A New Versatile Microarray-based Method for High Throughput Screening of Carbohydrate-active Enzymes*

PubMed Central

Vidal-Melgosa, Silvia; Pedersen, Henriette L.; Schückel, Julia; Arnal, Grégory; Dumon, Claire; Amby, Daniel B.; Monrad, Rune Nygaard; Westereng, Bjørge; Willats, William G. T.

2015-01-01

Carbohydrate-active enzymes have multiple biological roles and industrial applications. Advances in genome and transcriptome sequencing together with associated bioinformatics tools have identified vast numbers of putative carbohydrate-degrading and -modifying enzymes including glycoside hydrolases and lytic polysaccharide monooxygenases. However, there is a paucity of methods for rapidly screening the activities of these enzymes. By combining the multiplexing capacity of carbohydrate microarrays with the specificity of molecular probes, we have developed a sensitive, high throughput, and versatile semiquantitative enzyme screening technique that requires low amounts of enzyme and substrate. The method can be used to assess the activities of single enzymes, enzyme mixtures, and crude culture broths against single substrates, substrate mixtures, and biomass samples. Moreover, we show that the technique can be used to analyze both endo-acting and exo-acting glycoside hydrolases, polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. We demonstrate the potential of the technique by identifying the substrate specificities of purified uncharacterized enzymes and by screening enzyme activities from fungal culture broths. PMID:25657012

GRASP - A Prototype Interactive Graphic Sawing Program - (Forest Products Journal)

Treesearch

Luis G. Occeña; Daniel L. Schmoldt

1996-01-01

A versatile microcomputer-based interactive graphics sawing program has been developed as a tool for modeling various hardwood processes, from bucking and topping to log sawing, lumber edging, secondary processing, and even veneering. The microcomputer platform makes the tool affordable and accessible. A solid modeling basis provides the tool with a sound geometrical...

GRASP - A Prototype Interactive Graphic Sawing Program - (MU-IE Technical Report)

Treesearch

Luis G. Occeña; Daniel L. Schmoldt

1995-01-01

A versatile microcomputer-based interactive graphics program has been developed as a tool for modeling various hardwood processes, from bucking and topping to log sawing, lumber edging, secondary processing, even veneering. The microcomputer platform makes the tool affordable and accessible.A solid modeling basis provides the tool with a sound geometrical and...

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

PubMed

Ambrosini, Giovanna; Dreos, René; Kumar, Sunil; Bucher, Philipp

2016-11-18

ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data. Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade. The various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/ .

Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data.

PubMed

Pokharel, Yuba Raj; Saarela, Jani; Szwajda, Agnieszka; Rupp, Christian; Rokka, Anne; Lal Kumar Karna, Shibendra; Teittinen, Kaisa; Corthals, Garry; Kallioniemi, Olli; Wennerberg, Krister; Aittokallio, Tero; Westermarck, Jukka

2015-12-01

High content protein interaction screens have revolutionized our understanding of protein complex assembly. However, one of the major challenges in translation of high content protein interaction data is identification of those interactions that are functionally relevant for a particular biological question. To address this challenge, we developed a relevance ranking platform (RRP), which consist of modular functional and bioinformatic filters to provide relevance rank among the interactome proteins. We demonstrate the versatility of RRP to enable a systematic prioritization of the most relevant interaction partners from high content data, highlighted by the analysis of cancer relevant protein interactions for oncoproteins Pin1 and PME-1. We validated the importance of selected interactions by demonstration of PTOV1 and CSKN2B as novel regulators of Pin1 target c-Jun phosphorylation and reveal previously unknown interacting proteins that may mediate PME-1 effects via PP2A-inhibition. The RRP framework is modular and can be modified to answer versatile research problems depending on the nature of the biological question under study. Based on comparison of RRP to other existing filtering tools, the presented data indicate that RRP offers added value especially for the analysis of interacting proteins for which there is no sufficient prior knowledge available. Finally, we encourage the use of RRP in combination with either SAINT or CRAPome computational tools for selecting the candidate interactors that fulfill the both important requirements, functional relevance, and high confidence interaction detection. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Experiments in a Combustion-Driven Shock Tube with an Area Change

NASA Astrophysics Data System (ADS)

Schmidt, B. E.; Bobbitt, B.; Parziale, N. J.; Shepherd, J. E.

Shock tubes are versatile and useful tools for studying high temperature gas dynamics and the production of hypervelocity flows. High shock speeds are desirable for creating higher enthalpy, pressure, and temperature in the test gas which makes the study of thermo-chemical effects on fluid dynamics possible. Independent of construction and operational cost, free-piston drivers, such as the one used in the T5 facility at Caltech, give the best performance [3]. The high operational cost and long turnaround time of such a facility make a more economical option desirable for smaller-scale testing.

Catch and Patch: A Pipette-Based Approach for Automating Patch Clamp That Enables Cell Selection and Fast Compound Application.

PubMed

Danker, Timm; Braun, Franziska; Silbernagl, Nikole; Guenther, Elke

2016-03-01

Manual patch clamp, the gold standard of electrophysiology, represents a powerful and versatile toolbox to stimulate, modulate, and record ion channel activity from membrane fragments and whole cells. The electrophysiological readout can be combined with fluorescent or optogenetic methods and allows for ultrafast solution exchanges using specialized microfluidic tools. A hallmark of manual patch clamp is the intentional selection of individual cells for recording, often an essential prerequisite to generate meaningful data. So far, available automation solutions rely on random cell usage in the closed environment of a chip and thus sacrifice much of this versatility by design. To parallelize and automate the traditional patch clamp technique while perpetuating the full versatility of the method, we developed an approach to automation, which is based on active cell handling and targeted electrode placement rather than on random processes. This is achieved through an automated pipette positioning system, which guides the tips of recording pipettes with micrometer precision to a microfluidic cell handling device. Using a patch pipette array mounted on a conventional micromanipulator, our automated patch clamp process mimics the original manual patch clamp as closely as possible, yet achieving a configuration where recordings are obtained from many patch electrodes in parallel. In addition, our implementation is extensible by design to allow the easy integration of specialized equipment such as ultrafast compound application tools. The resulting system offers fully automated patch clamp on purposely selected cells and combines high-quality gigaseal recordings with solution switching in the millisecond timescale.

Firefly Luciferin-Inspired Biocompatible Chemistry for Protein Labeling and In Vivo Imaging.

PubMed

Wang, Yuqi; An, Ruibing; Luo, Zhiliang; Ye, Deju

2018-04-17

Biocompatible reactions have emerged as versatile tools to build various molecular imaging probes that hold great promise for the detection of biological processes in vitro and/or in vivo. In this Minireview, we describe the recent advances in the development of a firefly luciferin-inspired biocompatible reaction between cyanobenzothiazole (CBT) and cysteine (Cys), and highlight its versatility to label proteins and build multimodality molecular imaging probes. The review starts from the general introduction of biocompatible reactions, which is followed by briefly describing the development of the firefly luciferin-inspired biocompatible chemistry. We then discuss its applications for the specific protein labeling and for the development of multimodality imaging probes (fluorescence, bioluminescence, MRI, PET, photoacoustic, etc.) that enable high sensitivity and spatial resolution imaging of redox environment, furin and caspase-3/7 activity in living cells and mice. Finally, we offer the conclusions and our perspective on the various and potential applications of this reaction. We hope that this review will contribute to the research of biocompatible reactions for their versatile applications in protein labeling and molecular imaging. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chitosan-microreactor: a versatile approach for heterogeneous organic synthesis in microfluidics.

PubMed

Basavaraju, K C; Sharma, Siddharth; Singh, Ajay K; Im, Do Jin; Kim, Dong-Pyo

2014-07-01

Microreactors have been proven to be efficient tools for a variety of homogeneous organic transformations due to their mixing efficiency, which results in very fast reactions, better heat and mass transfer, and simple scale-up. However, in heterogeneous catalytic reactions each catalyst needs an individual substrate as support. Herein, a versatile approach to immobilize metal catalysts on chitosan as a common substrate is presented. Chitosan, accommodating many metal catalysts, is grafted onto the microchannel surface as nanobrush. The versatility, catalytic efficiency, and stability/durability of the microreactor are demonstrated for a number of organic transformations involving various metal compounds as catalysts. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

eShadow: A tool for comparing closely related sequences

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

Ovcharenko, Ivan; Boffelli, Dario; Loots, Gabriela G.

