35 A. aeneus and 38 A. caballeroi ) to characterize skull variation patterns, considering both species and sex effects. For this dataset, three different modularity hypotheses were tested, previously supported in other lacustrine divergent species; (2) a complete body shape dataset was also tested for four modularity hypotheses, which included a total of 196 individuals (110 Astyanax aeneus and 86 A. caballeroi ). Skull shape showed significant differences among species and sex ( P  < 0.001), where Astyanax caballeroi species showed an upwardly projected mandible and larger preorbital region. For the skull dataset, the modularity hypothesis ranked first included three partitioning modules. While for the complete body dataset the best ranked hypothesis included two modules (head vs the rest of the body), being significant only for A. caballeroi .

  15. On Classification of Modular Categories by Rank: Table A.1

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

    Bruillard, Paul; Ng, Siu-Hung; Rowell, Eric C.

    2016-04-10

    The feasibility of a classification-by-rank program for modular categories follows from the Rank-Finiteness Theorem. We develop arithmetic, representation theoretic and algebraic methods for classifying modular categories by rank. As an application, we determine all possible fusion rules for all rank=5 modular categories and describe the corresponding monoidal equivalence classes.

  16. Modular Robotic Vehicle

    NASA Technical Reports Server (NTRS)

    Borroni-Bird, Christopher E. (Inventor); Lapp, Anthony Joseph (Inventor); Vitale, Robert L. (Inventor); Lee, Chunhao J. (Inventor); Bluethmann, William J. (Inventor); Ridley, Justin S. (Inventor); Junkin, Lucien Q. (Inventor); Ambrose, Robert O. (Inventor); Lutz, Jonathan J. (Inventor); Guo, Raymond (Inventor)

    2015-01-01

    A modular robotic vehicle includes a chassis, driver input devices, an energy storage system (ESS), a power electronics module (PEM), modular electronic assemblies (eModules) connected to the ESS via the PEM, one or more master controllers, and various embedded controllers. Each eModule includes a drive wheel containing a propulsion-braking module, and a housing containing propulsion and braking control assemblies with respective embedded propulsion and brake controllers, and a mounting bracket covering a steering control assembly with embedded steering controllers. The master controller, which is in communication with each eModule and with the driver input devices, communicates with and independently controls each eModule, by-wire, via the embedded controllers to establish a desired operating mode. Modes may include a two-wheel, four-wheel, diamond, and omni-directional steering modes as well as a park mode. A bumper may enable docking with another vehicle, with shared control over the eModules of the vehicles.

  17. Modular chemiresistive sensor

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

    Alam, Maksudul M.; Sampathkumaran, Uma

    The present invention relates to a modular chemiresistive sensor. In particular, a modular chemiresistive sensor for hypergolic fuel and oxidizer leak detection, carbon dioxide monitoring and detection of disease biomarkers. The sensor preferably has two gold or platinum electrodes mounted on a silicon substrate where the electrodes are connected to a power source and are separated by a gap of 0.5 to 4.0 .mu.M. A polymer nanowire or carbon nanotube spans the gap between the electrodes and connects the electrodes electrically. The electrodes are further connected to a circuit board having a processor and data storage, where the processor canmore » measure current and voltage values between the electrodes and compare the current and voltage values with current and voltage values stored in the data storage and assigned to particular concentrations of a pre-determined substance such as those listed above or a variety of other substances.« less

  18. New Insights into the Biological Role of Mammalian ADARs; the RNA Editing Proteins

    PubMed Central

    Mannion, Niamh; Arieti, Fabiana; Gallo, Angela; Keegan, Liam P.; O’Connell, Mary A.

    2015-01-01

    The ADAR proteins deaminate adenosine to inosine in double-stranded RNA which is one of the most abundant modifications present in mammalian RNA. Inosine can have a profound effect on the RNAs that are edited, not only changing the base-pairing properties, but can also result in recoding, as inosine behaves as if it were guanosine. In mammals there are three ADAR proteins and two ADAR-related proteins (ADAD) expressed. All have a very similar modular structure; however, both their expression and biological function differ significantly. Only two of the ADAR proteins have enzymatic activity. However, both ADAR and ADAD proteins possess the ability to bind double-strand RNA. Mutations in ADARs have been associated with many diseases ranging from cancer, innate immunity to neurological disorders. Here, we will discuss in detail the domain structure of mammalian ADARs, the effects of RNA editing, and the role of ADARs in human diseases. PMID:26437436

  19. Aerolastic tailoring and integrated wing design

    NASA Technical Reports Server (NTRS)

    Love, Mike H.; Bohlmann, Jon

    1989-01-01

    Much has been learned from the TSO optimization code over the years in determining aeroelastic tailoring's place in the integrated design process. Indeed, it has become apparent that aeroelastic tailoring is and should be deeply embedded in design. Aeroelastic tailoring can have tremendous effects on the design loads, and design loads affect every aspect of the design process. While optimization enables the evaluation of design sensitivities, valid computational simulations are required to make these sensitivities valid. Aircraft maneuvers simulated must adequately cover the plane's intended flight envelope, realistic design criteria must be included, and models among the various disciplines must be calibrated among themselves and with any hard-core (e.g., wind tunnel) data available. The information gained and benefits derived from aeroelastic tailoring provide a focal point for the various disciplines to become involved and communicate with one another to reach the best design possible.

  20. Modular Rocket Engine Control Software (MRECS)

    NASA Technical Reports Server (NTRS)

    Tarrant, C.; Crook, J.

    1998-01-01

    The Modular Rocket Engine Control Software (MRECS) Program is a technology demonstration effort designed to advance the state-of-the-art in launch vehicle propulsion systems. Its emphasis is on developing and demonstrating a modular software architecture for advanced engine control systems that will result in lower software maintenance (operations) costs. It effectively accommodates software requirement changes that occur due to hardware technology upgrades and engine development testing. Ground rules directed by MSFC were to optimize modularity and implement the software in the Ada programming language. MRECS system software and the software development environment utilize Commercial-Off-the-Shelf (COTS) products. This paper presents the objectives, benefits, and status of the program. The software architecture, design, and development environment are described. MRECS tasks are defined and timing relationships given. Major accomplishments are listed. MRECS offers benefits to a wide variety of advanced technology programs in the areas of modular software architecture, reuse software, and reduced software reverification time related to software changes. MRECS was recently modified to support a Space Shuttle Main Engine (SSME) hot-fire test. Cold Flow and Flight Readiness Testing were completed before the test was cancelled. Currently, the program is focused on supporting NASA MSFC in accomplishing development testing of the Fastrac Engine, part of NASA's Low Cost Technologies (LCT) Program. MRECS will be used for all engine development testing.

  1. Multi-kilowatt modularized spacecraft power processing system development

    NASA Technical Reports Server (NTRS)

    Andrews, R. E.; Hayden, J. H.; Hedges, R. T.; Rehmann, D. W.

    1975-01-01

    A review of existing information pertaining to spacecraft power processing systems and equipment was accomplished with a view towards applicability to the modularization of multi-kilowatt power processors. Power requirements for future spacecraft were determined from the NASA mission model-shuttle systems payload data study which provided the limits for modular power equipment capabilities. Three power processing systems were compared to evaluation criteria to select the system best suited for modularity. The shunt regulated direct energy transfer system was selected by this analysis for a conceptual design effort which produced equipment specifications, schematics, envelope drawings, and power module configurations.

  2. Modular cathode assemblies and methods of using the same for electrochemical reduction

    DOEpatents

    Wiedmeyer, Stanley G; Barnes, Laurel A; Williamson, Mark A; Willit, James L

    2014-12-02

    Modular cathode assemblies are useable in electrolytic reduction systems and include a basket through which fluid electrolyte may pass and exchange charge with a material to be reduced in the basket. The basket can be divided into upper and lower sections to provide entry for the material. Example embodiment cathode assemblies may have any shape to permit modular placement at any position in reduction systems. Modular cathode assemblies include a cathode plate in the basket, to which unique and opposite electrical power may be supplied. Example embodiment modular cathode assemblies may have standardized electrical connectors. Modular cathode assemblies may be supported by a top plate of an electrolytic reduction system. Electrolytic oxide reduction systems are operated by positioning modular cathode and anode assemblies at desired positions, placing a material in the basket, and charging the modular assemblies to reduce the metal oxide.

  3. Multiple D3-Instantons and Mock Modular Forms II

    NASA Astrophysics Data System (ADS)

    Alexandrov, Sergei; Banerjee, Sibasish; Manschot, Jan; Pioline, Boris

    2018-03-01

    We analyze the modular properties of D3-brane instanton corrections to the hypermultiplet moduli space in type IIB string theory compactified on a Calabi-Yau threefold. In Part I, we found a necessary condition for the existence of an isometric action of S-duality on this moduli space: the generating function of DT invariants in the large volume attractor chamber must be a vector-valued mock modular form with specified modular properties. In this work, we prove that this condition is also sufficient at two-instanton order. This is achieved by producing a holomorphic action of {SL(2,Z)} on the twistor space which preserves the holomorphic contact structure. The key step is to cancel the anomalous modular variation of the Darboux coordinates by a local holomorphic contact transformation, which is generated by a suitable indefinite theta series. For this purpose we introduce a new family of theta series of signature (2, n - 2), find their modular completion, and conjecture sufficient conditions for their convergence, which may be of independent mathematical interest.

  4. Climbing therapy under PK-tailored prophylaxis.

    PubMed

    Stemberger, M; Schmit, E; Czepa, D; Kurnik, K; Spannagl, M

    2014-01-01

    Climbing has a low risk of injury and strengthens the entire musculature. Due to its benefits in physical and mental health as well as its high fun factor climbing is an established way of therapy. So far, the usefulness of climbing therapy has not been shown for people with haemophilia (PWH). A crucial requirement for physical activity in PWH is regular prophylaxis. As the patient's individual pharmacokinetic (PK) response varies significantly, PK-tailored prophylaxis may decrease bleeding frequency. We describe a man (age 25 years) with severe haemophilia A who took part in an 8.5-month weekly climbing program under PK-tailored prophylaxis. Bleeding frequency, factor consumption, joint health (Haemophilia Joint Health Score, HJHS), quality of life (Haemo-QoL-A) and climbing performance (UIAA scale) were assessed before and after the training. Prior to the study, the patient was on demand treatment. The patient was started on standard prophylaxis for a 2 months period and then observed for 6.5 months under PK-tailored prophylaxis. PK-tailored prophylaxis was targeted to a trough level of 1-3%. For high-impact activities a factor activity >15%, for low-impact activities a factor activity >5% was suggested. Climbing therapy was safe. The bleeding rate decreased from 14 (2012) to 1 (during the study period of 8.5 months). The one bleeding event was due to a missed infusion and was not triggered by physical activity. The elimination half-life using Bayesian statistics was determined to be 16h. Using this half-life for PK-tailored prophylaxis reduced the factor VIII consumption in comparison to standard prophylaxis. Joint health was particularly improved in the categories range of motion and swelling. Quality of life scores stayed at a high level. Climbing performance improved by 1 grade. The combination of PK-tailored prophylaxis with therapeutic climbing improved clinical outcome in this young adult with severe haemophilia. The tailored concept for high- and low

  5. 24 CFR 3282.12 - Excluded structures-modular homes.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 5 2013-04-01 2013-04-01 false Excluded structures-modular homes... HOUSING AND URBAN DEVELOPMENT MANUFACTURED HOME PROCEDURAL AND ENFORCEMENT REGULATIONS General § 3282.12 Excluded structures—modular homes. (a) The purpose of this section is to provide the certification...

  6. 24 CFR 3282.12 - Excluded structures-modular homes.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 5 2010-04-01 2010-04-01 false Excluded structures-modular homes... HOUSING AND URBAN DEVELOPMENT MANUFACTURED HOME PROCEDURAL AND ENFORCEMENT REGULATIONS General § 3282.12 Excluded structures—modular homes. (a) The purpose of this section is to provide the certification...

  7. Deinterlacing using modular neural network

    NASA Astrophysics Data System (ADS)

    Woo, Dong H.; Eom, Il K.; Kim, Yoo S.

    2004-05-01

    Deinterlacing is the conversion process from the interlaced scan to progressive one. While many previous algorithms that are based on weighted-sum cause blurring in edge region, deinterlacing using neural network can reduce the blurring through recovering of high frequency component by learning process, and is found robust to noise. In proposed algorithm, input image is divided into edge and smooth region, and then, to each region, one neural network is assigned. Through this process, each neural network learns only patterns that are similar, therefore it makes learning more effective and estimation more accurate. But even within each region, there are various patterns such as long edge and texture in edge region. To solve this problem, modular neural network is proposed. In proposed modular neural network, two modules are combined in output node. One is for low frequency feature of local area of input image, and the other is for high frequency feature. With this structure, each modular neural network can learn different patterns with compensating for drawback of counterpart. Therefore it can adapt to various patterns within each region effectively. In simulation, the proposed algorithm shows better performance compared with conventional deinterlacing methods and single neural network method.

  8. Multiple D3-Instantons and Mock Modular Forms I

    NASA Astrophysics Data System (ADS)

    Alexandrov, Sergei; Banerjee, Sibasish; Manschot, Jan; Pioline, Boris

    2017-07-01

    We study D3-instanton corrections to the hypermultiplet moduli space in type IIB string theory compactified on a Calabi-Yau threefold. In a previous work, consistency of D3-instantons with S-duality was established at first order in the instanton expansion, using the modular properties of the M5-brane elliptic genus. We extend this analysis to the two-instanton level, where wall-crossing phenomena start playing a role. We focus on the contact potential, an analogue of the Kähler potential which must transform as a modular form under S-duality. We show that it can be expressed in terms of a suitable modification of the partition function of D4-D2-D0 BPS black holes, constructed out of the generating function of MSW invariants (the latter coincide with Donaldson-Thomas invariants in a particular chamber). Modular invariance of the contact potential then requires that, in the case where the D3-brane wraps a reducible divisor, the generating function of MSW invariants must transform as a vector-valued mock modular form, with a specific modular completion built from the MSW invariants of the constituents. Physically, this gives a powerful constraint on the degeneracies of BPS black holes. Mathematically, our result gives a universal prediction for the modular properties of Donaldson-Thomas invariants of pure two-dimensional sheaves.

  9. Modular structure of functional networks in olfactory memory.

    PubMed

    Meunier, David; Fonlupt, Pierre; Saive, Anne-Lise; Plailly, Jane; Ravel, Nadine; Royet, Jean-Pierre

    2014-07-15

    Graph theory enables the study of systems by describing those systems as a set of nodes and edges. Graph theory has been widely applied to characterize the overall structure of data sets in the social, technological, and biological sciences, including neuroscience. Modular structure decomposition enables the definition of sub-networks whose components are gathered in the same module and work together closely, while working weakly with components from other modules. This processing is of interest for studying memory, a cognitive process that is widely distributed. We propose a new method to identify modular structure in task-related functional magnetic resonance imaging (fMRI) networks. The modular structure was obtained directly from correlation coefficients and thus retained information about both signs and weights. The method was applied to functional data acquired during a yes-no odor recognition memory task performed by young and elderly adults. Four response categories were explored: correct (Hit) and incorrect (False alarm, FA) recognition and correct and incorrect rejection. We extracted time series data for 36 areas as a function of response categories and age groups and calculated condition-based weighted correlation matrices. Overall, condition-based modular partitions were more homogeneous in young than elderly subjects. Using partition similarity-based statistics and a posteriori statistical analyses, we demonstrated that several areas, including the hippocampus, caudate nucleus, and anterior cingulate gyrus, belonged to the same module more frequently during Hit than during all other conditions. Modularity values were negatively correlated with memory scores in the Hit condition and positively correlated with bias scores (liberal/conservative attitude) in the Hit and FA conditions. We further demonstrated that the proportion of positive and negative links between areas of different modules (i.e., the proportion of correlated and anti-correlated areas

  10. Modular cathode assemblies and methods of using the same for electrochemical reduction

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

    Wiedmeyer, Stanley G.; Barnes, Laurel A.; Williamson, Mark A.

    Modular cathode assemblies are useable in electrolytic reduction systems and include a basket through which fluid electrolyte may pass and exchange charge with a material to be reduced in the basket. The basket can be divided into upper and lower sections to provide entry for the material. Example embodiment cathode assemblies may have any shape to permit modular placement at any position in reduction systems. Modular cathode assemblies include a cathode plate in the basket, to which unique and opposite electrical power may be supplied. Example embodiment modular cathode assemblies may have standardized electrical connectors. Modular cathode assemblies may bemore » supported by a top plate of an electrolytic reduction system. Electrolytic oxide reduction systems are operated by positioning modular cathode and anode assemblies at desired positions, placing a material in the basket, and charging the modular assemblies to reduce the metal oxide.« less

  11. Dissociation of modular total hip arthroplasty at the neck-stem interface without dislocation.

    PubMed

    Kouzelis, A; Georgiou, C S; Megas, P

    2012-12-01

    Modular femoral and acetabular components are now widely used, but only a few complications related to the modularity itself have been reported. We describe a case of dissociation of the modular total hip arthroplasty (THA) at the femoral neck-stem interface during walking. The possible causes of this dissociation are discussed. Successful treatment was provided with surgical revision and replacement of the modular neck components. Surgeons who use modular components in hip arthroplasties should be aware of possible early complications in which the modularity of the prostheses is the major factor of failure.

  12. MOBS - A modular on-board switching system

    NASA Astrophysics Data System (ADS)

    Berner, W.; Grassmann, W.; Piontek, M.

    The authors describe a multibeam satellite system that is designed for business services and for communications at a high bit rate. The repeater is regenerative with a modular onboard switching system. It acts not only as baseband switch but also as the central node of the network, performing network control and protocol evaluation. The hardware is based on a modular bus/memory architecture with associated processors.

  13. Modular System for Shelves and Coasts (MOSSCO v1.0) - a flexible and multi-component framework for coupled coastal ocean ecosystem modelling

    NASA Astrophysics Data System (ADS)

    Lemmen, Carsten; Hofmeister, Richard; Klingbeil, Knut; Hassan Nasermoaddeli, M.; Kerimoglu, Onur; Burchard, Hans; Kösters, Frank; Wirtz, Kai W.

    2018-03-01

    Shelf and coastal sea processes extend from the atmosphere through the water column and into the seabed. These processes reflect intimate interactions between physical, chemical, and biological states on multiple scales. As a consequence, coastal system modelling requires a high and flexible degree of process and domain integration; this has so far hardly been achieved by current model systems. The lack of modularity and flexibility in integrated models hinders the exchange of data and model components and has historically imposed the supremacy of specific physical driver models. We present the Modular System for Shelves and Coasts (MOSSCO; http://www.mossco.de), a novel domain and process coupling system tailored but not limited to the coupling challenges of and applications in the coastal ocean. MOSSCO builds on the Earth System Modeling Framework (ESMF) and on the Framework for Aquatic Biogeochemical Models (FABM). It goes beyond existing technologies by creating a unique level of modularity in both domain and process coupling, including a clear separation of component and basic model interfaces, flexible scheduling of several tens of models, and facilitation of iterative development at the lab and the station and on the coastal ocean scale. MOSSCO is rich in metadata and its concepts are also applicable outside the coastal domain. For coastal modelling, it contains dozens of example coupling configurations and tested set-ups for coupled applications. Thus, MOSSCO addresses the technology needs of a growing marine coastal Earth system community that encompasses very different disciplines, numerical tools, and research questions.

  14. Safety concerns related to modular/prefabricated building construction.

    PubMed

    Fard, Maryam Mirhadi; Terouhid, Seyyed Amin; Kibert, Charles J; Hakim, Hamed

    2017-03-01

    The US construction industry annually experiences a relatively high rate of fatalities and injuries; therefore, improving safety practices should be considered a top priority for this industry. Modular/prefabricated building construction is a construction strategy that involves manufacturing of the whole building or some of its components off-site. This research focuses on the safety performance of the modular/prefabricated building construction sector during both manufacturing and on-site processes. This safety evaluation can serve as the starting point for improving the safety performance of this sector. Research was conducted based on Occupational Safety and Health Administration investigated accidents. The study found 125 accidents related to modular/prefabricated building construction. The details of each accident were closely examined to identify the types of injury and underlying causes. Out of 125 accidents, there were 48 fatalities (38.4%), 63 hospitalized injuries (50.4%), and 14 non-hospitalized injuries (11.2%). It was found that, the most common type of injury in modular/prefabricated construction was 'fracture', and the most common cause of accidents was 'fall'. The most frequent cause of cause (underlying and root cause) was 'unstable structure'. In this research, the accidents were also examined in terms of corresponding location, occupation, equipment as well as activities during which the accidents occurred. For improving safety records of the modular/prefabricated construction sector, this study recommends that future research be conducted on stabilizing structures during their lifting, storing, and permanent installation, securing fall protection systems during on-site assembly of components while working from heights, and developing training programmes and standards focused on modular/prefabricated construction.

  15. Brain Modularity Mediates the Relation between Task Complexity and Performance

    NASA Astrophysics Data System (ADS)

    Ye, Fengdan; Yue, Qiuhai; Martin, Randi; Fischer-Baum, Simon; Ramos-Nuã+/-Ez, Aurora; Deem, Michael

    Recent work in cognitive neuroscience has focused on analyzing the brain as a network, rather than a collection of independent regions. Prior studies taking this approach have found that individual differences in the degree of modularity of the brain network relate to performance on cognitive tasks. However, inconsistent results concerning the direction of this relationship have been obtained, with some tasks showing better performance as modularity increases, and other tasks showing worse performance. A recent theoretical model suggests that these inconsistencies may be explained on the grounds that high-modularity networks favor performance on simple tasks whereas low-modularity networks favor performance on complex tasks. The current study tests these predictions by relating modularity from resting-state fMRI to performance on a set of behavioral tasks. Complex and simple tasks were defined on the basis of whether they drew on executive attention. Consistent with predictions, we found a negative correlation between individuals' modularity and their performance on the complex tasks but a positive correlation with performance on the simple tasks. The results presented here provide a framework for linking measures of whole brain organization to cognitive processing.

  16. Modularity and the spread of perturbations in complex dynamical systems

    NASA Astrophysics Data System (ADS)

    Kolchinsky, Artemy; Gates, Alexander J.; Rocha, Luis M.

    2015-12-01

    We propose a method to decompose dynamical systems based on the idea that modules constrain the spread of perturbations. We find partitions of system variables that maximize "perturbation modularity," defined as the autocovariance of coarse-grained perturbed trajectories. The measure effectively separates the fast intramodular from the slow intermodular dynamics of perturbation spreading (in this respect, it is a generalization of the "Markov stability" method of network community detection). Our approach captures variation of modular organization across different system states, time scales, and in response to different kinds of perturbations: aspects of modularity which are all relevant to real-world dynamical systems. It offers a principled alternative to detecting communities in networks of statistical dependencies between system variables (e.g., "relevance networks" or "functional networks"). Using coupled logistic maps, we demonstrate that the method uncovers hierarchical modular organization planted in a system's coupling matrix. Additionally, in homogeneously coupled map lattices, it identifies the presence of self-organized modularity that depends on the initial state, dynamical parameters, and type of perturbations. Our approach offers a powerful tool for exploring the modular organization of complex dynamical systems.

  17. Modularity and the spread of perturbations in complex dynamical systems.

    PubMed

    Kolchinsky, Artemy; Gates, Alexander J; Rocha, Luis M

    2015-12-01

    We propose a method to decompose dynamical systems based on the idea that modules constrain the spread of perturbations. We find partitions of system variables that maximize "perturbation modularity," defined as the autocovariance of coarse-grained perturbed trajectories. The measure effectively separates the fast intramodular from the slow intermodular dynamics of perturbation spreading (in this respect, it is a generalization of the "Markov stability" method of network community detection). Our approach captures variation of modular organization across different system states, time scales, and in response to different kinds of perturbations: aspects of modularity which are all relevant to real-world dynamical systems. It offers a principled alternative to detecting communities in networks of statistical dependencies between system variables (e.g., "relevance networks" or "functional networks"). Using coupled logistic maps, we demonstrate that the method uncovers hierarchical modular organization planted in a system's coupling matrix. Additionally, in homogeneously coupled map lattices, it identifies the presence of self-organized modularity that depends on the initial state, dynamical parameters, and type of perturbations. Our approach offers a powerful tool for exploring the modular organization of complex dynamical systems.

  18. Post-transcriptional labeling by using Suzuki-Miyaura cross-coupling generates functional RNA probes.

    PubMed

    Walunj, Manisha B; Tanpure, Arun A; Srivatsan, Seergazhi G

    2018-06-20

    Pd-catalyzed C-C bond formation, an important vertebra in the spine of synthetic chemistry, is emerging as a valuable chemoselective transformation for post-synthetic functionalization of biomacromolecules. While methods are available for labeling protein and DNA, development of an analogous procedure to label RNA by cross-coupling reactions remains a major challenge. Herein, we describe a new Pd-mediated RNA oligonucleotide (ON) labeling method that involves post-transcriptional functionalization of iodouridine-labeled RNA transcripts by using Suzuki-Miyaura cross-coupling reaction. 5-Iodouridine triphosphate (IUTP) is efficiently incorporated into RNA ONs at one or more sites by T7 RNA polymerase. Further, using a catalytic system made of Pd(OAc)2 and 2-aminopyrimidine-4,6-diol (ADHP) or dimethylamino-substituted ADHP (DMADHP), we established a modular method to functionalize iodouridine-labeled RNA ONs in the presence of various boronic acid and ester substrates under very mild conditions (37°C and pH 8.5). This method is highly chemoselective, and offers direct access to RNA ONs labeled with commonly used fluorescent and affinity tags and new fluorogenic environment-sensitive nucleoside probes in a ligand-controlled stereoselective fashion. Taken together, this simple approach of generating functional RNA ON probes by Suzuki-Miyaura coupling will be a very important addition to the resources and tools available for analyzing RNA motifs.

  19. Properties of Native High-Density Lipoproteins Inspire Synthesis of Actively Targeted In Vivo siRNA Delivery Vehicles.

    PubMed

    McMahon, Kaylin M; Plebanek, Michael P; Thaxton, C Shad

    2016-11-15

    Efficient systemic administration of therapeutic short interfering RNA (siRNA) is challenging. High-density lipoproteins (HDL) are natural in vivo RNA delivery vehicles. Specifically, native HDLs: 1) Load single-stranded RNA; 2) Are anionic, which requires charge reconciliation between the RNA and HDL, and 3) Actively target scavenger receptor type B-1 (SR-B1) to deliver RNA. Emphasizing these particular parameters, we employed templated lipoprotein particles (TLP), mimics of spherical HDLs, and self-assembled them with single-stranded complements of, presumably, any highly unmodified siRNA duplex pair after formulation with a cationic lipid. Resulting siRNA templated lipoprotein particles (siRNA-TLP) are anionic and tunable with regard to RNA assembly and function. Data demonstrate that the siRNA-TLPs actively target SR-B1 to potently reduce androgen receptor (AR) and enhancer of zeste homolog 2 (EZH2) proteins in multiple cancer cell lines. Systemic administration of siRNA-TLPs demonstrated no off-target toxicity and significantly reduced the growth of prostate cancer xenografts. Thus, native HDLs inspired the synthesis of a hybrid siRNA delivery vehicle that can modularly load single-stranded RNA complements after charge reconciliation with a cationic lipid, and that function due to active targeting of SR-B1.

  20. Development of a space universal modular architecture (SUMO)

    NASA Astrophysics Data System (ADS)

    Collins, Bernie F.

    This concept paper proposes that the space community should develop and implement a universal standard for spacecraft modularity - to improve interoperability of spacecraft components. Pursuing a global industry consensus standard for open and modular spacecraft architecture will encourage trade, remove standards-related market barriers, and in the long run increase both value provided to customers and profitability of the space industrial sector. This concept paper sets out: (1) the goals for a SUMO standard and how it will benefit the space community; (2) background on spacecraft modularity and existing related standards; (3) the proposed technical scope of the current standardization effort; and (4) an approach for creating a SUMO standard.

  1. A model of tailoring effects: A randomized controlled trial examining the mechanisms of tailoring in a web-based STD screening intervention.

    PubMed

    Lustria, Mia Liza A; Cortese, Juliann; Gerend, Mary A; Schmitt, Karla; Kung, Ying Mai; McLaughlin, Casey

    2016-11-01

    This study explores the mechanisms of tailoring within the context of RU@Risk a brief Web-based intervention designed to promote sexually transmitted disease (STD) testing among young adults. This is one of a few studies to empirically examine theorized message processing mechanisms of tailoring and persuasion outcomes in a single model. Sexually active college students (N = 1065) completed a pretest, were randomly assigned to explore a tailored or nontailored website, completed a posttest, and were offered the opportunity to order a free at-home STD test kit. As intervention effects were hypothesized to work via increases in perceived risk, change in perceived risk from pretest to posttest by condition was examined. Hypothesized mechanisms of tailoring (perceived personal relevance, attention, and elaboration) were examined using structural equation modeling (SEM). All analyses controlled for demographic variables and sexual history. As predicted, perceived risk of STDs increased from pretest to posttest, but only in the tailored condition. Results revealed that exposure to the tailored (vs. nontailored) website increased perceived personal relevance, attention to, and elaboration of the message. These effects in turn were associated with greater perceived risk of STDs and intentions to get tested. Additionally, participants in the tailored condition were more likely to order a test kit. Findings provide insight into the mechanisms of tailoring with important implications for optimizing message design. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  2. Modular control of endothelial sheet migration

    PubMed Central

    Vitorino, Philip; Meyer, Tobias

    2008-01-01

    Growth factor-induced migration of endothelial cell monolayers enables embryonic development, wound healing, and angiogenesis. Although collective migration is widespread and therapeutically relevant, the underlying mechanism by which cell monolayers respond to growth factor, sense directional signals, induce motility, and coordinate individual cell movements is only partially understood. Here we used RNAi to identify 100 regulatory proteins that enhance or suppress endothelial sheet migration into cell-free space. We measured multiple live-cell migration parameters for all siRNA perturbations and found that each targeted protein primarily regulates one of four functional outputs: cell motility, directed migration, cell–cell coordination, or cell density. We demonstrate that cell motility regulators drive random, growth factor-independent motility in the presence or absence of open space. In contrast, directed migration regulators selectively transduce growth factor signals to direct cells along the monolayer boundary toward open space. Lastly, we found that regulators of cell–cell coordination are growth factor-independent and reorient randomly migrating cells inside the sheet when boundary cells begin to migrate. Thus, cells transition from random to collective migration through a modular control system, whereby growth factor signals convert boundary cells into pioneers, while cells inside the monolayer reorient and follow pioneers through growth factor-independent migration and cell–cell coordination. PMID:19056882

  3. Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation.

    PubMed

    Yamazaki, Tomohiro; Souquere, Sylvie; Chujo, Takeshi; Kobelke, Simon; Chong, Yee Seng; Fox, Archa H; Bond, Charles S; Nakagawa, Shinichi; Pierron, Gerard; Hirose, Tetsuro

    2018-06-21

    A class of long noncoding RNAs (lncRNAs) has architectural functions in nuclear body construction; however, specific RNA domains dictating their architectural functions remain uninvestigated. Here, we identified the domains of the architectural NEAT1 lncRNA that construct paraspeckles. Systematic deletion of NEAT1 portions using CRISPR/Cas9 in haploid cells revealed modular domains of NEAT1 important for RNA stability, isoform switching, and paraspeckle assembly. The middle domain, containing functionally redundant subdomains, was responsible for paraspeckle assembly. Artificial tethering of the NONO protein to a NEAT1_2 mutant lacking the functional subdomains rescued paraspeckle assembly, and this required the NOPS dimerization domain of NONO. Paraspeckles exhibit phase-separated properties including susceptibility to 1,6-hexanediol treatment. RNA fragments of the NEAT1_2 subdomains preferentially bound NONO/SFPQ, leading to phase-separated aggregates in vitro. Thus, we demonstrate that the enrichment of NONO dimers on the redundant NEAT1_2 subdomains initiates construction of phase-separated paraspeckles, providing mechanistic insights into lncRNA-based nuclear body formation. Copyright © 2018 Elsevier Inc. All rights reserved.

  4. SMEX-Lite Modular Solar Array Architecture

    NASA Technical Reports Server (NTRS)

    Lyons, John

    2002-01-01

    For the most part, Goddard solar arrays have been custom designs that are unique to each mission. The solar panel design has been frozen prior to issuing an RFP for their procurement. There has typically been 6-9 months between RFP release and contract award, followed by an additional 24 months for performance of the contract. For Small Explorer (SMEX) missions, with three years between mission definition and launch, this has been a significant problem. The SMEX solar panels have been sufficiently small that the contract performance period has been reduced to 12-15 months. The bulk of this time is used up in the final design definition and fabrication of flight solar cell assemblies. Even so, it has been virtually impossible to have the spacecraft design at a level of maturity sufficient to freeze the solar panel geometry and release the RFP in time to avoid schedule problems with integrating the solar panels to the spacecraft. With that in mind, the SMEX-Lite project team developed a modular architecture for the assembly of solar arrays to greatly reduce the cost and schedule associated with the development of a mission- specific solar array. In the modular architecture, solar cells are fabricated onto small substrate panels. This modular panel (approximately 8.5" x 17" in this case) becomes the building block for constructing solar arrays for multiple missions with varying power requirements and geometrical arrangements. The mechanical framework that holds these modules together as a solar array is the only mission-unique design, changing in size and shape as required for each mission. There are several advantages to this approach. First, the typical solar array development cycle requires a mission unique design, procurement, and qualification including a custom qualification panel. With the modular architecture, a single qualification of the SMEX-Lite modules and the associated mechanical framework in a typical configuration provided a qualification by

  5. Proving relations between modular graph functions

    NASA Astrophysics Data System (ADS)

    Basu, Anirban

    2016-12-01

    We consider modular graph functions that arise in the low energy expansion of the four graviton amplitude in type II string theory. The vertices of these graphs are the positions of insertions of vertex operators on the toroidal worldsheet, while the links are the scalar Green functions connecting the vertices. Graphs with four and five links satisfy several non-trivial relations, which have been proved recently. We prove these relations by using elementary properties of Green functions and the details of the graphs. We also prove a relation between modular graph functions with six links.

  6. Fuel Cycle Performance of Thermal Spectrum Small Modular Reactors

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

    Worrall, Andrew; Todosow, Michael

    2016-01-01

    Small modular reactors may offer potential benefits, such as enhanced operational flexibility. However, it is vital to understand the holistic impact of small modular reactors on the nuclear fuel cycle and fuel cycle performance. The focus of this paper is on the fuel cycle impacts of light water small modular reactors in a once-through fuel cycle with low-enriched uranium fuel. A key objective of this paper is to describe preliminary reactor core physics and fuel cycle analyses conducted in support of the U.S. Department of Energy Office of Nuclear Energy Fuel Cycle Options Campaign. Challenges with small modular reactors include:more » increased neutron leakage, fewer assemblies in the core (and therefore fewer degrees of freedom in the core design), complex enrichment and burnable absorber loadings, full power operation with inserted control rods, the potential for frequent load-following operation, and shortened core height. Each of these will impact the achievable discharge burn-up in the reactor and the fuel cycle performance. This paper summarizes the results of an expert elicitation focused on developing a list of the factors relevant to small modular reactor fuel, core, and operation that will impact fuel cycle performance. Preliminary scoping analyses were performed using a regulatory-grade reactor core simulator. The hypothetical light water small modular reactor considered in these preliminary scoping studies is a cartridge type one-batch core with 4.9% enrichment. Some core parameters, such as the size of the reactor and general assembly layout, are similar to an example small modular reactor concept from industry. The high-level issues identified and preliminary scoping calculations in this paper are intended to inform on potential fuel cycle impacts of one-batch thermal spectrum SMRs. In particular, this paper highlights the impact of increased neutron leakage and reduced number of batches on the achievable burn-up of the reactor. Fuel cycle

  7. Directional selection can drive the evolution of modularity in complex traits

    PubMed Central

    Melo, Diogo; Marroig, Gabriel

    2015-01-01

    Modularity is a central concept in modern biology, providing a powerful framework for the study of living organisms on many organizational levels. Two central and related questions can be posed in regard to modularity: How does modularity appear in the first place, and what forces are responsible for keeping and/or changing modular patterns? We approached these questions using a quantitative genetics simulation framework, building on previous results obtained with bivariate systems and extending them to multivariate systems. We developed an individual-based model capable of simulating many traits controlled by many loci with variable pleiotropic relations between them, expressed in populations subject to mutation, recombination, drift, and selection. We used this model to study the problem of the emergence of modularity, and hereby show that drift and stabilizing selection are inefficient at creating modular variational structures. We also demonstrate that directional selection can have marked effects on the modular structure between traits, actively promoting a restructuring of genetic variation in the selected population and potentially facilitating the response to selection. Furthermore, we give examples of complex covariation created by simple regimes of combined directional and stabilizing selection and show that stabilizing selection is important in the maintenance of established covariation patterns. Our results are in full agreement with previous results for two-trait systems and further extend them to include scenarios of greater complexity. Finally, we discuss the evolutionary consequences of modular patterns being molded by directional selection. PMID:25548154

  8. Directional selection can drive the evolution of modularity in complex traits.

    PubMed

    Melo, Diogo; Marroig, Gabriel

    2015-01-13

    Modularity is a central concept in modern biology, providing a powerful framework for the study of living organisms on many organizational levels. Two central and related questions can be posed in regard to modularity: How does modularity appear in the first place, and what forces are responsible for keeping and/or changing modular patterns? We approached these questions using a quantitative genetics simulation framework, building on previous results obtained with bivariate systems and extending them to multivariate systems. We developed an individual-based model capable of simulating many traits controlled by many loci with variable pleiotropic relations between them, expressed in populations subject to mutation, recombination, drift, and selection. We used this model to study the problem of the emergence of modularity, and hereby show that drift and stabilizing selection are inefficient at creating modular variational structures. We also demonstrate that directional selection can have marked effects on the modular structure between traits, actively promoting a restructuring of genetic variation in the selected population and potentially facilitating the response to selection. Furthermore, we give examples of complex covariation created by simple regimes of combined directional and stabilizing selection and show that stabilizing selection is important in the maintenance of established covariation patterns. Our results are in full agreement with previous results for two-trait systems and further extend them to include scenarios of greater complexity. Finally, we discuss the evolutionary consequences of modular patterns being molded by directional selection.

  9. Multidisciplinary tailoring of hot composite structures

    NASA Technical Reports Server (NTRS)

    Singhal, Surendra N.; Chamis, Christos C.

    1993-01-01

    A computational simulation procedure is described for multidisciplinary analysis and tailoring of layered multi-material hot composite engine structural components subjected to simultaneous multiple discipline-specific thermal, structural, vibration, and acoustic loads. The effect of aggressive environments is also simulated. The simulation is based on a three-dimensional finite element analysis technique in conjunction with structural mechanics codes, thermal/acoustic analysis methods, and tailoring procedures. The integrated multidisciplinary simulation procedure is general-purpose including the coupled effects of nonlinearities in structure geometry, material, loading, and environmental complexities. The composite material behavior is assessed at all composite scales, i.e., laminate/ply/constituents (fiber/matrix), via a nonlinear material characterization hygro-thermo-mechanical model. Sample tailoring cases exhibiting nonlinear material/loading/environmental behavior of aircraft engine fan blades, are presented. The various multidisciplinary loads lead to different tailored designs, even those competing with each other, as in the case of minimum material cost versus minimum structure weight and in the case of minimum vibration frequency versus minimum acoustic noise.

  10. Domain organizations of modular extracellular matrix proteins and their evolution.

    PubMed

    Engel, J

    1996-11-01

    Multidomain proteins which are composed of modular units are a rather recent invention of evolution. Domains are defined as autonomously folding regions of a protein, and many of them are similar in sequence and structure, indicating common ancestry. Their modular nature is emphasized by frequent repetitions in identical or in different proteins and by a large number of different combinations with other domains. The extracellular matrix is perhaps the largest biological system composed of modular mosaic proteins, and its astonishing complexity and diversity are based on them. A cluster of minireviews on modular proteins is being published in Matrix Biology. These deal with the evolution of modular proteins, the three-dimensional structure of domains and the ways in which these interact in a multidomain protein. They discuss structure-function relationships in calcium binding domains, collagen helices, alpha-helical coiled-coil domains and C-lectins. The present minireview is focused on some general aspects and serves as an introduction to the cluster.

  11. Modular evolution of the Cetacean vertebral column.

    PubMed

    Buchholtz, Emily A

    2007-01-01

    Modular theory predicts that hierarchical developmental processes generate hierarchical phenotypic units that are capable of independent modification. The vertebral column is an overtly modular structure, and its rapid phenotypic transformation in cetacean evolution provides a case study for modularity. Terrestrial mammals have five morphologically discrete vertebral series that are now known to be coincident with Hox gene expression patterns. Here, I present the hypothesis that in living Carnivora and Artiodactyla, and by inference in the terrestrial ancestors of whales, the series are themselves components of larger precaudal and caudal modular units. Column morphology in a series of fossil and living whales is used to predict the type and sequence of developmental changes responsible for modification of that ancestral pattern. Developmental innovations inferred include independent meristic additions to the precaudal column in basal archaeocetes and basilosaurids, stepwise homeotic reduction of the sacral series in protocetids, and dissociation of the caudal series into anterior tail and fluke subunits in basilosaurids. The most dramatic change was the novel association of lumbar and anterior caudal vertebrae in a module that crosses the precaudal/caudal boundary. This large unit is defined by shared patterns of vertebral morphology, count, and size in all living whales (Neoceti).

  12. A Modular Robotic System with Applications to Space Exploration

    NASA Technical Reports Server (NTRS)

    Hancher, Matthew D.; Hornby, Gregory S.

    2006-01-01

    Modular robotic systems offer potential advantages as versatile, fault-tolerant, cost-effective platforms for space exploration, but a sufficiently mature system is not yet available. We describe the possible applications of such a system, and present prototype hardware intended as a step in the right direction. We also present elements of an automated design and optimization framework aimed at making modular robots easier to design and use, and discuss the results of applying the system to a gait optimization problem. Finally, we discuss the potential near-term applications of modular robotics to terrestrial robotics research.

  13. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures.

    PubMed

    Popenda, Mariusz; Szachniuk, Marta; Blazewicz, Marek; Wasik, Szymon; Burke, Edmund K; Blazewicz, Jacek; Adamiak, Ryszard W

    2010-05-06

    Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available

  14. Evolution of a modular software network

    PubMed Central

    Fortuna, Miguel A.; Bonachela, Juan A.; Levin, Simon A.

    2011-01-01

    “Evolution behaves like a tinkerer” (François Jacob, Science, 1977). Software systems provide a singular opportunity to understand biological processes using concepts from network theory. The Debian GNU/Linux operating system allows us to explore the evolution of a complex network in a unique way. The modular design detected during its growth is based on the reuse of existing code in order to minimize costs during programming. The increase of modularity experienced by the system over time has not counterbalanced the increase in incompatibilities between software packages within modules. This negative effect is far from being a failure of design. A random process of package installation shows that the higher the modularity, the larger the fraction of packages working properly in a local computer. The decrease in the relative number of conflicts between packages from different modules avoids a failure in the functionality of one package spreading throughout the entire system. Some potential analogies with the evolutionary and ecological processes determining the structure of ecological networks of interacting species are discussed. PMID:22106260

  15. Modular vaccine packaging increases packing efficiency

    PubMed Central

    Norman, Bryan A.; Rajgopal, Jayant; Lim, Jung; Gorham, Katrin; Haidari, Leila; Brown, Shawn T.; Lee, Bruce Y.

    2015-01-01

    Background Within a typical vaccine supply chain, vaccines are packaged into individual cylindrical vials (each containing one or more doses) that are bundled together in rectangular “inner packs” for transport via even larger groupings such as cold boxes and vaccine carriers. The variability of vaccine inner pack and vial size may hinder efficient vaccine distribution because it constrains packing of cold boxes and vaccine carriers to quantities that are often inappropriate or suboptimal in the context of country-specific vaccination guidelines. Methods We developed in Microsoft Excel (Microsoft Corp., Redmond, WA) a spreadsheet model that evaluated the impact of different packing schemes for the Benin routine regimen plus the introduction of the Rotarix vaccine. Specifically, we used the model to compare the current packing scheme to that of a proposed modular packing scheme. Results Conventional packing of a Dometic RCW25 that aims to maximize fully-immunized children (FICs) results in 123 FICs and a packing efficiency of 81.93% compared to a maximum of 155 FICs and 94.1% efficiency for an alternative modular packaging system. Conclusions Our analysis suggests that modular packaging systems could offer significant advantages over conventional vaccine packaging systems with respect to space efficiency and potential FICs, when they are stored in standard vaccine carrying devices. This allows for more vaccines to be stored within the same volume while also simplifying the procedures used by field workers to pack storage devices. Ultimately, modular packaging systems could be a simple way to help increase vaccine coverage worldwide. PMID:25957666

  16. Can tailored interventions increase mammography use among HMO women?

    PubMed

    Lipkus, I M; Rimer, B K; Halabi, S; Strigo, T S

    2000-01-01

    Telephone counseling and tailored print communications have emerged as promising methods for promoting mammography screening. However, there has been little research testing, within the same randomized field trial, of the efficacy of these two methods compared to a high-quality usual care system for enhancing screening. This study addressed the question: Compared to usual care, is tailored telephone counseling more effective than tailored print materials for promoting mammography screening? Three-year randomized field trial. One thousand ninety-nine women aged 50 and older recruited from a health maintenance organization in North Carolina. Women were randomized to 1 of 3 groups: (1) usual care, (2) tailored print communications, and (3) tailored telephone counseling. Adherence to mammography screening based on self-reports obtained during 1995, 1996, and 1997. Compared to usual care alone, telephone counseling promoted a significantly higher proportion of women having mammograms on schedule (71% vs 61%) than did tailored print (67% vs 61%) but only after the first year of intervention (during 1996). Furthermore, compared to usual care, telephone counseling was more effective than tailored print materials at promoting being on schedule with screening during 1996 and 1997 among women who were off-schedule during the previous year. The effects of the intervention were most pronounced after the first intervention. Compared to usual care, telephone counseling seemed particularly effective at promoting change among nonadherent women, the group for whom the intervention was developed. These results suggest that telephone counseling, rather than tailored print, might be the preferred first-line intervention for getting nonadherent women on schedule for mammography screening. Many questions would have to be answered about why the tailored print intervention was not more powerful. Nevertheless, it is clear that additional interventions will be needed to maintain women

  17. A universal strategy for regulating mRNA translation in prokaryotic and eukaryotic cells.

    PubMed

    Cao, Jicong; Arha, Manish; Sudrik, Chaitanya; Mukherjee, Abhirup; Wu, Xia; Kane, Ravi S

    2015-04-30

    We describe a simple strategy to control mRNA translation in both prokaryotic and eukaryotic cells which relies on a unique protein-RNA interaction. Specifically, we used the Pumilio/FBF (PUF) protein to repress translation by binding in between the ribosome binding site (RBS) and the start codon (in Escherichia coli), or by binding to the 5' untranslated region of target mRNAs (in mammalian cells). The design principle is straightforward, the extent of translational repression can be tuned and the regulator is genetically encoded, enabling the construction of artificial signal cascades. We demonstrate that this approach can also be used to regulate polycistronic mRNAs; such regulation has rarely been achieved in previous reports. Since the regulator used in this study is a modular RNA-binding protein, which can be engineered to target different 8-nucleotide RNA sequences, our strategy could be used in the future to target endogenous mRNAs for regulating metabolic flows and signaling pathways in both prokaryotic and eukaryotic cells. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. A universal strategy for regulating mRNA translation in prokaryotic and eukaryotic cells

    PubMed Central

    Cao, Jicong; Arha, Manish; Sudrik, Chaitanya; Mukherjee, Abhirup; Wu, Xia; Kane, Ravi S.

    2015-01-01

    We describe a simple strategy to control mRNA translation in both prokaryotic and eukaryotic cells which relies on a unique protein–RNA interaction. Specifically, we used the Pumilio/FBF (PUF) protein to repress translation by binding in between the ribosome binding site (RBS) and the start codon (in Escherichia coli), or by binding to the 5′ untranslated region of target mRNAs (in mammalian cells). The design principle is straightforward, the extent of translational repression can be tuned and the regulator is genetically encoded, enabling the construction of artificial signal cascades. We demonstrate that this approach can also be used to regulate polycistronic mRNAs; such regulation has rarely been achieved in previous reports. Since the regulator used in this study is a modular RNA-binding protein, which can be engineered to target different 8-nucleotide RNA sequences, our strategy could be used in the future to target endogenous mRNAs for regulating metabolic flows and signaling pathways in both prokaryotic and eukaryotic cells. PMID:25845589

  19. Future microfluidic and nanofluidic modular platforms for nucleic acid liquid biopsy in precision medicine

    PubMed Central

    Egatz-Gomez, Ana; Wang, Ceming; Klacsmann, Flora; Pan, Zehao; Marczak, Steve; Wang, Yunshan; Sun, Gongchen; Senapati, Satyajyoti; Chang, Hsueh-Chia

    2016-01-01

    Nucleic acid biomarkers have enormous potential in non-invasive diagnostics and disease management. In medical research and in the near future in the clinics, there is a great demand for accurate miRNA, mRNA, and ctDNA identification and profiling. They may lead to screening of early stage cancer that is not detectable by tissue biopsy or imaging. Moreover, because their cost is low and they are non-invasive, they can become a regular screening test during annual checkups or allow a dynamic treatment program that adjusts its drug and dosage frequently. We briefly review a few existing viral and endogenous RNA assays that have been approved by the Federal Drug Administration. These tests are based on the main nucleic acid detection technologies, namely, quantitative reverse transcription polymerase chain reaction (PCR), microarrays, and next-generation sequencing. Several of the challenges that these three technologies still face regarding the quantitative measurement of a panel of nucleic acids are outlined. Finally, we review a cluster of microfluidic technologies from our group with potential for point-of-care nucleic acid quantification without nucleic acid amplification, designed to overcome specific limitations of current technologies. We suggest that integration of these technologies in a modular design can offer a low-cost, robust, and yet sensitive/selective platform for a variety of precision medicine applications. PMID:27190565

  20. Toward modular biological models: defining analog modules based on referent physiological mechanisms.

    PubMed

    Petersen, Brenden K; Ropella, Glen E P; Hunt, C Anthony

    2014-08-16

    Currently, most biomedical models exist in isolation. It is often difficult to reuse or integrate models or their components, in part because they are not modular. Modular components allow the modeler to think more deeply about the role of the model and to more completely address a modeling project's requirements. In particular, modularity facilitates component reuse and model integration for models with different use cases, including the ability to exchange modules during or between simulations. The heterogeneous nature of biology and vast range of wet-lab experimental platforms call for modular models designed to satisfy a variety of use cases. We argue that software analogs of biological mechanisms are reasonable candidates for modularization. Biomimetic software mechanisms comprised of physiomimetic mechanism modules offer benefits that are unique or especially important to multi-scale, biomedical modeling and simulation. We present a general, scientific method of modularizing mechanisms into reusable software components that we call physiomimetic mechanism modules (PMMs). PMMs utilize parametric containers that partition and expose state information into physiologically meaningful groupings. To demonstrate, we modularize four pharmacodynamic response mechanisms adapted from an in silico liver (ISL). We verified the modularization process by showing that drug clearance results from in silico experiments are identical before and after modularization. The modularized ISL achieves validation targets drawn from propranolol outflow profile data. In addition, an in silico hepatocyte culture (ISHC) is created. The ISHC uses the same PMMs and required no refactoring. The ISHC achieves validation targets drawn from propranolol intrinsic clearance data exhibiting considerable between-lab variability. The data used as validation targets for PMMs originate from both in vitro to in vivo experiments exhibiting large fold differences in time scale. This report demonstrates

  1. Modular jet impingement assemblies with passive and active flow control for electronics cooling

    DOEpatents

    Zhou, Feng; Dede, Ercan Mehmet; Joshi, Shailesh

    2016-09-13

    Power electronics modules having modular jet impingement assembly utilized to cool heat generating devices are disclosed. The modular jet impingement assemblies include a modular manifold having a distribution recess, one or more angled inlet connection tubes positioned at an inlet end of the modular manifold that fluidly couple the inlet tube to the distribution recess and one or more outlet connection tubes positioned at an outlet end of the modular manifold that fluidly coupling the outlet tube to the distribution recess. The modular jet impingement assemblies include a manifold insert removably positioned within the distribution recess and include one or more inlet branch channels each including an impinging slot and one or more outlet branch channels each including a collecting slot. Further a heat transfer plate coupled to the modular manifold, the heat transfer plate comprising an impingement surface including an array of fins that extend toward the manifold insert.

  2. A Modular PMAD System for Small Spacecraft

    NASA Technical Reports Server (NTRS)

    Button, Robert M.

    1998-01-01

    Current trends in satellite design are focused on developing small, reliable, and inexpensive spacecraft. To that end, a modular power management and distribution system (PMAD) is proposed which will help transition the aerospace industry towards an assembly line approach to building spacecraft. The modular system is based on an innovative DC voltage boost converter called the Series Connected Boost Regulator (SCBR). The SCBR uses existing DC-DC converters and adds a unique series connection. This simple modification provides the SCBR topology with many advantages over existing boost converters. Efficiencies of 94-98%, power densities above 1,000 We/kg, and inherent fault tolerance are just a few of the characteristics presented. Limitations of the SCBR technology are presented, and it is shown that the SCBR makes an ideal photovoltaic array regulator. A modular design based on the series connected boost unit is outlined and functional descriptions of the components are given.

  3. Modular synchronization in complex networks.

    PubMed

    Oh, E; Rho, K; Hong, H; Kahng, B

    2005-10-01

    We study the synchronization transition (ST) of a modified Kuramoto model on two different types of modular complex networks. It is found that the ST depends on the type of intermodular connections. For the network with decentralized (centralized) intermodular connections, the ST occurs at finite coupling constant (behaves abnormally). Such distinct features are found in the yeast protein interaction network and the Internet, respectively. Moreover, by applying the finite-size scaling analysis to an artificial network with decentralized intermodular connections, we obtain the exponent associated with the order parameter of the ST to be beta approximately 1 different from beta(MF) approximately 1/2 obtained from the scale-free network with the same degree distribution but the absence of modular structure, corresponding to the mean field value.

  4. An instrumental puzzle: the modular integration of AOLI

    NASA Astrophysics Data System (ADS)

    López, Roberto L.; Velasco, Sergio; Colodro-Conde, Carlos; Valdivia, Juan J. F.; Puga, Marta; Oscoz, Alejandro; Rebolo, Rafael; MacKay, Craig; Pérez-Garrido, Antonio; Rodríguez-Ramos, Luis Fernando; Rodríguez-Ramos, José Manuel M.; King, David; Labadie, Lucas; Muthusubramanian, Balaji; Rodríguez-Coira, Gustavo

    2016-08-01

    The Adaptive Optics Lucky Imager, AOLI, is an instrument developed to deliver the highest spatial resolution ever obtained in the visible, 20 mas, from ground-based telescopes. In AOLI a new philosophy of instrumental prototyping has been applied, based on the modularization of the subsystems. This modular concept offers maximum flexibility regarding the instrument, telescope or the addition of future developments.

  5. Modular design of synthetic gene circuits with biological parts and pools.

    PubMed

    Marchisio, Mario Andrea

    2015-01-01

    Synthetic gene circuits can be designed in an electronic fashion by displaying their basic components-Standard Biological Parts and Pools of molecules-on the computer screen and connecting them with hypothetical wires. This procedure, achieved by our add-on for the software ProMoT, was successfully applied to bacterial circuits. Recently, we have extended this design-methodology to eukaryotic cells. Here, highly complex components such as promoters and Pools of mRNA contain hundreds of species and reactions whose calculation demands a rule-based modeling approach. We showed how to build such complex modules via the joint employment of the software BioNetGen (rule-based modeling) and ProMoT (modularization). In this chapter, we illustrate how to utilize our computational tool for synthetic biology with the in silico implementation of a simple eukaryotic gene circuit that performs the logic AND operation.

  6. Selforganization of modular activity of grid cells

    PubMed Central

    Urdapilleta, Eugenio; Si, Bailu

    2017-01-01

    Abstract A unique topographical representation of space is found in the concerted activity of grid cells in the rodent medial entorhinal cortex. Many among the principal cells in this region exhibit a hexagonal firing pattern, in which each cell expresses its own set of place fields (spatial phases) at the vertices of a triangular grid, the spacing and orientation of which are typically shared with neighboring cells. Grid spacing, in particular, has been found to increase along the dorso‐ventral axis of the entorhinal cortex but in discrete steps, that is, with a modular structure. In this study, we show that such a modular activity may result from the self‐organization of interacting units, which individually would not show discrete but rather continuously varying grid spacing. Within our “adaptation” network model, the effect of a continuously varying time constant, which determines grid spacing in the isolated cell model, is modulated by recurrent collateral connections, which tend to produce a few subnetworks, akin to magnetic domains, each with its own grid spacing. In agreement with experimental evidence, the modular structure is tightly defined by grid spacing, but also involves grid orientation and distortion, due to interactions across modules. Thus, our study sheds light onto a possible mechanism, other than simply assuming separate networks a priori, underlying the formation of modular grid representations. PMID:28768062

  7. GELATIO: a general framework for modular digital analysis of high-purity Ge detector signals

    NASA Astrophysics Data System (ADS)

    Agostini, M.; Pandola, L.; Zavarise, P.; Volynets, O.

    2011-08-01

    GELATIO is a new software framework for advanced data analysis and digital signal processing developed for the GERDA neutrinoless double beta decay experiment. The framework is tailored to handle the full analysis flow of signals recorded by high purity Ge detectors and photo-multipliers from the veto counters. It is designed to support a multi-channel modular and flexible analysis, widely customizable by the user either via human-readable initialization files or via a graphical interface. The framework organizes the data into a multi-level structure, from the raw data up to the condensed analysis parameters, and includes tools and utilities to handle the data stream between the different levels. GELATIO is implemented in C++. It relies upon ROOT and its extension TAM, which provides compatibility with PROOF, enabling the software to run in parallel on clusters of computers or many-core machines. It was tested on different platforms and benchmarked in several GERDA-related applications. A stable version is presently available for the GERDA Collaboration and it is used to provide the reference analysis of the experiment data.

  8. Corepressors: custom tailoring and alterations while you wait

    PubMed Central

    Goodson, Michael; Jonas, Brian A.; Privalsky, Martin A.

    2005-01-01

    A diverse cadre of metazoan transcription factors mediate repression by recruiting protein complexes containing the SMRT (silencing mediator of retinoid and thyroid hormone receptor) or N-CoR (nuclear receptor corepressor) corepressors. SMRT and N-CoR nucleate the assembly of still larger corepressor complexes that perform the specific molecular incantations necessary to confer transcriptional repression. Although SMRT and N-CoR are paralogs and possess similar molecular architectures and mechanistic strategies, they nonetheless exhibit distinct molecular and biological properties. It is now clear that the functions of both SMRT and N-CoR are further diversified through alternative mRNA splicing, yielding a series of corepressor protein variants that participate in distinctive transcription factor partnerships and display distinguishable repression properties. This review will discuss what is known about the structure and actions of SMRT, N-CoR, and their splicing variants, and how alternative splicing may allow the functions of these corepressors to be adapted and tailored to different cells and to different developmental stages. PMID:16604171

  9. Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life

    PubMed Central

    Weinberg, Marc S.; Michod, Richard E.

    2017-01-01

    In the RNA world hypothesis complex, self-replicating ribozymes were essential. For the emergence of an RNA world, less is known about the early processes that accounted for the formation of complex, long catalysts from small passively formed molecules. The functional role of small sequences has not been fully explored and, here, a possible role for smaller ligases is demonstrated. An established RNA polymerase model, the R18, was truncated from the 3′ end to generate smaller molecules. All the molecules were investigated for self-ligation functions with a set of oligonucleotide substrates without predesigned base pairing. The smallest molecule that exhibited self-ligation activity was a 40-nucleotide RNA. It also demonstrated the greatest functional flexibility as it was more general in the kinds of substrates it ligated to itself although its catalytic efficiency was the lowest. The largest ribozyme (R18) ligated substrates more selectively and with greatest efficiency. With increase in size and predicted structural stability, self-ligation efficiency improved, while functional flexibility decreased. These findings reveal that molecular size could have increased from the activity of small ligases joining oligonucleotides to their own end. In addition, there is a size-associated molecular-level trade-off that could have impacted the evolution of RNA-based life. PMID:28989747

  10. Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life

    NASA Astrophysics Data System (ADS)

    Dhar, Nisha; Weinberg, Marc S.; Michod, Richard E.; Durand, Pierre M.

    2017-09-01

    In the RNA world hypothesis complex, self-replicating ribozymes were essential. For the emergence of an RNA world, less is known about the early processes that accounted for the formation of complex, long catalysts from small passively formed molecules. The functional role of small sequences has not been fully explored and, here, a possible role for smaller ligases is demonstrated. An established RNA polymerase model, the R18, was truncated from the 3' end to generate smaller molecules. All the molecules were investigated for self-ligation functions with a set of oligonucleotide substrates without predesigned base pairing. The smallest molecule that exhibited self-ligation activity was a 40-nucleotide RNA. It also demonstrated the greatest functional flexibility as it was more general in the kinds of substrates it ligated to itself although its catalytic efficiency was the lowest. The largest ribozyme (R18) ligated substrates more selectively and with greatest efficiency. With increase in size and predicted structural stability, self-ligation efficiency improved, while functional flexibility decreased. These findings reveal that molecular size could have increased from the activity of small ligases joining oligonucleotides to their own end. In addition, there is a size-associated molecular-level trade-off that could have impacted the evolution of RNA-based life.

  11. Self-assembly of multi-stranded RNA motifs into lattices and tubular structures

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

    Stewart, Jaimie Marie; Subramanian, Hari K. K.; Franco, Elisa

    Rational design of nucleic acidmolecules yields selfassembling scaffolds with increasing complexity, size and functionality. It is an open question whether design methods tailored to build DNA nanostructures can be adapted to build RNA nanostructures with comparable features. We demonstrate the formation of RNA lattices and tubular assemblies from double crossover (DX) tiles, a canonical motif in DNA nanotechnology. Tubular structures can exceed 1 m in length, suggesting that this DX motif can produce very robust lattices. Some of these tubes spontaneously form with left-handed chirality. We obtain assemblies by using two methods: a protocol where gel-extracted RNA strands are slowlymore » annealed, and a one-pot transcription and anneal procedure. We then identify the tile nick position as a structural requirement for lattice formation. These results demonstrate that stable RNA structures can be obtained with design tools imported from DNA nanotechnology. These large assemblies could be potentially integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for colocalization of cellular components.« less

  12. Self-assembly of multi-stranded RNA motifs into lattices and tubular structures

    DOE PAGES

    Stewart, Jaimie Marie; Subramanian, Hari K. K.; Franco, Elisa

    2017-02-16

    Rational design of nucleic acidmolecules yields selfassembling scaffolds with increasing complexity, size and functionality. It is an open question whether design methods tailored to build DNA nanostructures can be adapted to build RNA nanostructures with comparable features. We demonstrate the formation of RNA lattices and tubular assemblies from double crossover (DX) tiles, a canonical motif in DNA nanotechnology. Tubular structures can exceed 1 m in length, suggesting that this DX motif can produce very robust lattices. Some of these tubes spontaneously form with left-handed chirality. We obtain assemblies by using two methods: a protocol where gel-extracted RNA strands are slowlymore » annealed, and a one-pot transcription and anneal procedure. We then identify the tile nick position as a structural requirement for lattice formation. These results demonstrate that stable RNA structures can be obtained with design tools imported from DNA nanotechnology. These large assemblies could be potentially integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for colocalization of cellular components.« less

  13. Self-assembly of multi-stranded RNA motifs into lattices and tubular structures

    PubMed Central

    Stewart, Jaimie Marie; Subramanian, Hari K. K.

    2017-01-01

    Abstract Rational design of nucleic acid molecules yields self-assembling scaffolds with increasing complexity, size and functionality. It is an open question whether design methods tailored to build DNA nanostructures can be adapted to build RNA nanostructures with comparable features. Here we demonstrate the formation of RNA lattices and tubular assemblies from double crossover (DX) tiles, a canonical motif in DNA nanotechnology. Tubular structures can exceed 1 μm in length, suggesting that this DX motif can produce very robust lattices. Some of these tubes spontaneously form with left-handed chirality. We obtain assemblies by using two methods: a protocol where gel-extracted RNA strands are slowly annealed, and a one-pot transcription and anneal procedure. We identify the tile nick position as a structural requirement for lattice formation. Our results demonstrate that stable RNA structures can be obtained with design tools imported from DNA nanotechnology. These large assemblies could be potentially integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for colocalization of cellular components. PMID:28204562

  14. The Challenges of Modularization.

    ERIC Educational Resources Information Center

    Brown, Sally; Saunders, Danny

    1995-01-01

    Discusses the movement towards credit accumulation and transfer in higher education institutions based on experiences at two universities in the United Kingdom, the University of Northumbria and the University of Glamorgan. Modularization, or unitization, and semesterization are considered, and three key areas are addressed: management, student…

  15. Tailored Codes for Small Quantum Memories

    NASA Astrophysics Data System (ADS)

    Robertson, Alan; Granade, Christopher; Bartlett, Stephen D.; Flammia, Steven T.

    2017-12-01

    We demonstrate that small quantum memories, realized via quantum error correction in multiqubit devices, can benefit substantially by choosing a quantum code that is tailored to the relevant error model of the system. For a biased noise model, with independent bit and phase flips occurring at different rates, we show that a single code greatly outperforms the well-studied Steane code across the full range of parameters of the noise model, including for unbiased noise. In fact, this tailored code performs almost optimally when compared with 10 000 randomly selected stabilizer codes of comparable experimental complexity. Tailored codes can even outperform the Steane code with realistic experimental noise, and without any increase in the experimental complexity, as we demonstrate by comparison in the observed error model in a recent seven-qubit trapped ion experiment.

  16. Modular Building Supplement: A Quick, Quality Solution for Schools.

    ERIC Educational Resources Information Center

    Goodmiller, Brian D.; Schendell, Derek G.

    2003-01-01

    This supplement presents three articles on modular construction that look at: "Fast Track Expansion for a New Jersey School" (involving a modular addition); "Precast Construction Helps Schools Meet Attendance Boom" (precast concrete components are quick, durable, and flexible); and "Airing HVAC Concerns" (poor indoor air quality in prefabricated…

  17. Modular low aspect ratio-high beta torsatron

    DOEpatents

    Sheffield, George V.; Furth, Harold P.

    1984-02-07

    A fusion reactor device in which the toroidal magnetic field and at least a portion of the poloidal magnetic field are provided by a single set of modular coils. The coils are arranged on the surface of a low aspect ratio toroid in planes having the cylindrical coordinate relationship .phi.=.phi..sub.i +kz where k is a constant equal to each coil's pitch and .phi..sub.i is the toroidal angle at which the i'th coil intersects the z=o plane. The device may be described as a modular, high beta torsation whose screw symmetry is pointed along the systems major (z) axis. The toroid defined by the modular coils preferably has a racetrack minor cross section. When vertical field coils and preferably a toroidal plasma current are provided for magnetic field surface closure within the toroid, a vacuum magnetic field of racetrack shaped minor cross section with improved stability and beta valves is obtained.

  18. Ecological and evolutionary dynamics of interconnectedness and modularity

    PubMed Central

    Nordbotten, Jan M.; Levin, Simon A.; Szathmáry, Eörs; Stenseth, Nils C.

    2018-01-01

    In this contribution, we develop a theoretical framework for linking microprocesses (i.e., population dynamics and evolution through natural selection) with macrophenomena (such as interconnectedness and modularity within an ecological system). This is achieved by developing a measure of interconnectedness for population distributions defined on a trait space (generalizing the notion of modularity on graphs), in combination with an evolution equation for the population distribution. With this contribution, we provide a platform for understanding under what environmental, ecological, and evolutionary conditions ecosystems evolve toward being more or less modular. A major contribution of this work is that we are able to decompose the overall driver of changes at the macro level (such as interconnectedness) into three components: (i) ecologically driven change, (ii) evolutionarily driven change, and (iii) environmentally driven change. PMID:29311333

  19. Modularization of genetic elements promotes synthetic metabolic engineering.

    PubMed

    Qi, Hao; Li, Bing-Zhi; Zhang, Wen-Qian; Liu, Duo; Yuan, Ying-Jin

    2015-11-15

    In the context of emerging synthetic biology, metabolic engineering is moving to the next stage powered by new technologies. Systematical modularization of genetic elements makes it more convenient to engineer biological systems for chemical production or other desired purposes. In the past few years, progresses were made in engineering metabolic pathway using synthetic biology tools. Here, we spotlighted the topic of implementation of modularized genetic elements in metabolic engineering. First, we overviewed the principle developed for modularizing genetic elements and then discussed how the genetic modules advanced metabolic engineering studies. Next, we picked up some milestones of engineered metabolic pathway achieved in the past few years. Last, we discussed the rapid raised synthetic biology field of "building a genome" and the potential in metabolic engineering. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. A truly Lego®-like modular microfluidics platform

    NASA Astrophysics Data System (ADS)

    Vittayarukskul, Kevin; Lee, Abraham Phillip

    2017-03-01

    Ideally, a modular microfluidics platform should be simple to assemble and support 3D configurations for increased versatility. The modular building blocks should also be mass producible like electrical components. These are fundamental features of world-renowned Legos® and why Legos® inspire many existing modular microfluidics platforms. In this paper, a truly Lego®-like microfluidics platform is introduced, and its basic feasibility is demonstrated. Here, PDMS building blocks resembling 2  ×  2 Lego® bricks are cast from 3D-printed master molds. The blocks are pegged and stacked on a traditional Lego® plate to create simple, 3D microfluidic networks, such as a single basket weave. Characteristics of the platform, including reversible sealing and automatic alignment of channels, are also analyzed and discussed in detail.

  1. Multifarenes: new modular cavitands.

    PubMed

    Parvari, Galit; Annamalai, Senthilmurugan; Borovoi, Iris; Chechik, Helena; Botoshansky, Mark; Pappo, Doron; Keinan, Ehud

    2014-03-07

    Multifarenes, a new class of macrocycles, which are constructed of alternating building blocks, are conveniently accessible by three complementary syntheses that provide modularity and scalability. In addition to metal-ion coordination, these cavitands show increased flexibility with increasing ring size, offering opportunities for induced fit to guest molecules.

  2. Toward modular biological models: defining analog modules based on referent physiological mechanisms

    PubMed Central

    2014-01-01

    Background Currently, most biomedical models exist in isolation. It is often difficult to reuse or integrate models or their components, in part because they are not modular. Modular components allow the modeler to think more deeply about the role of the model and to more completely address a modeling project’s requirements. In particular, modularity facilitates component reuse and model integration for models with different use cases, including the ability to exchange modules during or between simulations. The heterogeneous nature of biology and vast range of wet-lab experimental platforms call for modular models designed to satisfy a variety of use cases. We argue that software analogs of biological mechanisms are reasonable candidates for modularization. Biomimetic software mechanisms comprised of physiomimetic mechanism modules offer benefits that are unique or especially important to multi-scale, biomedical modeling and simulation. Results We present a general, scientific method of modularizing mechanisms into reusable software components that we call physiomimetic mechanism modules (PMMs). PMMs utilize parametric containers that partition and expose state information into physiologically meaningful groupings. To demonstrate, we modularize four pharmacodynamic response mechanisms adapted from an in silico liver (ISL). We verified the modularization process by showing that drug clearance results from in silico experiments are identical before and after modularization. The modularized ISL achieves validation targets drawn from propranolol outflow profile data. In addition, an in silico hepatocyte culture (ISHC) is created. The ISHC uses the same PMMs and required no refactoring. The ISHC achieves validation targets drawn from propranolol intrinsic clearance data exhibiting considerable between-lab variability. The data used as validation targets for PMMs originate from both in vitro to in vivo experiments exhibiting large fold differences in time scale

  3. Promoting a Culture of Tailoring for Systems Engineering Policy Expectations

    NASA Technical Reports Server (NTRS)

    Blankenship, Van A.

    2016-01-01

    NASA's Marshall Space Flight Center (MSFC) has developed an integrated systems engineering approach to promote a culture of tailoring for program and project policy requirements. MSFC's culture encourages and supports tailoring, with an emphasis on risk-based decision making, for enhanced affordability and efficiency. MSFC's policy structure integrates the various Agency requirements into a single, streamlined implementation approach which serves as a "one-stop-shop" for our programs and projects to follow. The engineers gain an enhanced understanding of policy and technical expectations, as well as lesson's learned from MSFC's history of spaceflight and science missions, to enable them to make appropriate, risk-based tailoring recommendations. The tailoring approach utilizes a standard methodology to classify projects into predefined levels using selected mission and programmatic scaling factors related to risk tolerance. Policy requirements are then selectively applied and tailored, with appropriate rationale, and approved by the governing authorities, to support risk-informed decisions to achieve the desired cost and schedule efficiencies. The policy is further augmented by implementation tools and lifecycle planning aids which help promote and support the cultural shift toward more tailoring. The MSFC Customization Tool is an integrated spreadsheet that ties together everything that projects need to understand, navigate, and tailor the policy. It helps them classify their project, understand the intent of the requirements, determine their tailoring approach, and document the necessary governance approvals. It also helps them plan for and conduct technical reviews throughout the lifecycle. Policy tailoring is thus established as a normal part of project execution, with the tools provided to facilitate and enable the tailoring process. MSFC's approach to changing the culture emphasizes risk-based tailoring of policy to achieve increased flexibility, efficiency

  4. Measuring, Enabling and Comparing Modularity, Regularity and Hierarchy in Evolutionary Design

    NASA Technical Reports Server (NTRS)

    Hornby, Gregory S.

    2005-01-01

    For computer-automated design systems to scale to complex designs they must be able to produce designs that exhibit the characteristics of modularity, regularity and hierarchy - characteristics that are found both in man-made and natural designs. Here we claim that these characteristics are enabled by implementing the attributes of combination, control-flow and abstraction in the representation. To support this claim we use an evolutionary algorithm to evolve solutions to different sizes of a table design problem using five different representations, each with different combinations of modularity, regularity and hierarchy enabled and show that the best performance happens when all three of these attributes are enabled. We also define metrics for modularity, regularity and hierarchy in design encodings and demonstrate that high fitness values are achieved with high values of modularity, regularity and hierarchy and that there is a positive correlation between increases in fitness and increases in modularity. regularity and hierarchy.

  5. Modularity: An Application of General Systems Theory to Military Force Development

    DTIC Science & Technology

    2005-01-01

    1999). Context, modularity, and the cultural constitution of development. In P. Lloyd & C. Fernyhough (Eds.), Lev Vygotsky : Critical assessments...of General Systems Theory to Military Force Development 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT...Prescribed by ANSI Std Z39-18 MODULARITY: AN APPLICATION OF GENERAL SYSTEMS THEORY TO MILITARY FORCE DEVELOPMENT 279 R SEARCH MODULARITY: AN APPLICATION OF

  6. Unraveling the disease consequences and mechanisms of modular structure in animal social networks

    PubMed Central

    Leu, Stephan T.; Cross, Paul C.; Hudson, Peter J.; Bansal, Shweta

    2017-01-01

    Disease risk is a potential cost of group living. Although modular organization is thought to reduce this cost in animal societies, empirical evidence toward this hypothesis has been conflicting. We analyzed empirical social networks from 43 animal species to motivate our study of the epidemiological consequences of modular structure in animal societies. From these empirical studies, we identified the features of interaction patterns associated with network modularity and developed a theoretical network model to investigate when and how subdivisions in social networks influence disease dynamics. Contrary to prior work, we found that disease risk is largely unaffected by modular structure, although social networks beyond a modular threshold experience smaller disease burden and longer disease duration. Our results illustrate that the lowering of disease burden in highly modular social networks is driven by two mechanisms of modular organization: network fragmentation and subgroup cohesion. Highly fragmented social networks with cohesive subgroups are able to structurally trap infections within a few subgroups and also cause a structural delay to the spread of disease outbreaks. Finally, we show that network models incorporating modular structure are necessary only when prior knowledge suggests that interactions within the population are highly subdivided. Otherwise, null networks based on basic knowledge about group size and local contact heterogeneity may be sufficient when data-limited estimates of epidemic consequences are necessary. Overall, our work does not support the hypothesis that modular structure universally mitigates the disease impact of group living. PMID:28373567

  7. Unraveling the disease consequences and mechanisms of modular structure in animal social networks.

    PubMed

    Sah, Pratha; Leu, Stephan T; Cross, Paul C; Hudson, Peter J; Bansal, Shweta

    2017-04-18

    Disease risk is a potential cost of group living. Although modular organization is thought to reduce this cost in animal societies, empirical evidence toward this hypothesis has been conflicting. We analyzed empirical social networks from 43 animal species to motivate our study of the epidemiological consequences of modular structure in animal societies. From these empirical studies, we identified the features of interaction patterns associated with network modularity and developed a theoretical network model to investigate when and how subdivisions in social networks influence disease dynamics. Contrary to prior work, we found that disease risk is largely unaffected by modular structure, although social networks beyond a modular threshold experience smaller disease burden and longer disease duration. Our results illustrate that the lowering of disease burden in highly modular social networks is driven by two mechanisms of modular organization: network fragmentation and subgroup cohesion. Highly fragmented social networks with cohesive subgroups are able to structurally trap infections within a few subgroups and also cause a structural delay to the spread of disease outbreaks. Finally, we show that network models incorporating modular structure are necessary only when prior knowledge suggests that interactions within the population are highly subdivided. Otherwise, null networks based on basic knowledge about group size and local contact heterogeneity may be sufficient when data-limited estimates of epidemic consequences are necessary. Overall, our work does not support the hypothesis that modular structure universally mitigates the disease impact of group living.

  8. Unraveling the disease consequences and mechanisms of modular structure in animal social networks

    USGS Publications Warehouse

    Sah, Pratha; Leu, Stephan T.; Cross, Paul C.; Hudson, Peter J.; Bansal, Shweta

    2017-01-01

    Disease risk is a potential cost of group living. Although modular organization is thought to reduce this cost in animal societies, empirical evidence toward this hypothesis has been conflicting. We analyzed empirical social networks from 43 animal species to motivate our study of the epidemiological consequences of modular structure in animal societies. From these empirical studies, we identified the features of interaction patterns associated with network modularity and developed a theoretical network model to investigate when and how subdivisions in social networks influence disease dynamics. Contrary to prior work, we found that disease risk is largely unaffected by modular structure, although social networks beyond a modular threshold experience smaller disease burden and longer disease duration. Our results illustrate that the lowering of disease burden in highly modular social networks is driven by two mechanisms of modular organization: network fragmentation and subgroup cohesion. Highly fragmented social networks with cohesive subgroups are able to structurally trap infections within a few subgroups and also cause a structural delay to the spread of disease outbreaks. Finally, we show that network models incorporating modular structure are necessary only when prior knowledge suggests that interactions within the population are highly subdivided. Otherwise, null networks based on basic knowledge about group size and local contact heterogeneity may be sufficient when data-limited estimates of epidemic consequences are necessary. Overall, our work does not support the hypothesis that modular structure universally mitigates the disease impact of group living.