2004-01-15

Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing, has been pioneered for predicting functional elements in the human genome through the analysis of multiple primate sequence alignments. We have expanded this theoretical approach to create a computational tool, eShadow, for the identification of elements under selective pressure in multiple sequence alignments of closely related genomes, such as in comparisons of human to primate or mouse to rat DNA. This tool integrates two different statistical methods and allows for the dynamic visualizationmore » of the resulting conservation profile. eShadow also includes a versatile optimization module capable of training the underlying Hidden Markov Model to differentially predict functional sequences. This module grants the tool high flexibility in the analysis of multiple sequence alignments and in comparing sequences with different divergence rates. Here, we describe the eShadow comparative tool and its potential uses for analyzing both multiple nucleotide and protein alignments to predict putative functional elements. The eShadow tool is publicly available at http://eshadow.dcode.org/« less

Tools for Energized Teaching: Revitalize Instruction with Ease

ERIC Educational Resources Information Center

Wilson, Kenneth

2006-01-01

"Challenge yourself to break out of your old routines. Think anew." Ken Wilson, educator, trainer and consultant has assembled a versatile, practical and generic book to use across disciplines and with all age levels. This collection of accessible, user-friendly tools incorporates and connects current education research--without the jargon. "This…

Computer assisted surgery with 3D robot models and visualisation of the telesurgical action.

PubMed

Rovetta, A

2000-01-01

This paper deals with the support of virtual reality computer action in the procedures of surgical robotics. Computer support gives a direct representation of the surgical theatre. The modelization of the procedure in course and in development gives a psychological reaction towards safety and reliability. Robots similar to the ones used by the manufacturing industry can be used with little modification as very effective surgical tools. They have high precision, repeatability and are versatile in integrating with the medical instrumentation. Now integrated surgical rooms, with computer and robot-assisted intervention, are operating. The computer is the element for a decision taking aid, and the robot works as a very effective tool.

PyOperators: Operators and solvers for high-performance computing

NASA Astrophysics Data System (ADS)

Chanial, P.; Barbey, N.

2012-12-01

PyOperators is a publicly available library that provides basic operators and solvers for small-to-very large inverse problems ({http://pchanial.github.com/pyoperators}). It forms the backbone of the package PySimulators, which implements specific operators to construct an instrument model and means to conveniently represent a map, a timeline or a time-dependent observation ({http://pchanial.github.com/pysimulators}). Both are part of the Tamasis (Tools for Advanced Map-making, Analysis and SImulations of Submillimeter surveys) toolbox, aiming at providing versatile, reliable, easy-to-use, and optimal map-making tools for Herschel and future generation of sub-mm instruments. The project is a collaboration between 4 institutes (ESO Garching, IAS Orsay, CEA Saclay, Univ. Leiden).

Robot Tracer with Visual Camera

NASA Astrophysics Data System (ADS)

Jabbar Lubis, Abdul; Dwi Lestari, Yuyun; Dafitri, Haida; Azanuddin

2017-12-01

Robot is a versatile tool that can function replace human work function. The robot is a device that can be reprogrammed according to user needs. The use of wireless networks for remote monitoring needs can be utilized to build a robot that can be monitored movement and can be monitored using blueprints and he can track the path chosen robot. This process is sent using a wireless network. For visual robot using high resolution cameras to facilitate the operator to control the robot and see the surrounding circumstances.

High-resolution γ-ray spectroscopy: a versatile tool for nuclear β-decay studies at TRIUMF-ISAC

NASA Astrophysics Data System (ADS)

Ball, G. C.; Achtzehn, T.; Albers, D.; Khalili, J. S. Al; Andreoiu, C.; Andreyev, A.; Ashley, S. F.; Austin, R. A. E.; Becker, J. A.; Bricault, P.; Chan, S.; Chakrawarthy, R. S.; Churchman, R.; Coombes, H.; Cunningham, E. S.; Daoud, J.; Dombsky, M.; Drake, T. E.; Eshpeter, B.; Finlay, P.; Garrett, P. E.; Geppert, C.; Grinyer, G. F.; Hackman, G.; Hanemaayer, V.; Hyland, B.; Jones, G. A.; Koopmans, K. A.; Kulp, W. D.; Lassen, J.; Lavoie, J. P.; Leslie, J. R.; Litvinov, Y.; Macdonald, J. A.; Mattoon, C.; Melconian, D.; Morton, A. C.; Osborne, C. J.; Pearson, C. J.; Pearson, M.; Phillips, A. A.; Ressler, J. J.; Sarazin, F.; Schumaker, M. A.; Schwarzenberg, J.; Scraggs, H. C.; Smith, M. B.; Svensson, C. E.; Valiente-Dobon, J. J.; Waddington, J. C.; Walker, P. M.; Wendt, K.; Williams, S. J.; Wood, J. L.; Zganjar, E. F.

2005-10-01

High-resolution γ-ray spectroscopy is essential to fully exploit the unique, high-quality beams available at the next generation of radioactive ion beam facilities such as the TRIUMF isotope separator and accelerator (ISAC). The 8π spectrometer, which consists of 20 Compton-suppressed HPGe detectors, has recently been reconfigured for a vigorous research programme in weak interaction and nuclear structure physics. With the addition of a variety of ancillary detectors it has become the world's most powerful device dedicated to β-decay studies. This paper provides a brief overview of the apparatus and highlights from recent experiments.

Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs).

PubMed

Cantsilieris, Stuart; Stessman, Holly A; Shendure, Jay; Eichler, Evan E

2017-01-01

Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers. The ability to append sequencing adaptors and sample-specific barcodes allows large-scale pooling and subsequent high-throughput sequencing at relatively low cost per sample. Here, we describe a "wet bench" protocol detailing the capture and subsequent sequencing of >2000 genomic targets from 192 samples, representative of a single lane on the Illumina HiSeq 2000 platform.

A new versatile microarray-based method for high throughput screening of carbohydrate-active enzymes.

PubMed

Vidal-Melgosa, Silvia; Pedersen, Henriette L; Schückel, Julia; Arnal, Grégory; Dumon, Claire; Amby, Daniel B; Monrad, Rune Nygaard; Westereng, Bjørge; Willats, William G T

2015-04-03

Carbohydrate-active enzymes have multiple biological roles and industrial applications. Advances in genome and transcriptome sequencing together with associated bioinformatics tools have identified vast numbers of putative carbohydrate-degrading and -modifying enzymes including glycoside hydrolases and lytic polysaccharide monooxygenases. However, there is a paucity of methods for rapidly screening the activities of these enzymes. By combining the multiplexing capacity of carbohydrate microarrays with the specificity of molecular probes, we have developed a sensitive, high throughput, and versatile semiquantitative enzyme screening technique that requires low amounts of enzyme and substrate. The method can be used to assess the activities of single enzymes, enzyme mixtures, and crude culture broths against single substrates, substrate mixtures, and biomass samples. Moreover, we show that the technique can be used to analyze both endo-acting and exo-acting glycoside hydrolases, polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. We demonstrate the potential of the technique by identifying the substrate specificities of purified uncharacterized enzymes and by screening enzyme activities from fungal culture broths. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

In situ DART-MS as a Versatile and Rapid Dereplication Tool in Lichenology: Chemical Fingerprinting of Ophioparma ventosa.