  9. Are we there yet? An examination of online tailored health communication.

    PubMed

    Suggs, L Suzanne; McIntyre, Chris

    2009-04-01

    Increasingly, the Internet is playing an important role in consumer health and patient-provider communication. Seventy-three percent of American adults are now online, and 79% have searched for health information on the Internet. This study provides a baseline understanding of the extent to which health consumers are able to find tailored communication online. It describes the current behavioral focus, the channels being used to deliver the tailored content, and the level of tailoring in online-tailored communication. A content analysis of 497 health Web sites found few examples of personalized, targeted, or tailored health sites freely available online. Tailored content was provided in 13 Web sites, although 15 collected individual data. More health risk assessment (HRA) sites included tailored feedback than other topics. The patterns that emerged from the analysis demonstrate that online health users can access a number of Web sites with communication tailored to their needs.

  10. Understanding tailoring in communicating about health

    PubMed Central

    Hawkins, Robert P.; Kreuter, Matthew; Resnicow, Kenneth; Fishbein, Martin; Dijkstra, Arie

    2011-01-01

    ‘Tailoring’ refers to any of a number of methods for creating communications individualized for their receivers, with the expectation that this individualization will lead to larger intended effects of these communications. Results so far have been generally positive but not consistently so, and this paper seeks to explicate tailoring to help focus future research. Tailoring involves either or both of two classes of goals (enhancing cognitive preconditions for message processing and enhancing message impact through modifying behavioral determinants of goal outcomes) and employs strategies of personalization, feedback and content matching. These goals and strategies intersect in a 2 × 3 matrix in which some strategies and their component tactics match better to some goals than to others. The paper illustrates how this framework can be systematically applied in generating research questions and identifying appropriate study designs for tailoring research. PMID:18349033

  11. Modular space station Phase B extension preliminary performance specification. Volume 2: Project

    NASA Technical Reports Server (NTRS)

    1971-01-01

    The four systems of the modular space station project are described, and the interfaces between this project and the shuttle project, the tracking and data relay satellite project, and an arbitrarily defined experiment project are defined. The experiment project was synthesized from internal experiments, detached research and application modules, and attached research and application modules to derive a set of interface requirements which will support multiple combinations of these elements expected during the modular space station mission. The modular space station project element defines a 6-man orbital program capable of growth to a 12-man orbital program capability. The modular space station project element specification defines the modular space station system, the premission operations support system, the mission operations support system, and the cargo module system and their interfaces.

  12. Tailored telephone counseling increases colorectal cancer screening.

    PubMed

    Rawl, Susan M; Christy, Shannon M; Monahan, Patrick O; Ding, Yan; Krier, Connie; Champion, Victoria L; Rex, Douglas

    2015-08-01

    To compare the efficacy of two interventions to promote colorectal cancer screening participation and forward stage movement of colorectal cancer screening adoption among first-degree relatives of individuals diagnosed with adenomatous polyps. One hundred fifty-eight first-degree relatives of individuals diagnosed with adenomatous polyps were randomly assigned to receive one of two interventions to promote colorectal cancer screening. Participants received either a tailored telephone counseling plus brochures intervention or a non-tailored print brochures intervention. Data were collected at baseline and 3 months post-baseline. Group differences and the effect of the interventions on adherence and stage movement for colorectal cancer screening were examined using t-tests, chi-square tests, and logistic regression. Individuals in the tailored telephone counseling plus brochures group were significantly more likely to complete colorectal cancer screening and to move forward on stage of change for fecal occult blood test, any colorectal cancer test stage and stage of the risk-appropriate test compared with individuals in the non-tailored brochure group at 3 months post-baseline. A tailored telephone counseling plus brochures intervention successfully promoted forward stage movement and colorectal cancer screening adherence among first-degree relatives of individuals diagnosed with adenomatous polyps. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  13. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

    PubMed Central

    2010-01-01

    Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE

  14. Classification of functional interactions from multi-electrodes data using conditional modularity analysis

    NASA Astrophysics Data System (ADS)

    Makhtar, Siti Noormiza; Senik, Mohd Harizal

    2018-02-01

    The availability of massive amount of neuronal signals are attracting widespread interest in functional connectivity analysis. Functional interactions estimated by multivariate partial coherence analysis in the frequency domain represent the connectivity strength in this study. Modularity is a network measure for the detection of community structure in network analysis. The discovery of community structure for the functional neuronal network was implemented on multi-electrode array (MEA) signals recorded from hippocampal regions in isoflurane-anaesthetized Lister-hooded rats. The analysis is expected to show modularity changes before and after local unilateral kainic acid (KA)-induced epileptiform activity. The result is presented using color-coded graphic of conditional modularity measure for 19 MEA nodes. This network is separated into four sub-regions to show the community detection within each sub-region. The results show that classification of neuronal signals into the inter- and intra-modular nodes is feasible using conditional modularity analysis. Estimation of segregation properties using conditional modularity analysis may provide further information about functional connectivity from MEA data.

  15. Mining the modular structure of protein interaction networks.

    PubMed

    Berenstein, Ariel José; Piñero, Janet; Furlong, Laura Inés; Chernomoretz, Ariel

    2015-01-01

    Cluster-based descriptions of biological networks have received much attention in recent years fostered by accumulated evidence of the existence of meaningful correlations between topological network clusters and biological functional modules. Several well-performing clustering algorithms exist to infer topological network partitions. However, due to respective technical idiosyncrasies they might produce dissimilar modular decompositions of a given network. In this contribution, we aimed to analyze how alternative modular descriptions could condition the outcome of follow-up network biology analysis. We considered a human protein interaction network and two paradigmatic cluster recognition algorithms, namely: the Clauset-Newman-Moore and the infomap procedures. We analyzed to what extent both methodologies yielded different results in terms of granularity and biological congruency. In addition, taking into account Guimera's cartographic role characterization of network nodes, we explored how the adoption of a given clustering methodology impinged on the ability to highlight relevant network meso-scale connectivity patterns. As a case study we considered a set of aging related proteins and showed that only the high-resolution modular description provided by infomap, could unveil statistically significant associations between them and inter/intra modular cartographic features. Besides reporting novel biological insights that could be gained from the discovered associations, our contribution warns against possible technical concerns that might affect the tools used to mine for interaction patterns in network biology studies. In particular our results suggested that sub-optimal partitions from the strict point of view of their modularity levels might still be worth being analyzed when meso-scale features were to be explored in connection with external source of biological knowledge.

  16. Common modular avionics - Partitioning and design philosophy

    NASA Astrophysics Data System (ADS)

    Scott, D. M.; Mulvaney, S. P.

    The design objectives and definition criteria for common modular hardware that will perform digital processing functions in multiple avionic subsystems are examined. In particular, attention is given to weapon system-level objectives, such as increased supportability, reduced life cycle costs, and increased upgradability. These objectives dictate the following overall modular design goals: reduce test equipment requirements; have a large number of subsystem applications; design for architectural growth; and standardize for technology transparent implementations. Finally, specific partitioning criteria are derived on the basis of the weapon system-level objectives and overall design goals.

  17. Tailored to Fit

    ERIC Educational Resources Information Center

    Milbradt, Allan; Klock, Ed

    2006-01-01

    Building a new school can be exciting and creative. The process enables parents, students, educators and the community to explore their dreams and priorities, and create a facility tailored to their unique needs. Unfortunately, the process also can leave education institutions and communities feeling like they've bought an "off-the-rack" facility…

  18. Elliptic CY3folds and non-perturbative modular transformation

    NASA Astrophysics Data System (ADS)

    Iqbal, Amer; Shabbir, Khurram

    2016-03-01

    We study the refined topological string partition function of a class of toric elliptically fibered Calabi-Yau threefolds. These Calabi-Yau threefolds give rise to five dimensional quiver gauge theories and are dual to configurations of M5-M2-branes. We determine the Gopakumar-Vafa invariants for these threefolds and show that the genus g free energy is given by the weight 2 g Eisenstein series. We also show that although the free energy at all genera are modular invariant, the full partition function satisfies the non-perturbative modular transformation property discussed by Lockhart and Vafa in arXiv:1210.5909 and therefore the modularity of free energy is up to non-perturbative corrections.

  19. Ecological and evolutionary dynamics of interconnectedness and modularity.

    PubMed

    Nordbotten, Jan M; Levin, Simon A; Szathmáry, Eörs; Stenseth, Nils C

    2018-01-23

    In this contribution, we develop a theoretical framework for linking microprocesses (i.e., population dynamics and evolution through natural selection) with macrophenomena (such as interconnectedness and modularity within an ecological system). This is achieved by developing a measure of interconnectedness for population distributions defined on a trait space (generalizing the notion of modularity on graphs), in combination with an evolution equation for the population distribution. With this contribution, we provide a platform for understanding under what environmental, ecological, and evolutionary conditions ecosystems evolve toward being more or less modular. A major contribution of this work is that we are able to decompose the overall driver of changes at the macro level (such as interconnectedness) into three components: ( i ) ecologically driven change, ( ii ) evolutionarily driven change, and ( iii ) environmentally driven change. Copyright © 2018 the Author(s). Published by PNAS.

  20. Maass Forms and Quantum Modular Forms

    NASA Astrophysics Data System (ADS)

    Rolen, Larry

    This thesis describes several new results in the theory of harmonic Maass forms and related objects. Maass forms have recently led to a flood of applications throughout number theory and combinatorics in recent years, especially following their development by the work of Bruinier and Funke the modern understanding Ramanujan's mock theta functions due to Zwegers. The first of three main theorems discussed in this thesis concerns the integrality properties of singular moduli. These are well-known to be algebraic integers, and they play a beautiful role in complex multiplication and explicit class field theory for imaginary quadratic fields. One can also study "singular moduli" for special non-holomorphic functions, which are algebraic but are not necessarily algebraic integers. Here we will explain the phenomenon of integrality properties and provide a sharp bound on denominators of symmetric functions in singular moduli. The second main theme of the thesis concerns Zagier's recent definition of a quantum modular form. Since their definition in 2010 by Zagier, quantum modular forms have been connected to numerous different topics such as strongly unimodal sequences, ranks, cranks, and asymptotics for mock theta functions. Motivated by Zagier's example of the quantum modularity of Kontsevich's "strange" function F(q), we revisit work of Andrews, Jimenez-Urroz, and Ono to construct a natural vector-valued quantum modular form whose components. The final chapter of this thesis is devoted to a study of asymptotics of mock theta functions near roots of unity. In his famous deathbed letter, Ramanujan introduced the notion of a mock theta function, and he offered some alleged examples. The theory of mock theta functions has been brought to fruition using the framework of harmonic Maass forms, thanks to Zwegers. Despite this understanding, little attention has been given to Ramanujan's original definition. Here we prove that Ramanujan's examples do indeed satisfy his

  1. Environmental versatility promotes modularity in genome-scale metabolic networks.

    PubMed

    Samal, Areejit; Wagner, Andreas; Martin, Olivier C

    2011-08-24

    The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new arrangements that may benefit their carrier. Conversely, modularity may emerge as a by-product of some trait. We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chemical environments. For such networks, we define a network module as a maximal set of reactions that are fully coupled, i.e., whose fluxes can only vary in fixed proportions. This definition overcomes limitations of purely graph based analyses of metabolism by exploiting the functional links between reactions. We call a metabolic network viable in a given chemical environment if it can synthesize all of an organism's biomass compounds from nutrients in this environment. An organism's metabolism is highly versatile if it can sustain life in many different chemical environments. We here ask whether versatility affects the modularity of metabolic networks. Using recently developed techniques to randomly sample large numbers of viable metabolic networks from a vast space of metabolic networks, we use flux balance analysis to study in silico metabolic networks that differ in their versatility. We find that highly versatile networks are also highly modular. They contain more modules and more reactions that are organized into modules. Most or all reactions in a module are associated with the same biochemical pathways. Modules that arise in highly versatile networks generally involve reactions that process nutrients or closely related chemicals. We also observe that the metabolism of E. coli is significantly more modular than even our most versatile networks. Our work shows that modularity in metabolic networks can be a by-product of functional constraints, e.g., the need to sustain life in multiple

  2. RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.

    PubMed

    Habegger, Lukas; Sboner, Andrea; Gianoulis, Tara A; Rozowsky, Joel; Agarwal, Ashish; Snyder, Michael; Gerstein, Mark

    2011-01-15

    The advent of next-generation sequencing for functional genomics has given rise to quantities of sequence information that are often so large that they are difficult to handle. Moreover, sequence reads from a specific individual can contain sufficient information to potentially identify and genetically characterize that person, raising privacy concerns. In order to address these issues, we have developed the Mapped Read Format (MRF), a compact data summary format for both short and long read alignments that enables the anonymization of confidential sequence information, while allowing one to still carry out many functional genomics studies. We have developed a suite of tools (RSEQtools) that use this format for the analysis of RNA-Seq experiments. These tools consist of a set of modules that perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads and segmenting that signal into actively transcribed regions. Moreover, the tools can readily be used to build customizable RNA-Seq workflows. In addition to the anonymization afforded by MRF, this format also facilitates the decoupling of the alignment of reads from downstream analyses. RSEQtools is implemented in C and the source code is available at http://rseqtools.gersteinlab.org/.

  3. Highly efficient siRNA delivery from core-shell mesoporous silica nanoparticles with multifunctional polymer caps

    NASA Astrophysics Data System (ADS)

    Möller, Karin; Müller, Katharina; Engelke, Hanna; Bräuchle, Christoph; Wagner, Ernst; Bein, Thomas

    2016-02-01

    A new general route for siRNA delivery is presented combining porous core-shell silica nanocarriers with a modularly designed multifunctional block copolymer. Specifically, the internal storage and release of siRNA from mesoporous silica nanoparticles (MSN) with orthogonal core-shell surface chemistry was investigated as a function of pore-size, pore morphology, surface properties and pH. Very high siRNA loading capacities of up to 380 μg per mg MSN were obtained with charge-matched amino-functionalized mesoporous cores, and release profiles show up to 80% siRNA elution after 24 h. We demonstrate that adsorption and desorption of siRNA is mainly driven by electrostatic interactions, which allow for high loading capacities even in medium-sized mesopores with pore diameters down to 4 nm in a stellate pore morphology. The negatively charged MSN shell enabled the association with a block copolymer containing positively charged artificial amino acids and oleic acid blocks, which acts simultaneously as capping and endosomal release agent. The potential of this multifunctional delivery platform is demonstrated by highly effective cell transfection and siRNA delivery into KB-cells. A luciferase reporter gene knock-down of up to 80-90% was possible using extremely low cell exposures with only 2.5 μg MSN containing 0.5 μg siRNA per 100 μL well.A new general route for siRNA delivery is presented combining porous core-shell silica nanocarriers with a modularly designed multifunctional block copolymer. Specifically, the internal storage and release of siRNA from mesoporous silica nanoparticles (MSN) with orthogonal core-shell surface chemistry was investigated as a function of pore-size, pore morphology, surface properties and pH. Very high siRNA loading capacities of up to 380 μg per mg MSN were obtained with charge-matched amino-functionalized mesoporous cores, and release profiles show up to 80% siRNA elution after 24 h. We demonstrate that adsorption and desorption of

  4. Magnetic Beads-Based Sensor with Tailored Sensitivity for Rapid and Single-Step Amperometric Determination of miRNAs.

    PubMed

    Vargas, Eva; Torrente-Rodríguez, Rebeca M; Ruiz-Valdepeñas Montiel, Víctor; Povedano, Eloy; Pedrero, María; Montoya, Juan J; Campuzano, Susana; Pingarrón, José M

    2017-11-09

    This work describes a sensitive amperometric magneto-biosensor for single-step and rapid determination of microRNAs (miRNAs). The developed strategy involves the use of direct hybridization of the target miRNA (miRNA-21) with a specific biotinylated DNA probe immobilized on streptavidin-modified magnetic beads (MBs), and labeling of the resulting heteroduplexes with a specific DNA-RNA antibody and the bacterial protein A (ProtA) conjugated with an horseradish peroxidase (HRP) homopolymer (Poly-HRP40) as an enzymatic label for signal amplification. Amperometric detection is performed upon magnetic capture of the modified MBs onto the working electrode surface of disposable screen-printed carbon electrodes (SPCEs) using the H₂O₂/hydroquinone (HQ) system. The magnitude of the cathodic signal obtained at -0.20 V (vs. the Ag pseudo-reference electrode) demonstrated linear dependence with the concentration of the synthetic target miRNA over the 1.0 to 100 pM range. The method provided a detection limit (LOD) of 10 attomoles (in a 25 μL sample) without any target miRNA amplification in just 30 min (once the DNA capture probe-MBs were prepared). This approach shows improved sensitivity compared with that of biosensors constructed with the same anti-DNA-RNA Ab as capture instead of a detector antibody and further labeling with a Strep-HRP conjugate instead of the Poly-HRP40 homopolymer. The developed strategy involves a single step working protocol, as well as the possibility to tailor the sensitivity by enlarging the length of the DNA/miRNA heteroduplexes using additional probes and/or performing the labelling with ProtA conjugated with homopolymers prepared with different numbers of HRP molecules. The practical usefulness was demonstrated by determination of the endogenous levels of the mature target miRNA in 250 ng raw total RNA (RNA t ) extracted from human mammary epithelial normal (MCF-10A) and cancer (MCF-7) cells and tumor tissues.

  5. ZERODUR TAILORED for cryogenic application

    NASA Astrophysics Data System (ADS)

    Jedamzik, R.; Westerhoff, T.

    2014-07-01

    ZERODUR® glass ceramic from SCHOTT is known for its very low thermal expansion coefficient (CTE) at room temperature and its excellent CTE homogeneity. It is widely used for ground-based astronomical mirrors but also for satellite applications. Many reference application demonstrate the excellent and long lasting performance of ZERODUR® components in orbit. For space application a low CTE of the mirror material is required at cryogenic temperatures together with a good match of the thermal expansion to the supporting structure material. It is possible to optimize the coefficient of thermal expansion of ZERODUR® for cryogenic applications. This paper reports on measurements of thermal expansion of ZERODUR® down to cryogenic temperatures of 10 K performed by the PTB (Physikalisch Technische Bundesanstallt, Braunschweig, Germany, the national metrology laboratory). The ZERODUR® TAILORED CRYO presented in this paper has a very low coefficient of thermal expansion down to 70 K. The maximum absolute integrated thermal expansion down to 10 K is only about 20 ppm. Mirror blanks made from ZERODUR® TAILORED CRYO can be light weighted to almost 90% with our modern processing technologies. With ZERODUR® TAILORED CRYO, SCHOTT offers the mirror blank material for the next generation of space telescope applications.

  6. Tailored nutrition education: is it really effective?

    PubMed

    Eyles, Helen; Ni Mhurchu, Cliona

    2012-03-01

    There has been a growing interest in tailored nutrition education over the previous decade, with a number of literature reviews suggesting this intervention strategy holds considerable potential. Nevertheless, the majority of intervention trials undertaken to date have employed subjective self-report outcome measures (such as dietary recalls). The aim of the present review is to further consider the likely true effect of tailored nutrition education by assessing the findings of tailored nutrition education intervention trials where objective outcome measures (such as sales data) have been employed. Four trials of tailored nutrition education employing objective outcome measures were identified: one was undertaken in eight low-cost supermarkets in New Zealand (2010; n 1104); one was an online intervention trial in Australia (2006; n 497); and two were undertaken in US supermarkets (1997 and 2001; n 105 and 296, respectively). Findings from the high-quality New Zealand trial were negative. Findings from the US trials were also generally negative, although reporting was poor making it difficult to assess quality. Findings from the high-quality online trial were positive, although have limited generalisability for public health. Trials employing objective outcome measures strongly suggest tailored nutrition education is not effective as a stand-alone strategy. However, further large, high-quality trials employing objective outcome measures are needed to determine the true effectiveness of this popular nutrition intervention strategy. Regardless, education plays an important role in generating social understanding and acceptance of broader interventions to improve nutrition.

  7. MRV - Modular Robotic Vehicle

    NASA Technical Reports Server (NTRS)

    Ridley, Justin; Bluethmann, Bill

    2015-01-01

    The Modular Robotic Vehicle, or MRV, completed in 2013, was developed at the Johnson Space Center in order to advance technologies which have applications for future vehicles both in space and on Earth. With seating for two people, MRV is a fully electric vehicle modeled as a "city car", suited for busy urban environments.

  8. Modular Closed-Loop Control of Diabetes

    PubMed Central

    Magni, L.; Dassau, E.; Hughes-Karvetski, C.; Toffanin, C.; De Nicolao, G.; Del Favero, S.; Breton, M.; Man, C. Dalla; Renard, E.; Zisser, H.; Doyle, F. J.; Cobelli, C.; Kovatchev, B. P.

    2015-01-01

    Modularity plays a key role in many engineering systems, allowing for plug-and-play integration of components, enhancing flexibility and adaptability, and facilitating standardization. In the control of diabetes, i.e., the so-called “artificial pancreas,” modularity allows for the step-wise introduction of (and regulatory approval for) algorithmic components, starting with subsystems for assured patient safety and followed by higher layer components that serve to modify the patient’s basal rate in real time. In this paper, we introduce a three-layer modular architecture for the control of diabetes, consisting in a sensor/pump interface module (IM), a continuous safety module (CSM), and a real-time control module (RTCM), which separates the functions of insulin recommendation (postmeal insulin for mitigating hyperglycemia) and safety (prevention of hypoglycemia). In addition, we provide details of instances of all three layers of the architecture: the APS© serving as the IM, the safety supervision module (SSM) serving as the CSM, and the range correction module (RCM) serving as the RTCM. We evaluate the performance of the integrated system via in silico preclinical trials, demonstrating 1) the ability of the SSM to reduce the incidence of hypoglycemia under nonideal operating conditions and 2) the ability of the RCM to reduce glycemic variability. PMID:22481809

  9. Modular closed-loop control of diabetes.

    PubMed

    Patek, S D; Magni, L; Dassau, E; Karvetski, C; Toffanin, C; De Nicolao, G; Del Favero, S; Breton, M; Man, C Dalla; Renard, E; Zisser, H; Doyle, F J; Cobelli, C; Kovatchev, B P

    2012-11-01

    Modularity plays a key role in many engineering systems, allowing for plug-and-play integration of components, enhancing flexibility and adaptability, and facilitating standardization. In the control of diabetes, i.e., the so-called "artificial pancreas," modularity allows for the step-wise introduction of (and regulatory approval for) algorithmic components, starting with subsystems for assured patient safety and followed by higher layer components that serve to modify the patient's basal rate in real time. In this paper, we introduce a three-layer modular architecture for the control of diabetes, consisting in a sensor/pump interface module (IM), a continuous safety module (CSM), and a real-time control module (RTCM), which separates the functions of insulin recommendation (postmeal insulin for mitigating hyperglycemia) and safety (prevention of hypoglycemia). In addition, we provide details of instances of all three layers of the architecture: the APS© serving as the IM, the safety supervision module (SSM) serving as the CSM, and the range correction module (RCM) serving as the RTCM. We evaluate the performance of the integrated system via in silico preclinical trials, demonstrating 1) the ability of the SSM to reduce the incidence of hypoglycemia under nonideal operating conditions and 2) the ability of the RCM to reduce glycemic variability.

  10. Modular reflector concept study

    NASA Technical Reports Server (NTRS)

    Vaughan, D. H.

    1981-01-01

    A study was conducted to evaluate the feasibility of space erecting a 100 meter paraboloidal radio frequency reflector by joining a number of individually deployed structural modules. Three module design concepts were considered: (1) the deployable cell module (DCM); (2) the modular paraboloidal erectable truss antenna (Mod-PETA); and (3) the modular erectable truss antenna (META). With the space shuttle (STS) as the launch system, the methodology of packaging and stowing in the orbiter, and of dispensing, deploying and joining, in orbit, were studied and the necessary support equipment identified. The structural performance of the completed reflectors was evaluated and their overall operational capability and feasibility were evaluated and compared. The potential of the three concepts to maintain stable shape in the space environment was determined. Their ability to operate at radio frequencies of 1 GHz and higher was assessed assuming the reflector surface to consist of a number of flat, hexagonal facets. A parametric study was performed to determine figure degradation as a function of reflector size, flat facet size, and f/D ratio.

  11. Structural tailoring of engine blades (STAEBL)

    NASA Technical Reports Server (NTRS)

    Platt, C. E.; Pratt, T. K.; Brown, K. W.

    1982-01-01

    A mathematical optimization procedure was developed for the structural tailoring of engine blades and was used to structurally tailor two engine fan blades constructed of composite materials without midspan shrouds. The first was a solid blade made from superhybrid composites, and the second was a hollow blade with metal matrix composite inlays. Three major computerized functions were needed to complete the procedure: approximate analysis with the established input variables, optimization of an objective function, and refined analysis for design verification.

  12. MODULAR ANALYTICS: A New Approach to Automation in the Clinical Laboratory.

    PubMed

    Horowitz, Gary L; Zaman, Zahur; Blanckaert, Norbert J C; Chan, Daniel W; Dubois, Jeffrey A; Golaz, Olivier; Mensi, Noury; Keller, Franz; Stolz, Herbert; Klingler, Karl; Marocchi, Alessandro; Prencipe, Lorenzo; McLawhon, Ronald W; Nilsen, Olaug L; Oellerich, Michael; Luthe, Hilmar; Orsonneau, Jean-Luc; Richeux, Gérard; Recio, Fernando; Roldan, Esther; Rymo, Lars; Wicktorsson, Anne-Charlotte; Welch, Shirley L; Wieland, Heinrich; Grawitz, Andrea Busse; Mitsumaki, Hiroshi; McGovern, Margaret; Ng, Katherine; Stockmann, Wolfgang

    2005-01-01

    MODULAR ANALYTICS (Roche Diagnostics) (MODULAR ANALYTICS, Elecsys and Cobas Integra are trademarks of a member of the Roche Group) represents a new approach to automation for the clinical chemistry laboratory. It consists of a control unit, a core unit with a bidirectional multitrack rack transportation system, and three distinct kinds of analytical modules: an ISE module, a P800 module (44 photometric tests, throughput of up to 800 tests/h), and a D2400 module (16 photometric tests, throughput up to 2400 tests/h). MODULAR ANALYTICS allows customised configurations for various laboratory workloads. The performance and practicability of MODULAR ANALYTICS were evaluated in an international multicentre study at 16 sites. Studies included precision, accuracy, analytical range, carry-over, and workflow assessment. More than 700 000 results were obtained during the course of the study. Median between-day CVs were typically less than 3% for clinical chemistries and less than 6% for homogeneous immunoassays. Median recoveries for nearly all standardised reference materials were within 5% of assigned values. Method comparisons versus current existing routine instrumentation were clinically acceptable in all cases. During the workflow studies, the work from three to four single workstations was transferred to MODULAR ANALYTICS, which offered over 100 possible methods, with reduction in sample splitting, handling errors, and turnaround time. Typical sample processing time on MODULAR ANALYTICS was less than 30 minutes, an improvement from the current laboratory systems. By combining multiple analytic units in flexible ways, MODULAR ANALYTICS met diverse laboratory needs and offered improvement in workflow over current laboratory situations. It increased overall efficiency while maintaining (or improving) quality.

  13. MODULAR ANALYTICS: A New Approach to Automation in the Clinical Laboratory

    PubMed Central

    Zaman, Zahur; Blanckaert, Norbert J. C.; Chan, Daniel W.; Dubois, Jeffrey A.; Golaz, Olivier; Mensi, Noury; Keller, Franz; Stolz, Herbert; Klingler, Karl; Marocchi, Alessandro; Prencipe, Lorenzo; McLawhon, Ronald W.; Nilsen, Olaug L.; Oellerich, Michael; Luthe, Hilmar; Orsonneau, Jean-Luc; Richeux, Gérard; Recio, Fernando; Roldan, Esther; Rymo, Lars; Wicktorsson, Anne-Charlotte; Welch, Shirley L.; Wieland, Heinrich; Grawitz, Andrea Busse; Mitsumaki, Hiroshi; McGovern, Margaret; Ng, Katherine; Stockmann, Wolfgang

    2005-01-01

    MODULAR ANALYTICS (Roche Diagnostics) (MODULAR ANALYTICS, Elecsys and Cobas Integra are trademarks of a member of the Roche Group) represents a new approach to automation for the clinical chemistry laboratory. It consists of a control unit, a core unit with a bidirectional multitrack rack transportation system, and three distinct kinds of analytical modules: an ISE module, a P800 module (44 photometric tests, throughput of up to 800 tests/h), and a D2400 module (16 photometric tests, throughput up to 2400 tests/h). MODULAR ANALYTICS allows customised configurations for various laboratory workloads. The performance and practicability of MODULAR ANALYTICS were evaluated in an international multicentre study at 16 sites. Studies included precision, accuracy, analytical range, carry-over, and workflow assessment. More than 700 000 results were obtained during the course of the study. Median between-day CVs were typically less than 3% for clinical chemistries and less than 6% for homogeneous immunoassays. Median recoveries for nearly all standardised reference materials were within 5% of assigned values. Method comparisons versus current existing routine instrumentation were clinically acceptable in all cases. During the workflow studies, the work from three to four single workstations was transferred to MODULAR ANALYTICS, which offered over 100 possible methods, with reduction in sample splitting, handling errors, and turnaround time. Typical sample processing time on MODULAR ANALYTICS was less than 30 minutes, an improvement from the current laboratory systems. By combining multiple analytic units in flexible ways, MODULAR ANALYTICS met diverse laboratory needs and offered improvement in workflow over current laboratory situations. It increased overall efficiency while maintaining (or improving) quality. PMID:18924721

  14. Applications of Spacelab Payload Standard Modular Electronics /SPSME/

    NASA Technical Reports Server (NTRS)

    Wilkinson, D. D.; Kasulka, L. H.

    1980-01-01

    The NASA sponsored Spacelab Payload Standard Modular Electronics program has been designed with the basic objective of providing a space-qualified set of standardized modular electronics to support investigations identified for Spacelab payloads. These units are reusable, have functional, physical, and interface characteristics which allow them to be conveniently assembled in a multitude of configurations, and functionally interchangeable with their ground-based equivalents. The interfacing and control modules are described and typical hardware applications are presented.

  15. Progress toward Modular UAS for Geoscience Applications

    NASA Astrophysics Data System (ADS)

    Dahlgren, R. P.; Clark, M. A.; Comstock, R. J.; Fladeland, M.; Gascot, H., III; Haig, T. H.; Lam, S. J.; Mazhari, A. A.; Palomares, R. R.; Pinsker, E. A.; Prathipati, R. T.; Sagaga, J.; Thurling, J. S.; Travers, S. V.

    2017-12-01

    Small Unmanned Aerial Systems (UAS) have become accepted tools for geoscience, ecology, agriculture, disaster response, land management, and industry. A variety of consumer UAS options exist as science and engineering payload platforms, but their incompatibilities with one another contribute to high operational costs compared with those of piloted aircraft. This research explores the concept of modular UAS, demonstrating airframes that can be reconfigured in the field for experimental optimization, to enable multi-mission support, facilitate rapid repair, or respond to changing field conditions. Modular UAS is revolutionary in allowing aircraft to be optimized around the payload, reversing the conventional wisdom of designing the payload to accommodate an unmodifiable aircraft. UAS that are reconfigurable like Legos™ are ideal for airborne science service providers, system integrators, instrument designers and end users to fulfill a wide range of geoscience experiments. Modular UAS facilitate the adoption of open-source software and rapid prototyping technology where design reuse is important in the context of a highly regulated industry like aerospace. The industry is now at a stage where consolidation, acquisition, and attrition will reduce the number of small manufacturers, with a reduction of innovation and motivation to reduce costs. Modularity leads to interface specifications, which can evolve into de facto or formal standards which contain minimum (but sufficient) details such that multiple vendors can then design to those standards and demonstrate interoperability. At that stage, vendor coopetition leads to robust interface standards, interoperability standards and multi-source agreements which in turn drive costs down significantly.

  16. Lay Health Influencers: How They Tailor Brief Tobacco Cessation Interventions

    ERIC Educational Resources Information Center

    Yuan, Nicole P.; Castaneda, Heide; Nichter, Mark; Nichter, Mimi; Wind, Steven; Carruth, Lauren; Muramoto, Myra

    2012-01-01

    Interventions tailored to individual smoker characteristics have increasingly received attention in the tobacco control literature. The majority of tailored interventions are generated by computers and administered with printed materials or web-based programs. The purpose of this study was to examine the tailoring activities of community lay…

  17. Episodic Memory Retrieval Benefits from a Less Modular Brain Network Organization.

    PubMed

    Westphal, Andrew J; Wang, Siliang; Rissman, Jesse

    2017-03-29

    Most complex cognitive tasks require the coordinated interplay of multiple brain networks, but the act of retrieving an episodic memory may place especially heavy demands for communication between the frontoparietal control network (FPCN) and the default mode network (DMN), two networks that do not strongly interact with one another in many task contexts. We applied graph theoretical analysis to task-related fMRI functional connectivity data from 20 human participants and found that global brain modularity-a measure of network segregation-is markedly reduced during episodic memory retrieval relative to closely matched analogical reasoning and visuospatial perception tasks. Individual differences in modularity were correlated with memory task performance, such that lower modularity levels were associated with a lower false alarm rate. Moreover, the FPCN and DMN showed significantly elevated coupling with each other during the memory task, which correlated with the global reduction in brain modularity. Both networks also strengthened their functional connectivity with the hippocampus during the memory task. Together, these results provide a novel demonstration that reduced modularity is conducive to effective episodic retrieval, which requires close collaboration between goal-directed control processes supported by the FPCN and internally oriented self-referential processing supported by the DMN. SIGNIFICANCE STATEMENT Modularity, an index of the degree to which nodes of a complex system are organized into discrete communities, has emerged as an important construct in the characterization of brain connectivity dynamics. We provide novel evidence that the modularity of the human brain is reduced when individuals engage in episodic memory retrieval, relative to other cognitive tasks, and that this state of lower modularity is associated with improved memory performance. We propose a neural systems mechanism for this finding where the nodes of the frontoparietal control

  18. Small worlds in space: Synchronization, spatial and relational modularity

    NASA Astrophysics Data System (ADS)

    Brede, M.

    2010-06-01

    In this letter we investigate networks that have been optimized to realize a trade-off between enhanced synchronization and cost of wire to connect the nodes in space. Analyzing the evolved arrangement of nodes in space and their corresponding network topology, a class of small-world networks characterized by spatial and network modularity is found. More precisely, for low cost of wire optimal configurations are characterized by a division of nodes into two spatial groups with maximum distance from each other, whereas network modularity is low. For high cost of wire, the nodes organize into several distinct groups in space that correspond to network modules connected on a ring. In between, spatially and relationally modular small-world networks are found.

  19. A modular reactor to simulate biofilm development in orthopedic materials.

    PubMed

    Barros, Joana; Grenho, Liliana; Manuel, Cândida M; Ferreira, Carla; Melo, Luís F; Nunes, Olga C; Monteiro, Fernando J; Ferraz, Maria P

    2013-09-01

    Surfaces of medical implants are generally designed to encourage soft- and/or hard-tissue adherence, eventually leading to tissue- or osseo-integration. Unfortunately, this feature may also encourage bacterial adhesion and biofilm formation. To understand the mechanisms of bone tissue infection associated with contaminated biomaterials, a detailed understanding of bacterial adhesion and subsequent biofilm formation on biomaterial surfaces is needed. In this study, a continuous-flow modular reactor composed of several modular units placed in parallel was designed to evaluate the activity of circulating bacterial suspensions and thus their predilection for biofilm formation during 72 h of incubation. Hydroxyapatite discs were placed in each modular unit and then removed at fixed times to quantify biofilm accumulation. Biofilm formation on each replicate of material, unchanged in structure, morphology, or cell density, was reproducibly observed. The modular reactor therefore proved to be a useful tool for following mature biofilm formation on different surfaces and under conditions similar to those prevailing near human-bone implants.

  20. Adapt Design: A Methodology for Enabling Modular Design for Mission Specific SUAS

    DTIC Science & Technology

    2016-08-24

    ADAPT DESIGN: A METHODOLOGY FOR ENABLING MODULAR DESIGN FOR MISSION SPECIFIC SUAS Zachary C. Fisher David Locascio K. Daniel Cooksey...vehicle’s small scale. This paper considers a different approach to SUAS design aimed at addressing this issue. In this approach, a hybrid modular and...Two types of platforms have been identified: scalable platforms where variants are produced by varying scalable design variables, and modular

  1. Information Tailoring Enhancements for Large-Scale Social Data

    DTIC Science & Technology

    2016-06-15

    Intelligent Automation Incorporated Information Tailoring Enhancements for Large-Scale... Automation Incorporated Progress Report No. 3 Information Tailoring Enhancements for Large-Scale Social Data Submitted in accordance with...1 Work Performed within This Reporting Period .................................................... 2 1.1 Enhanced Named Entity Recognition (NER

  2. Brain Network Modularity Predicts Exercise-Related Executive Function Gains in Older Adults

    PubMed Central

    Baniqued, Pauline L.; Gallen, Courtney L.; Voss, Michelle W.; Burzynska, Agnieszka Z.; Wong, Chelsea N.; Cooke, Gillian E.; Duffy, Kristin; Fanning, Jason; Ehlers, Diane K.; Salerno, Elizabeth A.; Aguiñaga, Susan; McAuley, Edward; Kramer, Arthur F.; D'Esposito, Mark

    2018-01-01

    Recent work suggests that the brain can be conceptualized as a network comprised of groups of sub-networks or modules. The extent of segregation between modules can be quantified with a modularity metric, where networks with high modularity have dense connections within modules and sparser connections between modules. Previous work has shown that higher modularity predicts greater improvements after cognitive training in patients with traumatic brain injury and in healthy older and young adults. It is not known, however, whether modularity can also predict cognitive gains after a physical exercise intervention. Here, we quantified modularity in older adults (N = 128, mean age = 64.74) who underwent one of the following interventions for 6 months (NCT01472744 on ClinicalTrials.gov): (1) aerobic exercise in the form of brisk walking (Walk), (2) aerobic exercise in the form of brisk walking plus nutritional supplement (Walk+), (3) stretching, strengthening and stability (SSS), or (4) dance instruction. After the intervention, the Walk, Walk+ and SSS groups showed gains in cardiorespiratory fitness (CRF), with larger effects in both walking groups compared to the SSS and Dance groups. The Walk, Walk+ and SSS groups also improved in executive function (EF) as measured by reasoning, working memory, and task-switching tests. In the Walk, Walk+, and SSS groups that improved in EF, higher baseline modularity was positively related to EF gains, even after controlling for age, in-scanner motion and baseline EF. No relationship between modularity and EF gains was observed in the Dance group, which did not show training-related gains in CRF or EF control. These results are consistent with previous studies demonstrating that individuals with a more modular brain network organization are more responsive to cognitive training. These findings suggest that the predictive power of modularity may be generalizable across interventions aimed to enhance aspects of cognition and that

  3. Clearing the skies over modular polyketide synthases.

    PubMed

    Sherman, David H; Smith, Janet L

    2006-09-19

    Modular polyketide synthases (PKSs) are large multifunctional proteins that synthesize complex polyketide metabolites in microbial cells. A series of recent studies confirm the close protein structural relationship between catalytic domains in the type I mammalian fatty acid synthase (FAS) and the basic synthase unit of the modular PKS. They also establish a remarkable similarity in the overall organization of the type I FAS and the PKS module. This information provides important new conclusions about catalytic domain architecture, function, and molecular recognition that are essential for future efforts to engineer useful polyketide metabolites with valuable biological activities.

  4. Modular shield

    DOEpatents

    Snyder, Keith W.

    2002-01-01

    A modular system for containing projectiles has a sheet of material including at least a polycarbonate layer held by a metal frame having a straight frame member corresponding to each straight edge of the sheet. Each frame member has a U-shaped shield channel covering and holding a straight edge of the sheet and an adjacent U-shaped clamp channel rigidly held against the shield channel. A flexible gasket separates each sheet edge from its respective shield channel; and each frame member is fastened to each adjacent frame member only by clamps extending between adjacent clamp channels.

  5. Rapidly Deployed Modular Telemetry System

    NASA Technical Reports Server (NTRS)

    Varnavas, Kosta A. (Inventor); Sims, William Herbert, III (Inventor)

    2013-01-01

    The present invention is a telemetry system, and more specifically is a rapidly deployed modular telemetry apparatus which utilizes of SDR technology and the FPGA programming capability to reduce the number of hardware components and programming required to deploy a telemetry system.

  6. Phage-bacteria infection networks: From nestedness to modularity

    NASA Astrophysics Data System (ADS)

    Flores, Cesar O.; Valverde, Sergi; Weitz, Joshua S.

    2013-03-01

    Bacteriophages (viruses that infect bacteria) are the most abundant biological life-forms on Earth. However, very little is known regarding the structure of phage-bacteria infections. In a recent study we re-evaluated 38 prior studies and demonstrated that phage-bacteria infection networks tend to be statistically nested in small scale communities (Flores et al 2011). Nestedness is consistent with a hierarchy of infection and resistance within phages and bacteria, respectively. However, we predicted that at large scales, phage-bacteria infection networks should be typified by a modular structure. We evaluate and confirm this hypothesis using the most extensive study of phage-bacteria infections (Moebus and Nattkemper 1981). In this study, cross-infections were evaluated between 215 marine phages and 286 marine bacteria. We develop a novel multi-scale network analysis and find that the Moebus and Nattkemper (1981) study, is highly modular (at the whole network scale), yet also exhibits nestedness and modularity at the within-module scale. We examine the role of geography in driving these modular patterns and find evidence that phage-bacteria interactions can exhibit strong similarity despite large distances between sites. CFG acknowledges the support of CONACyT Foundation. JSW holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and acknowledges the support of the James S. McDonnell Foundation

  7. Modular Flooring System

    NASA Technical Reports Server (NTRS)

    Thate, Robert

    2012-01-01

    The modular flooring system (MFS) was developed to provide a portable, modular, durable carpeting solution for NASA fs Robotics Alliance Project fs (RAP) outreach efforts. It was also designed to improve and replace a modular flooring system that was too heavy for safe use and transportation. The MFS was developed for use as the flooring for various robotics competitions that RAP utilizes to meet its mission goals. One of these competitions, the FIRST Robotics Competition (FRC), currently uses two massive rolls of broadloom carpet for the foundation of the arena in which the robots are contained during the competition. The area of the arena is approximately 30 by 72 ft (approximately 9 by 22 m). This carpet is very cumbersome and requires large-capacity vehicles, and handling equipment and personnel to transport and deploy. The broadloom carpet sustains severe abuse from the robots during a regular three-day competition, and as a result, the carpet is not used again for competition. Similarly, broadloom carpets used for trade shows at convention centers around the world are typically discarded after only one use. This innovation provides a green solution to this wasteful practice. Each of the flooring modules in the previous system weighed 44 lb (.20 kg). The improvements in the overall design of the system reduce the weight of each module by approximately 22 lb (.10 kg) (50 %), and utilize an improved "module-to-module" connection method that is superior to the previous system. The MFS comprises 4-by-4-ft (.1.2-by- 1.2-m) carpet module assemblies that utilize commercially available carpet tiles that are bonded to a lightweight substrate. The substrate surface opposite from the carpeted surface has a module-to-module connecting interface that allows for the modules to be connected, one to the other, as the modules are constructed. This connection is hidden underneath the modules, creating a smooth, co-planar flooring surface. The modules are stacked and strapped

  8. Modular biowaste monitoring system conceptual design

    NASA Technical Reports Server (NTRS)

    Fogal, G. L.

    1974-01-01

    The objective of the study was to define requirements and generate a conceptual design for a Modular Biowaste Monitoring System for specifically supporting shuttle life science experimental and diagnostic programs.

  9. Effects of tailoring health messages on physical activity.

    PubMed

    Smeets, Tamara; Brug, J; de Vries, H

    2008-06-01

    Computer-tailored printed education can be a promising way of promoting physical activity. The present study tested whether computer-tailored feedback on physical activity is effective and whether there are differences between respondents with low and high motivation to change. Respondents (n = 487) were randomly assigned to a tailored intervention group or a no information control group. Physical activity and determinants were measured at baseline and after 3 months. At post-test, the motivated respondents in the control group were more likely not to meet the recommendation for physical activity than to meet it, and motivated respondents in the experimental group were more likely to engage in transport-related activities and showed more improvement over time for the total activity score than respondents in the control group (beta = 0.24, P = 0.02). Both groups improved their behaviour over time. No group differences in physical activity were found for the unmotivated respondents. The results showed that the effects of the tailored feedback were restricted to respondents who had a positive motivation to change at baseline. Possible explanations could be that unmotivated respondents were unwilling to read and process the information because they felt 'no need to change'. Alternatively, one tailored feedback letter may not have been sufficient for this unmotivated group.

  10. Contour interpolation: A case study in Modularity of Mind.

    PubMed

    Keane, Brian P

    2018-05-01

    In his monograph Modularity of Mind (1983), philosopher Jerry Fodor argued that mental architecture can be partly decomposed into computational organs termed modules, which were characterized as having nine co-occurring features such as automaticity, domain specificity, and informational encapsulation. Do modules exist? Debates thus far have been framed very generally with few, if any, detailed case studies. The topic is important because it has direct implications on current debates in cognitive science and because it potentially provides a viable framework from which to further understand and make hypotheses about the mind's structure and function. Here, the case is made for the modularity of contour interpolation, which is a perceptual process that represents non-visible edges on the basis of how surrounding visible edges are spatiotemporally configured. There is substantial evidence that interpolation is domain specific, mandatory, fast, and developmentally well-sequenced; that it produces representationally impoverished outputs; that it relies upon a relatively fixed neural architecture that can be selectively impaired; that it is encapsulated from belief and expectation; and that its inner workings cannot be fathomed through conscious introspection. Upon differentiating contour interpolation from a higher-order contour representational ability ("contour abstraction") and upon accommodating seemingly inconsistent experimental results, it is argued that interpolation is modular to the extent that the initiating conditions for interpolation are strong. As interpolated contours become more salient, the modularity features emerge. The empirical data, taken as a whole, show that at least certain parts of the mind are modularly organized. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. Tailoring of EIA-649-1: Definition of Major (Class I) Engineering Change Proposal

    DTIC Science & Technology

    2015-05-15

    MISSILE SYSTEMS CENTER TAILORING TAILORING OF EIA -649-1: DEFINITION OF MAJOR (CLASS I) ENGINEERING CHANGE PROPOSAL APPROVED FOR...PUBLIC RELEASE; DISTRIBUTION IS UNLIMITED 1 Tailoring of EIA -649-1: Definition of Major (Class I) ECP. 1. Intent of this Tailoring Document...This tailoring document remedies a requirements gap in the industry consensus standard, EIA -649-1: 2015. Specifically, this tailoring provides a

  12. Finding specific RNA motifs: Function in a zeptomole world?

    PubMed Central

    KNIGHT, ROB; YARUS, MICHAEL

    2003-01-01

    We have developed a new method for estimating the abundance of any modular (piecewise) RNA motif within a longer random region. We have used this method to estimate the size of the active motifs available to modern SELEX experiments (picomoles of unique sequences) and to a plausible RNA World (zeptomoles of unique sequences: 1 zmole = 602 sequences). Unexpectedly, activities such as specific isoleucine binding are almost certainly present in zeptomoles of molecules, and even ribozymes such as self-cleavage motifs may appear (depending on assumptions about the minimal structures). The number of specified nucleotides is not the only important determinant of a motif’s rarity: The number of modules into which it is divided, and the details of this division, are also crucial. We propose three maxims for easily isolated motifs: the Maxim of Minimization, the Maxim of Multiplicity, and the Maxim of the Median. These maxims together state that selected motifs should be small and composed of as many separate, equally sized modules as possible. For evenly divided motifs with four modules, the largest accessible activity in picomole scale (1–1000 pmole) pools of length 100 is about 34 nucleotides; while for zeptomole scale (1–1000 zmole) pools it is about 20 specific nucleotides (50% probability of occurrence). This latter figure includes some ribozymes and aptamers. Consequently, an RNA metabolism apparently could have begun with only zeptomoles of RNA molecules. PMID:12554865

  13. Modular invariant representations of infinite-dimensional Lie algebras and superalgebras

    PubMed Central

    Kac, Victor G.; Wakimoto, Minoru

    1988-01-01

    In this paper, we launch a program to describe and classify modular invariant representations of infinite-dimensional Lie algebras and superalgebras. We prove a character formula for a large class of highest weight representations L(λ) of a Kac-Moody algebra [unk] with a symmetrizable Cartan matrix, generalizing the Weyl-Kac character formula [Kac, V. G. (1974) Funct. Anal. Appl. 8, 68-70]. In the case of an affine [unk], this class includes modular invariant representations of arbitrary rational level m = t/u, where t [unk] Z and u [unk] N are relatively prime and m + g ≥ g/u (g is the dual Coxeter number). We write the characters of these representations in terms of theta functions and calculate their asymptotics, generalizing the results of Kac and Peterson [Kac, V. G. & Peterson, D. H. (1984) Adv. Math. 53, 125-264] and of Kac and Wakimoto [Kac, V. G. & Wakimoto, M. (1988) Adv. Math. 70, 156-234] for the u = 1 (integrable) case. We work out in detail the case [unk] = A1(1), in particular classifying all its modular invariant representations. Furthermore, we show that the modular invariant representations of the Virasoro algebra Vir are precisely the “minimal series” of Belavin et al. [Belavin, A. A., Polyakov, A. M. & Zamolodchikov, A. B. (1984) Nucl. Phys. B 241, 333-380] using the character formulas of Feigin and Fuchs [Feigin, B. L. & Fuchs, D. B. (1984) Lect. Notes Math. 1060, 230-245]. We show that tensoring the basic representation and modular invariant representations of A1(1) produces all modular invariant representations of Vir generalizing the results of Goddard et al. [Goddard P., Kent, A. & Olive, D. (1986) Commun. Math. Phys. 103, 105-119] and of Kac and Wakimoto [Kac, V. G. & Wakimoto, M. (1986) Lect. Notes Phys. 261, 345-371] in the unitary case. We study the general branching functions as well. All these results are generalized to the Kac-Moody superalgebras introduced by Kac [Kac, V. G. (1978) Adv. Math. 30, 85-136] and to N = 1 super

  14. Stratway: A Modular Approach to Strategic Conflict Resolution

    NASA Technical Reports Server (NTRS)

    Hagen, George E.; Butler, Ricky W.; Maddalon, Jeffrey M.

    2011-01-01

    In this paper we introduce Stratway, a modular approach to finding long-term strategic resolutions to conflicts between aircraft. The modular approach provides both advantages and disadvantages. Our primary concern is to investigate the implications on the verification of safety-critical properties of a strategic resolution algorithm. By partitioning the problem into verifiable modules much stronger verification claims can be established. Since strategic resolution involves searching for solutions over an enormous state space, Stratway, like most similar algorithms, searches these spaces by applying heuristics, which present especially difficult verification challenges. An advantage of a modular approach is that it makes a clear distinction between the resolution function and the trajectory generation function. This allows the resolution computation to be independent of any particular vehicle. The Stratway algorithm was developed in both Java and C++ and is available through a open source license. Additionally there is a visualization application that is helpful when analyzing and quickly creating conflict scenarios.

  15. In C. elegans, high levels of dsRNA allow RNAi in the absence of RDE-4.

    PubMed

    Habig, Jeffrey W; Aruscavage, P Joseph; Bass, Brenda L

    2008-01-01

    C. elegans Dicer requires an accessory double-stranded RNA binding protein, RDE-4, to enact the first step of RNA interference, the cleavage of dsRNA to produce siRNA. While RDE-4 is typically essential for RNAi, we report that in the presence of high concentrations of trigger dsRNA, rde-4 deficient animals are capable of silencing a transgene. By multiple criteria the silencing occurs by the canonical RNAi pathway. For example, silencing is RDE-1 dependent and exhibits a decrease in the targeted mRNA in response to an increase in siRNA. We also find that high concentrations of dsRNA trigger lead to increased accumulation of primary siRNAs, consistent with the existence of a rate-limiting step during the conversion of primary to secondary siRNAs. Our studies also revealed that transgene silencing occurs at low levels in the soma, even in the presence of ADARs, and that at least some siRNAs accumulate in a temperature-dependent manner. We conclude that an RNAi response varies with different conditions, and this may allow an organism to tailor a response to specific environmental signals.

  16. In C. elegans, High Levels of dsRNA Allow RNAi in the Absence of RDE-4

    PubMed Central

    Habig, Jeffrey W.; Aruscavage, P. Joseph; Bass, Brenda L.

    2008-01-01

    C. elegans Dicer requires an accessory double-stranded RNA binding protein, RDE-4, to enact the first step of RNA interference, the cleavage of dsRNA to produce siRNA. While RDE-4 is typically essential for RNAi, we report that in the presence of high concentrations of trigger dsRNA, rde-4 deficient animals are capable of silencing a transgene. By multiple criteria the silencing occurs by the canonical RNAi pathway. For example, silencing is RDE-1 dependent and exhibits a decrease in the targeted mRNA in response to an increase in siRNA. We also find that high concentrations of dsRNA trigger lead to increased accumulation of primary siRNAs, consistent with the existence of a rate-limiting step during the conversion of primary to secondary siRNAs. Our studies also revealed that transgene silencing occurs at low levels in the soma, even in the presence of ADARs, and that at least some siRNAs accumulate in a temperature-dependent manner. We conclude that an RNAi response varies with different conditions, and this may allow an organism to tailor a response to specific environmental signals. PMID:19112503

  17. MACOP modular architecture with control primitives

    PubMed Central

    Waegeman, Tim; Hermans, Michiel; Schrauwen, Benjamin

    2013-01-01

    Walking, catching a ball and reaching are all tasks in which humans and animals exhibit advanced motor skills. Findings in biological research concerning motor control suggest a modular control hierarchy which combines movement/motor primitives into complex and natural movements. Engineers inspire their research on these findings in the quest for adaptive and skillful control for robots. In this work we propose a modular architecture with control primitives (MACOP) which uses a set of controllers, where each controller becomes specialized in a subregion of its joint and task-space. Instead of having a single controller being used in this subregion [such as MOSAIC (modular selection and identification for control) on which MACOP is inspired], MACOP relates more to the idea of continuously mixing a limited set of primitive controllers. By enforcing a set of desired properties on the mixing mechanism, a mixture of primitives emerges unsupervised which successfully solves the control task. We evaluate MACOP on a numerical model of a robot arm by training it to generate desired trajectories. We investigate how the tracking performance is affected by the number of controllers in MACOP and examine how the individual controllers and their generated control primitives contribute to solving the task. Furthermore, we show how MACOP compensates for the dynamic effects caused by a fixed control rate and the inertia of the robot. PMID:23888140

  18. BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction.

    PubMed

    Townsley, Brad T; Covington, Michael F; Ichihashi, Yasunori; Zumstein, Kristina; Sinha, Neelima R

    2015-01-01

    Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

  19. Miniature modular microwave end-to-end receiver

    NASA Technical Reports Server (NTRS)

    Sukamto, Lin M. (Inventor); Cooley, Thomas W. (Inventor); Janssen, Michael A. (Inventor); Parks, Gary S. (Inventor)

    1993-01-01

    An end-to-end microwave receiver system contained in a single miniature hybrid package mounted on a single heatsink is presented. It includes an input end connected to a microwave receiver antenna and an output end which produces a digital count proportional to the amplitude of a signal of a selected microwave frequency band received at the antenna and corresponding to one of the water vapor absorption lines near frequencies of 20 GHz or 30 GHz. The hybrid package is on the order of several centimeters in length and a few centimeters in height and width. The package includes an L-shaped carrier having a base surface, a vertical wall extending up from the base surface and forming a corner therewith, and connection pins extending through the vertical wall. Modular blocks rest on the base surface against the vertical wall and support microwave monolithic integrated circuits on top surfaces thereof connected to the external connection pins. The modular blocks lie end-to-end on the base surface so as to be modularly removable by sliding along the base surface beneath the external connection pins away from the vertical wall.

  20. Space biology initiative program definition review. Trade study 4: Design modularity and commonality

    NASA Technical Reports Server (NTRS)

    Jackson, L. Neal; Crenshaw, John, Sr.; Davidson, William L.; Herbert, Frank J.; Bilodeau, James W.; Stoval, J. Michael; Sutton, Terry

    1989-01-01

    The relative cost impacts (up or down) of developing Space Biology hardware using design modularity and commonality is studied. Recommendations for how the hardware development should be accomplished to meet optimum design modularity requirements for Life Science investigation hardware will be provided. In addition, the relative cost impacts of implementing commonality of hardware for all Space Biology hardware are defined. Cost analysis and supporting recommendations for levels of modularity and commonality are presented. A mathematical or statistical cost analysis method with the capability to support development of production design modularity and commonality impacts to parametric cost analysis is provided.

  1. On the role of sparseness in the evolution of modularity in gene regulatory networks

    PubMed Central

    2018-01-01

    Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology. One hypothesis for the evolution of modules suggests that interactions between some sets of genes become maladaptive when selection favours additional gene activity patterns. The removal of such interactions by selection would result in the formation of modules. A second hypothesis suggests that modularity evolves in response to sparseness, the scarcity of interactions within a system. Here I simulate the evolution of gene regulatory networks and analyse diverse experimentally sustained networks to study the relationship between sparseness and modularity. My results suggest that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, sparseness amplifies the effects of forms of selection that, like selection for additional gene activity patterns, already produce an increase in modularity. That evolution of new gene activity patterns is frequent across evolution also supports that it is a major factor in the evolution of modularity. That sparseness is widespread across gene regulatory networks indicates that it may have facilitated the evolution of modules in a wide variety of cases. PMID:29775459

  2. On the role of sparseness in the evolution of modularity in gene regulatory networks.

    PubMed

    Espinosa-Soto, Carlos

    2018-05-01

    Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology. One hypothesis for the evolution of modules suggests that interactions between some sets of genes become maladaptive when selection favours additional gene activity patterns. The removal of such interactions by selection would result in the formation of modules. A second hypothesis suggests that modularity evolves in response to sparseness, the scarcity of interactions within a system. Here I simulate the evolution of gene regulatory networks and analyse diverse experimentally sustained networks to study the relationship between sparseness and modularity. My results suggest that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, sparseness amplifies the effects of forms of selection that, like selection for additional gene activity patterns, already produce an increase in modularity. That evolution of new gene activity patterns is frequent across evolution also supports that it is a major factor in the evolution of modularity. That sparseness is widespread across gene regulatory networks indicates that it may have facilitated the evolution of modules in a wide variety of cases.

  3. Comparison of alternative approaches for analysing multi-level RNA-seq data

    PubMed Central

    Mohorianu, Irina; Bretman, Amanda; Smith, Damian T.; Fowler, Emily K.; Dalmay, Tamas

    2017-01-01

    RNA sequencing (RNA-seq) is widely used for RNA quantification in the environmental, biological and medical sciences. It enables the description of genome-wide patterns of expression and the identification of regulatory interactions and networks. The aim of RNA-seq data analyses is to achieve rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite variation in levels of noise and inherent biases in sequencing data. This can be especially challenging for datasets in which gene expression differences are subtle, as in the behavioural transcriptomics test dataset from D. melanogaster that we used here. We investigated the power of existing approaches for quality checking mRNA-seq data and explored additional, quantitative quality checks. To accommodate nested, multi-level experimental designs, we incorporated sample layout into our analyses. We employed a subsampling without replacement-based normalization and an identification of DE that accounted for the hierarchy and amplitude of effect sizes within samples, then evaluated the resulting differential expression call in comparison to existing approaches. In a final step to test for broader applicability, we applied our approaches to a published set of H. sapiens mRNA-seq samples, The dataset-tailored methods improved sample comparability and delivered a robust prediction of subtle gene expression changes. The proposed approaches have the potential to improve key steps in the analysis of RNA-seq data by incorporating the structure and characteristics of biological experiments. PMID:28792517

  4. Web-based tailored nutrition education: results of a randomized controlled trial.

    PubMed

    Oenema, A; Brug, J; Lechner, L

    2001-12-01

    There is ample evidence that printed, computer-tailored nutrition education is a more effective tool for motivating people to change to healthier diets than general nutrition education. New technology is now providing more advanced ways of delivering tailored messages, e.g. via the World Wide Web (WWW). Before disseminating a tailored intervention via the web, it is important to investigate the potential of web-based tailored nutrition education. The present study investigated the immediate impact of web-based computer-tailored nutrition education on personal awareness and intentions related to intake of fat, fruit and vegetables. A randomized controlled trial, with a pre-test-post-test control group design was conducted. Significant differences in awareness and intention to change were found between the intervention and control group at post-test. The tailored intervention was appreciated better, was rated as more personally relevant, and had more subjective impact on opinion and intentions to change than the general nutrition information. Computer literacy had no effect on these ratings. The results indicate that interactive, web-based computer-tailored nutrition education can lead to changes in determinants of behavior. Future research should be aimed at longer-term (behavioral) effects and the practicability of distributing tailored interventions via the WWW.

  5. The modular socket system in a rural setting in Indonesia.

    PubMed

    Giesberts, Bob; Ennion, Liezel; Hjelmstrom, Olle; Karma, Agusni; Lechler, Knut; Hekman, Edsko; Bergsma, Arjen

    2018-06-01

    Prosthetic services are inaccessible to people living in rural areas. Systems like the modular socket system have the potential to be fabricated outside of the prosthetic workshop. This study aimed to evaluate the patient's performance and satisfaction with the use of the modular socket system, and the technical feasibility of its implementation in a rural setting. A quantitative longitudinal descriptive study design was followed. A total of 15 persons with a lower limb amputation were fitted with the modular socket system and followed over 4-6 months. Performance was measured using a 2-min walk test, 10-m walk test and mobility and function questionnaire. Satisfaction was measured by the Socket Fit Comfort Score, Prosthesis Evaluation Questionnaire and EuroQoL 5 Dimensions 5 Levels. Notes on technical feasibility were taken at the moment of fitting ( t 0 ), at 1-3 months post fitting ( t 1 ) and at the end evaluation at 4-6 months post fitting ( t 2 ). Performance did not change between t 0 and t 2 . The comfort of the socket fit reduced between t 0 and t 2 . Satisfaction with prosthesis and general health status stayed constant over time. The average fitting-time for the modular socket system was 6.4 h. The modular socket system can be considered a useful alternative for use in rural settings. Clinical relevance The use of the modular socket system is feasible and can improve accessibility to prosthetic technology in rural areas. Experienced prosthetic users were satisfied with the performance and the device. The shorter manufacturing time and use of only hand-held tools makes it an ideal alternative for use in remote and rural settings.

  6. Metal Matrix Laminate Tailoring (MMLT) code: User's manual

    NASA Technical Reports Server (NTRS)

    Murthy, P. L. N.; Morel, M. R.; Saravanos, D. A.

    1993-01-01

    The User's Manual for the Metal Matrix Laminate Tailoring (MMLT) program is presented. The code is capable of tailoring the fabrication process, constituent characteristics, and laminate parameters (individually or concurrently) for a wide variety of metal matrix composite (MMC) materials, to improve the performance and identify trends or behavior of MMC's under different thermo-mechanical loading conditions. This document is meant to serve as a guide in the use of the MMLT code. Detailed explanations of the composite mechanics and tailoring analysis are beyond the scope of this document, and may be found in the references. MMLT was developed by the Structural Mechanics Branch at NASA Lewis Research Center (LeRC).

  7. Quantum plug n’ play: modular computation in the quantum regime

    NASA Astrophysics Data System (ADS)

    Thompson, Jayne; Modi, Kavan; Vedral, Vlatko; Gu, Mile

    2018-01-01

    Classical computation is modular. It exploits plug n’ play architectures which allow us to use pre-fabricated circuits without knowing their construction. This bestows advantages such as allowing parts of the computational process to be outsourced, and permitting individual circuit components to be exchanged and upgraded. Here, we introduce a formal framework to describe modularity in the quantum regime. We demonstrate a ‘no-go’ theorem, stipulating that it is not always possible to make use of quantum circuits without knowing their construction. This has significant consequences for quantum algorithms, forcing the circuit implementation of certain quantum algorithms to be rebuilt almost entirely from scratch after incremental changes in the problem—such as changing the number being factored in Shor’s algorithm. We develop a workaround capable of restoring modularity, and apply it to design a modular version of Shor’s algorithm that exhibits increased versatility and reduced complexity. In doing so we pave the way to a realistic framework whereby ‘quantum chips’ and remote servers can be invoked (or assembled) to implement various parts of a more complex quantum computation.

  8. Neural correlates of message tailoring and self-relatedness in smoking cessation programming.

    PubMed

    Chua, Hannah Faye; Liberzon, Israel; Welsh, Robert C; Strecher, Victor J

    2009-01-15

    Smoking leads to illnesses including addiction, cancer, and cardiovascular and respiratory diseases. Different intervention programs have become available. In the past decade, providing tailored smoking cessation messages has been shown to be more effective in inducing smoking cessation than one-size-fits-all interventions. However, little is known about the brain responses of smokers when they receive tailored smoking cessation messages. A neuroimaging study using blocked and event-related designs examined neural activity in 24 smokers exposed to high-tailored and low-tailored smoking cessation messages. In both blocked and event-related conditions, rostral medial prefrontal cortex and precuneus/posterior cingulate were engaged more during the processing of high-tailored smoking cessation messages than low-tailored smoking cessation messages. The activation patterns of smokers to tailored cessation messages show involvement of brain areas commonly implicated in self-related processing. Results seem to add support to the suggested role of self-relevance in tailored cessation programs, where previous studies have shown a potential mediating role of self-relevance on smoking abstinence. The findings are relevant to understanding the cognitive mechanisms underlying tailored message processing and might point to new directions for testing response to health communications programming.

  9. Simulation of value stream mapping and discrete optimization of energy consumption in modular construction

    NASA Astrophysics Data System (ADS)

    Chowdhury, Md Mukul

    With the increased practice of modularization and prefabrication, the construction industry gained the benefits of quality management, improved completion time, reduced site disruption and vehicular traffic, and improved overall safety and security. Whereas industrialized construction methods, such as modular and manufactured buildings, have evolved over decades, core techniques used in prefabrication plants vary only slightly from those employed in traditional site-built construction. With a focus on energy and cost efficient modular construction, this research presents the development of a simulation, measurement and optimization system for energy consumption in the manufacturing process of modular construction. The system is based on Lean Six Sigma principles and loosely coupled system operation to identify the non-value adding tasks and possible causes of low energy efficiency. The proposed system will also include visualization functions for demonstration of energy consumption in modular construction. The benefits of implementing this system include a reduction in the energy consumption in production cost, decrease of energy cost in the production of lean-modular construction, and increase profit. In addition, the visualization functions will provide detailed information about energy efficiency and operation flexibility in modular construction. A case study is presented to validate the reliability of the system.

  10. Versatile microrobotics using simple modular subunits

    NASA Astrophysics Data System (ADS)

    Cheang, U. Kei; Meshkati, Farshad; Kim, Hoyeon; Lee, Kyoungwoo; Fu, Henry Chien; Kim, Min Jun

    2016-07-01

    The realization of reconfigurable modular microrobots could aid drug delivery and microsurgery by allowing a single system to navigate diverse environments and perform multiple tasks. So far, microrobotic systems are limited by insufficient versatility; for instance, helical shapes commonly used for magnetic swimmers cannot effectively assemble and disassemble into different size and shapes. Here by using microswimmers with simple geometries constructed of spherical particles, we show how magnetohydrodynamics can be used to assemble and disassemble modular microrobots with different physical characteristics. We develop a mechanistic physical model that we use to improve assembly strategies. Furthermore, we experimentally demonstrate the feasibility of dynamically changing the physical properties of microswimmers through assembly and disassembly in a controlled fluidic environment. Finally, we show that different configurations have different swimming properties by examining swimming speed dependence on configuration size.

  11. A Modular Set of Mixed Reality Simulators for Blind and Guided Procedures

    DTIC Science & Technology

    2016-08-01

    AWARD NUMBER: W81XWH-14-1-0113 TITLE: A Modular Set of Mixed Reality Simulators for “blind” and Guided Procedures PRINCIPAL INVESTIGATOR...2015 – 07/31/2016 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER A Modular Set of Mixed Reality Simulators for “Blind” and Guided Procedures 5b...editor developed to facilitate creation by non-technical educators of ITs for the set of modular simulators, (c) a curriculum for self-study and self

  12. Redefining the modular organization of the core Mediator complex.

    PubMed

    Wang, Xuejuan; Sun, Qianqian; Ding, Zhenrui; Ji, Jinhua; Wang, Jianye; Kong, Xiao; Yang, Jianghong; Cai, Gang

    2014-07-01

    The Mediator complex plays an essential role in the regulation of eukaryotic transcription. The Saccharomyces cerevisiae core Mediator comprises 21 subunits, which are organized into Head, Middle and Tail modules. Previously, the Head module was assigned to a distinct dense domain at the base, and the Middle and Tail modules were identified to form a tight structure above the Head module, which apparently contradicted findings from many biochemical and functional studies. Here, we compared the structures of the core Mediator and its subcomplexes, especially the first 3D structure of the Head + Middle modules, which permitted an unambiguous assignment of the three modules. Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base. The new modular model of the core Mediator has reconciled the previous inconsistencies between the structurally and functionally defined Mediator modules. Collectively, these analyses completely redefine the modular organization of the core Mediator, which allow us to integrate the structural and functional information into a coherent mechanism for the Mediator's modularity and regulation in transcription initiation.

  13. Redefining the modular organization of the core Mediator complex

    PubMed Central

    Wang, Xuejuan; Sun, Qianqian; Ding, Zhenrui; Ji, Jinhua; Wang, Jianye; Kong, Xiao; Yang, Jianghong; Cai, Gang

    2014-01-01

    The Mediator complex plays an essential role in the regulation of eukaryotic transcription. The Saccharomyces cerevisiae core Mediator comprises 21 subunits, which are organized into Head, Middle and Tail modules. Previously, the Head module was assigned to a distinct dense domain at the base, and the Middle and Tail modules were identified to form a tight structure above the Head module, which apparently contradicted findings from many biochemical and functional studies. Here, we compared the structures of the core Mediator and its subcomplexes, especially the first 3D structure of the Head + Middle modules, which permitted an unambiguous assignment of the three modules. Furthermore, nanogold labeling pinpointing four Mediator subunits from different modules conclusively validated the modular assignment, in which the Head and Middle modules fold back on one another and form the upper portion of the core Mediator, while the Tail module forms a distinct dense domain at the base. The new modular model of the core Mediator has reconciled the previous inconsistencies between the structurally and functionally defined Mediator modules. Collectively, these analyses completely redefine the modular organization of the core Mediator, which allow us to integrate the structural and functional information into a coherent mechanism for the Mediator's modularity and regulation in transcription initiation. PMID:24810298

  14. Modular assembly for supporting, straining, and directing flow to a core in a nuclear reactor

    DOEpatents

    Pennell, William E.

    1977-01-01

    A reactor core support arrangement for supporting, straining, and providing fluid flow to the core and periphery of a nuclear reactor during normal operation. A plurality of removable inlet modular units are contained within permanent liners in the lower supporting plate of the reactor vessel lower internals. During normal operation (1) each inlet modular unit directs main coolant flow to a plurality of core assemblies, the latter being removably supported in receptacles in the upper portion of the modular unit and (2) each inlet modular unit may direct bypass flow to a low pressure annular region of the reactor vessel. Each inlet modular unit may include special fluid seals interposed between mating surfaces of the inlet modular units and the core assemblies and between the inlet modular units and the liners, to minimize leakage and achieve an hydraulic balance. Utilizing the hydraulic balance, the modular units are held in the liners and the assemblies are held in the modular unit receptacles by their own respective weight. Included as part of the permanent liners below the horizontal support plate are generally hexagonal axial debris barriers. The axial debris barriers collectively form a bottom boundary of a secondary high pressure plenum, the upper boundary of which is the bottom surface of the horizontal support plate. Peripheral liners include radial debris barriers which collectively form a barrier against debris entry radially. During normal operation primary coolant inlet openings in the liner, below the axial debris barriers, pass a large amount of coolant into the inlet modular units, and secondary coolant inlet openings in the portion of the liners within the secondary plenum pass a small amount of coolant into the inlet modular units. The secondary coolant inlet openings also provide alternative coolant inlet flow paths in the unlikely event of blockage of the primary inlet openings. The primary inlet openings have characteristics which limit the

  15. Sambot II: A self-assembly modular swarm robot

    NASA Astrophysics Data System (ADS)

    Zhang, Yuchao; Wei, Hongxing; Yang, Bo; Jiang, Cancan

    2018-04-01

    The new generation of self-assembly modular swarm robot Sambot II, based on the original generation of self-assembly modular swarm robot Sambot, adopting laser and camera module for information collecting, is introduced in this manuscript. The visual control algorithm of Sambot II is detailed and feasibility of the algorithm is verified by the laser and camera experiments. At the end of this manuscript, autonomous docking experiments of two Sambot II robots are presented. The results of experiments are showed and analyzed to verify the feasibility of whole scheme of Sambot II.

  16. French Modular Impoundment: Final Cost and Performance Evaluation

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

    Drown, Peter; French, Bill

    This report comprises the Final Cost and Performance Report for the Department of Energy Award # EE0007244, the French Modular Impoundment (aka the “French Dam”.) The French Dam is a system of applying precast modular construction to water control structures. The “French Dam” is a term used to cover the construction means/methods used to construct or rehabilitate dams, diversion structures, powerhouses, and other hydraulic structures which impound water and are covered under FDE’s existing IP (Patents # US8414223B2; US9103084B2.)

  17. Modularity, quaternion-Kähler spaces, and mirror symmetry

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

    Alexandrov, Sergei; Banerjee, Sibasish

    2013-10-15

    We provide an explicit twistorial construction of quaternion-Kähler manifolds obtained by deformation of c-map spaces and carrying an isometric action of the modular group SL(2,Z). The deformation is not assumed to preserve any continuous isometry and therefore this construction presents a general framework for describing NS5-brane instanton effects in string compactifications with N= 2 supersymmetry. In this context the modular invariant parametrization of twistor lines found in this work yields the complete non-perturbative mirror map between type IIA and type IIB physical fields.

  18. When modularization fails to occur: a developmental perspective.

    PubMed

    D'Souza, Dean; Karmiloff-Smith, Annette

    2011-05-01

    We argue that models of adult cognition defined in terms of independently functioning modules cannot be applied to development, whether typical or atypical. The infant brain starts out highly interconnected, and it is only over developmental time that neural networks become increasingly specialized-that is, relatively modularized. In the case of atypical development, even when behavioural scores fall within the normal range, they are frequently underpinned by different cognitive and neural processes. In other words, in neurodevelopmental disorders the gradual process of relative modularization may fail to occur.

  19. Integromics network meta-analysis on cardiac aging offers robust multi-layer modular signatures and reveals micronome synergism.

    PubMed

    Dimitrakopoulou, Konstantina; Vrahatis, Aristidis G; Bezerianos, Anastasios

    2015-03-04

    The avalanche of integromics and panomics approaches shifted the deciphering of aging mechanisms from single molecular entities to communities of them. In this orientation, we explore the cardiac aging mechanisms - risk factor for multiple cardiovascular diseases - by capturing the micronome synergism and detecting longevity signatures in the form of communities (modules). For this, we developed a meta-analysis scheme that integrates transcriptome expression data from multiple cardiac-specific independent studies in mouse and human along with proteome and micronome interaction data in the form of multiple independent weighted networks. Modularization of each weighted network produced modules, which in turn were further analyzed so as to define consensus modules across datasets that change substantially during lifespan. Also, we established a metric that determines - from the modular perspective - the synergism of microRNA-microRNA interactions as defined by significantly functionally associated targets. The meta-analysis provided 40 consensus integromics modules across mouse datasets and revealed microRNA relations with substantial collective action during aging. Three modules were reproducible, based on homology, when mapped against human-derived modules. The respective homologs mainly represent NADH dehydrogenases, ATP synthases, cytochrome oxidases, Ras GTPases and ribosomal proteins. Among various observations, we corroborate to the involvement of miR-34a (included in consensus modules) as proposed recently; yet we report that has no synergistic effect. Moving forward, we determined its age-related neighborhood in which HCN3, a known heart pacemaker channel, was included. Also, miR-125a-5p/-351, miR-200c/-429, miR-106b/-17, miR-363/-92b, miR-181b/-181d, miR-19a/-19b, let-7d/-7f, miR-18a/-18b, miR-128/-27b and miR-106a/-291a-3p pairs exhibited significant synergy and their association to aging and/or cardiovascular diseases is supported in many cases by a

  20. Numerical simulations of human tibia osteosynthesis using modular plates based on Nitinol staples.

    PubMed

    Tarniţă, Daniela; Tarniţă, D N; Popa, D; Grecu, D; Tarniţă, Roxana; Niculescu, D; Cismaru, F

    2010-01-01

    The shape memory alloys exhibit a number of remarkable properties, which open new possibilities in engineering and more specifically in biomedical engineering. The most important alloy used in biomedical applications is NiTi. This alloy combines the characteristics of the shape memory effect and superelasticity with excellent corrosion resistance, wear characteristics, mechanical properties and a good biocompatibility. These properties make it an ideal biological engineering material, especially in orthopedic surgery and orthodontics. In this work, modular plates for the osteosynthesis of the long bones fractures are presented. The proposed modular plates are realized from identical modules, completely interchangeable, made of titanium or stainless steel having as connecting elements U-shaped staples made of Nitinol. Using computed tomography (CT) images to provide three-dimensional geometric details and SolidWorks software package, the three dimensional virtual models of the tibia bone and of the modular plates are obtained. The finite element models of the tibia bone and of the modular plate are generated. For numerical simulation, VisualNastran software is used. Finally, displacements diagram, von Misses strain diagram, for the modular plate and for the fractured tibia and modular plate ensemble are obtained.

  1. Modular Engine Instrumentation System

    NASA Technical Reports Server (NTRS)

    Rice, W. J.; Birchenough, A. G.

    1982-01-01

    System that provides information and measurements never obtained before in real time has been developed. System shows not only real-time measurements but also results of computations of key combustion parameters in meaningful and easily understood display. Standard commercially-available shaft encoder plus data from pressure transducer act as principal drivers to device. Eventually, modular system could be developed into onboard controller for automobile engines.