PubMed

Le Pogam, Pierre; Le Lamer, Anne-Cécile; Legouin, Béatrice; Boustie, Joël; Rondeau, David

2016-11-01

Lichens widely occur all over the world and are known to produce unique secondary metabolites with various biological activities. To develop high-throughput screening approaches requiring little to no sample preparation to alleviate the dereplication holdup and accelerate the discovery workflow of new structures from lichens. The extracellular distribution of lichen metabolites is incentive for in situ chemical profiling of lichens using the ambient mass spectrometry DART-MS. For this purpose, the chlorolichen Ophioparma ventosa, producing an array of lichen polyphenolics that encompass the main structural classes associated to lichen chemodiversity, represented a relevant model to assess the versatility of this platform. The feasibility of this approach was first established by analysing the pure compounds known from this species prior to being extended to different solid organs of the lichen. All tested compounds could be detected in positive and negative ion modes, most often with prevalent protonated or deprotonated molecules. Only depsides underwent a significant in-source fragmentation in both ionisation modes, which should be regarded as an added value for their structural elucidation. In situ DART-MS analyses of Ophioparma ventosa provided an extensive chemical profile and noteworthy pinpointed miriquidic acid, an unusual lichen depside so far unknown within this species. At last, in situ DART-MS granted a first insight into the distribution of the metabolites within the lichen. DART-MS represents a versatile tool to the wide field of lichenology, facilitating accelerated and sharp analyses of lichens and bypassing costly and tedious procedures of solvent extraction. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

A high-resolution, confocal laser-scanning microscope and flash photolysis system for physiological studies.

PubMed

Parker, I; Callamaras, N; Wier, W G

1997-06-01

We describe the construction of a high-resolution confocal laser-scanning microscope, and illustrate its use for studying elementary Ca2+ signalling events in cells. An avalanche photodiode module and simple optical path provide a high efficiency system for detection of fluorescence signals, allowing use of a small confocal aperture giving near diffraction-limited spatial resolution (< 300 nm lateral and < 400 nm axial). When operated in line-scan mode, the maximum temporal resolution is 1 ms, and the associated computer software allows complete flexibility to record line-scans continuously for long (minutes) periods or to obtain any desired pixel resolution in x-y scans. An independent UV irradiation system permits simultaneous photolysis of caged compounds over either a uniform, wide field (arc lamp source) or at a tightly focussed spot (frequency-tripled Nd:YAG laser). The microscope thus provides a versatile tool for optical studies of dynamic cellular processes, as well as excellent resolution for morphological studies. The confocal scanner can be added to virtually any inverted microscope for a component cost that is only a small fraction of that of comparable commercial instruments, yet offers better performance and greater versatility.

Transposons As Tools for Functional Genomics in Vertebrate Models.

PubMed

Kawakami, Koichi; Largaespada, David A; Ivics, Zoltán

2017-11-01

Genetic tools and mutagenesis strategies based on transposable elements are currently under development with a vision to link primary DNA sequence information to gene functions in vertebrate models. By virtue of their inherent capacity to insert into DNA, transposons can be developed into powerful tools for chromosomal manipulations. Transposon-based forward mutagenesis screens have numerous advantages including high throughput, easy identification of mutated alleles, and providing insight into genetic networks and pathways based on phenotypes. For example, the Sleeping Beauty transposon has become highly instrumental to induce tumors in experimental animals in a tissue-specific manner with the aim of uncovering the genetic basis of diverse cancers. Here, we describe a battery of mutagenic cassettes that can be applied in conjunction with transposon vectors to mutagenize genes, and highlight versatile experimental strategies for the generation of engineered chromosomes for loss-of-function as well as gain-of-function mutagenesis for functional gene annotation in vertebrate models, including zebrafish, mice, and rats. Copyright © 2017 Elsevier Ltd. All rights reserved.

Silk Film Embossing System

NASA Astrophysics Data System (ADS)

Paquette, Mark S.

New tools are often required to facilitate new discoveries and test new methods. Commercial offerings can be prohibitively expensive and difficult to customize. The development of ad-hoc tools provides the most flexibility and provides an opportunity to modify and refine a technology. An embossing system was developed for silk film imprinting and stamping in order to facilitate and add versatility to the efforts involving micro- and nanoscale device manufacturing in biopolymers. This system features temperature controlled embossing surfaces, adjustable embossing pressures, and variable embossing times. The device can also be fitted with interchangeable temperature controlled embossing and stamping tools. The design, development, fabrication, applications, and future improvements are explored for the system. This device may facilitate new discoveries in the realm of biopolymer micro- and nanomanufacturing and may provide a path towards high volume production of silk film based technologies.

A Deeper Understanding of Metacomprehension in Reading: Development of a New Multidimensional Tool

ERIC Educational Resources Information Center

Soto, Christian; Gutierrez de Blume, Antonio P.; Asún, Rodrigo; Jacovina, Matthew; Vásquez, Claudio

2018-01-01

The purpose of this research endeavor was to develop and validate a new measurement tool predicated on previous research to assess learners' metacomprehension during reading. In two separate studies with Chilean undergraduate students (N = 923), we demonstrate the versatility and utility of our proposed Metacomprehension Inventory (MI). In Study…

Making Connections: Using Mobile Phones as a Museum Tool

ERIC Educational Resources Information Center

Manabe, Makoto; Lydens, Lois

2007-01-01

Mobile phones have been steadily gaining appreciation among the museum community as a versatile tool. The new generation of mobile phones allows museums to imagine a whole new range of applications, including audiovisual personal tours and live-feed broadcasting. Personal tours using mobile phones are appealing to museum educators since patrons…

Configuration Management and Infrastructure Monitoring Using CFEngine and Icinga for Real-time Heterogeneous Data Taking Environment

NASA Astrophysics Data System (ADS)

Poat, M. D.; Lauret, J.; Betts, W.

2015-12-01

The STAR online computing environment is an intensive ever-growing system used for real-time data collection and analysis. Composed of heterogeneous and sometimes groups of custom-tuned machines, the computing infrastructure was previously managed by manual configurations and inconsistently monitored by a combination of tools. This situation led to configuration inconsistency and an overload of repetitive tasks along with lackluster communication between personnel and machines. Globally securing this heterogeneous cyberinfrastructure was tedious at best and an agile, policy-driven system ensuring consistency, was pursued. Three configuration management tools, Chef, Puppet, and CFEngine have been compared in reliability, versatility and performance along with a comparison of infrastructure monitoring tools Nagios and Icinga. STAR has selected the CFEngine configuration management tool and the Icinga infrastructure monitoring system leading to a versatile and sustainable solution. By leveraging these two tools STAR can now swiftly upgrade and modify the environment to its needs with ease as well as promptly react to cyber-security requests. By creating a sustainable long term monitoring solution, the detection of failures was reduced from days to minutes, allowing rapid actions before the issues become dire problems, potentially causing loss of precious experimental data or uptime.

Myokit: A simple interface to cardiac cellular electrophysiology.

PubMed

Clerx, Michael; Collins, Pieter; de Lange, Enno; Volders, Paul G A

2016-01-01

Myokit is a new powerful and versatile software tool for modeling and simulation of cardiac cellular electrophysiology. Myokit consists of an easy-to-read modeling language, a graphical user interface, single and multi-cell simulation engines and a library of advanced analysis tools accessible through a Python interface. Models can be loaded from Myokit's native file format or imported from CellML. Model export is provided to C, MATLAB, CellML, CUDA and OpenCL. Patch-clamp data can be imported and used to estimate model parameters. In this paper, we review existing tools to simulate the cardiac cellular action potential to find that current tools do not cater specifically to model development and that there is a gap between easy-to-use but limited software and powerful tools that require strong programming skills from their users. We then describe Myokit's capabilities, focusing on its model description language, simulation engines and import/export facilities in detail. Using three examples, we show how Myokit can be used for clinically relevant investigations, multi-model testing and parameter estimation in Markov models, all with minimal programming effort from the user. This way, Myokit bridges a gap between performance, versatility and user-friendliness. Copyright © 2015 Elsevier Ltd. All rights reserved.

BRepertoire: a user-friendly web server for analysing antibody repertoire data.