  2. Resilience of networks formed of interdependent modular networks

    NASA Astrophysics Data System (ADS)

    Shekhtman, Louis M.; Shai, Saray; Havlin, Shlomo

    2015-12-01

    Many infrastructure networks have a modular structure and are also interdependent with other infrastructures. While significant research has explored the resilience of interdependent networks, there has been no analysis of the effects of modularity. Here we develop a theoretical framework for attacks on interdependent modular networks and support our results through simulations. We focus, for simplicity, on the case where each network has the same number of communities and the dependency links are restricted to be between pairs of communities of different networks. This is particularly realistic for modeling infrastructure across cities. Each city has its own infrastructures and different infrastructures are dependent only within the city. However, each infrastructure is connected within and between cities. For example, a power grid will connect many cities as will a communication network, yet a power station and communication tower that are interdependent will likely be in the same city. It has previously been shown that single networks are very susceptible to the failure of the interconnected nodes (between communities) (Shai et al 2014 arXiv:1404.4748) and that attacks on these nodes are even more crippling than attacks based on betweenness (da Cunha et al 2015 arXiv:1502.00353). In our example of cities these nodes have long range links which are more likely to fail. For both treelike and looplike interdependent modular networks we find distinct regimes depending on the number of modules, m. (i) In the case where there are fewer modules with strong intraconnections, the system first separates into modules in an abrupt first-order transition and then each module undergoes a second percolation transition. (ii) When there are more modules with many interconnections between them, the system undergoes a single transition. Overall, we find that modular structure can significantly influence the type of transitions observed in interdependent networks and should be

  3. Comprehensive benefits analysis of steel structure modular residence based on the entropy evaluation

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoxiao; Wang, Li; Jiang, Pengming

    2017-04-01

    Steel structure modular residence is the outstanding residential industrialization. It has many advantages, such as the low whole cost, high resource recovery, a high degree of industrialization. This paper compares the comprehensive benefits of steel structural in modular buildings with prefabricated reinforced concrete residential from economic benefits, environmental benefits, social benefits and technical benefits by the method of entropy evaluation. Finally, it is concluded that the comprehensive benefits of steel structural in modular buildings is better than that of prefabricated reinforced concrete residential. The conclusion of this study will provide certain reference significance to the development of steel structural in modular buildings in China.

  4. Neural correlates of message tailoring and self-relatedness in smoking cessation programming

    PubMed Central

    Chua, Hannah Faye; Liberzon, Israel; Welsh, Robert C.; Strecher, Victor J.

    2011-01-01

    BACKGROUND Smoking leads to illnesses including addiction, cancer, and cardiovascular and respiratory diseases. Different intervention programs have become available. In the past decade, providing tailored smoking cessation messages has been shown to be more effective in inducing smoking cessation than one-size-fits-all interventions. However, little is known about the brain responses of smokers when they receive tailored smoking cessation messages. METHODS A neuroimaging study using blocked and event-related designs examined neural activity in 24 smokers exposed to high-tailored and low-tailored smoking cessation messages. RESULTS: In both blocked and event-related conditions, rostral medial prefrontal cortex and precuneus/posterior cingulate were engaged more during the processing of high-tailored smoking cessation messages than low-tailored smoking cessation messages. CONCLUSION The activation patterns of smokers to tailored cessation messages show involvement of brain areas commonly implicated in self-related processing. Results seem to add support to the suggested role of self-relevance in tailored cessation programs, where previous studies have shown a potential mediating role of self-relevance on smoking abstinence. The findings are relevant to understanding the cognitive mechanisms underlying tailored message processing and may point to new directions for testing response to health communications programming. PMID:18926523

  5. RNA-dependent DNA endonuclease Cas9 of the CRISPR system: Holy Grail of genome editing?

    PubMed

    Gasiunas, Giedrius; Siksnys, Virginijus

    2013-11-01

    Tailor-made nucleases for precise genome modification, such as zinc finger or TALE nucleases, currently represent the state-of-the-art for genome editing. These nucleases combine a programmable protein module which guides the enzyme to the target site with a nuclease domain which cuts DNA at the addressed site. Reprogramming of these nucleases to cut genomes at specific locations requires major protein engineering efforts. RNA-guided DNA endonuclease Cas9 of the type II (clustered regularly interspaced short palindromic repeat) CRISPR-Cas system uses CRISPR RNA (crRNA) as a guide to locate the DNA target and the Cas9 protein to cut DNA. Easy programmability of the Cas9 endonuclease using customizable RNAs brings unprecedented flexibility and versatility for targeted genome modification. We highlight the potential of the Cas9 RNA-guided DNA endonuclease as a novel tool for genome surgery, and discuss possible constraints and future prospects. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. RNA interference: ready to silence cancer?

    PubMed

    Mocellin, Simone; Costa, Rodolfo; Nitti, Donato

    2006-01-01

    RNA interference (RNAi) is considered the most promising functional genomics tool recently developed. As in other medical fields, this biotechnology might revolutionize the approach to dissecting the biology of cancer, ultimately speeding up the discovery pace of novel targets suitable for molecularly tailored antitumor therapies. In addition, preclinical results suggest that RNAi itself might be used as a therapeutic weapon. With the aim of illustrating not only the potentials but also the current limitations of RNAi as a tool in the fight against cancer, here we summarize the physiology of RNAi, discuss the main technical issues of RNAi-based gene silencing, and review some of the most interesting preclinical results obtained so far with its implementation in the field of oncology.

  7. Seven protective miRNA signatures for prognosis of cervical cancer.

    PubMed

    Liu, Bei; Ding, Jin-Feng; Luo, Jian; Lu, Li; Yang, Fen; Tan, Xiao-Dong

    2016-08-30

    Cervical cancer is the second cause of cancer death in females in their 20s and 30s, but there were limited studies about its prognosis. This study aims to identify miRNA related to prognosis and study their functions. TCGA data of patients with cervical cancer were used to build univariate Cox's model with single clinical parameter or miRNA expression level. Multivariate Cox's model was built using both clinical information and miRNA expression levels. At last, STRING was used to enrich gene ontology or pathway for validated targets of significant miRNAs, and visualize the interactions among them. Using univariate Cox's model with clinical parameters, we found that two clinical parameters, tobacco use and clinical stage, and seven miRNAs were highly correlated with the survival status. Only using the expression level of miRNA signatures, the model could separate patients into high-risk and low-risk groups successfully. An optimal feature-selected model was proposed based on two clinical parameters and seven miRNAs. Functional analysis of these seven miRNAs showed they were associated to various pathways related to cancer, including MAPK, VEGF and P53 pathways. These results helped the research of identifying targets for targeted therapy which could potentially allow tailoring of treatment for cervical cancer patients.

  8. Sculpting the Intrinsic Modular Organization of Spontaneous Brain Activity by Art.

    PubMed

    Lin, Chia-Shu; Liu, Yong; Huang, Wei-Yuan; Lu, Chia-Feng; Teng, Shin; Ju, Tzong-Ching; He, Yong; Wu, Yu-Te; Jiang, Tianzi; Hsieh, Jen-Chuen

    2013-01-01

    Artistic training is a complex learning that requires the meticulous orchestration of sophisticated polysensory, motor, cognitive, and emotional elements of mental capacity to harvest an aesthetic creation. In this study, we investigated the architecture of the resting-state functional connectivity networks from professional painters, dancers and pianists. Using a graph-based network analysis, we focused on the art-related changes of modular organization and functional hubs in the resting-state functional connectivity network. We report that the brain architecture of artists consists of a hierarchical modular organization where art-unique and artistic form-specific brain states collectively mirror the mind states of virtuosos. We show that even in the resting state, this type of extraordinary and long-lasting training can macroscopically imprint a neural network system of spontaneous activity in which the related brain regions become functionally and topologically modularized in both domain-general and domain-specific manners. The attuned modularity reflects a resilient plasticity nurtured by long-term experience.

  9. Sculpting the Intrinsic Modular Organization of Spontaneous Brain Activity by Art

    PubMed Central

    Lin, Chia-Shu; Liu, Yong; Huang, Wei-Yuan; Lu, Chia-Feng; Teng, Shin; Ju, Tzong-Ching; He, Yong; Wu, Yu-Te; Jiang, Tianzi; Hsieh, Jen-Chuen

    2013-01-01

    Artistic training is a complex learning that requires the meticulous orchestration of sophisticated polysensory, motor, cognitive, and emotional elements of mental capacity to harvest an aesthetic creation. In this study, we investigated the architecture of the resting-state functional connectivity networks from professional painters, dancers and pianists. Using a graph-based network analysis, we focused on the art-related changes of modular organization and functional hubs in the resting-state functional connectivity network. We report that the brain architecture of artists consists of a hierarchical modular organization where art-unique and artistic form-specific brain states collectively mirror the mind states of virtuosos. We show that even in the resting state, this type of extraordinary and long-lasting training can macroscopically imprint a neural network system of spontaneous activity in which the related brain regions become functionally and topologically modularized in both domain-general and domain-specific manners. The attuned modularity reflects a resilient plasticity nurtured by long-term experience. PMID:23840527

  10. Network modularity reveals critical scales for connectivity in ecology and evolution

    USGS Publications Warehouse

    Fletcher, Robert J.; Revell, Andre; Reichert, Brian E.; Kitchens, Wiley M.; Dixon, J.; Austin, James D.

    2013-01-01

    For nearly a century, biologists have emphasized the profound importance of spatial scale for ecology, evolution and conservation. Nonetheless, objectively identifying critical scales has proven incredibly challenging. Here we extend new techniques from physics and social sciences that estimate modularity on networks to identify critical scales for movement and gene flow in animals. Using four species that vary widely in dispersal ability and include both mark-recapture and population genetic data, we identify significant modularity in three species, two of which cannot be explained by geographic distance alone. Importantly, the inclusion of modularity in connectivity and population viability assessments alters conclusions regarding patch importance to connectivity and suggests higher metapopulation viability than when ignoring this hidden spatial scale. We argue that network modularity reveals critical meso-scales that are probably common in populations, providing a powerful means of identifying fundamental scales for biology and for conservation strategies aimed at recovering imperilled species.

  11. A Taguchi study of the aeroelastic tailoring design process

    NASA Technical Reports Server (NTRS)

    Bohlmann, Jonathan D.; Scott, Robert C.

    1991-01-01

    A Taguchi study was performed to determine the important players in the aeroelastic tailoring design process and to find the best composition of the optimization's objective function. The Wing Aeroelastic Synthesis Procedure (TSO) was used to ascertain the effects that factors such as composite laminate constraints, roll effectiveness constraints, and built-in wing twist and camber have on the optimum, aeroelastically tailored wing skin design. The results show the Taguchi method to be a viable engineering tool for computational inquiries, and provide some valuable lessons about the practice of aeroelastic tailoring.

  12. Chromatin isolation by RNA purification (ChIRP).

    PubMed

    Chu, Ci; Quinn, Jeffrey; Chang, Howard Y

    2012-03-25

    Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental gene expression (1,2,3,4,5,6,7). The recent discovery of thousands of lncRNAs in association with specific chromatin modification complexes, such as Polycomb Repressive Complex 2 (PRC2) that mediates histone H3 lysine 27 trimethylation (H3K27me3), suggests broad roles for numerous lncRNAs in managing chromatin states in a gene-specific fashion (8,9). While some lncRNAs are thought to work in cis on neighboring genes, other lncRNAs work in trans to regulate distantly located genes. For instance, Drosophila lncRNAs roX1 and roX2 bind numerous regions on the X chromosome of male cells, and are critical for dosage compensation (10,11). However, the exact locations of their binding sites are not known at high resolution. Similarly, human lncRNA HOTAIR can affect PRC2 occupancy on hundreds of genes genome-wide( 3,12,13), but how specificity is achieved is unclear. LncRNAs can also serve as modular scaffolds to recruit the assembly of multiple protein complexes. The classic trans-acting RNA scaffold is the TERC RNA that serves as the template and scaffold for the telomerase complex (14); HOTAIR can also serve as a scaffold for PRC2 and a H3K4 demethylase complex (13). Prior studies mapping RNA occupancy at chromatin have revealed substantial insights (15,16), but only at a single gene locus at a time. The occupancy sites of most lncRNAs are not known, and the roles of lncRNAs in chromatin regulation have been mostly inferred from the indirect effects of lncRNA perturbation. Just as chromatin immunoprecipitation followed by microarray or deep sequencing (ChIP-chip or ChIP-seq, respectively) has greatly improved our understanding of protein-DNA interactions on a genomic scale, here we illustrate a recently published strategy to map long RNA occupancy genome-wide at high resolution (17). This method, Chromatin Isolation by

  13. Fast Modular Exponentiation and Elliptic Curve Group Operation in Maple

    ERIC Educational Resources Information Center

    Yan, S. Y.; James, G.

    2006-01-01

    The modular exponentiation, y[equivalent to]x[superscript k](mod n) with x,y,k,n integers and n [greater than] 1; is the most fundamental operation in RSA and ElGamal public-key cryptographic systems. Thus the efficiency of RSA and ElGamal depends entirely on the efficiency of the modular exponentiation. The same situation arises also in elliptic…

  14. Modularity, Working Memory, and Second Language Acquisition: A Research Program

    ERIC Educational Resources Information Center

    Truscott, John

    2017-01-01

    Considerable reason exists to view the mind, and language within it, as modular, and this view has an important place in research and theory in second language acquisition (SLA) and beyond. But it has had very little impact on the study of working memory and its role in SLA. This article considers the need for modular study of working memory,…

  15. Episodic Memory Retrieval Benefits from a Less Modular Brain Network Organization

    PubMed Central

    2017-01-01

    Most complex cognitive tasks require the coordinated interplay of multiple brain networks, but the act of retrieving an episodic memory may place especially heavy demands for communication between the frontoparietal control network (FPCN) and the default mode network (DMN), two networks that do not strongly interact with one another in many task contexts. We applied graph theoretical analysis to task-related fMRI functional connectivity data from 20 human participants and found that global brain modularity—a measure of network segregation—is markedly reduced during episodic memory retrieval relative to closely matched analogical reasoning and visuospatial perception tasks. Individual differences in modularity were correlated with memory task performance, such that lower modularity levels were associated with a lower false alarm rate. Moreover, the FPCN and DMN showed significantly elevated coupling with each other during the memory task, which correlated with the global reduction in brain modularity. Both networks also strengthened their functional connectivity with the hippocampus during the memory task. Together, these results provide a novel demonstration that reduced modularity is conducive to effective episodic retrieval, which requires close collaboration between goal-directed control processes supported by the FPCN and internally oriented self-referential processing supported by the DMN. SIGNIFICANCE STATEMENT Modularity, an index of the degree to which nodes of a complex system are organized into discrete communities, has emerged as an important construct in the characterization of brain connectivity dynamics. We provide novel evidence that the modularity of the human brain is reduced when individuals engage in episodic memory retrieval, relative to other cognitive tasks, and that this state of lower modularity is associated with improved memory performance. We propose a neural systems mechanism for this finding where the nodes of the frontoparietal

  16. Modular, bluetooth enabled, wireless electroencephalograph (EEG) platform.

    PubMed

    Lovelace, Joseph A; Witt, Tyler S; Beyette, Fred R

    2013-01-01

    A design for a modular, compact, and accurate wireless electroencephalograph (EEG) system is proposed. EEG is the only non-invasive measure for neuronal function of the brain. Using a number of digital signal processing (DSP) techniques, this neuronal function can be acquired and processed into meaningful representations of brain activity. The system described here utilizes Bluetooth to wirelessly transmit the digitized brain signal for an end application use. In this way, the system is portable, and modular in terms of the device to which it can interface. Brain Computer Interface (BCI) has become a popular extension of EEG systems in modern research. This design serves as a platform for applications using BCI capability.

  17. DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data.

    PubMed

    Gong, Ting; Szustakowski, Joseph D

    2013-04-15

    For heterogeneous tissues, measurements of gene expression through mRNA-Seq data are confounded by relative proportions of cell types involved. In this note, we introduce an efficient pipeline: DeconRNASeq, an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It adopts a globally optimized non-negative decomposition algorithm through quadratic programming for estimating the mixing proportions of distinctive tissue types in next-generation sequencing data. We demonstrated the feasibility and validity of DeconRNASeq across a range of mixing levels and sources using mRNA-Seq data mixed in silico at known concentrations. We validated our computational approach for various benchmark data, with high correlation between our predicted cell proportions and the real fractions of tissues. Our study provides a rigorous, quantitative and high-resolution tool as a prerequisite to use mRNA-Seq data. The modularity of package design allows an easy deployment of custom analytical pipelines for data from other high-throughput platforms. DeconRNASeq is written in R, and is freely available at http://bioconductor.org/packages. Supplementary data are available at Bioinformatics online.

  18. Small modular reactors are 'crucial technology'

    NASA Astrophysics Data System (ADS)

    Johnston, Hamish

    2018-03-01

    Small modular nuclear reactors (SMRs) offer a way for the UK to reduce carbon dioxide emissions from electricity generation, while allowing the country to meet the expected increase in demand for electricity from electric vehicles and other uses.

  19. Modular Access and Progression Routes: Support Issues and Student Directed Learning.

    ERIC Educational Resources Information Center

    Ward, Jill

    1995-01-01

    The effects of modularizing Access Courses provided by the University of Derby were examined for 299 adult students. No significant differences appeared in retention, but the modular approach had increased recruitment/retention of unskilled and lower achieving students. Students with lower entry qualifications had higher achievement than similar…

  20. Neural Modularity Helps Organisms Evolve to Learn New Skills without Forgetting Old Skills

    PubMed Central

    Ellefsen, Kai Olav; Mouret, Jean-Baptiste; Clune, Jeff

    2015-01-01

    A long-standing goal in artificial intelligence is creating agents that can learn a variety of different skills for different problems. In the artificial intelligence subfield of neural networks, a barrier to that goal is that when agents learn a new skill they typically do so by losing previously acquired skills, a problem called catastrophic forgetting. That occurs because, to learn the new task, neural learning algorithms change connections that encode previously acquired skills. How networks are organized critically affects their learning dynamics. In this paper, we test whether catastrophic forgetting can be reduced by evolving modular neural networks. Modularity intuitively should reduce learning interference between tasks by separating functionality into physically distinct modules in which learning can be selectively turned on or off. Modularity can further improve learning by having a reinforcement learning module separate from sensory processing modules, allowing learning to happen only in response to a positive or negative reward. In this paper, learning takes place via neuromodulation, which allows agents to selectively change the rate of learning for each neural connection based on environmental stimuli (e.g. to alter learning in specific locations based on the task at hand). To produce modularity, we evolve neural networks with a cost for neural connections. We show that this connection cost technique causes modularity, confirming a previous result, and that such sparsely connected, modular networks have higher overall performance because they learn new skills faster while retaining old skills more and because they have a separate reinforcement learning module. Our results suggest (1) that encouraging modularity in neural networks may help us overcome the long-standing barrier of networks that cannot learn new skills without forgetting old ones, and (2) that one benefit of the modularity ubiquitous in the brains of natural animals might be to

  1. Neural modularity helps organisms evolve to learn new skills without forgetting old skills.

    PubMed

    Ellefsen, Kai Olav; Mouret, Jean-Baptiste; Clune, Jeff

    2015-04-01

    A long-standing goal in artificial intelligence is creating agents that can learn a variety of different skills for different problems. In the artificial intelligence subfield of neural networks, a barrier to that goal is that when agents learn a new skill they typically do so by losing previously acquired skills, a problem called catastrophic forgetting. That occurs because, to learn the new task, neural learning algorithms change connections that encode previously acquired skills. How networks are organized critically affects their learning dynamics. In this paper, we test whether catastrophic forgetting can be reduced by evolving modular neural networks. Modularity intuitively should reduce learning interference between tasks by separating functionality into physically distinct modules in which learning can be selectively turned on or off. Modularity can further improve learning by having a reinforcement learning module separate from sensory processing modules, allowing learning to happen only in response to a positive or negative reward. In this paper, learning takes place via neuromodulation, which allows agents to selectively change the rate of learning for each neural connection based on environmental stimuli (e.g. to alter learning in specific locations based on the task at hand). To produce modularity, we evolve neural networks with a cost for neural connections. We show that this connection cost technique causes modularity, confirming a previous result, and that such sparsely connected, modular networks have higher overall performance because they learn new skills faster while retaining old skills more and because they have a separate reinforcement learning module. Our results suggest (1) that encouraging modularity in neural networks may help us overcome the long-standing barrier of networks that cannot learn new skills without forgetting old ones, and (2) that one benefit of the modularity ubiquitous in the brains of natural animals might be to

  2. CosmoSIS: Modular cosmological parameter estimation

    DOE PAGES

    Zuntz, J.; Paterno, M.; Jennings, E.; ...

    2015-06-09

    Cosmological parameter estimation is entering a new era. Large collaborations need to coordinate high-stakes analyses using multiple methods; furthermore such analyses have grown in complexity due to sophisticated models of cosmology and systematic uncertainties. In this paper we argue that modularity is the key to addressing these challenges: calculations should be broken up into interchangeable modular units with inputs and outputs clearly defined. Here we present a new framework for cosmological parameter estimation, CosmoSIS, designed to connect together, share, and advance development of inference tools across the community. We describe the modules already available in CosmoSIS, including CAMB, Planck, cosmicmore » shear calculations, and a suite of samplers. Lastly, we illustrate it using demonstration code that you can run out-of-the-box with the installer available at http://bitbucket.org/joezuntz/cosmosis« less

  3. Versatile microrobotics using simple modular subunits

    PubMed Central

    Cheang, U Kei; Meshkati, Farshad; Kim, Hoyeon; Lee, Kyoungwoo; Fu, Henry Chien; Kim, Min Jun

    2016-01-01

    The realization of reconfigurable modular microrobots could aid drug delivery and microsurgery by allowing a single system to navigate diverse environments and perform multiple tasks. So far, microrobotic systems are limited by insufficient versatility; for instance, helical shapes commonly used for magnetic swimmers cannot effectively assemble and disassemble into different size and shapes. Here by using microswimmers with simple geometries constructed of spherical particles, we show how magnetohydrodynamics can be used to assemble and disassemble modular microrobots with different physical characteristics. We develop a mechanistic physical model that we use to improve assembly strategies. Furthermore, we experimentally demonstrate the feasibility of dynamically changing the physical properties of microswimmers through assembly and disassembly in a controlled fluidic environment. Finally, we show that different configurations have different swimming properties by examining swimming speed dependence on configuration size. PMID:27464852

  4. Modular Approach to Select Bacteriophages Targeting Pseudomonas aeruginosa for Their Application to Children Suffering With Cystic Fibrosis

    PubMed Central

    Krylov, Victor; Shaburova, Olga; Pleteneva, Elena; Bourkaltseva, Maria; Krylov, Sergey; Kaplan, Alla; Chesnokova, Elena; Kulakov, Leonid; Magill, Damian; Polygach, Olga

    2016-01-01

    This review discusses the potential application of bacterial viruses (phage therapy) toward the eradication of antibiotic resistant Pseudomonas aeruginosa in children with cystic fibrosis (CF). In this regard, several potential relationships between bacteria and their bacteriophages are considered. The most important aspect that must be addressed with respect to phage therapy of bacterial infections in the lungs of CF patients is in ensuring the continuity of treatment in light of the continual occurrence of resistant bacteria. This depends on the ability to rapidly select phages exhibiting an enhanced spectrum of lytic activity among several well-studied phage groups of proven safety. We propose a modular based approach, utilizing both mono-species and hetero-species phage mixtures. With an approach involving the visual recognition of characteristics exhibited by phages of well-studied phage groups on lawns of the standard P. aeruginosa PAO1 strain, the simple and rapid enhancement of the lytic spectrum of cocktails is permitted, allowing the development of tailored preparations for patients capable of circumventing problems associated with phage resistant bacterial mutants. PMID:27790211

  5. Hippocampal Network Modularity Is Associated With Relational Memory Dysfunction in Schizophrenia.

    PubMed

    Avery, Suzanne N; Rogers, Baxter P; Heckers, Stephan

    2018-05-01

    Functional dysconnectivity has been proposed as a major pathophysiological mechanism for cognitive dysfunction in schizophrenia. The hippocampus is a focal point of dysconnectivity in schizophrenia, with decreased hippocampal functional connectivity contributing to the marked memory deficits observed in patients. Normal memory function relies on the interaction of complex corticohippocampal networks. However, only recent technological advances have enabled the large-scale exploration of functional networks with accuracy and precision. We investigated the modularity of hippocampal resting-state functional networks in a sample of 45 patients with schizophrenia spectrum disorders and 38 healthy control subjects. Modularity was calculated for two distinct functional networks: a core hippocampal-medial temporal lobe cortex network and an extended hippocampal-cortical network. As hippocampal function differs along its longitudinal axis, follow-up analyses examined anterior and posterior networks separately. To explore effects of resting network function on behavior, we tested associations between modularity and relational memory ability. Age, sex, handedness, and parental education were similar between groups. Network modularity was lower in schizophrenia patients, especially in the posterior hippocampal network. Schizophrenia patients also showed markedly lower relational memory ability compared with control subjects. We found a distinct brain-behavior relationship in schizophrenia that differed from control subjects by network and anterior/posterior division-while relational memory in control subjects was associated with anterior hippocampal-cortical modularity, schizophrenia patients showed an association with posterior hippocampal-medial temporal lobe cortex network modularity. Our findings support a model of abnormal resting-state corticohippocampal network coherence in schizophrenia, which may contribute to relational memory deficits. Copyright © 2018 Society of

  6. RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.

    PubMed

    Uyar, Bora; Yusuf, Dilmurat; Wurmus, Ricardo; Rajewsky, Nikolaus; Ohler, Uwe; Akalin, Altuna

    2017-06-02

    In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies. The design of RCAS is modular, which enables flexible usage and convenient integration with other bioinformatics workflows. RCAS is an R/Bioconductor package but we also created graphical user interfaces including a Galaxy wrapper and a stand-alone web service. The application of RCAS on published datasets shows that RCAS is not only able to reproduce published findings but also helps generate novel knowledge and hypotheses. The meta-gene profiles, gene-centric annotation, motif analysis and gene-set analysis provided by RCAS provide contextual knowledge which is necessary for understanding the functional aspects of different biological events that involve RNAs. In addition, the array of different interfaces and deployment options adds the convenience of use for different levels of users. RCAS is available at http://bioconductor.org/packages/release/bioc/html/RCAS.html and http://rcas.mdc-berlin.de. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Analysis of In-Space Assembly of Modular Systems

    NASA Technical Reports Server (NTRS)

    Moses, Robert W.; VanLaak, James; Johnson, Spencer L.; Chytka, Trina M.; Reeves, John D.; Todd, B. Keith; Moe, Rud V.; Stambolian, Damon B.

    2005-01-01

    Early system-level life cycle assessments facilitate cost effective optimization of system architectures to enable implementation of both modularity and in-space assembly, two key Exploration Systems Research & Technology (ESR&T) Strategic Challenges. Experiences with the International Space Station (ISS) demonstrate that the absence of this rigorous analysis can result in increased cost and operational risk. An effort is underway, called Analysis of In-Space Assembly of Modular Systems, to produce an innovative analytical methodology, including an evolved analysis toolset and proven processes in a collaborative engineering environment, to support the design and evaluation of proposed concepts. The unique aspect of this work is that it will produce the toolset, techniques and initial products to analyze and compare the detailed, life cycle costs and performance of different implementations of modularity for in-space assembly. A multi-Center team consisting of experienced personnel from the Langley Research Center, Johnson Space Center, Kennedy Space Center, and the Goddard Space Flight Center has been formed to bring their resources and experience to this development. At the end of this 30-month effort, the toolset will be ready to support the Exploration Program with an integrated assessment strategy that embodies all life-cycle aspects of the mission from design and manufacturing through operations to enable early and timely selection of an optimum solution among many competing alternatives. Already there are many different designs for crewed missions to the Moon that present competing views of modularity requiring some in-space assembly. The purpose of this paper is to highlight the approach for scoring competing designs.

  8. RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction.

    PubMed

    Zhang, Xiaomeng; Wu, Deng; Chen, Liqun; Li, Xiang; Yang, Jinxurong; Fan, Dandan; Dong, Tingting; Liu, Mingyue; Tan, Puwen; Xu, Jintian; Yi, Ying; Wang, Yuting; Zou, Hua; Hu, Yongfei; Fan, Kaili; Kang, Juanjuan; Huang, Yan; Miao, Zhengqiang; Bi, Miaoman; Jin, Nana; Li, Kongning; Li, Xia; Xu, Jianzhen; Wang, Dong

    2014-07-01

    Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (http://www.rna-society.org/raid), an RNA-associated (RNA-RNA/RNA-protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA-RNA interactions and 1619 RNA-protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA-RNA/RNA-protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA-RNA/RNA-protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network. © 2014 Zhang et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  9. Re-emergence of modular brain networks in stroke recovery.

    PubMed

    Siegel, Joshua S; Seitzman, Benjamin A; Ramsey, Lenny E; Ortega, Mario; Gordon, Evan M; Dosenbach, Nico U F; Petersen, Steven E; Shulman, Gordon L; Corbetta, Maurizio

    2018-04-01

    Studies of stroke have identified local reorganization in perilesional tissue. However, because the brain is highly networked, strokes also broadly alter the brain's global network organization. Here, we assess brain network structure longitudinally in adult stroke patients using resting state fMRI. The topology and boundaries of cortical regions remain grossly unchanged across recovery. In contrast, the modularity of brain systems i.e. the degree of integration within and segregation between networks, was significantly reduced sub-acutely (n = 107), but partially recovered by 3 months (n = 85), and 1 year (n = 67). Importantly, network recovery correlated with recovery from language, spatial memory, and attention deficits, but not motor or visual deficits. Finally, in-depth single subject analyses were conducted using tools for visualization of changes in brain networks over time. This exploration indicated that changes in modularity during successful recovery reflect specific alterations in the relationships between different networks. For example, in a patient with left temporo-parietal stroke and severe aphasia, sub-acute loss of modularity reflected loss of association between frontal and temporo-parietal regions bi-hemispherically across multiple modules. These long-distance connections then returned over time, paralleling aphasia recovery. This work establishes the potential importance of normalization of large-scale modular brain systems in stroke recovery. Copyright © 2017. Published by Elsevier Ltd.

  10. Going Modular--For Better or Worse? AIR 1994 Annual Forum Paper.

    ERIC Educational Resources Information Center

    McLachlan, Jeffrey E.; Wood, Vivienne

    A modular system for undergraduate programs was implemented in three degree programs at Napier University in Scotland. This paper describes the degree course structure prior to 1992-93 and factors leading to change, including university response to government policy encouraging wider access to higher education. A rationale for modularization is…

  11. Engineered Photoactivatable Genetic Switches Based on the Bacterium Phage T7 RNA Polymerase.

    PubMed

    Han, Tiyun; Chen, Quan; Liu, Haiyan

    2017-02-17

    Genetic switches in which the activity of T7 RNA polymerase (RNAP) is directly regulated by external signals are obtained with an engineering strategy of splitting the protein into fragments and using regulatory domains to modulate their reconstitutions. Robust switchable systems with excellent dark-off/light-on properties are obtained with the light-activatable VVD domain and its variants as regulatory domains. For the best split position found, working switches exploit either the light-induced interactions between the VVD domains or allosteric effects. The split fragments show high modularity when they are combined with different regulatory domains such as those with chemically inducible interaction, enabling chemically controlled switches. To summarize, the T7 RNA polymerase-based switches are powerful tools to implement light-activated gene expression in different contexts. Moreover, results about the studied split positions and domain organizations may facilitate future engineering studies on this and on related proteins.

  12. In-air microfluidics enables rapid fabrication of emulsions, suspensions, and 3D modular (bio)materials

    PubMed Central

    Visser, Claas Willem; Kamperman, Tom; Karbaat, Lisanne P.; Lohse, Detlef; Karperien, Marcel

    2018-01-01

    Microfluidic chips provide unparalleled control over droplets and jets, which have advanced all natural sciences. However, microfluidic applications could be vastly expanded by increasing the per-channel throughput and directly exploiting the output of chips for rapid additive manufacturing. We unlock these features with in-air microfluidics, a new chip-free platform to manipulate microscale liquid streams in the air. By controlling the composition and in-air impact of liquid microjets by surface tension–driven encapsulation, we fabricate monodisperse emulsions, particles, and fibers with diameters of 20 to 300 μm at rates that are 10 to 100 times higher than chip-based droplet microfluidics. Furthermore, in-air microfluidics uniquely enables module-based production of three-dimensional (3D) multiscale (bio)materials in one step because droplets are partially solidified in-flight and can immediately be printed onto a substrate. In-air microfluidics is cytocompatible, as demonstrated by additive manufacturing of 3D modular constructs with tailored microenvironments for multiple cell types. Its in-line control, high throughput and resolution, and cytocompatibility make in-air microfluidics a versatile platform technology for science, industry, and health care. PMID:29399628

  13. Tailored metal matrix composites for high-temperature performance

    NASA Technical Reports Server (NTRS)

    Morel, M. R.; Saravanos, D. A.; Chamis, C. C.

    1992-01-01

    A multi-objective tailoring methodology is presented to maximize stiffness and load carrying capacity of a metal matrix cross-ply laminated at elevated temperatures. The fabrication process and fiber volume ratio are used as the design variables. A unique feature is the concurrent effects from fabrication, residual stresses, material nonlinearity, and thermo-mechanical loading on the laminate properties at the post-fabrication phase. For a (0/90)(sub s) graphite/copper laminate, strong coupling was observed between the fabrication process, laminate characteristics, and thermo-mechanical loading. The multi-objective tailoring was found to be more effective than single objective tailoring. Results indicate the potential to increase laminate stiffness and load carrying capacity by controlling the critical parameters of the fabrication process and the laminate.

  14. A Customized Quantitative PCR MicroRNA Panel Provides a Technically Robust Context for Studying Neurodegenerative Disease Biomarkers and Indicates a High Correlation Between Cerebrospinal Fluid and Choroid Plexus MicroRNA Expression.

    PubMed

    Wang, Wang-Xia; Fardo, David W; Jicha, Gregory A; Nelson, Peter T

    2017-12-01

    MicroRNA (miRNA) expression varies in association with different tissue types and in diseases. Having been found in body fluids including blood and cerebrospinal fluid (CSF), miRNAs constitute potential biomarkers. CSF miRNAs have been proposed as biomarkers for neurodegenerative diseases; however, there is a lack of consensus about the best candidate miRNA biomarkers and there has been variability in results from different research centers, perhaps due to technical factors. Here, we sought to optimize technical parameters for CSF miRNA studies. We examined different RNA isolation methods and performed miRNA expression profiling with TaqMan® miRNA Arrays. More specifically, we developed a customized CSF-miRNA low-density array (TLDA) panel that contains 47 targets: miRNAs shown previously to be relevant to neurodegenerative disease, miRNAs that are abundant in CSF, data normalizers, and controls for potential blood and tissue contamination. The advantages of using this CSF-miRNA TLDA panel include specificity, sensitivity, fast processing and data analysis, and cost effectiveness. We optimized technical parameters for this assay. Further, the TLDA panel can be tailored to other specific purposes. We tested whether the profile of miRNAs in the CSF resembled miRNAs isolated from brain tissue (hippocampus or cerebellum), blood, or the choroid plexus. We found that the CSF miRNA expression profile most closely resembles that of choroid plexus tissue, underscoring the potential importance of choroid plexus-derived signaling through CSF miRNAs. In summary, the TLDA miRNA array panel will enable evaluation and discovery of CSF miRNA biomarkers and can potentially be utilized in clinical diagnosis and disease stage monitoring.

  15. 48 CFR 39.103 - Modular contracting.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... CATEGORIES OF CONTRACTING ACQUISITION OF INFORMATION TECHNOLOGY General 39.103 Modular contracting. (a) This section implements Section 5202, Incremental Acquisition of Information Technology, of the Clinger-Cohen... technology. Consistent with the agency's information technology architecture, agencies should, to the maximum...

  16. Small Molecule Targeting of a MicroRNA Associated with Hepatocellular Carcinoma.

    PubMed

    Childs-Disney, Jessica L; Disney, Matthew D

    2016-02-19

    Development of precision therapeutics is of immense interest, particularly as applied to the treatment of cancer. By analyzing the preferred cellular RNA targets of small molecules, we discovered that 5"-azido neomycin B binds the Drosha processing site in the microRNA (miR)-525 precursor. MiR-525 confers invasive properties to hepatocellular carcinoma (HCC) cells. Although HCC is one of the most common cancers, treatment options are limited, making the disease often fatal. Herein, we find that addition of 5"-azido neomycin B and its FDA-approved precursor, neomycin B, to an HCC cell line selectively inhibits production of the mature miRNA, boosts a downstream protein, and inhibits invasion. Interestingly, neomycin B is a second-line agent for hepatic encephalopathy (HE) and bacterial infections due to cirrhosis. Our results provocatively suggest that neomycin B, or second-generation derivatives, may be dual functioning molecules to treat both HE and HCC. Collectively, these studies show that rational design approaches can be tailored to disease-associated RNAs to afford potential lead therapeutics.

  17. Modularization--A Road to Relevance?

    ERIC Educational Resources Information Center

    Palow, William P.

    This paper describes a modular program at a community college for instructing non-science majors in college algebra. The two-course sequence is comprised of four modules each and successful completion of a module is required before a student proceeds to the next. Placement, grading policies, and scheduling are all discussed. A formative evaluation…

  18. Preliminary development of an advanced modular pressure relief cushion: Testing and user evaluation.

    PubMed

    Freeto, Tyler; Mitchell, Steven J; Bogie, Kath M

    2018-02-01

    Effective pressure relief cushions are identified as a core assistive technology need by the World Health Organization Global Cooperation on Assistive Technology. High quality affordable wheelchair cushions could provide effective pressure relief for many individuals with limited access to advanced assistive technology. Value driven engineering (VdE) principles were employed to develop a prototype modular cushion. Low cost dynamically responsive gel balls were arranged in a close packed array and seated in bilayer foam for containment and support. Two modular cushions, one with high compliance balls and one with moderate compliance balls were compared with High Profile and Low Profile Roho ® and Jay ® Medical 2 cushions. ISO 16480-2 biomechanical standardized tests were applied to assess cushion performance. A preliminary materials cost analysis was carried out. A prototype modular cushion was evaluated by 12 participants who reported satisfaction using a questionnaire based on the Quebec User Evaluation of Satisfaction with Assistive Technology (QUEST 2.0) instrument. Overall the modular cushions performed better than, or on par with, the most widely prescribed commercially available cushions under ISO 16480-2 testing. Users rated the modular cushion highly for overall appearance, size and dimensions, comfort, safety, stability, ease of adjustment and general ease of use. Cost-analysis indicated that every modular cushion component a could be replaced several times and still maintain cost-efficacy over the complete cushion lifecycle. A VdE modular cushion has the potential provide effective pressure relief for many users at a low lifetime cost. Copyright © 2017. Published by Elsevier Ltd.

  19. The impact of tailored interventions on a community health center population.

    PubMed

    Rimer, B K; Conaway, M; Lyna, P; Glassman, B; Yarnall, K S; Lipkus, I; Barber, L T

    1999-06-01

    We conducted a 4-year randomized study in a community health center that serves primarily low income Blacks in Durham, North Carolina. Patients (1318 at baseline) were assigned randomly to one of three study groups: provider prompting intervention alone, provider prompting and tailored print materials or the previous group and tailored telephone counseling. The purpose of the study was to determine whether increasingly intensive, tailored print and telephone interventions also were increasingly effective in promoting adherence to mammograms, Pap tests and overall cancer screening compliance. Thus, the combination of tailored print interventions (print and telephone) should have been more effective than the provider prompting intervention alone, or the print intervention and prompting combination. This is one of the few studies to examine a measure of overall cancer screening compliance and to assess the benefit of combinations of tailored interventions in promoting adherence to cancer screening. Patients gave extremely high ratings to the interventions. At the bivariate level, we found a significant effect of the most intensive group (provider prompting intervention, tailored print communications and tailored telephone counseling) on Pap test compliance (P = 0.05) and borderline significance at the multivariate level (P = 0.06) as well on overall screening compliance (P = 0.06). There was not a significant effect on mammography, probably because a majority of the patients were receiving regular mammograms. We also found some important subgroup differences. For example, a larger proportion of women reported Pap tests in the tailored print and counseling group when they believed the materials were 'meant for me.' These results show that a combination of tailored interventions may have potential for reaching the women who have too often been labeled the 'hard to reach.'

  20. A Modular Habitation System for Human Planetary and Space Exploration

    NASA Technical Reports Server (NTRS)

    Howe, A. Scott

    2015-01-01

    A small-diameter modular pressure vessel system is devised that can be applied to planetary surface and deep space human exploration missions. As one of the recommendations prepared for the NASA Human Spaceflight Architecture Team (HAT) Evolvable Mars Campaign (EMC), a compact modular system can provide a Mars-forward approach to a variety of missions and environments. Small cabins derived from the system can fit into the Space Launch System (SLS) Orion "trunk", or can be mounted with mobility systems to function as pressurized rovers, in-space taxis, ascent stage cabins, or propellant tanks. Larger volumes can be created using inflatable elements for long-duration deep space missions and planetary surface outposts. This paper discusses how a small-diameter modular system can address functional requirements, mass and volume constraints, and operational scenarios.

  1. Context, confidentiality, and consent in tailored health communications: a cautionary note.

    PubMed

    Orleans, C T

    1999-01-01

    This article highlights key contextual factors that emerge when the evolution of tailored health communications is viewed against the backdrop of dynamic changes in the nation's health care system--including the shift from fee-for-service medicine to managed care and the proliferation of direct-to-consumer and tailored marketing strategies in the pharmaceutical industry. It focuses on contextual variables with potential to significantly mediate the impact of personally tailored health advice--including those related to confidentiality, privacy, and informed consent and to the perceived aims, intents, and sources of tailored health messages. To protect the future of tailored health messages, more research attention must be given to defining these contextual factors and understanding the roles that they play and the ways in which they can be controlled to assure the best outcomes. Such research could point the way towards a set of empirical and ethical "best practices" based on a scientific understanding of how to maximize the benefits, and minimize the potential harms, of the widescale use of tailored health communications.

  2. Reanalysis of RNA-Sequencing Data Reveals Several Additional Fusion Genes with Multiple Isoforms

    PubMed Central

    Kangaspeska, Sara; Hultsch, Susanne; Edgren, Henrik; Nicorici, Daniel; Murumägi, Astrid; Kallioniemi, Olli

    2012-01-01

    RNA-sequencing and tailored bioinformatic methodologies have paved the way for identification of expressed fusion genes from the chaotic genomes of solid tumors. We have recently successfully exploited RNA-sequencing for the discovery of 24 novel fusion genes in breast cancer. Here, we demonstrate the importance of continuous optimization of the bioinformatic methodology for this purpose, and report the discovery and experimental validation of 13 additional fusion genes from the same samples. Integration of copy number profiling with the RNA-sequencing results revealed that the majority of the gene fusions were promoter-donating events that occurred at copy number transition points or involved high-level DNA-amplifications. Sequencing of genomic fusion break points confirmed that DNA-level rearrangements underlie selected fusion transcripts. Furthermore, a significant portion (>60%) of the fusion genes were alternatively spliced. This illustrates the importance of reanalyzing sequencing data as gene definitions change and bioinformatic methods improve, and highlights the previously unforeseen isoform diversity among fusion transcripts. PMID:23119097

  3. Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms.

    PubMed

    Kangaspeska, Sara; Hultsch, Susanne; Edgren, Henrik; Nicorici, Daniel; Murumägi, Astrid; Kallioniemi, Olli

    2012-01-01

    RNA-sequencing and tailored bioinformatic methodologies have paved the way for identification of expressed fusion genes from the chaotic genomes of solid tumors. We have recently successfully exploited RNA-sequencing for the discovery of 24 novel fusion genes in breast cancer. Here, we demonstrate the importance of continuous optimization of the bioinformatic methodology for this purpose, and report the discovery and experimental validation of 13 additional fusion genes from the same samples. Integration of copy number profiling with the RNA-sequencing results revealed that the majority of the gene fusions were promoter-donating events that occurred at copy number transition points or involved high-level DNA-amplifications. Sequencing of genomic fusion break points confirmed that DNA-level rearrangements underlie selected fusion transcripts. Furthermore, a significant portion (>60%) of the fusion genes were alternatively spliced. This illustrates the importance of reanalyzing sequencing data as gene definitions change and bioinformatic methods improve, and highlights the previously unforeseen isoform diversity among fusion transcripts.

  4. A Modular Plasmid Assembly Kit for Multigene Expression, Gene Silencing and Silencing Rescue in Plants

    PubMed Central

    Binder, Andreas; Lambert, Jayne; Morbitzer, Robert; Popp, Claudia; Ott, Thomas; Lahaye, Thomas; Parniske, Martin

    2014-01-01

    The Golden Gate (GG) modular assembly approach offers a standardized, inexpensive and reliable way to ligate multiple DNA fragments in a pre-defined order in a single-tube reaction. We developed a GG based toolkit for the flexible construction of binary plasmids for transgene expression in plants. Starting from a common set of modules, such as promoters, protein tags and transcribed regions of interest, synthetic genes are assembled, which can be further combined to multigene constructs. As an example, we created T-DNA constructs encoding multiple fluorescent proteins targeted to distinct cellular compartments (nucleus, cytosol, plastids) and demonstrated simultaneous expression of all genes in Nicotiana benthamiana, Lotus japonicus and Arabidopsis thaliana. We assembled an RNA interference (RNAi) module for the construction of intron-spliced hairpin RNA constructs and demonstrated silencing of GFP in N. benthamiana. By combination of the silencing construct together with a codon adapted rescue construct into one vector, our system facilitates genetic complementation and thus confirmation of the causative gene responsible for a given RNAi phenotype. As proof of principle, we silenced a destabilized GFP gene (dGFP) and restored GFP fluorescence by expression of a recoded version of dGFP, which was not targeted by the silencing construct. PMID:24551083

  5. Framework for Defining and Assessing Benefits of a Modular Assembly Design Approach for Exploration Systems

    NASA Technical Reports Server (NTRS)

    Dorsey, John T.; Collins, Timothy J.; Moe, Rud V.; Doggett,. William R.

    2006-01-01

    A comprehensive modular assembly system model has been proposed that extends the art from modular hardware, to include in-space assembly, servicing and repair and it s critical components of infrastructure, agents and assembly operations. Benefits of modular assembly have been identified and a set of metrics defined that extends the art beyond the traditional measures of performance, with emphasis on criteria that allow life-cycle mission costs to be used as a figure of merit (and include all substantive terms that have an impact on the evaluation). The modular assembly approach was used as a basis for developing a Solar Electric Transfer Vehicle (SETV) concept and three modular assembly scenarios were developed. The modular assembly approach also allows the SETV to be entered into service much earlier than competing conventional configurations and results in a great deal of versatility in accommodating different launch vehicle payload capabilities, allowing for modules to be pre-assembled before launch or assembled on orbit, without changing the space vehicle design.

  6. Decentralized Modular Systems Versus Centralized Systems.

    ERIC Educational Resources Information Center

    Crossey, R. E.

    Building design, planning, and construction programing for modular decentralized mechanical building systems are outlined in terms of costs, performance, expansion and flexibility. Design strategy, approach, and guidelines for implementing such systems for buildings are suggested, with emphasis on mechanical equipment and building element…

  7. eHealth and the use of individually tailored information: A systematic review.

    PubMed

    Conway, Nicholas; Webster, Clare; Smith, Blair; Wake, Deborah

    2017-09-01

    Tailored messages are those that specifically target individuals following an assessment of their unique characteristics. This systematic review assesses the evidence regarding the effectiveness of tailoring within eHealth interventions aimed at chronic disease management. OVID Medline/Embase databases were searched for randomised control trials, controlled clinical, trials, before -after studies, and time series analyses from inception - May 2014. Objectively measured clinical processes/outcomes were considered. Twenty-two papers were eligible for inclusion: 6/22 used fully tailored messaging and 16/22 used partially tailored messages. Two studies isolated tailoring as the active component. The remainder compared intervention with standard care. In all, 12/16 studies measuring clinical processes and 2/6 studies reporting clinical outcomes showed improvements, regardless of target group. Study quality was low and design did not allow for identification of interventions' active component. Heterogeneity precluded meta-analysis. This review has demonstrated that there is a lack of evidence to suggest that tailoring within an eHealth context confers benefit over non-tailored eHealth interventions.

  8. Preliminary design study. Shuttle modular scanning spectroradiometer

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Fundamental concepts on which to base a detailed design for a Shuttle Modular Scanning Spectroradiometer were developed, and a preliminary design is presented. The recommended design features modularity and flexibility. It includes a 75-cm f/1.7-telescope assembly in an all-reflective Schmidt configuration, a solid state scan system (pushbroom) with high resolution over a 15 deg field of view, and ten detector channels covering the spectral range from 0.45 to 12.5 micrometers. It uses charge transfer device techniques to accommodate a large number of detector elements for earth observation measurements. Methods for in-flight radiometric calibration, for image motion compensation, and for data processing are described. Recommendations for ground support equipment are included, and interfaces with the shuttle orbiter vehicle are illustrated.

  9. How to Tackle the Challenge of siRNA Delivery with Sequence-Defined Oligoamino Amides.

    PubMed

    Reinhard, Sören; Wagner, Ernst

    2017-01-01

    RNA interference (RNAi) as a mechanism of gene regulation provides exciting opportunities for medical applications. Synthetic small interfering RNA (siRNA) triggers the knockdown of complementary mRNA sequences in a catalytic fashion and has to be delivered into the cytosol of the targeted cells. The design of adequate carrier systems to overcome multiple extracellular and intracellular roadblocks within the delivery process has utmost importance. Cationic polymers form polyplexes through electrostatic interaction with negatively charged nucleic acids and present a promising class of carriers. Issues of polycations regarding toxicity, heterogeneity, and polydispersity can be overcome by solid-phase-assisted synthesis of sequence-defined cationic oligomers. These medium-sized highly versatile nucleic acid carriers display low cytotoxicity and can be modified and tailored in multiple ways to meet specific requirements of nucleic acid binding, polyplex size, shielding, targeting, and intracellular release of the cargo. In this way, sequence-defined cationic oligomers can mimic the dynamic and bioresponsive behavior of viruses. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Modular Chemical Process Intensification: A Review.

    PubMed

    Kim, Yong-Ha; Park, Lydia K; Yiacoumi, Sotira; Tsouris, Costas

    2017-06-07

    Modular chemical process intensification can dramatically improve energy and process efficiencies of chemical processes through enhanced mass and heat transfer, application of external force fields, enhanced driving forces, and combinations of different unit operations, such as reaction and separation, in single-process equipment. These dramatic improvements lead to several benefits such as compactness or small footprint, energy and cost savings, enhanced safety, less waste production, and higher product quality. Because of these benefits, process intensification can play a major role in industrial and manufacturing sectors, including chemical, pulp and paper, energy, critical materials, and water treatment, among others. This article provides an overview of process intensification, including definitions, principles, tools, and possible applications, with the objective to contribute to the future development and potential applications of modular chemical process intensification in industrial and manufacturing sectors. Drivers and barriers contributing to the advancement of process intensification technologies are discussed.

  11. Modular Heat Exchanger With Integral Heat Pipe

    NASA Technical Reports Server (NTRS)

    Schreiber, Jeffrey G.

    1992-01-01

    Modular heat exchanger with integral heat pipe transports heat from source to Stirling engine. Alternative to heat exchangers depending on integrities of thousands of brazed joints, contains only 40 brazed tubes.

  12. Walking Works Wonders: a tailored workplace intervention evaluated over 24 months.

    PubMed

    Haslam, Cheryl; Kazi, Aadil; Duncan, Myanna; Clemes, Stacy; Twumasi, Ricardo

    2018-06-22

    This article presents longitudinal data from 1120 participants across 10 worksites enrolled in Walking Works Wonders, a tailored intervention designed to increase physical activity and reduce sedentary behaviour. The intervention was evaluated over 2 years, using a quasi-experimental design comprising 3 conditions: tailored information; standard information and control. This study explored the impact of the intervention on objective measures (BMI, %Fat, waist circumference, blood pressure and heart rate) and self-reported measures of physical activity, sedentary behaviour, physical and psychological health. Interventions tailored to employees' stage of change significantly reduced BMI and waist circumference compared to standard and control conditions. Employees who received either a standard or tailored intervention demonstrated significantly higher work ability, organizational commitment, job motivation, job satisfaction, and a reduction in intention to quit the organization. The results suggest that adopting a tailored approach to interventions.

  13. Scalable detection of statistically significant communities and hierarchies, using message passing for modularity

    PubMed Central

    Zhang, Pan; Moore, Cristopher

    2014-01-01

    Modularity is a popular measure of community structure. However, maximizing the modularity can lead to many competing partitions, with almost the same modularity, that are poorly correlated with each other. It can also produce illusory ‘‘communities’’ in random graphs where none exist. We address this problem by using the modularity as a Hamiltonian at finite temperature and using an efficient belief propagation algorithm to obtain the consensus of many partitions with high modularity, rather than looking for a single partition that maximizes it. We show analytically and numerically that the proposed algorithm works all of the way down to the detectability transition in networks generated by the stochastic block model. It also performs well on real-world networks, revealing large communities in some networks where previous work has claimed no communities exist. Finally we show that by applying our algorithm recursively, subdividing communities until no statistically significant subcommunities can be found, we can detect hierarchical structure in real-world networks more efficiently than previous methods. PMID:25489096

  14. Modular Software for Spacecraft Navigation Using the Global Positioning System (GPS)

    NASA Technical Reports Server (NTRS)

    Truong, S. H.; Hartman, K. R.; Weidow, D. A.; Berry, D. L.; Oza, D. H.; Long, A. C.; Joyce, E.; Steger, W. L.

    1996-01-01

    The Goddard Space Flight Center Flight Dynamics and Mission Operations Divisions have jointly investigated the feasibility of engineering modular Global Positioning SYSTEM (GPS) navigation software to support both real time flight and ground postprocessing configurations. The goals of this effort are to define standard GPS data interfaces and to engineer standard, reusable navigation software components that can be used to build a broad range of GPS navigation support applications. The paper discusses the GPS modular software (GMOD) system and operations concepts, major requirements, candidate software architecture, feasibility assessment and recommended software interface standards. In additon, ongoing efforts to broaden the scope of the initial study and to develop modular software to support autonomous navigation using GPS are addressed,

  15. Atomic force microscopy reveals the mechanical design of a modular protein

    PubMed Central

    Li, Hongbin; Oberhauser, Andres F.; Fowler, Susan B.; Clarke, Jane; Fernandez, Julio M.

    2000-01-01

    Tandem modular proteins underlie the elasticity of natural adhesives, cell adhesion proteins, and muscle proteins. The fundamental unit of elastic proteins is their individually folded modules. Here, we use protein engineering to construct multimodular proteins composed of Ig modules of different mechanical strength. We examine the mechanical properties of the resulting tandem modular proteins by using single protein atomic force microscopy. We show that by combining modules of known mechanical strength, we can generate proteins with novel elastic properties. Our experiments reveal the simple mechanical design of modular proteins and open the way for the engineering of elastic proteins with defined mechanical properties, which can be used in tissue and fiber engineering. PMID:10823913

  16. Atomic force microscopy reveals the mechanical design of a modular protein.

    PubMed

    Li, H; Oberhauser, A F; Fowler, S B; Clarke, J; Fernandez, J M

    2000-06-06

    Tandem modular proteins underlie the elasticity of natural adhesives, cell adhesion proteins, and muscle proteins. The fundamental unit of elastic proteins is their individually folded modules. Here, we use protein engineering to construct multimodular proteins composed of Ig modules of different mechanical strength. We examine the mechanical properties of the resulting tandem modular proteins by using single protein atomic force microscopy. We show that by combining modules of known mechanical strength, we can generate proteins with novel elastic properties. Our experiments reveal the simple mechanical design of modular proteins and open the way for the engineering of elastic proteins with defined mechanical properties, which can be used in tissue and fiber engineering.

  17. Metal flow of a tailor-welded blank in deep drawing process

    NASA Astrophysics Data System (ADS)

    Yan, Qi; Guo, Ruiquan

    2005-01-01

    Tailor welded blanks were used in the automotive industry to consolidate parts, reduce weight, and increase safety. In recent years, this technology was developing rapidly in China. In Chinese car models, tailor welded blanks had been applied in a lot of automobile parts such as rail, door inner, bumper, floor panel, etc. Concerns on the properties of tailor welded blanks had become more and more important for automobile industry. A lot of research had shown that the strength of the welded seam was higher than that of the base metal, such that the weld failure in the aspect of strength was not a critical issue. However, formability of tailor welded blanks in the stamping process was complex. Among them, the metal flow of tailor welded blanks in the stamping process must be investigated thoroughly in order to reduce the scrap rate during the stamping process in automobile factories. In this paper, the behavior of metal flow for tailor welded blanks made by the laser welding process with two types of different thickness combinations were studied in the deep drawing process. Simulations and experiment verification of the movement of weld line for tailor welded blanks were discussed in detail. Results showed that the control on the movement of welded seam during stamping process by taking some measures in the aspect of blank holder was effective.

  18. Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages

    PubMed Central

    del Sol, Antonio; Araúzo-Bravo, Marcos J; Amoros, Dolors; Nussinov, Ruth

    2007-01-01

    Background Allosteric communications are vital for cellular signaling. Here we explore a relationship between protein architectural organization and shortcuts in signaling pathways. Results We show that protein domains consist of modules interconnected by residues that mediate signaling through the shortest pathways. These mediating residues tend to be located at the inter-modular boundaries, which are more rigid and display a larger number of long-range interactions than intra-modular regions. The inter-modular boundaries contain most of the residues centrally conserved in the protein fold, which may be crucial for information transfer between amino acids. Our approach to modular decomposition relies on a representation of protein structures as residue-interacting networks, and removal of the most central residue contacts, which are assumed to be crucial for allosteric communications. The modular decomposition of 100 multi-domain protein structures indicates that modules constitute the building blocks of domains. The analysis of 13 allosteric proteins revealed that modules characterize experimentally identified functional regions. Based on the study of an additional functionally annotated dataset of 115 proteins, we propose that high-modularity modules include functional sites and are the basic functional units. We provide examples (the Gαs subunit and P450 cytochromes) to illustrate that the modular architecture of active sites is linked to their functional specialization. Conclusion Our method decomposes protein structures into modules, allowing the study of signal transmission between functional sites. A modular configuration might be advantageous: it allows signaling proteins to expand their regulatory linkages and may elicit a broader range of control mechanisms either via modular combinations or through modulation of inter-modular linkages. PMID:17531094

  19. Digital Control Technologies for Modular DC-DC Converters

    NASA Technical Reports Server (NTRS)

    Button, Robert M.; Kascak, Peter E.; Lebron-Velilla, Ramon

    2002-01-01

    Recent trends in aerospace Power Management and Distribution (PMAD) systems focus on using commercial off-the-shelf (COTS) components as standard building blocks. This move to more modular designs has been driven by a desire to reduce costs and development times, but is also due to the impressive power density and efficiency numbers achieved by today's commercial DC-DC converters. However, the PMAD designer quickly learns of the hidden "costs" of using COTS converters. The most significant cost is the required addition of external input filters to meet strict electromagnetic interference (MIAMI) requirements for space systems. In fact, the high power density numbers achieved by the commercial manufacturers are greatly due to the lack of necessary input filters included in the COTS module. The NASA Glenn Research Center is currently pursuing a digital control technology that addresses this problem with modular DC-DC converters. This paper presents the digital control technologies that have been developed to greatly reduce the input filter requirements for paralleled, modular DC-DC converters. Initial test result show that the input filter's inductor size was reduced by 75 percent, and the capacitor size was reduced by 94 percent while maintaining the same power quality specifications.

  20. MIDEX Advanced Modular and Distributed Spacecraft Avionics Architecture

    NASA Technical Reports Server (NTRS)

    Ruffa, John A.; Castell, Karen; Flatley, Thomas; Lin, Michael

    1998-01-01

    MIDEX (Medium Class Explorer) is the newest line in NASA's Explorer spacecraft development program. As part of the MIDEX charter, the MIDEX spacecraft development team has developed a new modular, distributed, and scaleable spacecraft architecture that pioneers new spaceflight technologies and implementation approaches, all designed to reduce overall spacecraft cost while increasing overall functional capability. This resultant "plug and play" system dramatically decreases the complexity and duration of spacecraft integration and test, providing a basic framework that supports spacecraft modularity and scalability for missions of varying size and complexity. Together, these subsystems form a modular, flexible avionics suite that can be modified and expanded to support low-end and very high-end mission requirements with a minimum of redesign, as well as allowing a smooth, continuous infusion of new technologies as they are developed without redesigning the system. This overall approach has the net benefit of allowing a greater portion of the overall mission budget to be allocated to mission science instead of a spacecraft bus. The MIDEX scaleable architecture is currently being manufactured and tested for use on the Microwave Anisotropy Probe (MAP), an inhouse program at GSFC.

  1. A modular projection autostereoscopic system for stereo cinema

    NASA Astrophysics Data System (ADS)

    Elkhov, Victor A.; Kondratiev, Nikolai V.; Ovechkis, Yuri N.; Pautova, Larisa V.

    2009-02-01

    The lenticular raster system for 3D movies non-glasses show designed by NIKFI demonstrated commercially in Moscow in the 40'st of the last century. Essential lack of this method was narrow individual viewing zone as only two images on the film used. To solve this problem, we propose to use digital video projective system with modular principle of its design. Increase of the general number of the pixels forming the stereo image is reached by using of more than one projector. The modular projection autostereoscopic system for demonstration of the 3D movies includes diffuser screen; lenticular plate located in front of the screen; projective system consisted from several projectors and the block of parallax panoramogram fragments creator. By means of this block the parallax panoramogram is broken into fragments which quantity corresponds to number of projectors. For the large dimension lenticular screen making rectangular fragments of inclined raster were joined in a uniform leaf. To obtain the needed focal distance of the screen lenses we used immersion - aqueous solution of glycerin. The immersion also let essentially decrease visibility of fragments joints. An experimental prototype of the modular projection autostereoscopic system was created to validate proposed system.

  2. 77 FR 28861 - Secretary of Energy Advisory Board, Small Modular Reactor Subcommittee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-16

    ... DEPARTMENT OF ENERGY Secretary of Energy Advisory Board, Small Modular Reactor Subcommittee AGENCY: Department of Energy. ACTION: Notice of Open Meeting. SUMMARY: This notice announces an open meeting of the Secretary of Energy Advisory Board (SEAB), Small Modular Reactor Subcommittee (SMR). The Federal Advisory...

  3. 48 CFR 39.103 - Modular contracting.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... increments to take advantage of any evolution in technology or needs that occur during implementation and use... CATEGORIES OF CONTRACTING ACQUISITION OF INFORMATION TECHNOLOGY General 39.103 Modular contracting. (a) This section implements Section 5202, Incremental Acquisition of Information Technology, of the Clinger-Cohen...

  4. 48 CFR 39.103 - Modular contracting.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... increments to take advantage of any evolution in technology or needs that occur during implementation and use... CATEGORIES OF CONTRACTING ACQUISITION OF INFORMATION TECHNOLOGY General 39.103 Modular contracting. (a) This section implements Section 5202, Incremental Acquisition of Information Technology, of the Clinger-Cohen...

  5. 48 CFR 39.103 - Modular contracting.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... increments to take advantage of any evolution in technology or needs that occur during implementation and use... CATEGORIES OF CONTRACTING ACQUISITION OF INFORMATION TECHNOLOGY General 39.103 Modular contracting. (a) This... technology. Consistent with the agency's information technology architecture, agencies should, to the maximum...

  6. 48 CFR 39.103 - Modular contracting.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... increments to take advantage of any evolution in technology or needs that occur during implementation and use... CATEGORIES OF CONTRACTING ACQUISITION OF INFORMATION TECHNOLOGY General 39.103 Modular contracting. (a) This section implements Section 5202, Incremental Acquisition of Information Technology, of the Clinger-Cohen...

  7. Modular-extramodular organization in developing multisensory shell regions of the mouse inferior colliculus.

    PubMed

    Dillingham, Christopher H; Gay, Sean M; Behrooz, Roxana; Gabriele, Mark L

    2017-12-01

    The complex neuroanatomical connections of the inferior colliculus (IC) and its major subdivisions offer a juxtaposition of segregated processing streams with distinct organizational features. While the tonotopically layered central nucleus is well-documented, less is known about functional compartments in the neighboring lateral cortex (LCIC). In addition to a laminar framework, LCIC afferent-efferent patterns suggest a multimodal mosaic, consisting of a patchy modular network with surrounding extramodular domains. This study utilizes several neurochemical markers that reveal an emerging LCIC modular-extramodular microarchitecture. In newborn and post-hearing C57BL/6J and CBA/CaJ mice, histochemical and immunocytochemical stains were performed for acetylcholinesterase (AChE), nicotinamide adenine dinucleotide phosphate-diaphorase (NADPH-d), glutamic acid decarboxylase (GAD), cytochrome oxidase (CO), and calretinin (CR). Discontinuous layer 2 modules are positive for AChE, NADPH-d, GAD, and CO throughout the rostrocaudal LCIC. While not readily apparent at birth, discrete cell clusters emerge over the first postnatal week, yielding an identifiable modular network prior to hearing onset. Modular boundaries continue to become increasingly distinct with age, as surrounding extramodular fields remain largely negative for each marker. Alignment of modular markers in serial sections suggests each highlight the same periodic patchy network throughout the nascent LCIC. In contrast, CR patterns appear complementary, preferentially staining extramodular LCIC zones. Double-labeling experiments confirm that NADPH-d, the most consistent developmental modular marker, and CR label separate, nonoverlapping LCIC compartments. Determining how this emerging modularity may align with similar LCIC patch-matrix-like Eph/ephrin guidance patterns, and how each interface with, and potentially influence developing multimodal LCIC projection configurations is discussed. © 2017 Wiley

  8. Does nasal echolocation influence the modularity of the mammal skull?

    PubMed

    Santana, S E; Lofgren, S E

    2013-11-01

    In vertebrates, changes in cranial modularity can evolve rapidly in response to selection. However, mammals have apparently maintained their pattern of cranial integration throughout their evolutionary history and across tremendous morphological and ecological diversity. Here, we use phylogenetic, geometric morphometric and comparative analyses to test the hypothesis that the modularity of the mammalian skull has been remodelled in rhinolophid bats due to the novel and critical function of the nasal cavity in echolocation. We predicted that nasal echolocation has resulted in the evolution of a third cranial module, the 'nasal dome', in addition to the braincase and rostrum modules, which are conserved across mammals. We also test for similarities in the evolution of skull shape in relation to habitat across rhinolophids. We find that, despite broad variation in the shape of the nasal dome, the integration of the rhinolophid skull is highly consistent with conserved patterns of modularity found in other mammals. Across their broad geographical distribution, cranial shape in rhinolophids follows two major divisions that could reflect adaptations to dietary and environmental differences in African versus South Asian distributions. Our results highlight the potential of a relatively simple modular template to generate broad morphological and functional variation in mammals. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  9. Modular, Reconfigurable, and Rapid Response Space Systems: The Remote Sensing Advanced Technology Microsatellite

    NASA Technical Reports Server (NTRS)

    Esper, Jaime; Andary, Jim; Oberright, John; So, Maria; Wegner, Peter; Hauser, Joe

    2004-01-01

    Modular, Reconfigurable, and Rapid-response (MR(sup 2)) space systems represent a paradigm shift in the way space assets of all sizes are designed, manufactured, integrated, tested, and flown. This paper will describe the MR(sup 2) paradigm in detail, and will include guidelines for its implementation. The Remote Sensing Advanced Technology microsatellite (RSAT) is a proposed flight system test-bed used for developing and implementing principles and best practices for MR(sup 2) spacecraft, and their supporting infrastructure. The initial goal of this test-bed application is to produce a lightweight (approx. 100 kg), production-minded, cost-effective, and scalable remote sensing micro-satellite capable of high performance and broad applicability. Such applications range from future distributed space systems, to sensor-webs, and rapid-response satellite systems. Architectures will be explored that strike a balance between modularity and integration while preserving the MR(sup 2) paradigm. Modularity versus integration has always been a point of contention when approaching a design: whereas one-of-a-kind missions may require close integration resulting in performance optimization, multiple and flexible application spacecraft benefit &om modularity, resulting in maximum flexibility. The process of building spacecraft rapidly (< 7 days), requires a concerted and methodical look at system integration and test processes and pitfalls. Although the concept of modularity is not new and was first developed in the 1970s by NASA's Goddard Space Flight Center (Multi-Mission Modular Spacecraft), it was never modernized and was eventually abandoned. Such concepts as the Rapid Spacecraft Development Office (RSDO) became the preferred method for acquiring satellites. Notwithstanding, over the past 30 years technology has advanced considerably, and the time is ripe to reconsider modularity in its own right, as enabler of R(sup 2), and as a key element of transformational systems. The

  10. Towards a sustainable modular robot system for planetary exploration

    NASA Astrophysics Data System (ADS)

    Hossain, S. G. M.

    This thesis investigates multiple perspectives of developing an unmanned robotic system suited for planetary terrains. In this case, the unmanned system consists of unit-modular robots. This type of robot has potential to be developed and maintained as a sustainable multi-robot system while located far from direct human intervention. Some characteristics that make this possible are: the cooperation, communication and connectivity among the robot modules, flexibility of individual robot modules, capability of self-healing in the case of a failed module and the ability to generate multiple gaits by means of reconfiguration. To demonstrate the effects of high flexibility of an individual robot module, multiple modules of a four-degree-of-freedom unit-modular robot were developed. The robot was equipped with a novel connector mechanism that made self-healing possible. Also, design strategies included the use of series elastic actuators for better robot-terrain interaction. In addition, various locomotion gaits were generated and explored using the robot modules, which is essential for a modular robot system to achieve robustness and thus successfully navigate and function in a planetary environment. To investigate multi-robot task completion, a biomimetic cooperative load transportation algorithm was developed and simulated. Also, a liquid motion-inspired theory was developed consisting of a large number of robot modules. This can be used to traverse obstacles that inevitably occur in maneuvering over rough terrains such as in a planetary exploration. Keywords: Modular robot, cooperative robots, biomimetics, planetary exploration, sustainability.

  11. Tailoring the Crystal Structure Toward Optimal Super Conductors

    DTIC Science & Technology

    2016-06-23

    AFRL-AFOSR-VA-TR-2016-0210 TAILORING THE CRYSTAL STRUCTURE TOWARD OPTIMAL SUPERCONDUCTORS Emilia Morosan WILLIAM MARSH RICE UNIV HOUSTON TX Final...TAILORING THE CRYSTAL STRUCTURE TOWARD OPTIMAL SUPERCONDUCTORS 5a. CONTRACT NUMBER FA9550-11-1-0023 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...studied the properties of layered transition metal compounds in search of unconventional superconductors . The aim is to identify ground states competing

  12. Tailoring Software Inspections for Aspect-Oriented Programming

    ERIC Educational Resources Information Center

    Watkins, Charlette Ward

    2009-01-01

    Aspect-Oriented Software Development (AOSD) is a new approach that addresses limitations inherent in conventional programming, especially the principle of separation of concerns by emphasizing the encapsulation and modularization of crosscutting concerns through a new abstraction, the "aspect." Aspect-oriented programming is an emerging AOSD…

  13. Modularity in developmental biology and artificial organs: a missing concept in tissue engineering.

    PubMed

    Lenas, Petros; Luyten, Frank P; Doblare, Manuel; Nicodemou-Lena, Eleni; Lanzara, Andreina Elena

    2011-06-01

    Tissue engineering is reviving itself, adopting the concept of biomimetics of in vivo tissue development. A basic concept of developmental biology is the modularity of the tissue architecture according to which intermediates in tissue development constitute semiautonomous entities. Both engineering and nature have chosen the modular architecture to optimize the product or organism development and evolution. Bioartificial tissues do not have a modular architecture. On the contrary, artificial organs of modular architecture have been already developed in the field of artificial organs. Therefore the conceptual support of tissue engineering by the field of artificial organs becomes critical in its new endeavor of recapitulating in vitro the in vivo tissue development. © 2011, Copyright the Authors. Artificial Organs © 2011, International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

  14. The Effects of Tailoring Knowledge Acquisition on Colorectal Cancer Screening Self-Efficacy

    PubMed Central

    Jerant, Anthony; To, Patricia; Franks, Peter

    2015-01-01

    Interventions tailored to psychological factors such as personal and vicarious behavioral experiences can enhance behavioral self-efficacy, but are complex to develop and implement. Information seeking theory suggests tailoring acquisition of health knowledge (without concurrent psychological factor tailoring) could enhance self-efficacy, simplifying the design of tailored behavior change interventions. To begin to examine this issue, the authors conducted exploratory analyses of data from a randomized controlled trial, comparing the effects of an experimental colorectal cancer (CRC) screening intervention tailoring knowledge acquisition with the effects of a non-tailored control on CRC screening knowledge and self-efficacy in 1159 patients comprising three ethnicity/language strata (Hispanic/Spanish 23.4%, Hispanic/English 27.2%, non-Hispanic/English 49.3%) and five recruitment center strata. Adjusted for study strata, the mean post-intervention knowledge score was significantly higher in the experimental group versus control. Adjusted experimental intervention exposure (B = 0.22, 95% CI [0.14, 0.30]), pre-intervention knowledge (B = 0.11, 95% CI [0.05, 0.16]), and post-intervention knowledge (B = 0.03, 95% CI [0.01, 0.05]) were independently associated with subsequent CRC screening self-efficacy (p < .001 all associations). These exploratory findings suggest tailoring knowledge acquisition may enhance self-efficacy, with potential implications for tailored intervention design, but require confirmation in studies specifically designed to examine this issue. PMID:25928315

  15. RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.

    PubMed

    D'Antonio, Mattia; D'Onorio De Meo, Paolo; Pallocca, Matteo; Picardi, Ernesto; D'Erchia, Anna Maria; Calogero, Raffaele A; Castrignanò, Tiziana; Pesole, Graziano

    2015-01-01

    The study of RNA has been dramatically improved by the introduction of Next Generation Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions, also providing information on strand orientation (RNA-Seq). The complexity of transcriptomes and of their regulative pathways make RNA-Seq one of most complex field of NGS applications, addressing several aspects of the expression process (e.g. identification and quantification of expressed genes and transcripts, alternative splicing and polyadenylation, fusion genes and trans-splicing, post-transcriptional events, etc.). In order to provide researchers with an effective and friendly resource for analyzing RNA-Seq data, we present here RAP (RNA-Seq Analysis Pipeline), a cloud computing web application implementing a complete but modular analysis workflow. This pipeline integrates both state-of-the-art bioinformatics tools for RNA-Seq analysis and in-house developed scripts to offer to the user a comprehensive strategy for data analysis. RAP is able to perform quality checks (adopting FastQC and NGS QC Toolkit), identify and quantify expressed genes and transcripts (with Tophat, Cufflinks and HTSeq), detect alternative splicing events (using SpliceTrap) and chimeric transcripts (with ChimeraScan). This pipeline is also able to identify splicing junctions and constitutive or alternative polyadenylation sites (implementing custom analysis modules) and call for statistically significant differences in genes and transcripts expression, splicing pattern and polyadenylation site usage (using Cuffdiff2 and DESeq). Through a user friendly web interface, the RAP workflow can be suitably customized by the user and it is automatically executed on our cloud computing environment. This strategy allows to access to bioinformatics tools and computational resources without specific bioinformatics and IT skills. RAP provides a set of tabular and graphical results that can be helpful to browse, filter and export

  16. Coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures

    NASA Technical Reports Server (NTRS)

    Hartle, M. S.; Mcknight, R. L.; Huang, H.; Holt, R.

    1992-01-01

    Described here are the accomplishments of a 5-year program to develop a methodology for coupled structural, thermal, electromagnetic analysis tailoring of graded component structures. The capabilities developed over the course of the program are the analyzer module and the tailoring module for the modeling of graded materials. Highlighted accomplishments for the past year include the addition of a buckling analysis capability, the addition of mode shape slope calculation for flutter analysis, verification of the analysis modules using simulated components, and verification of the tailoring module.

  17. Comparing homeless persons' care experiences in tailored versus nontailored primary care programs.

    PubMed

    Kertesz, Stefan G; Holt, Cheryl L; Steward, Jocelyn L; Jones, Richard N; Roth, David L; Stringfellow, Erin; Gordon, Adam J; Kim, Theresa W; Austin, Erika L; Henry, Stephen Randal; Kay Johnson, N; Shanette Granstaff, U; O'Connell, James J; Golden, Joya F; Young, Alexander S; Davis, Lori L; Pollio, David E

    2013-12-01

    We compared homeless patients' experiences of care in health care organizations that differed in their degree of primary care design service tailoring. We surveyed homeless-experienced patients (either recently or currently homeless) at 3 Veterans Affairs (VA) mainstream primary care settings in Pennsylvania and Alabama, a homeless-tailored VA clinic in California, and a highly tailored non-VA Health Care for the Homeless Program in Massachusetts (January 2011-March 2012). We developed a survey, the "Primary Care Quality-Homeless Survey," to reflect the concerns and aspirations of homeless patients. Mean scores at the tailored non-VA site were superior to those from the 3 mainstream VA sites (P < .001). Adjusting for patient characteristics, these differences remained significant for subscales assessing the patient-clinician relationship (P < .001) and perceptions of cooperation among providers (P = .004). There were 1.5- to 3-fold increased odds of an unfavorable experience in the domains of the patient-clinician relationship, cooperation, and access or coordination for the mainstream VA sites compared with the tailored non-VA site; the tailored VA site attained intermediate results. Tailored primary care service design was associated with a superior service experience for patients who experienced homelessness.

  18. Investigation on changes of modularity and robustness by edge-removal mutations in signaling networks.

    PubMed

    Truong, Cong-Doan; Kwon, Yung-Keun

    2017-12-21

    Biological networks consisting of molecular components and interactions are represented by a graph model. There have been some studies based on that model to analyze a relationship between structural characteristics and dynamical behaviors in signaling network. However, little attention has been paid to changes of modularity and robustness in mutant networks. In this paper, we investigated the changes of modularity and robustness by edge-removal mutations in three signaling networks. We first observed that both the modularity and robustness increased on average in the mutant network by the edge-removal mutations. However, the modularity change was negatively correlated with the robustness change. This implies that it is unlikely that both the modularity and the robustness values simultaneously increase by the edge-removal mutations. Another interesting finding is that the modularity change was positively correlated with the degree, the number of feedback loops, and the edge betweenness of the removed edges whereas the robustness change was negatively correlated with them. We note that these results were consistently observed in randomly structure networks. Additionally, we identified two groups of genes which are incident to the highly-modularity-increasing and the highly-robustness-decreasing edges with respect to the edge-removal mutations, respectively, and observed that they are likely to be central by forming a connected component of a considerably large size. The gene-ontology enrichment of each of these gene groups was significantly different from the rest of genes. Finally, we showed that the highly-robustness-decreasing edges can be promising edgetic drug-targets, which validates the usefulness of our analysis. Taken together, the analysis of changes of robustness and modularity against edge-removal mutations can be useful to unravel novel dynamical characteristics underlying in signaling networks.