PubMed

Margreitter, Christian; Lu, Hui-Chun; Townsend, Catherine; Stewart, Alexander; Dunn-Walters, Deborah K; Fraternali, Franca

2018-04-14

Antibody repertoire analysis by high throughput sequencing is now widely used, but a persisting challenge is enabling immunologists to explore their data to discover discriminating repertoire features for their own particular investigations. Computational methods are necessary for large-scale evaluation of antibody properties. We have developed BRepertoire, a suite of user-friendly web-based software tools for large-scale statistical analyses of repertoire data. The software is able to use data preprocessed by IMGT, and performs statistical and comparative analyses with versatile plotting options. BRepertoire has been designed to operate in various modes, for example analysing sequence-specific V(D)J gene usage, discerning physico-chemical properties of the CDR regions and clustering of clonotypes. Those analyses are performed on the fly by a number of R packages and are deployed by a shiny web platform. The user can download the analysed data in different table formats and save the generated plots as image files ready for publication. We believe BRepertoire to be a versatile analytical tool that complements experimental studies of immune repertoires. To illustrate the server's functionality, we show use cases including differential gene usage in a vaccination dataset and analysis of CDR3H properties in old and young individuals. The server is accessible under http://mabra.biomed.kcl.ac.uk/BRepertoire.

CRISPR-Cas9 for medical genetic screens: applications and future perspectives.

PubMed

Xue, Hui-Ying; Ji, Li-Juan; Gao, Ai-Mei; Liu, Ping; He, Jing-Dong; Lu, Xiao-Jie

2016-02-01

CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR associated nuclease 9) systems have emerged as versatile and convenient (epi)genome editing tools and have become an important player in medical genetic research. CRISPR-Cas9 and its variants such as catalytically inactivated Cas9 (dead Cas9, dCas9) and scaffold-incorporating single guide sgRNA (scRNA) have been applied in various genomic screen studies. CRISPR screens enable high-throughput interrogation of gene functions in health and diseases. Compared with conventional RNAi screens, CRISPR screens incur less off-target effects and are more versatile in that they can be used in multiple formats such as knockout, knockdown and activation screens, and can target coding and non-coding regions throughout the genome. This powerful screen platform holds the potential of revolutionising functional genomic studies in the near future. Herein, we introduce the mechanisms of (epi)genome editing mediated by CRISPR-Cas9 and its variants, introduce the procedures and applications of CRISPR screen in functional genomics, compare it with conventional screen tools and at last discuss current challenges and opportunities and propose future directions. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Additively Manufactured Device for Dynamic Culture of Large Arrays of 3D Tissue Engineered Constructs.

PubMed

Costa, Pedro F; Hutmacher, Dietmar W; Theodoropoulos, Christina; Gomes, Manuela E; Reis, Rui L; Vaquette, Cédryck

2015-04-22

The ability to test large arrays of cell and biomaterial combinations in 3D environments is still rather limited in the context of tissue engineering and regenerative medicine. This limitation can be generally addressed by employing highly automated and reproducible methodologies. This study reports on the development of a highly versatile and upscalable method based on additive manufacturing for the fabrication of arrays of scaffolds, which are enclosed into individualized perfusion chambers. Devices containing eight scaffolds and their corresponding bioreactor chambers are simultaneously fabricated utilizing a dual extrusion additive manufacturing system. To demonstrate the versatility of the concept, the scaffolds, while enclosed into the device, are subsequently surface-coated with a biomimetic calcium phosphate layer by perfusion with simulated body fluid solution. 96 scaffolds are simultaneously seeded and cultured with human osteoblasts under highly controlled bidirectional perfusion dynamic conditions over 4 weeks. Both coated and noncoated resulting scaffolds show homogeneous cell distribution and high cell viability throughout the 4 weeks culture period and CaP-coated scaffolds result in a significantly increased cell number. The methodology developed in this work exemplifies the applicability of additive manufacturing as a tool for further automation of studies in the field of tissue engineering and regenerative medicine. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Parallel System for Integrating Impact Models and Sectors (pSIMS)

NASA Technical Reports Server (NTRS)

Elliott, Joshua; Kelly, David; Chryssanthacopoulos, James; Glotter, Michael; Jhunjhnuwala, Kanika; Best, Neil; Wilde, Michael; Foster, Ian

2014-01-01

We present a framework for massively parallel climate impact simulations: the parallel System for Integrating Impact Models and Sectors (pSIMS). This framework comprises a) tools for ingesting and converting large amounts of data to a versatile datatype based on a common geospatial grid; b) tools for translating this datatype into custom formats for site-based models; c) a scalable parallel framework for performing large ensemble simulations, using any one of a number of different impacts models, on clusters, supercomputers, distributed grids, or clouds; d) tools and data standards for reformatting outputs to common datatypes for analysis and visualization; and e) methodologies for aggregating these datatypes to arbitrary spatial scales such as administrative and environmental demarcations. By automating many time-consuming and error-prone aspects of large-scale climate impacts studies, pSIMS accelerates computational research, encourages model intercomparison, and enhances reproducibility of simulation results. We present the pSIMS design and use example assessments to demonstrate its multi-model, multi-scale, and multi-sector versatility.

The fragmented character of Middle Palaeolithic stone tool technology.

PubMed

Turq, Alain; Roebroeks, Wil; Bourguignon, Laurence; Faivre, Jean-Philippe

2013-11-01

The importance of the transport of stone artefacts in structuring Neandertal lithic assemblages has often been addressed, but the degree to which this led to fragmentation of lithic reduction over Middle Palaeolithic landscapes has not been explicitly studied thus far. Large-scale excavations of Middle Palaeolithic open-air sites and refitting studies of the retrieved assemblages have yielded new, high-resolution data on the mobile aspects of Neandertal stone tool technology. In this paper, we integrate lithic technology and raw material data from recent studies of Middle Palaeolithic open-air and rock shelter sites in Western Europe. We demonstrate that the results of a variety of typological, technological (especially refitting), and lithological studies have important consequences for our knowledge of the acquisition of raw materials and subsequent production, usage and discard of stone artefacts in the Middle Palaeolithic. Neandertal production and use of stone tools was fragmented in three domains: the spatial, the temporal and the social domain. We show that this versatile segmentation of stone artefact handling strategies is a main determinant of the character of the Neandertal archaeological record. Our data testify to ubiquitous and continuous transport of stone artefacts of a wide variety of forms, picked by Neandertals using selection criteria that were sometimes far removed from what archaeologists have traditionally considered, and to some degree still consider, to be desired end products of knapping activities. The data presented here testify to the variability and versatility of Middle Palaeolithic stone tool technology, whose fragmented character created very heterogeneous archaeological assemblages, usually the product of a wide variety of independent import, use, discard and/or subsequent transport events. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

Wilson, Eric J

The ResStock analysis tool is helping states, municipalities, utilities, and manufacturers identify which home upgrades save the most energy and money. Across the country there's a vast diversity in the age, size, construction practices, installed equipment, appliances, and resident behavior of the housing stock, not to mention the range of climates. These variations have hindered the accuracy of predicting savings for existing homes. Researchers at the National Renewable Energy Laboratory (NREL) developed ResStock. It's a versatile tool that takes a new approach to large-scale residential energy analysis by combining: large public and private data sources, statistical sampling, detailed subhourly buildingmore » simulations, high-performance computing. This combination achieves unprecedented granularity and most importantly - accuracy - in modeling the diversity of the single-family housing stock.« less

Catechol-grafted poly(ethylene glycol) for PEGylation on versatile substrates.

PubMed

Lee, Hyukjin; Lee, Kang Dae; Pyo, Kyung Bo; Park, Sung Young; Lee, Haeshin

2010-03-16

We report on catechol-grafted poly(ethylene) glycol (PEG-g-catechol) for the preparation of nonfouling surfaces on versatile substrates including adhesion-resistant PTFE. PEG-g-catechol was prepared by the step-growth polymerization of PEO to which dopamine, a mussel-derived adhesive molecule, was conjugated. The immersion of substrates into an aqueous solution of PEG-g-catechol resulted in robust PEGylation on versatile surfaces of noble metals, oxides, and synthetic polymers. Surface PEGylation was unambiguously confirmed by various surface analytical tools such as ellipsometry, goniometry, infrared spectroscopy, and X-ray photoelectron spectroscopy. Contrary to existing PEG derivatives that are difficult-to-modify synthetic polymer surfaces, PEG-g-catechol can be considered to be a new class of PEGs for the facile surface PEGylation of various types of surfaces.