  19. CRISPR Display: A modular method for locus-specific targeting of long noncoding RNAs and synthetic RNA devices in vivo

    PubMed Central

    Shechner, David M.; Hacisüleyman, Ezgi; Younger, Scott T.; Rinn, John L.

    2016-01-01

    Noncoding RNAs (ncRNAs) comprise an important class of regulatory molecules that mediate a vast array of biological processes. This broad functional capacity has also facilitated the design of artificial ncRNAs with novel functions. To further investigate and harness these capabilities, we developed CRISPR-Display (“CRISP-Disp”), a targeted localization method that uses Sp. Cas9 to deploy large RNA cargos to DNA loci. We demonstrate that exogenous RNA domains can be functionally appended onto the CRISPR scaffold at multiple insertion points, allowing the construction of Cas9 complexes with protein-binding cassettes, artificial aptamers, pools of random sequences, and RNAs up to 4.8 kilobases in length, including natural lncRNAs. Unlike most existing CRISPR methods, CRISP-Disp allows simultaneous multiplexing of distinct functions at multiple targets, limited only by the number of available functional RNA motifs. We anticipate that this technology will provide a powerful method with which to ectopically localize functional RNAs and ribonucleoprotein (RNP) complexes at specified genomic loci. PMID:26030444

  20. Induction of RNA interference in dendritic cells.

    PubMed

    Li, Mu; Qian, Hua; Ichim, Thomas E; Ge, Wei-Wen; Popov, Igor A; Rycerz, Katarzyna; Neu, John; White, David; Zhong, Robert; Min, Wei-Ping

    2004-01-01

    Dendritic cells (DC) reside at the center of the immunological universe, possessing the ability both to stimulate and inhibit various types of responses. Tolerogenic/regulatory DC with therapeutic properties can be generated through various means of manipulations in vitro and in vivo. Here we describe several attractive strategies for manipulation of DC using the novel technique of RNA interference (RNAi). Additionally, we overview some of our data regarding yet undescribed characteristics of RNAi in DC such as specific transfection strategies, persistence of gene silencing, and multi-gene silencing. The advantages of using RNAi for DC genetic manipulation gives rise to the promise of generating tailor-made DC that can be used effectively to treat a variety of immunologically mediated diseases.

  1. Modular cryogenic interconnects for multi-qubit devices.

    PubMed

    Colless, J I; Reilly, D J

    2014-11-01

    We have developed a modular interconnect platform for the control and readout of multiple solid-state qubits at cryogenic temperatures. The setup provides 74 filtered dc-bias connections, 32 control and readout connections with -3 dB frequency above 5 GHz, and 4 microwave feed lines that allow low loss (less than 3 dB) transmission 10 GHz. The incorporation of a radio-frequency interposer enables the platform to be separated into two printed circuit boards, decoupling the simple board that is bonded to the qubit chip from the multilayer board that incorporates expensive connectors and components. This modular approach lifts the burden of duplicating complex interconnect circuits for every prototype device. We report the performance of this platform at milli-Kelvin temperatures, including signal transmission and crosstalk measurements.

  2. Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform.

    PubMed

    Mládek, Arnošt; Sponer, Judit E; Kulhánek, Petr; Lu, Xiang-Jun; Olson, Wilma K; Sponer, Jiřĺ

    2012-01-10

    Folded RNA molecules are shaped by an astonishing variety of highly conserved noncanonical molecular interactions and backbone topologies. The dinucleotide platform is a widespread recurrent RNA modular building submotif formed by the side-by-side pairing of bases from two consecutive nucleotides within a single strand, with highly specific sequence preferences. This unique arrangement of bases is cemented by an intricate network of noncanonical hydrogen bonds and facilitated by a distinctive backbone topology. The present study investigates the gas-phase intrinsic stabilities of the three most common RNA dinucleotide platforms - 5'-GpU-3', ApA, and UpC - via state-of-the-art quantum-chemical (QM) techniques. The mean stability of base-base interactions decreases with sequence in the order GpU > ApA > UpC. Bader's atoms-in-molecules analysis reveals that the N2(G)…O4(U) hydrogen bond of the GpU platform is stronger than the corresponding hydrogen bonds in the other two platforms. The mixed-pucker sugar-phosphate backbone conformation found in most GpU platforms, in which the 5'-ribose sugar (G) is in the C2'-endo form and the 3'-sugar (U) in the C3'-endo form, is intrinsically more stable than the standard A-RNA backbone arrangement, partially as a result of a favorable O2'…O2P intra-platform interaction. Our results thus validate the hypothesis of Lu et al. (Lu Xiang-Jun, et al. Nucleic Acids Res. 2010, 38, 4868-4876), that the superior stability of GpU platforms is partially mediated by the strong O2'…O2P hydrogen bond. In contrast, ApA and especially UpC platform-compatible backbone conformations are rather diverse and do not display any characteristic structural features. The average stabilities of ApA and UpC derived backbone conformers are also lower than those of GpU platforms. Thus, the observed structural and evolutionary patterns of the dinucleotide platforms can be accounted for, to a large extent, by their intrinsic properties as described by

  3. A modular approach to adaptive structures.

    PubMed

    Pagitz, Markus; Pagitz, Manuel; Hühne, Christian

    2014-10-07

    A remarkable property of nastic, shape changing plants is their complete fusion between actuators and structure. This is achieved by combining a large number of cells whose geometry, internal pressures and material properties are optimized for a given set of target shapes and stiffness requirements. An advantage of such a fusion is that cell walls are prestressed by cell pressures which increases, decreases the overall structural stiffness, weight. Inspired by the nastic movement of plants, Pagitz et al (2012 Bioinspir. Biomim. 7) published a novel concept for pressure actuated cellular structures. This article extends previous work by introducing a modular approach to adaptive structures. An algorithm that breaks down any continuous target shapes into a small number of standardized modules is presented. Furthermore it is shown how cytoskeletons within each cell enhance the properties of adaptive modules. An adaptive passenger seat and an aircrafts leading, trailing edge is used to demonstrate the potential of a modular approach.

  4. SMEX-Lite Modular Solar Array Architecture

    NASA Technical Reports Server (NTRS)

    Lyons, John W.; Day, John (Technical Monitor)

    2002-01-01

    The NASA Small Explorer (SMEX) missions have typically had three years between mission definition and launch. This short schedule has posed significant challenges with respect to solar array design and procurement. Typically, the solar panel geometry is frozen prior to going out with a procurement. However, with the SMEX schedule, it has been virtually impossible to freeze the geometry in time to avoid scheduling problems with integrating the solar panels to the spacecraft. A modular solar array architecture was developed to alleviate this problem. This approach involves procuring sufficient modules for multiple missions and assembling the modules onto a solar array framework that is unique to each mission. The modular approach removes the solar array from the critical path of the SMEX integration and testing schedule. It also reduces the cost per unit area of the solar arrays and facilitates the inclusion of experiments involving new solar cell or panel technologies in the SMEX missions.

  5. The Modular Optical Underwater Survey System

    PubMed Central

    Amin, Ruhul; Richards, Benjamin L.; Misa, William F. X. E.; Taylor, Jeremy C.; Miller, Dianna R.; Rollo, Audrey K.; Demarke, Christopher; Ossolinski, Justin E.; Reardon, Russell T.; Koyanagi, Kyle H.

    2017-01-01

    The Pacific Islands Fisheries Science Center deploys the Modular Optical Underwater Survey System (MOUSS) to estimate the species-specific, size-structured abundance of commercially-important fish species in Hawaii and the Pacific Islands. The MOUSS is an autonomous stereo-video camera system designed for the in situ visual sampling of fish assemblages. This system is rated to 500 m and its low-light, stereo-video cameras enable identification, counting, and sizing of individuals at a range of 0.5–10 m. The modular nature of MOUSS allows for the efficient and cost-effective use of various imaging sensors, power systems, and deployment platforms. The MOUSS is in use for surveys in Hawaii, the Gulf of Mexico, and Southern California. In Hawaiian waters, the system can effectively identify individuals to a depth of 250 m using only ambient light. In this paper, we describe the MOUSS’s application in fisheries research, including the design, calibration, analysis techniques, and deployment mechanism. PMID:29019962

  6. [Modularization by the open standard. (I)].

    PubMed

    Hirano, H

    2000-10-01

    We are proceeding with the project called "Open LA21 Project" in the course of the clinical laboratory automation toward the 21st century. With the modular system that realizes integration, downsizing, a reasonable price, and is the future course in the clinical testing automation system as well, we aim to establish common standards among manufacturers as the only way to create user friendly market environments where the proper competition exists among the manufacturers. The common standards which are in preparation by the participating companies as "Open module system standards" are the standards which are going to be made public. They are intended to guarantee connection, compatibility of the products in conformity with the standards. In this project, we intend to realize the modular system that integrates each field, such as chemistry, hematology, coagulation/fibrinolysis, immunology, urinalysis in an early stage, and contribute positively to restructuring and upgrading the "raison d'etre" of the 21st century clinical testing.

  7. Modular Chemical Process Intensification: A Review

    DOE PAGES

    Kim, Yong-ha; Park, Lydia K.; Yiacoumi, Sotira; ...

    2016-06-24

    Modular chemical process intensification can dramatically improve energy and process efficiencies of chemical processes through enhanced mass and heat transfer, application of external force fields, enhanced driving forces, and combinations of different unit operations, such as reaction and separation, in single-process equipment. Dramatic improvements such as these lead to several benefits such as compactness or small footprint, energy and cost savings, enhanced safety, less waste production, and higher product quality. Because of these benefits, process intensification can play a major role in industrial and manufacturing sectors, including chemical, pulp and paper, energy, critical materials, and water treatment, among others. Thismore » article provides an overview of process intensification, including definitions, principles, tools, and possible applications, with the objective to contribute to the future development and potential applications of modular chemical process intensification in industrial and manufacturing sectors. Drivers and barriers contributing to the advancement of process intensification technologies are discussed.« less

  8. Tailored tools to improve pharmacotherapy in infants.

    PubMed

    Allegaert, Karel

    2014-08-01

    Extensive within-population variability is the essence of neonatal pharmacology. Despite this, infants remain one of the last therapeutic orphans. Together with additional legal initiatives, tailoring of already available tools (modeling, covariates, pharmacovigilance) may significantly improve pharmacotherapy in infants. Modeling approaches that hold the promise to improve pharmacotherapy in infants are between-compound extrapolation for compounds that undergo the same route of elimination and integration of time-varying physiology to adapt for the fast maturational changes. Besides these maturational covariates (size, age), newly emerging covariates relate to novel treatment modalities (extracorporeal circulation, hypothermia), environmental issues (microbiome, critical illness) or pharmacogenetics. All these covariates interact with the maturational variation. Finally, pharmacovigilance also needs to be tailored to the characteristics of this population. This relates to preventive strategies, signal detection and assessment of causality. Knowledge on pharmacotherapy in infants is lagging. Tailoring available tools to the specific characteristics (maturation) and clinical needs (newly emerging covariates) of infants is feasible but needs creativity and a multidisciplinary collaboration between modelers, academia, clinical researchers and, obviously, the public, including parents.

  9. Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein.

    PubMed

    Yan, Winston X; Chong, Shaorong; Zhang, Huaibin; Makarova, Kira S; Koonin, Eugene V; Cheng, David R; Scott, David A

    2018-04-19

    Bacterial class 2 CRISPR-Cas systems utilize a single RNA-guided protein effector to mitigate viral infection. We aggregated genomic data from multiple sources and constructed an expanded database of predicted class 2 CRISPR-Cas systems. A search for novel RNA-targeting systems identified subtype VI-D, encoding dual HEPN domain-containing Cas13d effectors and putative WYL-domain-containing accessory proteins (WYL1 and WYL-b1 through WYL-b5). The median size of Cas13d proteins is 190 to 300 aa smaller than that of Cas13a-Cas13c. Despite their small size, Cas13d orthologs from Eubacterium siraeum (Es) and Ruminococcus sp. (Rsp) are active in both CRISPR RNA processing and targeting, as well as collateral RNA cleavage, with no target-flanking sequence requirements. The RspWYL1 protein stimulates RNA cleavage by both EsCas13d and RspCas13d, demonstrating a common regulatory mechanism for divergent Cas13d orthologs. The small size, minimal targeting constraints, and modular regulation of Cas13d effectors further expands the CRISPR toolkit for RNA manipulation and detection. Copyright © 2018 Elsevier Inc. All rights reserved.

  10. A Comparison of a Bayesian and a Maximum Likelihood Tailored Testing Procedure.

    ERIC Educational Resources Information Center

    McKinley, Robert L.; Reckase, Mark D.

    A study was conducted to compare tailored testing procedures based on a Bayesian ability estimation technique and on a maximum likelihood ability estimation technique. The Bayesian tailored testing procedure selected items so as to minimize the posterior variance of the ability estimate distribution, while the maximum likelihood tailored testing…

  11. LPWA using supersonic gas jet with tailored density profile

    NASA Astrophysics Data System (ADS)

    Kononenko, O.; Bohlen, S.; Dale, J.; D'Arcy, R.; Dinter, M.; Erbe, J. H.; Indorf, G.; di Lucchio, L.; Goldberg, L.; Gruse, J. N.; Karstensen, S.; Libov, V.; Ludwig, K.; Martinez de La Ossa, A.; Marutzky, F.; Niroula, A.; Osterhoff, J.; Quast, M.; Schaper, L.; Schwinkendorf, J.-P.; Streeter, M.; Tauscher, G.; Weichert, S.; Palmer, C.; Horbatiuk, Taras

    2016-10-01

    Laser driven plasma wakefield accelerators have been explored as a potential compact, reproducible source of relativistic electron bunches, utilising an electric field of many GV/m. Control over injection of electrons into the wakefield is of crucial importance in producing stable, mono-energetic electron bunches. Density tailoring of the target, to control the acceleration process, can also be used to improve the quality of the bunch. By using gas jets to provide tailored targets it is possible to provide good access for plasma diagnostics while also producing sharp density gradients for density down-ramp injection. OpenFOAM hydrodynamic simulations were used to investigate the possibility of producing tailored density targets in a supersonic gas jet. Particle-in-cell simulations of the resulting density profiles modelled the effect of the tailored density on the properties of the accelerated electron bunch. Here, we present the simulation results together with preliminary experimental measurements of electron and x-ray properties from LPWA experiments using gas jet targets and a 25 TW, 25 fs Ti:Sa laser system at DESY.

  12. RNA mediated assembly of nanostructures

    NASA Astrophysics Data System (ADS)

    Rouge, Jessica Lynn

    The first chapter of this work presents a comprehensive look at RNA mediated nanoparticle formation. The overall goal of this research is to gain a deeper understanding of the RNA-particle formation mechanism and the basic properties of the materials selected by modified RNA molecules. Understanding such RNA-substrate interactions and how they translate into the physical and chemical characteristics of the nanoparticles they create are important fundamental concepts when considering these biotemplated materials as potential chemical catalysts. The RNA sequences discussed in the first chapter (referred to as Pdases) were discovered using RNA in vitro selection techniques. These Pdases were found to be capable of forming inorganic palladium (Pd) containing nanoparticles with impressive control over an individual particle's size and shape, despite incubation with the same organometallic precursor. This discovery held exciting implications for inorganic nanoparticle design while also generating numerous questions regarding the mechanism of RNA mediated particle growth. The central question that arose after this initial discovery was how could a biomolecule be used to tailor the physical size and shape of inorganic materials? Starting with a chemical proof designed to uncover the composition of the nanoparticles formed by RNA mediation, this chapter investigates the basic material properties of the nanoparticles while also introducing surprising results regarding the effect of multiple sequences on nanoparticle growth outcomes. In the second chapter, the experiments shift to developing methods to investigate nanoparticle growth mechanisms by fluorescence spectroscopy. A fluorescence polarization anisotropy (FPA) assay is presented in which the strengths of the technique are adapted for studying the formation of RNA mediated Pd nanoparticles in real time. This is a unique application of FPA, as it has been adapted to encompass both the biochemical and materials analysis

  13. Modularity, Working Memory and Language Acquisition

    ERIC Educational Resources Information Center

    Baddeley, Alan D.

    2017-01-01

    The concept of modularity is used to contrast the approach to working memory proposed by Truscott with the Baddeley and Hitch multicomponent model. This proposes four sub components comprising the "central executive," an executive control system of limited attentional capacity that utilises storage based on separate but interlinked…

  14. A Modular Curriculum in Information Studies.

    ERIC Educational Resources Information Center

    Large, J. A.

    Prepared under a contract between UNESCO and IFLA (the International Federation of Library Associations), this modular curriculum is intended as a resource from which curricula can be constructed by individual departments of information studies to meet local needs and circumstances. Following an introductory discussion and explanation of the…

  15. Multi-scale modularity and motif distributional effect in metabolic networks.

    PubMed

    Gao, Shang; Chen, Alan; Rahmani, Ali; Zeng, Jia; Tan, Mehmet; Alhajj, Reda; Rokne, Jon; Demetrick, Douglas; Wei, Xiaohui

    2016-01-01

    Metabolism is a set of fundamental processes that play important roles in a plethora of biological and medical contexts. It is understood that the topological information of reconstructed metabolic networks, such as modular organization, has crucial implications on biological functions. Recent interpretations of modularity in network settings provide a view of multiple network partitions induced by different resolution parameters. Here we ask the question: How do multiple network partitions affect the organization of metabolic networks? Since network motifs are often interpreted as the super families of evolved units, we further investigate their impact under multiple network partitions and investigate how the distribution of network motifs influences the organization of metabolic networks. We studied Homo sapiens, Saccharomyces cerevisiae and Escherichia coli metabolic networks; we analyzed the relationship between different community structures and motif distribution patterns. Further, we quantified the degree to which motifs participate in the modular organization of metabolic networks.

  16. Evaluating Psychosocial and Behavioral Mechanisms of Change in a Tailored Communication Intervention

    ERIC Educational Resources Information Center

    Elder, John P.; Ayala, Guadalupe X.; Slymen, Donald J.; Arredondo, Elva M.; Campbell, Nadia R.

    2009-01-01

    This study examined the impact of a tailored nutrition intervention at 3 and 6 months postintervention. In all, 357 Latinas were randomly assigned to one of three conditions: (1) a control condition comprised of previously developed Spanish language targeted materials, (2) tailored print materials, or (3) tailored print materials accompanied by…

  17. Cost-effectiveness of targeted and tailored interventions on colorectal cancer screening use.

    PubMed

    Lairson, David R; DiCarlo, Melissa; Myers, Ronald E; Wolf, Thomas; Cocroft, James; Sifri, Randa; Rosenthal, Michael; Vernon, Sally W; Wender, Richard

    2008-02-15

    Colorectal cancer (CRC) screening is cost-effective but underused. The objective of this study was to determine the cost-effectiveness of targeted and tailored behavioral interventions to increase CRC screening use by conducting an economic analysis associated with a randomized trial among patients in a large, racially and ethnically diverse, urban family practice in Philadelphia. The incremental costs per unit increase were measured in individuals who were screened during the 24 months after intervention. Percent increase in screening was adjusted for baseline differences in the study groups. Each intervention arm received a targeted screening invitation letter, stool blood test (SBT) cards, informational booklet, and reminder letter. Tailored interventions incrementally added tailored messages and reminder telephone calls. Program costs of the targeted intervention were 42 dollars per participant. Additional costs of adding tailored print materials and of delivering a reminder telephone call were 150 dollars and 200 dollars per participant, respectively. The cost per additional individual screened was 319 dollars when comparing the no intervention group with the targeted intervention group. The targeted intervention was more effective and less costly than the tailored intervention. Although tailoring plus reminder telephone call was the most effective strategy, it was very costly per additional individual screened. Mailed SBT cards significantly boosted CRC screening use. However, going beyond the targeted intervention to include tailoring or tailoring plus reminder calls in the manner used in this study did not appear to be an economically attractive strategy. Cancer 2008. (c) 2007 American Cancer Society.

  18. Addressing medication nonadherence by mobile phone: development and delivery of tailored messages.

    PubMed

    Gatwood, Justin; Balkrishnan, Rajesh; Erickson, Steven R; An, Lawrence C; Piette, John D; Farris, Karen B

    2014-01-01

    Medication nonadherence remains a significant public health problem, and efforts to improve adherence have shown only limited impact. The tailoring of messages has become a popular method of developing communication to influence specific health-related behaviors but the development and impact of tailored text messages on medication use is poorly understood. The aim of this paper is to describe an approach to developing theory-based tailored messages for delivery via mobile phone to improve medication adherence among patients with diabetes. Kreuter's five-step tailoring process was followed to create tailored messages for mobile phone delivery. Two focus group sessions, using input from 11 people, and expert review of message content were used to adapt the survey instrument on which the messages were tailored and edit the developed messages for the target population. Following established tailoring methods a library of 168 theory-driven and 128 medication-specific tailored messages were developed and formatted for automated delivery to mobile phones. Concepts from the Health Belief Model and Self-Determination Theory were used to craft the messages and an algorithm was applied to determine the order and timing of messages with the aim of progressively influencing disease and treatment-related beliefs driving adherence to diabetes medication. The process described may be applied to future investigations aiming to improve medication adherence in patients with diabetes and the effectiveness of the current messages will be tested in a planned analysis. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Retroactivity in the Context of Modularly Structured Biomolecular Systems

    PubMed Central

    Pantoja-Hernández, Libertad; Martínez-García, Juan Carlos

    2015-01-01

    Synthetic biology has intensively promoted the technical implementation of modular strategies in the fabrication of biological devices. Modules are considered as networks of reactions. The behavior displayed by biomolecular systems results from the information processes carried out by the interconnection of the involved modules. However, in natural systems, module wiring is not a free-of-charge process; as a consequence of interconnection, a reactive phenomenon called retroactivity emerges. This phenomenon is characterized by signals that propagate from downstream modules (the modules that receive the incoming signals upon interconnection) to upstream ones (the modules that send the signals upon interconnection). Such retroactivity signals, depending of their strength, may change and sometimes even disrupt the behavior of modular biomolecular systems. Thus, analysis of retroactivity effects in natural biological and biosynthetic systems is crucial to achieve a deeper understanding of how this interconnection between functionally characterized modules takes place and how it impacts the overall behavior of the involved cell. By discussing the modules interconnection in natural and synthetic biomolecular systems, we propose that such systems should be considered as quasi-modular. PMID:26137457

  20. Supervisory Control System Architecture for Advanced Small Modular Reactors

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

    Cetiner, Sacit M; Cole, Daniel L; Fugate, David L

    2013-08-01

    This technical report was generated as a product of the Supervisory Control for Multi-Modular SMR Plants project within the Instrumentation, Control and Human-Machine Interface technology area under the Advanced Small Modular Reactor (SMR) Research and Development Program of the U.S. Department of Energy. The report documents the definition of strategies, functional elements, and the structural architecture of a supervisory control system for multi-modular advanced SMR (AdvSMR) plants. This research activity advances the state-of-the art by incorporating decision making into the supervisory control system architectural layers through the introduction of a tiered-plant system approach. The report provides a brief history ofmore » hierarchical functional architectures and the current state-of-the-art, describes a reference AdvSMR to show the dependencies between systems, presents a hierarchical structure for supervisory control, indicates the importance of understanding trip setpoints, applies a new theoretic approach for comparing architectures, identifies cyber security controls that should be addressed early in system design, and describes ongoing work to develop system requirements and hardware/software configurations.« less

  1. Fully decentralized estimation and control for a modular wheeled mobile robot

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

    Mutambara, A.G.O.; Durrant-Whyte, H.F.

    2000-06-01

    In this paper, the problem of fully decentralized data fusion and control for a modular wheeled mobile robot (WMR) is addressed. This is a vehicle system with nonlinear kinematics, distributed multiple sensors, and nonlinear sensor models. The problem is solved by applying fully decentralized estimation and control algorithms based on the extended information filter. This is achieved by deriving a modular, decentralized kinematic model by using plane motion kinematics to obtain the forward and inverse kinematics for a generalized simple wheeled vehicle. This model is then used in the decentralized estimation and control algorithms. WMR estimation and control is thusmore » obtained locally using reduced order models with reduced communication of information between nodes is carried out after every measurement (full rate communication), the estimates and control signals obtained at each node are equivalent to those obtained by a corresponding centralized system. Transputer architecture is used as the basis for hardware and software design as it supports the extensive communication and concurrency requirements that characterize modular and decentralized systems. The advantages of a modular WMR vehicle include scalability, application flexibility, low prototyping costs, and high reliability.« less

  2. A modular BLSS simulation model

    NASA Technical Reports Server (NTRS)

    Rummel, John D.; Volk, Tyler

    1987-01-01

    A bioregenerative life support system (BLSS) for extraterrestrial use will be faced with coordination problems more acute than those in any ecosystem found on Earth. A related problem in BLSS design is providing an interface between the various life support processors, one that will allow for their coordination while still allowing for system expansion. A modular model is presented of a BLSS that interfaces system processors only with the material storage reservoirs, allowing those reservoirs to act as the principal buffers in the system and thus minimizing difficulties with processor coordination. The modular nature of the model allows independent development of the detailed submodels that exist within the model framework. Using this model, BLSS dynamics were investigated under normal conditions and under various failure modes. Partial and complete failures of various components, such as the waste processors or the plants themselves, drive transient responses in the model system, allowing the examination of the effectiveness of the system reservoirs as buffers. The results from simulations help to determine control strategies and BLSS design requirements. An evolved version could be used as an interactive control aid in a future BLSS.

  3. Decentralized and Modular Electrical Architecture

    NASA Astrophysics Data System (ADS)

    Elisabelar, Christian; Lebaratoux, Laurence

    2014-08-01

    This paper presents the studies made on the definition and design of a decentralized and modular electrical architecture that can be used for power distribution, active thermal control (ATC), standard inputs-outputs electrical interfaces.Traditionally implemented inside central unit like OBC or RTU, these interfaces can be dispatched in the satellite by using MicroRTU.CNES propose a similar approach of MicroRTU. The system is based on a bus called BRIO (Bus Réparti des IO), which is composed, by a power bus and a RS485 digital bus. BRIO architecture is made with several miniature terminals called BTCU (BRIO Terminal Control Unit) distributed in the spacecraft.The challenge was to design and develop the BTCU with very little volume, low consumption and low cost. The standard BTCU models are developed and qualified with a configuration dedicated to ATC, while the first flight model will fly on MICROSCOPE for PYRO actuations and analogue acquisitions. The design of the BTCU is made in order to be easily adaptable for all type of electric interface needs.Extension of this concept is envisaged for power conditioning and distribution unit, and a Modular PCDU based on BRIO concept is proposed.

  4. Single-cell RNA-sequencing: The future of genome biology is now

    PubMed Central

    Picelli, Simone

    2017-01-01

    ABSTRACT Genome-wide single-cell analysis represents the ultimate frontier of genomics research. In particular, single-cell RNA-sequencing (scRNA-seq) studies have been boosted in the last few years by an explosion of new technologies enabling the study of the transcriptomic landscape of thousands of single cells in complex multicellular organisms. More sensitive and automated methods are being continuously developed and promise to deliver better data quality and higher throughput with less hands-on time. The outstanding amount of knowledge that is going to be gained from present and future studies will have a profound impact in many aspects of our society, from the introduction of truly tailored cancer treatments, to a better understanding of antibiotic resistance and host-pathogen interactions; from the discovery of the mechanisms regulating stem cell differentiation to the characterization of the early event of human embryogenesis. PMID:27442339

  5. Comparing Homeless Persons’ Care Experiences in Tailored Versus Nontailored Primary Care Programs

    PubMed Central

    Holt, Cheryl L.; Steward, Jocelyn L.; Jones, Richard N.; Roth, David L.; Stringfellow, Erin; Gordon, Adam J.; Kim, Theresa W.; Austin, Erika L.; Henry, Stephen Randal; Kay Johnson, N.; Shanette Granstaff, U.; O’Connell, James J.; Golden, Joya F.; Young, Alexander S.; Davis, Lori L.; Pollio, David E.

    2013-01-01

    Objectives. We compared homeless patients’ experiences of care in health care organizations that differed in their degree of primary care design service tailoring. Methods. We surveyed homeless-experienced patients (either recently or currently homeless) at 3 Veterans Affairs (VA) mainstream primary care settings in Pennsylvania and Alabama, a homeless-tailored VA clinic in California, and a highly tailored non-VA Health Care for the Homeless Program in Massachusetts (January 2011-March 2012). We developed a survey, the “Primary Care Quality-Homeless Survey," to reflect the concerns and aspirations of homeless patients. Results. Mean scores at the tailored non-VA site were superior to those from the 3 mainstream VA sites (P < .001). Adjusting for patient characteristics, these differences remained significant for subscales assessing the patient–clinician relationship (P < .001) and perceptions of cooperation among providers (P = .004). There were 1.5- to 3-fold increased odds of an unfavorable experience in the domains of the patient–clinician relationship, cooperation, and access or coordination for the mainstream VA sites compared with the tailored non-VA site; the tailored VA site attained intermediate results. Conclusions. Tailored primary care service design was associated with a superior service experience for patients who experienced homelessness. PMID:24148052

  6. Modular high speed counter employing edge-triggered code

    DOEpatents

    Vanstraelen, Guy F.

    1993-06-29

    A high speed modular counter (100) utilizing a novel counting method in which the first bit changes with the frequency of the driving clock, and changes in the higher order bits are initiated one clock pulse after a "0" to "1" transition of the next lower order bit. This allows all carries to be known one clock period in advance of a bit change. The present counter is modular and utilizes two types of standard counter cells. A first counter cell determines the zero bit. The second counter cell determines any other higher order bit. Additional second counter cells are added to the counter to accommodate any count length without affecting speed.

  7. Modular high speed counter employing edge-triggered code

    DOEpatents

    Vanstraelen, G.F.

    1993-06-29

    A high speed modular counter (100) utilizing a novel counting method in which the first bit changes with the frequency of the driving clock, and changes in the higher order bits are initiated one clock pulse after a 0'' to 1'' transition of the next lower order bit. This allows all carries to be known one clock period in advance of a bit change. The present counter is modular and utilizes two types of standard counter cells. A first counter cell determines the zero bit. The second counter cell determines any other higher order bit. Additional second counter cells are added to the counter to accommodate any count length without affecting speed.

  8. Modular digital holographic fringe data processing system

    NASA Technical Reports Server (NTRS)

    Downward, J. G.; Vavra, P. C.; Schebor, F. S.; Vest, C. M.

    1985-01-01

    A software architecture suitable for reducing holographic fringe data into useful engineering data is developed and tested. The results, along with a detailed description of the proposed architecture for a Modular Digital Fringe Analysis System, are presented.

  9. Fretting-corrosion at the modular tapers interface: Inspection of standard ASTM F1875-98.

    PubMed

    Bingley, Rachel; Martin, Alan; Manfredi, Olivia; Nejadhamzeeigilani, Mahdiyar; Oladokun, Abimbola; Beadling, Andrew Robert; Siddiqui, Sohail; Anderson, James; Thompson, Jonathan; Neville, Anne; Bryant, Michael

    2018-05-01

    Interest in the degradation mechanisms at the modular tapers interfaces has been renewed due to increased reported cases of adverse reactions to metal debris and the appearance of wear and corrosion at the modular tapers interfaces at revision. Over the past two decades, a lot of research has been expended to understand the degradation mechanisms, with two primary implant loading procedures and orientations used consistently across the literature. ASTM F1875-98 is often used as a guide to understand and benchmark the tribocorrosion processes occurring within the modular tapers interface. This article presents a comparison of the two methods outlined in ASTM F1875-98 as well as a critique of the standard considering the current paradigm in pre-clinical assessment of modular tapers.

  10. Virtual design and optimization studies for industrial silicon microphones applying tailored system-level modeling

    NASA Astrophysics Data System (ADS)

    Kuenzig, Thomas; Dehé, Alfons; Krumbein, Ulrich; Schrag, Gabriele

    2018-05-01

    Maxing out the technological limits in order to satisfy the customers’ demands and obtain the best performance of micro-devices and-systems is a challenge of today’s manufacturers. Dedicated system simulation is key to investigate the potential of device and system concepts in order to identify the best design w.r.t. the given requirements. We present a tailored, physics-based system-level modeling approach combining lumped with distributed models that provides detailed insight into the device and system operation at low computational expense. The resulting transparent, scalable (i.e. reusable) and modularly composed models explicitly contain the physical dependency on all relevant parameters, thus being well suited for dedicated investigation and optimization of MEMS devices and systems. This is demonstrated for an industrial capacitive silicon microphone. The performance of such microphones is determined by distributed effects like viscous damping and inhomogeneous capacitance variation across the membrane as well as by system-level phenomena like package-induced acoustic effects and the impact of the electronic circuitry for biasing and read-out. The here presented model covers all relevant figures of merit and, thus, enables to evaluate the optimization potential of silicon microphones towards high fidelity applications. This work was carried out at the Technical University of Munich, Chair for Physics of Electrotechnology. Thomas Kuenzig is now with Infineon Technologies AG, Neubiberg.

  11. Advantages of a Modular Mars Surface Habitat Approach

    NASA Technical Reports Server (NTRS)

    Rucker, Michelle A.; Hoffman, Stephan J.; Andrews, Alida; Watts, Kevin

    2018-01-01

    Early crewed Mars mission concepts developed by the National Aeronautics and Space Administration (NASA) assumed a single, large habitat would house six crew members for a 500-day Mars surface stay. At the end of the first mission, all surface equipment, including the habitat, -would be abandoned and the process would be repeated at a different Martian landing site. This work was documented in a series of NASA publications culminating with the Mars Design Reference Mission 5.0 (NASA-SP-2009-566). The Evolvable Mars Campaign (EMC) explored whether re-using surface equipment at a single landing site could be more affordable than the Apollo-style explore-abandon-repeat mission cadence. Initial EMC assumptions preserved the single, monolithic habitat, the only difference being a new requirement to reuse the surface habitat for multiple expedition crews. A trade study comparing a single large habitat versus smaller, modular habitats leaned towards the monolithic approach as more mass-efficient. More recent work has focused on the operational aspects of building up Mars surface infrastructure over multiple missions, and has identified compelling advantages of the modular approach that should be considered before making a final decision. This paper explores Mars surface mission operational concepts and integrated system analysis, and presents an argument for the modular habitat approach.

  12. Modular Building Institute 2002 Educational Showcase.

    ERIC Educational Resources Information Center

    Modular Building Inst., Charlottesville, VA.

    This publication contains brief articles concerned with modular school structures. Some articles offer examples of such structures at actual schools. The articles in this issue are: (1) "Re-Educating Schools" (Chuck Savage); (2) "Tax-Exempt Financing for Public Schools" (John Kennedy); (3) "Help Us Rebuild America" (Michael Roman); (4) "Case…

  13. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 1 2013-10-01 2013-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212... powered, it must comply with the AC line conducted requirements found in § 15.207. AC or DC power lines...

  14. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212... powered, it must comply with the AC line conducted requirements found in § 15.207. AC or DC power lines...

  15. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 1 2011-10-01 2011-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212... powered, it must comply with the AC line conducted requirements found in § 15.207. AC or DC power lines...

  16. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212... powered, it must comply with the AC line conducted requirements found in § 15.207. AC or DC power lines...

  17. 47 CFR 15.212 - Modular transmitters.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 1 2014-10-01 2014-10-01 false Modular transmitters. 15.212 Section 15.212 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL RADIO FREQUENCY DEVICES Intentional Radiators § 15.212... powered, it must comply with the AC line conducted requirements found in § 15.207. AC or DC power lines...

  18. Lattices, vertex algebras, and modular categories

    NASA Astrophysics Data System (ADS)

    van Ekeren, Jethro

    2018-03-01

    In this note we give an account of recent progress on the construction of holomorphic vertex algebras as cyclic orbifolds as well as related topics in lattices and modular categories. We present a novel computation of the Schur indicator of a lattice involution orbifold using finite Heisenberg groups and discriminant forms.

  19. In Silico Investigation of a Surgical Interface for Remote Control of Modular Miniature Robots in Minimally Invasive Surgery

    PubMed Central

    Zygomalas, Apollon; Giokas, Konstantinos; Koutsouris, Dimitrios

    2014-01-01

    Aim. Modular mini-robots can be used in novel minimally invasive surgery techniques like natural orifice transluminal endoscopic surgery (NOTES) and laparoendoscopic single site (LESS) surgery. The control of these miniature assistants is complicated. The aim of this study is the in silico investigation of a remote controlling interface for modular miniature robots which can be used in minimally invasive surgery. Methods. The conceptual controlling system was developed, programmed, and simulated using professional robotics simulation software. Three different modes of control were programmed. The remote controlling surgical interface was virtually designed as a high scale representation of the respective modular mini-robot, therefore a modular controlling system itself. Results. With the proposed modular controlling system the user could easily identify the conformation of the modular mini-robot and adequately modify it as needed. The arrangement of each module was always known. The in silico investigation gave useful information regarding the controlling mode, the adequate speed of rearrangements, and the number of modules needed for efficient working tasks. Conclusions. The proposed conceptual model may promote the research and development of more sophisticated modular controlling systems. Modular surgical interfaces may improve the handling and the dexterity of modular miniature robots during minimally invasive procedures. PMID:25295187

  20. In silico investigation of a surgical interface for remote control of modular miniature robots in minimally invasive surgery.

    PubMed

    Zygomalas, Apollon; Giokas, Konstantinos; Koutsouris, Dimitrios

    2014-01-01

    Aim. Modular mini-robots can be used in novel minimally invasive surgery techniques like natural orifice transluminal endoscopic surgery (NOTES) and laparoendoscopic single site (LESS) surgery. The control of these miniature assistants is complicated. The aim of this study is the in silico investigation of a remote controlling interface for modular miniature robots which can be used in minimally invasive surgery. Methods. The conceptual controlling system was developed, programmed, and simulated using professional robotics simulation software. Three different modes of control were programmed. The remote controlling surgical interface was virtually designed as a high scale representation of the respective modular mini-robot, therefore a modular controlling system itself. Results. With the proposed modular controlling system the user could easily identify the conformation of the modular mini-robot and adequately modify it as needed. The arrangement of each module was always known. The in silico investigation gave useful information regarding the controlling mode, the adequate speed of rearrangements, and the number of modules needed for efficient working tasks. Conclusions. The proposed conceptual model may promote the research and development of more sophisticated modular controlling systems. Modular surgical interfaces may improve the handling and the dexterity of modular miniature robots during minimally invasive procedures.

  1. Simulation and Modeling Capability for Standard Modular Hydropower Technology

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

    Stewart, Kevin M.; Smith, Brennan T.; Witt, Adam M.

    Grounded in the stakeholder-validated framework established in Oak Ridge National Laboratory’s SMH Exemplary Design Envelope Specification, this report on Simulation and Modeling Capability for Standard Modular Hydropower (SMH) Technology provides insight into the concepts, use cases, needs, gaps, and challenges associated with modeling and simulating SMH technologies. The SMH concept envisions a network of generation, passage, and foundation modules that achieve environmentally compatible, cost-optimized hydropower using standardization and modularity. The development of standardized modeling approaches and simulation techniques for SMH (as described in this report) will pave the way for reliable, cost-effective methods for technology evaluation, optimization, and verification.

  2. Modular disposable can (MODCAN) crash cushion: A concept investigation

    NASA Technical Reports Server (NTRS)

    Knoell, A.; Wilson, A.

    1976-01-01

    A conceptual design investigation of an improved highway crash cushion system is presented. The system is referred to as a modular disposable can (MODCAN) crash system. It is composed of a modular arrangement of disposable metal beverage cans configured to serve as an effective highway impact attenuation system. Experimental data, design considerations, and engineering calculations supporting the design development are presented. Design performance is compared to that of a conventional steel drum system. It is shown that the MODCAN concepts offers the potential for smoother and safer occupant deceleration for a larger class of vehicle impact weights than the steel drum device.