Illuminating the Past: The Neutron as a Tool in Archaeology

ERIC Educational Resources Information Center

Kockelmann, W.; Kirfel, A.; Siano, S.; Frost, C. D.

2004-01-01

Neutrons can be produced in nuclear reactions and used as very versatile probes for condensed matter research. Since their introduction in the 1950s neutron scattering techniques have evolved to be very powerful tools for investigating the properties of condensed matter. Here we present the concept of neutron diffraction and how this technique can…

Using Concepts in Literature-based Discovery: Simulating Swanson's Raynaud-Fish Oil and Migraine-Magnesium Discoveries.

ERIC Educational Resources Information Center

Weeber, Marc; Klein, Henny; de Jong-van den Berg, Lolkje T. W.; Vos, Rein

2001-01-01

Proposes a two-step model of discovery in which new scientific hypotheses can be generated and subsequently tested. Applying advanced natural language processing techniques to find biomedical concepts in text, the model is implemented in a versatile interactive discovery support tool. This tool is used to successfully simulate Don R. Swanson's…

msBiodat analysis tool, big data analysis for high-throughput experiments.

PubMed

Muñoz-Torres, Pau M; Rokć, Filip; Belužic, Robert; Grbeša, Ivana; Vugrek, Oliver

2016-01-01

Mass spectrometry (MS) are a group of a high-throughput techniques used to increase knowledge about biomolecules. They produce a large amount of data which is presented as a list of hundreds or thousands of proteins. Filtering those data efficiently is the first step for extracting biologically relevant information. The filtering may increase interest by merging previous data with the data obtained from public databases, resulting in an accurate list of proteins which meet the predetermined conditions. In this article we present msBiodat Analysis Tool, a web-based application thought to approach proteomics to the big data analysis. With this tool, researchers can easily select the most relevant information from their MS experiments using an easy-to-use web interface. An interesting feature of msBiodat analysis tool is the possibility of selecting proteins by its annotation on Gene Ontology using its Gene Id, ensembl or UniProt codes. The msBiodat analysis tool is a web-based application that allows researchers with any programming experience to deal with efficient database querying advantages. Its versatility and user-friendly interface makes easy to perform fast and accurate data screening by using complex queries. Once the analysis is finished, the result is delivered by e-mail. msBiodat analysis tool is freely available at http://msbiodata.irb.hr.

A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization

NASA Astrophysics Data System (ADS)

van der Velde, Jasper H. M.; Oelerich, Jens; Huang, Jingyi; Smit, Jochem H.; Aminian Jazi, Atieh; Galiani, Silvia; Kolmakov, Kirill; Guoridis, Giorgos; Eggeling, Christian; Herrmann, Andreas; Roelfes, Gerard; Cordes, Thorben

2016-01-01

Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with `self-healing' properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer-dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard.

DEKOIS: demanding evaluation kits for objective in silico screening--a versatile tool for benchmarking docking programs and scoring functions.

PubMed

Vogel, Simon M; Bauer, Matthias R; Boeckler, Frank M

2011-10-24

For widely applied in silico screening techniques success depends on the rational selection of an appropriate method. We herein present a fast, versatile, and robust method to construct demanding evaluation kits for objective in silico screening (DEKOIS). This automated process enables creating tailor-made decoy sets for any given sets of bioactives. It facilitates a target-dependent validation of docking algorithms and scoring functions helping to save time and resources. We have developed metrics for assessing and improving decoy set quality and employ them to investigate how decoy embedding affects docking. We demonstrate that screening performance is target-dependent and can be impaired by latent actives in the decoy set (LADS) or enhanced by poor decoy embedding. The presented method allows extending and complementing the collection of publicly available high quality decoy sets toward new target space. All present and future DEKOIS data sets will be made accessible at www.dekois.com.

Acoustic Purification of Extracellular Microvesicles

PubMed Central

Lee, Kyungheon; Shao, Huilin; Weissleder, Ralph; Lee, Hakho

2015-01-01

Microvesicles (MVs) are an increasingly important source for biomarker discovery and clinical diagnostics. The small size of MVs and their presence in complex biological environment, however, pose practical technical challenges, particularly when sample volumes are small. We herein present an acoustic nano-filter system that size-specifically separates MVs in a continuous and contact-free manner. The separation is based on ultrasound standing waves that exert differential acoustic force on MVs according to their size and density. By optimizing the design of the ultrasound transducers and underlying electronics, we were able to achieve a high separation yield and resolution. The “filter size-cutoff” can be controlled electronically in situ and enables versatile MV-size selection. We applied the acoustic nano-filter to isolate nanoscale (<200 nm) vesicles from cell culture media as well as MVs in stored red blood cell products. With the capacity for rapid and contact-free MV isolation, the developed system could become a versatile preparatory tool for MV analyses. PMID:25672598

A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization

PubMed Central

van der Velde, Jasper H. M.; Oelerich, Jens; Huang, Jingyi; Smit, Jochem H.; Aminian Jazi, Atieh; Galiani, Silvia; Kolmakov, Kirill; Gouridis, Giorgos; Eggeling, Christian; Herrmann, Andreas; Roelfes, Gerard; Cordes, Thorben

2016-01-01

Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with ‘self-healing’ properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer–dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard. PMID:26751640

LED-based interference-reflection microscopy combined with optical tweezers for quantitative three-dimensional microtubule imaging.

PubMed

Simmert, Steve; Abdosamadi, Mohammad Kazem; Hermsdorf, Gero; Schäffer, Erik

2018-05-28

Optical tweezers combined with various microscopy techniques are a versatile tool for single-molecule force spectroscopy. However, some combinations may compromise measurements. Here, we combined optical tweezers with total-internal-reflection-fluorescence (TIRF) and interference-reflection microscopy (IRM). Using a light-emitting diode (LED) for IRM illumination, we show that single microtubules can be imaged with high contrast. Furthermore, we converted the IRM interference pattern of an upward bent microtubule to its three-dimensional (3D) profile calibrated against the optical tweezers and evanescent TIRF field. In general, LED-based IRM is a powerful method for high-contrast 3D microscopy.

IDL Object Oriented Software for Hinode/XRT Image Analysis

NASA Astrophysics Data System (ADS)

Higgins, P. A.; Gallagher, P. T.

2008-09-01

We have developed a set of object oriented IDL routines that enable users to search, download and analyse images from the X-Ray Telescope (XRT) on-board Hinode. In this paper, we give specific examples of how the object can be used and how multi-instrument data analysis can be performed. The XRT object is a highly versatile and powerful IDL object, which will prove to be a useful tool for solar researchers. This software utilizes the generic Framework object available within the GEN branch of SolarSoft.

Enhanced poly(3-hydroxybutyrate) production in transgenic tobacco BY-2 cells using engineered acetoacetyl-CoA reductase.

PubMed

Yokoo, Toshinori; Matsumoto, Ken'ichiro; Ooba, Takashi; Morimoto, Kenjiro; Taguchi, Seiichi

2015-01-01

Highly active mutant of NADPH-dependent acetoacetyl-CoA reductase (PhaB) was expressed in Nicotiana tabacum cv. Bright Yellow-2 cultured cells to produce poly(3-hydroxybutyrate) [P(3HB)]. The mutated PhaB increased P(3HB) content by three-fold over the control, indicating that the mutant was a versatile tool for P(3HB) production. Additionally, the PhaB-catalyzed reaction was suggested to be a rate-limiting step of P(3HB) biosynthesis in tobacco BY-2 cells.

Measurement of strains by means of electro-optics holography

NASA Astrophysics Data System (ADS)

Sciammarella, Cesar A.; Bhat, Gopalakrishna K.; Albertazzi, Armando, Jr.

1991-03-01

The use of a TV camera as a recording medium and the observation of whole field displacements in real time makes holographic TV a very interesting and powerful tool in a variety of areas from NDE to research and development. The paper presents new developments in the field that add to the versatility of the technique by introducing portability and methods to obtain accurate quantitative results. Examples of applications are given to the measurement of strains both at room and at high temperatures and strain measurements at the microscopic level. 1.

MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data

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

White, Richard A.; Panyala, Ajay R.; Glass, Kevin A.

MerCat is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. MerCat inputs include assembled contigs and raw sequence reads from any platform resulting in feature abundance counts tables. MerCat allows for direct analysis of data properties without reference sequence database dependency commonly used by search tools such as BLAST and/or DIAMOND for compositional analysis of whole community shotgun sequencing (e.g. metagenomes and metatranscriptomes).

Constraint-Muse: A Soft-Constraint Based System for Music Therapy

NASA Astrophysics Data System (ADS)

Hölzl, Matthias; Denker, Grit; Meier, Max; Wirsing, Martin

Monoidal soft constraints are a versatile formalism for specifying and solving multi-criteria optimization problems with dynamically changing user preferences. We have developed a prototype tool for interactive music creation, called Constraint Muse, that uses monoidal soft constraints to ensure that a dynamically generated melody harmonizes with input from other sources. Constraint Muse provides an easy to use interface based on Nintendo Wii controllers and is intended to be used in music therapy for people with Parkinson’s disease and for children with high-functioning autism or Asperger’s syndrome.

Pool-site fuel inspection and examination techniques applied by the Kraftwerk Union Aktiengesellschaft Fuel Service. [PWR; BWR

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

Knaab, H.; Knecht, K.

The need for pool-site inspection and examination of fuel assemblies was recognized by Kraftwerk Union Aktiengesellschaft with the commissioning of the first nuclear power stations. A wet sipping method has demonstrated high reliability in detection of leaking fuel assemblies. The visual inspection system is a versatile tool. It can be supplemented by attaching devices for oxide thickness measurement or surface replication. Repair of leaking pressurized water reactor fuel assemblies has improved fuel utilization. Applied methods and typical results are described.

Quantitative imaging of heterogeneous dynamics in drying and aging paints

PubMed Central

van der Kooij, Hanne M.; Fokkink, Remco; van der Gucht, Jasper; Sprakel, Joris

2016-01-01

Drying and aging paint dispersions display a wealth of complex phenomena that make their study fascinating yet challenging. To meet the growing demand for sustainable, high-quality paints, it is essential to unravel the microscopic mechanisms underlying these phenomena. Visualising the governing dynamics is, however, intrinsically difficult because the dynamics are typically heterogeneous and span a wide range of time scales. Moreover, the high turbidity of paints precludes conventional imaging techniques from reaching deep inside the paint. To address these challenges, we apply a scattering technique, Laser Speckle Imaging, as a versatile and quantitative tool to elucidate the internal dynamics, with microscopic resolution and spanning seven decades of time. We present a toolbox of data analysis and image processing methods that allows a tailored investigation of virtually any turbid dispersion, regardless of the geometry and substrate. Using these tools we watch a variety of paints dry and age with unprecedented detail. PMID:27682840

High-energy x-ray scattering studies of battery materials

DOE PAGES

Glazer, Matthew P. B.; Okasinski, John S.; Almer, Jonathan D.; ...

2016-06-08

High-energy x-ray (HEX) scattering is a sensitive and powerful tool to nondestructively probe the atomic and mesoscale structures of battery materials under synthesis and operational conditions. The penetration power of HEXs enables the use of large, practical samples and realistic environments, allowing researchers to explore the inner workings of batteries in both laboratory and commercial formats. This article highlights the capability and versatility of HEX techniques, particularly from synchrotron sources, to elucidate materials synthesis processes and thermal instability mechanisms in situ, to understand (dis)charging mechanisms in operando under a variety of cycling conditions, and to spatially resolve electrode/electrolyte responses tomore » highlight connections between inhomogeneity and performance. Such studies have increased our understanding of the fundamental mechanisms underlying battery performance. Here, by deepening our understanding of the linkages between microstructure and overall performance, HEXs represent a powerful tool for validating existing batteries and shortening battery-development timelines.« less

High-energy x-ray scattering studies of battery materials

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

Glazer, Matthew P. B.; Okasinski, John S.; Almer, Jonathan D.

High-energy x-ray (HEX) scattering is a sensitive and powerful tool to nondestructively probe the atomic and mesoscale structures of battery materials under synthesis and operational conditions. The penetration power of HEXs enables the use of large, practical samples and realistic environments, allowing researchers to explore the inner workings of batteries in both laboratory and commercial formats. This article highlights the capability and versatility of HEX techniques, particularly from synchrotron sources, to elucidate materials synthesis processes and thermal instability mechanisms in situ, to understand (dis)charging mechanisms in operando under a variety of cycling conditions, and to spatially resolve electrode/electrolyte responses tomore » highlight connections between inhomogeneity and performance. Such studies have increased our understanding of the fundamental mechanisms underlying battery performance. Here, by deepening our understanding of the linkages between microstructure and overall performance, HEXs represent a powerful tool for validating existing batteries and shortening battery-development timelines.« less

The nanomaterial toolkit for neuroengineering

NASA Astrophysics Data System (ADS)

Shah, Shreyas

2016-10-01

There is a growing interest in developing effective tools to better probe the central nervous system (CNS), to understand how it works and to treat neural diseases, injuries and cancer. The intrinsic complexity of the CNS has made this a challenging task for decades. Yet, with the extraordinary recent advances in nanotechnology and nanoscience, there is a general consensus on the immense value and potential of nanoscale tools for engineering neural systems. In this review, an overview of specialized nanomaterials which have proven to be the most effective tools in neuroscience is provided. After a brief background on the prominent challenges in the field, a variety of organic and inorganic-based nanomaterials are described, with particular emphasis on the distinctive properties that make them versatile and highly suitable in the context of the CNS. Building on this robust nano-inspired foundation, the rational design and application of nanomaterials can enable the generation of new methodologies to greatly advance the neuroscience frontier.

[The GIPSY-RECPAM model: a versatile approach for integrated evaluation in cardiologic care].

PubMed

Carinci, F

2009-01-01

Tree-structured methodology applied for the GISSI-PSICOLOGIA project, although performed in the framework of earliest GISSI studies, represents a powerful tool to analyze different aspects of cardiologic care. The GISSI-PSICOLOGIA project has delivered a novel methodology based on the joint application of psychometric tools and sophisticated statistical techniques. Its prospective use could allow building effective epidemiological models relevant to the prognosis of the cardiologic patient. The various features of the RECPAM method allow a versatile use in the framework of modern e-health projects. The study used the Cognitive Behavioral Assessment H Form (CBA-H) psychometrics scales. The potential for its future application in the framework of Italian cardiology is relevant and particularly indicated to assist planning of systems for integrated care and routine evaluation of the cardiologic patient.

Purity of Vector Vortex Beams through a Birefringent Amplifier

NASA Astrophysics Data System (ADS)

Sroor, Hend; Lisa, Nyameko; Naidoo, Darryl; Litvin, Igor; Forbes, Andrew

2018-04-01

Creating high-quality vector vortex (VV) beams is possible with a myriad of techniques at low power, and while a few studies have produced such beams at high power, none have considered the impact of amplification on the vector purity. Here we employ tools to study the amplification of VV beams and, in particular, the purity of such modes. We outline a versatile toolbox for such investigations and demonstrate its use in the general case of VV beams through a birefringent gain medium. Intriguingly, we show that it is possible to enhance the purity of such beams during amplification, paving the way for high-brightness VV beams, a requirement for their use in high-power applications such as optical communication and laser-enabled manufacturing.

Designing LibGuides as Instructional Tools for Critical Thinking and Effective Online Learning

ERIC Educational Resources Information Center

Baker, Ruth L.

2014-01-01

Did you ever wish for an easy-to-maintain tool to create course-level or assignment-level instruction for online or distance students? LibGuides can provide the solution! LibGuides provide a versatile and easy-to-maintain platform for delivering step-by-step, scaffolded tutorials that enhance learning outcomes through chunking, reduced strain on…

Targeted Delivery of CRISPR/Cas9-Mediated Cancer Gene Therapy via Liposome-Templated Hydrogel Nanoparticles.

PubMed

Chen, Zeming; Liu, Fuyao; Chen, Yanke; Liu, Jun; Wang, Xiaoying; Chen, Ann T; Deng, Gang; Zhang, Hongyi; Liu, Jie; Hong, Zhangyong; Zhou, Jiangbing

2017-12-08

Due to its simplicity, versatility, and high efficiency, the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technology has emerged as one of the most promising approaches for treatment of a variety of genetic diseases, including human cancers. However, further translation of CRISPR/Cas9 for cancer gene therapy requires development of safe approaches for efficient, highly specific delivery of both Cas9 and single guide RNA to tumors. Here, novel core-shell nanostructure, liposome-templated hydrogel nanoparticles (LHNPs) that are optimized for efficient codelivery of Cas9 protein and nucleic acids is reported. It is demonstrated that, when coupled with the minicircle DNA technology, LHNPs deliver CRISPR/Cas9 with efficiency greater than commercial agent Lipofectamine 2000 in cell culture and can be engineered for targeted inhibition of genes in tumors, including tumors the brain. When CRISPR/Cas9 targeting a model therapeutic gene, polo-like kinase 1 (PLK1), is delivered, LHNPs effectively inhibit tumor growth and improve tumor-bearing mouse survival. The results suggest LHNPs as versatile CRISPR/Cas9-delivery tool that can be adapted for experimentally studying the biology of cancer as well as for clinically translating cancer gene therapy.

Price and cost estimation

NASA Technical Reports Server (NTRS)

Stewart, R. D.

1979-01-01

Price and Cost Estimating Program (PACE II) was developed to prepare man-hour and material cost estimates. Versatile and flexible tool significantly reduces computation time and errors and reduces typing and reproduction time involved in preparation of cost estimates.

Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB.

PubMed

Chatziioannou, Aristotelis; Moulos, Panagiotis; Kolisis, Fragiskos N

2009-10-27

The microarray data analysis realm is ever growing through the development of various tools, open source and commercial. However there is absence of predefined rational algorithmic analysis workflows or batch standardized processing to incorporate all steps, from raw data import up to the derivation of significantly differentially expressed gene lists. This absence obfuscates the analytical procedure and obstructs the massive comparative processing of genomic microarray datasets. Moreover, the solutions provided, heavily depend on the programming skills of the user, whereas in the case of GUI embedded solutions, they do not provide direct support of various raw image analysis formats or a versatile and simultaneously flexible combination of signal processing methods. We describe here Gene ARMADA (Automated Robust MicroArray Data Analysis), a MATLAB implemented platform with a Graphical User Interface. This suite integrates all steps of microarray data analysis including automated data import, noise correction and filtering, normalization, statistical selection of differentially expressed genes, clustering, classification and annotation. In its current version, Gene ARMADA fully supports 2 coloured cDNA and Affymetrix oligonucleotide arrays, plus custom arrays for which experimental details are given in tabular form (Excel spreadsheet, comma separated values, tab-delimited text formats). It also supports the analysis of already processed results through its versatile import editor. Besides being fully automated, Gene ARMADA incorporates numerous functionalities of the Statistics and Bioinformatics Toolboxes of MATLAB. In addition, it provides numerous visualization and exploration tools plus customizable export data formats for seamless integration by other analysis tools or MATLAB, for further processing. Gene ARMADA requires MATLAB 7.4 (R2007a) or higher and is also distributed as a stand-alone application with MATLAB Component Runtime. Gene ARMADA provides a highly adaptable, integrative, yet flexible tool which can be used for automated quality control, analysis, annotation and visualization of microarray data, constituting a starting point for further data interpretation and integration with numerous other tools.

Role versatility among men who have sex with men in urban Peru.

PubMed

Goodreau, Steven M; Peinado, Jesus; Goicochea, Pedro; Vergara, Jorge; Ojeda, Nora; Casapia, Martin; Ortiz, Abner; Zamalloa, Victoria; Galvan, Rosa; Sanchez, Jorge R

2007-08-01

Role versatility refers to the practice in which individual men who have sex with men (MSM) play both insertive and receptive sexual roles over time. Versatility has been thought to be relatively uncommon among Latin American MSM but possibly rising. Versatility has also been shown to be a potentially large population-level risk factor for HIV infection. In this study we examine the correlates of versatile behavior and identity among 2,655 MSM in six Peruvian cities. Versatile behavior with recent male partners was found in 9% of men and versatile ("moderno") identity was reported by 16%. Significant predictors included high education, white-collar occupation, sex work, and residence in Lima. Age was not significant in any analysis. Since sex work is negatively correlated with other predictors, versatile men appear to comprise two distinct sub-populations. Insertive-only men appear to play a strong role in bridging the HIV epidemic between MSM and women.

Inductively coupled plasma mass spectrometry (ICP MS): a versatile tool.

PubMed

Ammann, Adrian A

2007-04-01

Inductively coupled plasma (ICP) mass spectrometry (MS) is routinely used in many diverse research fields such as earth, environmental, life and forensic sciences and in food, material, chemical, semiconductor and nuclear industries. The high ion density and the high temperature in a plasma provide an ideal atomizer and element ionizer for all types of samples and matrices introduced by a variety of specialized devices. Outstanding properties such as high sensitivity (ppt-ppq), relative salt tolerance, compound-independent element response and highest quantitation accuracy lead to the unchallenged performance of ICP MS in efficiently detecting, identifying and reliably quantifying trace elements. The increasing availability of relevant reference compounds and high separation selectivity extend the molecular identification capability of ICP MS hyphenated to species-specific separation techniques. While molecular ion source MS is specialized in determining the structure of unknown molecules, ICP MS is an efficient and highly sensitive tool for target-element orientated discoveries of relevant and unknown compounds. This special-feature, tutorial article presents the principle and advantages of ICP MS, highlighting these using examples from recently published investigations. Copyright 2007 John Wiley & Sons, Ltd.

Sine systemate chaos? A versatile tool for earthworm taxonomy: non-destructive imaging of freshly fixed and museum specimens using micro-computed tomography.

PubMed

Fernández, Rosa; Kvist, Sebastian; Lenihan, Jennifer; Giribet, Gonzalo; Ziegler, Alexander

2014-01-01

In spite of the high relevance of lumbricid earthworms ('Oligochaeta': Lumbricidae) for soil structure and functioning, the taxonomy of this group of terrestrial invertebrates remains in a quasi-chaotic state. Earthworm taxonomy traditionally relies on the interpretation of external and internal morphological characters, but the acquisition of these data is often hampered by tedious dissections or restricted access to valuable and rare museum specimens. The present state of affairs, in conjunction with the difficulty of establishing primary homologies for multiple morphological features, has led to an almost unrivaled instability in the taxonomy and systematics of certain earthworm groups, including Lumbricidae. As a potential remedy, we apply for the first time a non-destructive imaging technique to lumbricids and explore the future application of this approach to earthworm taxonomy. High-resolution micro-computed tomography (μCT) scanning of freshly fixed and museum specimens was carried out using two cosmopolitan species, Aporrectodea caliginosa and A. trapezoides. By combining two-dimensional and three-dimensional dataset visualization techniques, we demonstrate that the morphological features commonly used in earthworm taxonomy can now be analyzed without the need for dissection, whether freshly fixed or museum specimens collected more than 60 years ago are studied. Our analyses show that μCT in combination with soft tissue staining can be successfully applied to lumbricid earthworms. An extension of the approach to other families is poised to strengthen earthworm taxonomy by providing a versatile tool to resolve the taxonomic chaos currently present in this ecologically important, but taxonomically neglected group of terrestrial invertebrates.