  3. Modular space vehicle boards, control software, reprogramming, and failure recovery

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

    Judd, Stephen; Dallmann, Nicholas; McCabe, Kevin

    A space vehicle may have a modular board configuration that commonly uses some or all components and a common operating system for at least some of the boards. Each modular board may have its own dedicated processing, and processing loads may be distributed. The space vehicle may be reprogrammable, and may be launched without code that enables all functionality and/or components. Code errors may be detected and the space vehicle may be reset to a working code version to prevent system failure.

  4. Computer-Supported Feedback Message Tailoring for Healthcare Providers in Malawi: Proof-of-Concept.

    PubMed

    Landis-Lewis, Zach; Douglas, Gerald P; Hochheiser, Harry; Kam, Matthew; Gadabu, Oliver; Bwanali, Mwatha; Jacobson, Rebecca S

    2015-01-01

    Although performance feedback has the potential to help clinicians improve the quality and safety of care, healthcare organizations generally lack knowledge about how this guidance is best provided. In low-resource settings, tools for theory-informed feedback tailoring may enhance limited clinical supervision resources. Our objectives were to establish proof-of-concept for computer-supported feedback message tailoring in Malawi, Africa. We conducted this research in five stages: clinical performance measurement, modeling the influence of feedback on antiretroviral therapy (ART) performance, creating a rule-based message tailoring process, generating tailored messages for recipients, and finally analysis of performance and message tailoring data. We retrospectively generated tailored messages for 7,448 monthly performance reports from 11 ART clinics. We found that tailored feedback could be routinely generated for four guideline-based performance indicators, with 35% of reports having messages prioritized to optimize the effect of feedback. This research establishes proof-of-concept for a novel approach to improving the use of clinical performance feedback in low-resource settings and suggests possible directions for prospective evaluations comparing alternative designs of feedback messages.

  5. Modular low-aspect-ratio high-beta torsatron

    DOEpatents

    Sheffield, G.V.

    1982-04-01

    A fusion-reactor device is described which the toroidal magnetic field and at least a portion of the poloidal magnetic field are provided by a single set of modular coils. The coils are arranged on the surface of a low-aspect-ratio toroid in planed having the cylindrical coordinate relationship phi = phi/sub i/ + kz, where k is a constant equal to each coil's pitch and phi/sub i/ is the toroidal angle at which the i'th coil intersects the z = o plane. The toroid defined by the modular coils preferably has a race track minor cross section. When vertical field coils and, preferably, a toroidal plasma current are provided for magnetic-field-surface closure within the toroid, a vacuum magnetic field of racetrack-shaped minor cross section with improved stability and beta valves is obtained.

  6. Toward the Modularization of Decision Support Systems

    NASA Astrophysics Data System (ADS)

    Raskin, R. G.

    2009-12-01

    Decision support systems are typically developed entirely from scratch without the use of modular components. This “stovepiped” approach is inefficient and costly because it prevents a developer from leveraging the data, models, tools, and services of other developers. Even when a decision support component is made available, it is difficult to know what problem it solves, how it relates to other components, or even that the component exists, The Spatial Decision Support (SDS) Consortium was formed in 2008 to organize the body of knowledge in SDS within a common portal. The portal identifies the canonical steps in the decision process and enables decision support components to be registered, categorized, and searched. This presentation describes how a decision support system can be assembled from modular models, data, tools and services, based on the needs of the Earth science application.

  7. The Promise of Tailoring Incentives for Healthy Behaviors.

    PubMed

    Kullgren, Jeffrey T; Williams, Geoffrey C; Resnicow, Kenneth; An, Lawrence C; Rothberg, Amy; Volpp, Kevin G; Heisler, Michele

    2016-01-01

    To describe how tailoring financial incentives for healthy behaviors to employees' goals, values, and aspirations might improve the efficacy of incentives. We integrate insights from self-determination theory (SDT) with principles from behavioral economics in the design of financial incentives by linking how incentives could help meet an employee's life goals, values, or aspirations. Tailored financial incentives could be more effective than standard incentives in promoting autonomous motivation necessary to initiate healthy behaviors and sustain them after incentives are removed. Previous efforts to improve the design of financial incentives have tested different incentive designs that vary the size, schedule, timing, and target of incentives. Our strategy for tailoring incentives builds on strong evidence that difficult behavior changes are more successful when integrated with important life goals and values. We outline necessary research to examine the effectiveness of this approach among at-risk employees. Instead of offering simple financial rewards for engaging in healthy behaviors, existing programs could leverage incentives to promote employees' autonomous motivation for sustained health improvements. Effective application of these concepts could lead to programs more effective at improving health, potentially at lower cost. Our approach for the first time integrates key insights from SDT, behavioral economics, and tailoring to turn an extrinsic reward for behavior change into an internalized, self-sustaining motivator for long-term engagement in risk-reducing behaviors.

  8. Automated Finite Element Analysis of Elastically-Tailored Plates

    NASA Technical Reports Server (NTRS)

    Jegley, Dawn C. (Technical Monitor); Tatting, Brian F.; Guerdal, Zafer

    2003-01-01

    A procedure for analyzing and designing elastically tailored composite laminates using the STAGS finite element solver has been presented. The methodology used to produce the elastic tailoring, namely computer-controlled steering of unidirectionally reinforced composite material tows, has been reduced to a handful of design parameters along with a selection of construction methods. The generality of the tow-steered ply definition provides the user a wide variety of options for laminate design, which can be automatically incorporated with any finite element model that is composed of STAGS shell elements. Furthermore, the variable stiffness parameterization is formulated so that manufacturability can be assessed during the design process, plus new ideas using tow steering concepts can be easily integrated within the general framework of the elastic tailoring definitions. Details for the necessary implementation of the tow-steering definitions within the STAGS hierarchy is provided, and the format of the ply definitions is discussed in detail to provide easy access to the elastic tailoring choices. Integration of the automated STAGS solver with laminate design software has been demonstrated, so that the large design space generated by the tow-steering options can be traversed effectively. Several design problems are presented which confirm the usefulness of the design tool as well as further establish the potential of tow-steered plies for laminate design.

  9. Sequential Modular Position and Momentum Measurements of a Trapped Ion Mechanical Oscillator

    NASA Astrophysics Data System (ADS)

    Flühmann, C.; Negnevitsky, V.; Marinelli, M.; Home, J. P.

    2018-04-01

    The noncommutativity of position and momentum observables is a hallmark feature of quantum physics. However, this incompatibility does not extend to observables that are periodic in these base variables. Such modular-variable observables have been suggested as tools for fault-tolerant quantum computing and enhanced quantum sensing. Here, we implement sequential measurements of modular variables in the oscillatory motion of a single trapped ion, using state-dependent displacements and a heralded nondestructive readout. We investigate the commutative nature of modular variable observables by demonstrating no-signaling in time between successive measurements, using a variety of input states. Employing a different periodicity, we observe signaling in time. This also requires wave-packet overlap, resulting in quantum interference that we enhance using squeezed input states. The sequential measurements allow us to extract two-time correlators for modular variables, which we use to violate a Leggett-Garg inequality. Signaling in time and Leggett-Garg inequalities serve as efficient quantum witnesses, which we probe here with a mechanical oscillator, a system that has a natural crossover from the quantum to the classical regime.

  10. A modular toolset for recombination transgenesis and neurogenetic analysis of Drosophila.

    PubMed

    Wang, Ji-Wu; Beck, Erin S; McCabe, Brian D

    2012-01-01

    Transgenic Drosophila have contributed extensively to our understanding of nervous system development, physiology and behavior in addition to being valuable models of human neurological disease. Here, we have generated a novel series of modular transgenic vectors designed to optimize and accelerate the production and analysis of transgenes in Drosophila. We constructed a novel vector backbone, pBID, that allows both phiC31 targeted transgene integration and incorporates insulator sequences to ensure specific and uniform transgene expression. Upon this framework, we have built a series of constructs that are either backwards compatible with existing restriction enzyme based vectors or utilize Gateway recombination technology for high-throughput cloning. These vectors allow for endogenous promoter or Gal4 targeted expression of transgenic proteins with or without fluorescent protein or epitope tags. In addition, we have generated constructs that facilitate transgenic splice isoform specific RNA inhibition of gene expression. We demonstrate the utility of these constructs to analyze proteins involved in nervous system development, physiology and neurodegenerative disease. We expect that these reagents will facilitate the proficiency and sophistication of Drosophila genetic analysis in both the nervous system and other tissues.

  11. A Modular Toolset for Recombination Transgenesis and Neurogenetic Analysis of Drosophila

    PubMed Central

    Wang, Ji-Wu; Beck, Erin S.; McCabe, Brian D.

    2012-01-01

    Transgenic Drosophila have contributed extensively to our understanding of nervous system development, physiology and behavior in addition to being valuable models of human neurological disease. Here, we have generated a novel series of modular transgenic vectors designed to optimize and accelerate the production and analysis of transgenes in Drosophila. We constructed a novel vector backbone, pBID, that allows both phiC31 targeted transgene integration and incorporates insulator sequences to ensure specific and uniform transgene expression. Upon this framework, we have built a series of constructs that are either backwards compatible with existing restriction enzyme based vectors or utilize Gateway recombination technology for high-throughput cloning. These vectors allow for endogenous promoter or Gal4 targeted expression of transgenic proteins with or without fluorescent protein or epitope tags. In addition, we have generated constructs that facilitate transgenic splice isoform specific RNA inhibition of gene expression. We demonstrate the utility of these constructs to analyze proteins involved in nervous system development, physiology and neurodegenerative disease. We expect that these reagents will facilitate the proficiency and sophistication of Drosophila genetic analysis in both the nervous system and other tissues. PMID:22848718

  12. Modular co-culture engineering, a new approach for metabolic engineering.

    PubMed

    Zhang, Haoran; Wang, Xiaonan

    2016-09-01

    With the development of metabolic engineering, employment of a selected microbial host for accommodation of a designed biosynthetic pathway to produce a target compound has achieved tremendous success in the past several decades. Yet, increasing requirements for sophisticated microbial biosynthesis call for establishment and application of more advanced metabolic engineering methodologies. Recently, important progress has been made towards employing more than one engineered microbial strains to constitute synthetic co-cultures and modularizing the biosynthetic labor between the co-culture members in order to improve bioproduction performance. This emerging approach, referred to as modular co-culture engineering in this review, presents a valuable opportunity for expanding the scope of the broad field of metabolic engineering. We highlight representative research accomplishments using this approach, especially those utilizing metabolic engineering tools for microbial co-culture manipulation. Key benefits and major challenges associated with modular co-culture engineering are also presented and discussed. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  13. The effects of predictor method factors on selection outcomes: A modular approach to personnel selection procedures.

    PubMed

    Lievens, Filip; Sackett, Paul R

    2017-01-01

    Past reviews and meta-analyses typically conceptualized and examined selection procedures as holistic entities. We draw on the product design literature to propose a modular approach as a complementary perspective to conceptualizing selection procedures. A modular approach means that a product is broken down into its key underlying components. Therefore, we start by presenting a modular framework that identifies the important measurement components of selection procedures. Next, we adopt this modular lens for reviewing the available evidence regarding each of these components in terms of affecting validity, subgroup differences, and applicant perceptions, as well as for identifying new research directions. As a complement to the historical focus on holistic selection procedures, we posit that the theoretical contributions of a modular approach include improved insight into the isolated workings of the different components underlying selection procedures and greater theoretical connectivity among different selection procedures and their literatures. We also outline how organizations can put a modular approach into operation to increase the variety in selection procedures and to enhance the flexibility in designing them. Overall, we believe that a modular perspective on selection procedures will provide the impetus for programmatic and theory-driven research on the different measurement components of selection procedures. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  14. Revisiting the variation of clustering coefficient of biological networks suggests new modular structure.

    PubMed

    Hao, Dapeng; Ren, Cong; Li, Chuanxing

    2012-05-01

    A central idea in biology is the hierarchical organization of cellular processes. A commonly used method to identify the hierarchical modular organization of network relies on detecting a global signature known as variation of clustering coefficient (so-called modularity scaling). Although several studies have suggested other possible origins of this signature, it is still widely used nowadays to identify hierarchical modularity, especially in the analysis of biological networks. Therefore, a further and systematical investigation of this signature for different types of biological networks is necessary. We analyzed a variety of biological networks and found that the commonly used signature of hierarchical modularity is actually the reflection of spoke-like topology, suggesting a different view of network architecture. We proved that the existence of super-hubs is the origin that the clustering coefficient of a node follows a particular scaling law with degree k in metabolic networks. To study the modularity of biological networks, we systematically investigated the relationship between repulsion of hubs and variation of clustering coefficient. We provided direct evidences for repulsion between hubs being the underlying origin of the variation of clustering coefficient, and found that for biological networks having no anti-correlation between hubs, such as gene co-expression network, the clustering coefficient doesn't show dependence of degree. Here we have shown that the variation of clustering coefficient is neither sufficient nor exclusive for a network to be hierarchical. Our results suggest the existence of spoke-like modules as opposed to "deterministic model" of hierarchical modularity, and suggest the need to reconsider the organizational principle of biological hierarchy.

  15. Consciousness in SLA: A Modular Perspective

    ERIC Educational Resources Information Center

    Truscott, John

    2015-01-01

    Understanding the place of consciousness in second language acquisition (SLA) is crucial for an understanding of how acquisition occurs. Considerable work has been done on this topic, but nearly all of it assumes a highly non-modular view, according to which language and its development is "nothing special". As this assumption runs…

  16. Learning in Modular Systems

    DTIC Science & Technology

    2010-05-07

    important for deep modular systems is that taking a series of small update steps and stopping before convergence, so called early stopping, is a form of regu...larization around the initial parameters of the system . For example, the stochastic gradient descent 5 1 u + 1 v = 1 6‖x2‖q = ‖x‖22q 22 Chapter 2...Aside from the overall speed of the classifier, no quantitative performance analysis was given, and the role played by the features in the larger system

  17. RNA editing of microRNA prevents RNA-induced silencing complex recognition of target mRNA

    PubMed Central

    Cui, Yalei; Huang, Tianzhi; Zhang, Xiaobo

    2015-01-01

    MicroRNAs (miRNAs) integrate with Argonaut (Ago) to create the RNA-induced silencing complex, and regulate gene expression by silencing target mRNAs. RNA editing of miRNA may affect miRNA processing, assembly of the Ago complex and target mRNA binding. However, the function of edited miRNA, assembled within the Ago complex, has not been extensively investigated. In this study, sequence analysis of the Ago complex of Marsupenaeus japonicus shrimp infected with white spot syndrome virus (WSSV) revealed that host ADAR (adenosine deaminase acting on RNA) catalysed A-to-I RNA editing of a viral miRNA (WSSV-miR-N12) at the +16 site. This editing of the non-seed sequence did not affect association of the edited miRNA with the Ago protein, but inhibited interaction between the miRNA and its target gene (wsv399). The WSSV early gene wsv399 inhibited WSSV infection. As a result, the RNA editing of miRNA caused virus latency. Our results highlight a novel example of miRNA editing in the miRNA-induced silencing complex. PMID:26674414

  18. On the definition and K-theory realization of a modular functor

    NASA Astrophysics Data System (ADS)

    Kriz, Igor; Lai, Luhang

    We present a definition of a (super)-modular functor which includes certain interesting cases that previous definitions do not allow. We also introduce a notion of topological twisting of a modular functor, and construct formally a realization by a 2-dimensional topological field theory valued in twisted K-modules. We discuss, among other things, the N = 1-supersymmetric minimal models from the point of view of this formalism.

  19. An examination of effect estimation in factorial and standardly-tailored designs

    PubMed Central

    Allore, Heather G; Murphy, Terrence E

    2012-01-01

    Background Many clinical trials are designed to test an intervention arm against a control arm wherein all subjects are equally eligible for all interventional components. Factorial designs have extended this to test multiple intervention components and their interactions. A newer design referred to as a ‘standardly-tailored’ design, is a multicomponent interventional trial that applies individual interventional components to modify risk factors identified a priori and tests whether health outcomes differ between treatment arms. Standardly-tailored designs do not require that all subjects be eligible for every interventional component. Although standardly-tailored designs yield an estimate for the net effect of the multicomponent intervention, it has not yet been shown if they permit separate, unbiased estimation of individual component effects. The ability to estimate the most potent interventional components has direct bearing on conducting second stage translational research. Purpose We present statistical issues related to the estimation of individual component effects in trials of geriatric conditions using factorial and standardly-tailored designs. The medical community is interested in second stage translational research involving the transfer of results from a randomized clinical trial to a community setting. Before such research is undertaken, main effects and synergistic and or antagonistic interactions between them should be identified. Knowledge of the relative strength and direction of the effects of the individual components and their interactions facilitates the successful transfer of clinically significant findings and may potentially reduce the number of interventional components needed. Therefore the current inability of the standardly-tailored design to provide unbiased estimates of individual interventional components is a serious limitation in their applicability to second stage translational research. Methods We discuss estimation of

  20. A cost-effectiveness comparison of three tailored interventions to increase mammography screening.

    PubMed

    Saywell, Robert M; Champion, Victoria L; Skinner, Celette Sugg; Menon, Usha; Daggy, Joanne

    2004-10-01

    Mammography is the primary method used for breast cancer screening. However, adherence to recommended screening practices is still below acceptable levels. This study examined the cost-effectiveness of three combinations of tailored telephone and mailed intervention strategies for increasing adherence to mammography. There were 1044 participants who were randomly assigned to one of four groups. A logistic regression model with adherence as the dependent variable and group as the independent variable was used to test for significant differences, and a ratio of cost/improvement in mammogram adherence evaluated the cost-effectiveness. All three of the interventions (tailored telephone, tailored mail, and tailored telephone and mail) had significantly better adherence rates compared with the control group (usual care). However, when also considering costs, one emerged as the superior strategy. The cost-effectiveness ratios for the three interventions show that the tailored mail (letter) was the most cost-effective strategy, achieving 43.3% mammography adherence at a marginal cost of dollar 0.39 per 1% increase in women screened. The tailored mail plus telephone achieved greater adherence (49.4%), but at a higher cost (dollar 0.56 per 1% increase in women screened). A tailored mail reminder is an effective and economical intervention to increase mammography adherence. Future research should confirm this finding and address its applicability to practice in other settings.

  1. Modular Mayhem? A Case Study of the Development of the A-Level Science Curriculum in England

    ERIC Educational Resources Information Center

    Hayward, Geoff; McNicholl, Jane

    2007-01-01

    This article investigates the costs and benefits of the increased use of modular or unitized qualification designs through a case study of the GCE A-level science curriculum in England. Following a brief review of the development of modular A-levels, the various proposed advantages of modularity--short-term goals and regular feedback, flexibility…

  2. Tailoring periodical collections to meet institutional needs.

    PubMed Central

    Delman, B S

    1984-01-01

    A system for tailoring journal collections to meet institutional needs is described. The approach is based on the view that reference work and collection development are variant and complementary forms of the same library function; both tasks have as their objective a literature response to information problems. Utilizing the tools and procedures of the reference search in response to a specific collection development problem topic, the author created a model ranked list of relevant journals. Finally, by linking the model to certain operational and environmental factors in three different health care organizations, he tailored the collection to meet the institutions' respective information needs. PMID:6375775

  3. PTERA - Modular Aircraft Flight Test

    NASA Image and Video Library

    2016-01-13

    Aerospace testing can be costly and time consuming but a new modular, subscale remotely piloted aircraft offers NASA researchers more affordable options for developing a wide range of cutting edge aviation and space technologies. The Prototype-Technology Evaluation and Research Aircraft (PTERA), developed by Area-I, Inc., of Kennesaw, Georgia, is an extremely versatile and high quality, yet inexpensive, flying laboratory bridging the gap between wind tunnels and crewed flight testing.

  4. Multidimensional bioseparation with modular microfluidics

    DOEpatents

    Chirica, Gabriela S.; Renzi, Ronald F.

    2013-08-27

    A multidimensional chemical separation and analysis system is described including a prototyping platform and modular microfluidic components capable of rapid and convenient assembly, alteration and disassembly of numerous candidate separation systems. Partial or total computer control of the separation system is possible. Single or multiple alternative processing trains can be tested, optimized and/or run in parallel. Examples related to the separation and analysis of human bodily fluids are given.

  5. How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives.

    PubMed

    Dal Molin, Alessandra; Di Camillo, Barbara

    2018-01-31

    The sequencing of the transcriptome of single cells, or single-cell RNA-sequencing, has now become the dominant technology for the identification of novel cell types in heterogeneous cell populations or for the study of stochastic gene expression. In recent years, various experimental methods and computational tools for analysing single-cell RNA-sequencing data have been proposed. However, most of them are tailored to different experimental designs or biological questions, and in many cases, their performance has not been benchmarked yet, thus increasing the difficulty for a researcher to choose the optimal single-cell transcriptome sequencing (scRNA-seq) experiment and analysis workflow. In this review, we aim to provide an overview of the current available experimental and computational methods developed to handle single-cell RNA-sequencing data and, based on their peculiarities, we suggest possible analysis frameworks depending on specific experimental designs. Together, we propose an evaluation of challenges and open questions and future perspectives in the field. In particular, we go through the different steps of scRNA-seq experimental protocols such as cell isolation, messenger RNA capture, reverse transcription, amplification and use of quantitative standards such as spike-ins and Unique Molecular Identifiers (UMIs). We then analyse the current methodological challenges related to preprocessing, alignment, quantification, normalization, batch effect correction and methods to control for confounding effects. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  6. Integrated modular teaching in dermatology for undergraduate students: A novel approach.

    PubMed

    Karthikeyan, Kaliaperumal; Kumar, Annapurna

    2014-07-01

    Undergraduate teaching in dermatology comprises didactic lectures and clinical classes. Integrated modular teaching is a novel approach, which integrates basic sciences with dermatology in the form of a module. Further the module also incorporates various teaching modalities, which facilitate active participation from students and promotes learning. The pre- and post-test values showed the effectiveness of the integrated module. The students feedback was encouraging. The aim of this study was to determine the acceptance and opinion of undergraduate students regarding integrated modular teaching as a new teaching aid in dermatology. This was a descriptive study. Varied teaching methodologies involving multiple disciplines were undertaken in six major undergraduate topics in dermatology for seventh and eighth semester students. A total of six modules were conducted over a period of 12 months for students of seventh and eighth semesters. The topics for the various modules were sexually transmitted diseases, acquired immunodeficiency syndrome, oral ulcers, leprosy, connective tissue disorders and psoriasis. Faculty members from different disciplines participated. Pre- and post-test were conducted before and after the modules respectively to gauge the effectiveness of the modules. It was found that almost every student had a better score on the posttest as compared to the pretest. General feedback obtained from the students showed that all of them felt that modular teaching was a more interesting and useful teaching learning experience than conventional teaching. Integrated modular teaching can be an effective adjunct in imparting theoretical and practical knowledge to the students. Further, various teaching methodologies can be used in integrated modules effectively with active student participation. Thus integrated modular teaching addresses two important issues in medical education, namely integration and active student participation.

  7. RNA editing of microRNA prevents RNA-induced silencing complex recognition of target mRNA.

    PubMed

    Cui, Yalei; Huang, Tianzhi; Zhang, Xiaobo

    2015-12-01

    MicroRNAs (miRNAs) integrate with Argonaut (Ago) to create the RNA-induced silencing complex, and regulate gene expression by silencing target mRNAs. RNA editing of miRNA may affect miRNA processing, assembly of the Ago complex and target mRNA binding. However, the function of edited miRNA, assembled within the Ago complex, has not been extensively investigated. In this study, sequence analysis of the Ago complex of Marsupenaeus japonicus shrimp infected with white spot syndrome virus (WSSV) revealed that host ADAR (adenosine deaminase acting on RNA) catalysed A-to-I RNA editing of a viral miRNA (WSSV-miR-N12) at the +16 site. This editing of the non-seed sequence did not affect association of the edited miRNA with the Ago protein, but inhibited interaction between the miRNA and its target gene (wsv399). The WSSV early gene wsv399 inhibited WSSV infection. As a result, the RNA editing of miRNA caused virus latency. Our results highlight a novel example of miRNA editing in the miRNA-induced silencing complex. © 2015 The Authors.

  8. The application of modular protein domains in proteomics

    PubMed Central

    Jadwin, Joshua A.; Ogiue-Ikeda, Mari; Machida, Kazuya

    2012-01-01

    The ability of modular protein domains to independently fold and bind short peptide ligands both in vivo and in vitro has allowed a significant number of protein-protein interaction studies to take advantage of them as affinity and detection reagents. Here, we refer to modular domain based proteomics as “domainomics” to draw attention to the potential of using domains and their motifs as tools in proteomics. In this review we describe core concepts of domainomics, established and emerging technologies, and recent studies by functional category. Accumulation of domain-motif binding data should ultimately provide the foundation for domain-specific interactomes, which will likely reveal the underlying substructure of protein networks as well as the selectivity and plasticity of signal transduction. PMID:22710164

  9. Standard Modular Hydropower Technology Acceleration Workshop: Summary Report

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

    Smith, Brennan T.; DeNeale, Scott T.; Witt, Adam M.

    In support of the Department of Energy (DOE) funded Standard Modular Hydropower (SMH) Technology Acceleration project, Oak Ridge National Laboratory (ORNL) staff convened with five small hydropower technology entrepreneurs on June 14 and 15, 2017 to discuss gaps, challenges, and opportunities for small modular hydropower development. The workshop was designed to walk through SMH concepts, discuss the SMH research vision, assess how each participant’s technology aligns with SMH concepts and research, and identify future pathways for mutually beneficial collaboration that leverages ORNL expertise and entrepreneurial industry experience. The goal coming out of the workshop is to advance standardized, scalable, modularmore » hydropower technologies and development approaches with sustained and open dialogue among diverse stakeholder groups.« less

  10. Lightweight composites for modular panelized construction

    NASA Astrophysics Data System (ADS)

    Vaidya, Amol S.

    Rapid advances in construction materials technology have enabled civil engineers to achieve impressive gains in the safety, economy, and functionality of structures built to serve the common needs of society. Modular building systems is a fast-growing modern, form of construction gaining recognition for its increased efficiency and ability to apply modern technology to the needs of the market place. In the modular construction technique, a single structural panel can perform a number of functions such as providing thermal insulation, vibration damping, and structural strength. These multifunctional panels can be prefabricated in a manufacturing facility and then transferred to the construction site. A system that uses prefabricated panels for construction is called a "panelized construction system". This study focuses on the development of pre-cast, lightweight, multifunctional sandwich composite panels to be used for panelized construction. Two thermoplastic composite panels are proposed in this study, namely Composite Structural Insulated Panels (CSIPs) for exterior walls, floors and roofs, and Open Core Sandwich composite for multifunctional interior walls of a structure. Special manufacturing techniques are developed for manufacturing these panels. The structural behavior of these panels is analyzed based on various building design codes. Detailed descriptions of the design, cost analysis, manufacturing, finite element modeling and structural testing of these proposed panels are included in this study in the of form five peer-reviewed journal articles. The structural testing of the proposed panels involved in this study included flexural testing, axial compression testing, and low and high velocity impact testing. Based on the current study, the proposed CSIP wall and floor panels were found satisfactory, based on building design codes ASCE-7-05 and ACI-318-05. Joining techniques are proposed in this study for connecting the precast panels on the construction

  11. Anatomical Network Analysis Shows Decoupling of Modular Lability and Complexity in the Evolution of the Primate Skull

    PubMed Central

    Esteve-Altava, Borja; Boughner, Julia C.; Diogo, Rui; Villmoare, Brian A.; Rasskin-Gutman, Diego

    2015-01-01

    Modularity and complexity go hand in hand in the evolution of the skull of primates. Because analyses of these two parameters often use different approaches, we do not know yet how modularity evolves within, or as a consequence of, an also-evolving complex organization. Here we use a novel network theory-based approach (Anatomical Network Analysis) to assess how the organization of skull bones constrains the co-evolution of modularity and complexity among primates. We used the pattern of bone contacts modeled as networks to identify connectivity modules and quantify morphological complexity. We analyzed whether modularity and complexity evolved coordinately in the skull of primates. Specifically, we tested Herbert Simon’s general theory of near-decomposability, which states that modularity promotes the evolution of complexity. We found that the skulls of extant primates divide into one conserved cranial module and up to three labile facial modules, whose composition varies among primates. Despite changes in modularity, statistical analyses reject a positive feedback between modularity and complexity. Our results suggest a decoupling of complexity and modularity that translates to varying levels of constraint on the morphological evolvability of the primate skull. This study has methodological and conceptual implications for grasping the constraints that underlie the developmental and functional integration of the skull of humans and other primates. PMID:25992690

  12. Modular radiochemistry synthesis system

    DOEpatents

    Satyamurthy, Nagichettiar; Barrio, Jorge R.; Amarasekera, Bernard; Van Dam, Michael R.; Olma, Sebastian; Williams, Dirk; Eddings, Mark; Shen, Clifton Kwang-Fu

    2016-11-01

    A modular chemical production system includes multiple modules for performing a chemical reaction, particularly of radiochemical compounds, from a remote location. One embodiment comprises a reaction vessel including a moveable heat source with the position thereof relative to the reaction vessel being controllable from a remote position. Alternatively the heat source may be fixed in location and the reaction vial is moveable into and out of the heat source. The reaction vessel has one or more sealing plugs, the positioning of which in relationship to the reaction vessel is controllable from a remote position. Also the one or more reaction vessel sealing plugs can include one or more conduits there through for delivery of reactants, gases at atmospheric or an elevated pressure, inert gases, drawing a vacuum and removal of reaction end products to and from the reaction vial, the reaction vial with sealing plug in position being operable at elevated pressures. The modular chemical production system is assembled from modules which can each include operating condition sensors and controllers configured for monitoring and controlling the individual modules and the assembled system from a remote position. Other modules include, but are not limited to a Reagent Storage and Delivery Module, a Cartridge Purification Module, a Microwave Reaction Module, an External QC/Analysis/Purification Interface Module, an Aliquotting Module, an F-18 Drying Module, a Concentration Module, a Radiation Counting Module, and a Capillary Reactor Module.

  13. Modular radiochemistry synthesis system

    DOEpatents

    Satyamurthy, Nagichettiar; Barrio, Jorge R.; Amarasekera, Bernard; Van Dam, R. Michael; Olma, Sebastian; Williams, Dirk; Eddings, Mark; Shen, Clifton Kwang-Fu

    2015-12-15

    A modular chemical production system includes multiple modules for performing a chemical reaction, particularly of radiochemical compounds, from a remote location. One embodiment comprises a reaction vessel including a moveable heat source with the position thereof relative to the reaction vessel being controllable from a remote position. Alternatively the heat source may be fixed in location and the reaction vial is moveable into and out of the heat source. The reaction vessel has one or more sealing plugs, the positioning of which in relationship to the reaction vessel is controllable from a remote position. Also the one or more reaction vessel sealing plugs can include one or more conduits there through for delivery of reactants, gases at atmospheric or an elevated pressure, inert gases, drawing a vacuum and removal of reaction end products to and from the reaction vial, the reaction vial with sealing plug in position being operable at elevated pressures. The modular chemical production system is assembled from modules which can each include operating condition sensors and controllers configured for monitoring and controlling the individual modules and the assembled system from a remote position. Other modules include, but are not limited to a Reagent Storage and Delivery Module, a Cartridge Purification Module, a Microwave Reaction Module, an External QC/Analysis/Purification Interface Module, an Aliquotting Module, an F-18 Drying Module, a Concentration Module, a Radiation Counting Module, and a Capillary Reactor Module.

  14. Modular radiochemistry synthesis system

    DOEpatents

    Satyamurthy, Nagichettiar; Barrio, Jorge R; Amarasekera, Bernard; Van Dam, R. Michael; Olma, Sebastian; Williams, Dirk; Eddings, Mark A; Shen, Clifton Kwang-Fu

    2015-02-10

    A modular chemical production system includes multiple modules for performing a chemical reaction, particularly of radiochemical compounds, from a remote location. One embodiment comprises a reaction vessel including a moveable heat source with the position thereof relative to the reaction vessel being controllable from a remote position. Alternatively the heat source may be fixed in location and the reaction vial is moveable into and out of the heat source. The reaction vessel has one or more sealing plugs, the positioning of which in relationship to the reaction vessel is controllable from a remote position. Also the one or more reaction vessel sealing plugs can include one or more conduits there through for delivery of reactants, gases at atmospheric or an elevated pressure, inert gases, drawing a vacuum and removal of reaction end products to and from the reaction vial, the reaction vial with sealing plug in position being operable at elevated pressures. The modular chemical production system is assembled from modules which can each include operating condition sensors and controllers configured for monitoring and controlling the individual modules and the assembled system from a remote position. Other modules include, but are not limited to a Reagent Storage and Delivery Module, a Cartridge Purification Module, a Microwave Reaction Module, an External QC/Analysis/Purification Interface Module, an Aliquotting Module, an F-18 Drying Module, a Concentration Module, a Radiation Counting Module, and a Capillary Reactor Module.

  15. Review of the Modular Administrative Structure.

    ERIC Educational Resources Information Center

    Grand Valley State Colleges, Allendale, MI. Office of Institutional Analysis.

    The modular administrative structure implemented at Grand Valley State Colleges in 1973 is described as a system in which administrative affairs are divided into functional self-contained units called modules, each of which has a head or acting head who is responsible for the management of the functions contained within the module. A long-range…

  16. Large-scale modular biofiltration system for effective odor removal in a composting facility.

    PubMed

    Lin, Yueh-Hsien; Chen, Yu-Pei; Ho, Kuo-Ling; Lee, Tsung-Yih; Tseng, Ching-Ping

    2013-01-01

    Several different foul odors such as nitrogen-containing groups, sulfur-containing groups, and short-chain fatty-acids commonly emitted from composting facilities. In this study, an experimental laboratory-scale bioreactor was scaled up to build a large-scale modular biofiltration system that can process 34 m(3)min(-1)waste gases. This modular reactor system was proven effective in eliminating odors, with a 97% removal efficiency for 96 ppm ammonia, a 98% removal efficiency for 220 ppm amines, and a 100% removal efficiency of other odorous substances. The results of operational parameters indicate that this modular biofiltration system offers long-term operational stability. Specifically, a low pressure drop (<45 mmH2O m(-1)) was observed, indicating that the packing carrier in bioreactor units does not require frequent replacement. Thus, this modular biofiltration system can be used in field applications to eliminate various odors with compact working volume.

  17. Modular thermal analyzer routine, volume 1

    NASA Technical Reports Server (NTRS)

    Oren, J. A.; Phillips, M. A.; Williams, D. R.

    1972-01-01

    The Modular Thermal Analyzer Routine (MOTAR) is a general thermal analysis routine with strong capabilities for performing thermal analysis of systems containing flowing fluids, fluid system controls (valves, heat exchangers, etc.), life support systems, and thermal radiation situations. Its modular organization permits the analysis of a very wide range of thermal problems for simple problems containing a few conduction nodes to those containing complicated flow and radiation analysis with each problem type being analyzed with peak computational efficiency and maximum ease of use. The organization and programming methods applied to MOTAR achieved a high degree of computer utilization efficiency in terms of computer execution time and storage space required for a given problem. The computer time required to perform a given problem on MOTAR is approximately 40 to 50 percent that required for the currently existing widely used routines. The computer storage requirement for MOTAR is approximately 25 percent more than the most commonly used routines for the most simple problems but the data storage techniques for the more complicated options should save a considerable amount of space.

  18. Modular cell biology: retroactivity and insulation

    PubMed Central

    Del Vecchio, Domitilla; Ninfa, Alexander J; Sontag, Eduardo D

    2008-01-01

    Modularity plays a fundamental role in the prediction of the behavior of a system from the behavior of its components, guaranteeing that the properties of individual components do not change upon interconnection. Just as electrical, hydraulic, and other physical systems often do not display modularity, nor do many biochemical systems, and specifically, genetic networks. Here, we study the effect of interconnections on the input–output dynamic characteristics of transcriptional components, focusing on a property, which we call ‘retroactivity', that plays a role analogous to non-zero output impedance in electrical systems. In transcriptional networks, retroactivity is large when the amount of transcription factor is comparable to, or smaller than, the amount of promoter-binding sites, or when the affinity of such binding sites is high. To attenuate the effect of retroactivity, we propose a feedback mechanism inspired by the design of amplifiers in electronics. We introduce, in particular, a mechanism based on a phosphorylation–dephosphorylation cycle. This mechanism enjoys a remarkable insulation property, due to the fast timescales of the phosphorylation and dephosphorylation reactions. PMID:18277378

  19. Improving long-term care provision: towards demand-based care by means of modularity

    PubMed Central

    2010-01-01

    Background As in most fields of health care, societal and political changes encourage suppliers of long-term care to put their clients at the center of care and service provision and become more responsive towards client needs and requirements. However, the diverse, multiple and dynamic nature of demand for long-term care complicates the movement towards demand-based care provision. This paper aims to advance long-term care practice and, to that end, examines the application of modularity. This concept is recognized in a wide range of product and service settings for its ability to design demand-based products and processes. Methods Starting from the basic dimensions of modularity, we use qualitative research to explore the use and application of modularity principles in the current working practices and processes of four organizations in the field of long-term care for the elderly. In-depth semi-structured interviews were conducted with 38 key informants and triangulated with document research and observation. Data was analyzed thematically by means of coding and subsequent exploration of patterns. Data analysis was facilitated by qualitative analysis software. Results Our data suggest that a modular setup of supply is employed in the arrangement of care and service supply and assists providers of long-term care in providing their clients with choice options and variation. In addition, modularization of the needs assessment and package specification process allows the case organizations to manage client involvement but still provide customized packages of care and services. Conclusion The adequate setup of an organization's supply and its specification phase activities are indispensible for long-term care providers who aim to do better in terms of quality and efficiency. Moreover, long-term care providers could benefit from joint provision of care and services by means of modular working teams. Based upon our findings, we are able to elaborate on how to further

  20. Improving long-term care provision: towards demand-based care by means of modularity.

    PubMed

    de Blok, Carolien; Luijkx, Katrien; Meijboom, Bert; Schols, Jos

    2010-09-21

    As in most fields of health care, societal and political changes encourage suppliers of long-term care to put their clients at the center of care and service provision and become more responsive towards client needs and requirements. However, the diverse, multiple and dynamic nature of demand for long-term care complicates the movement towards demand-based care provision. This paper aims to advance long-term care practice and, to that end, examines the application of modularity. This concept is recognized in a wide range of product and service settings for its ability to design demand-based products and processes. Starting from the basic dimensions of modularity, we use qualitative research to explore the use and application of modularity principles in the current working practices and processes of four organizations in the field of long-term care for the elderly. In-depth semi-structured interviews were conducted with 38 key informants and triangulated with document research and observation. Data was analyzed thematically by means of coding and subsequent exploration of patterns. Data analysis was facilitated by qualitative analysis software. Our data suggest that a modular setup of supply is employed in the arrangement of care and service supply and assists providers of long-term care in providing their clients with choice options and variation. In addition, modularization of the needs assessment and package specification process allows the case organizations to manage client involvement but still provide customized packages of care and services. The adequate setup of an organization's supply and its specification phase activities are indispensible for long-term care providers who aim to do better in terms of quality and efficiency. Moreover, long-term care providers could benefit from joint provision of care and services by means of modular working teams. Based upon our findings, we are able to elaborate on how to further enable demand-based provision of long