Sine Systemate Chaos? A Versatile Tool for Earthworm Taxonomy: Non-Destructive Imaging of Freshly Fixed and Museum Specimens Using Micro-Computed Tomography

PubMed Central

Fernández, Rosa; Kvist, Sebastian; Lenihan, Jennifer; Giribet, Gonzalo; Ziegler, Alexander

2014-01-01

In spite of the high relevance of lumbricid earthworms (‘Oligochaeta’: Lumbricidae) for soil structure and functioning, the taxonomy of this group of terrestrial invertebrates remains in a quasi-chaotic state. Earthworm taxonomy traditionally relies on the interpretation of external and internal morphological characters, but the acquisition of these data is often hampered by tedious dissections or restricted access to valuable and rare museum specimens. The present state of affairs, in conjunction with the difficulty of establishing primary homologies for multiple morphological features, has led to an almost unrivaled instability in the taxonomy and systematics of certain earthworm groups, including Lumbricidae. As a potential remedy, we apply for the first time a non-destructive imaging technique to lumbricids and explore the future application of this approach to earthworm taxonomy. High-resolution micro-computed tomography (μCT) scanning of freshly fixed and museum specimens was carried out using two cosmopolitan species, Aporrectodea caliginosa and A. trapezoides. By combining two-dimensional and three-dimensional dataset visualization techniques, we demonstrate that the morphological features commonly used in earthworm taxonomy can now be analyzed without the need for dissection, whether freshly fixed or museum specimens collected more than 60 years ago are studied. Our analyses show that μCT in combination with soft tissue staining can be successfully applied to lumbricid earthworms. An extension of the approach to other families is poised to strengthen earthworm taxonomy by providing a versatile tool to resolve the taxonomic chaos currently present in this ecologically important, but taxonomically neglected group of terrestrial invertebrates. PMID:24837238

Preparing Colorful Astronomical Images and Illustrations

NASA Astrophysics Data System (ADS)

Levay, Z. G.; Frattare, L. M.

2001-12-01

We present techniques for using mainstream graphics software, specifically Adobe Photoshop and Illustrator, for producing composite color images and illustrations from astronomical data. These techniques have been used with numerous images from the Hubble Space Telescope to produce printed and web-based news, education and public presentation products as well as illustrations for technical publication. While Photoshop is not intended for quantitative analysis of full dynamic range data (as are IRAF or IDL, for example), we have had much success applying Photoshop's numerous, versatile tools to work with scaled images, masks, text and graphics in multiple semi-transparent layers and channels. These features, along with its user-oriented, visual interface, provide convenient tools to produce high-quality, full-color images and graphics for printed and on-line publication and presentation.

Versatile polyion complex micelles for peptide and siRNA vectorization to engineer tolerogenic dendritic cells.

PubMed

Mebarek, Naila; Vicente, Rita; Aubert-Pouëssel, Anne; Quentin, Julie; Mausset-Bonnefont, Anne-Laure; Devoisselle, Jean-Marie; Jorgensen, Christian; Bégu, Sylvie; Louis-Plence, Pascale

2015-05-01

Dendritic cells (DCs) are professional antigen-presenting cells that play a critical role in maintaining the balance between immunity and tolerance and, as such are a promising immunotherapy tool to induce immunity or to restore tolerance. The main challenge to harness the tolerogenic properties of DCs is to preserve their immature phenotype. We recently developed polyion complex micelles, formulated with double hydrophilic block copolymers of poly(methacrylic acid) and poly(ethylene oxide) blocks and able to entrap therapeutic molecules, which did not induce DC maturation. In the current study, the intrinsic destabilizing membrane properties of the polymers were used to optimize endosomal escape property of the micelles in order to propose various strategies to restore tolerance. On the first hand, we showed that high molecular weight (Mw) copolymer-based micelles were efficient to favor the release of the micelle-entrapped peptide into the endosomes, and thus to improve peptide presentation by immature (i) DCs. On the second hand, we put in evidence that low Mw copolymer-based micelles were able to favor the cytosolic release of micelle-entrapped small interfering RNAs, dampening the DCs immunogenicity. Therefore, we demonstrate the versatile use of polyionic complex micelles to preserve tolerogenic properties of DCs. Altogether, our results underscored the potential of such micelle-loaded iDCs as a therapeutic tool to restore tolerance in autoimmune diseases. Copyright © 2015 Elsevier B.V. All rights reserved.

Insertional engineering of chromosomes with Sleeping Beauty transposition: an overview.

PubMed

Grabundzija, Ivana; Izsvák, Zsuzsanna; Ivics, Zoltán

2011-01-01

Novel genetic tools and mutagenesis strategies based on the Sleeping Beauty (SB) transposable element are currently under development with a vision to link primary DNA sequence information to gene functions in vertebrate models. By virtue of its inherent capacity to insert into DNA, the SB transposon can be developed into powerful tools for chromosomal manipulations. Mutagenesis screens based on SB have numerous advantages including high throughput and easy identification of mutated alleles. Forward genetic approaches based on insertional mutagenesis by engineered SB transposons have the advantage of providing insight into genetic networks and pathways based on phenotype. Indeed, the SB transposon has become a highly instrumental tool to induce tumors in experimental animals in a tissue-specific -manner with the aim of uncovering the genetic basis of diverse cancers. Here, we describe a battery of mutagenic cassettes that can be applied in conjunction with SB transposon vectors to mutagenize genes, and highlight versatile experimental strategies for the generation of engineered chromosomes for loss-of-function as well as gain-of-function mutagenesis for functional gene annotation in vertebrate models.

Metadata Authoring with Versatility and Extensibility

NASA Technical Reports Server (NTRS)

Pollack, Janine; Olsen, Lola

2004-01-01

NASA's Global Change Master Directory (GCMD) assists the scientific community in the discovery of and linkage to Earth science data sets and related services. The GCMD holds over 13,800 data set descriptions in Directory Interchange Format (DIF) and 700 data service descriptions in Service Entry Resource Format (SERF), encompassing the disciplines of geology, hydrology, oceanography, meteorology, and ecology. Data descriptions also contain geographic coverage information and direct links to the data, thus allowing researchers to discover data pertaining to a geographic location of interest, then quickly acquire those data. The GCMD strives to be the preferred data locator for world-wide directory-level metadata. In this vein, scientists and data providers must have access to intuitive and efficient metadata authoring tools. Existing GCMD tools are attracting widespread usage; however, a need for tools that are portable, customizable and versatile still exists. With tool usage directly influencing metadata population, it has become apparent that new tools are needed to fill these voids. As a result, the GCMD has released a new authoring tool allowing for both web-based and stand-alone authoring of descriptions. Furthermore, this tool incorporates the ability to plug-and-play the metadata format of choice, offering users options of DIF, SERF, FGDC, ISO or any other defined standard. Allowing data holders to work with their preferred format, as well as an option of a stand-alone application or web-based environment, docBUlLDER will assist the scientific community in efficiently creating quality data and services metadata.

A versatile strategy for gene trapping and trap conversion in emerging model organisms.

PubMed

Kontarakis, Zacharias; Pavlopoulos, Anastasios; Kiupakis, Alexandros; Konstantinides, Nikolaos; Douris, Vassilis; Averof, Michalis

2011-06-01

Genetic model organisms such as Drosophila, C. elegans and the mouse provide formidable tools for studying mechanisms of development, physiology and behaviour. Established models alone, however, allow us to survey only a tiny fraction of the morphological and functional diversity present in the animal kingdom. Here, we present iTRAC, a versatile gene-trapping approach that combines the implementation of unbiased genetic screens with the generation of sophisticated genetic tools both in established and emerging model organisms. The approach utilises an exon-trapping transposon vector that carries an integrase docking site, allowing the targeted integration of new constructs into trapped loci. We provide proof of principle for iTRAC in the emerging model crustacean Parhyale hawaiensis: we generate traps that allow specific developmental and physiological processes to be visualised in unparalleled detail, we show that trapped genes can be easily cloned from an unsequenced genome, and we demonstrate targeting of new constructs into a trapped locus. Using this approach, gene traps can serve as platforms for generating diverse reporters, drivers for tissue-specific expression, gene knockdown and other genetic tools not yet imagined.

Using a Fluorescent PCR-capillary Gel Electrophoresis Technique to Genotype CRISPR/Cas9-mediated Knockout Mutants in a High-throughput Format.

PubMed

Ramlee, Muhammad Khairul; Wang, Jing; Cheung, Alice M S; Li, Shang

2017-04-08

The development of programmable genome-editing tools has facilitated the use of reverse genetics to understand the roles specific genomic sequences play in the functioning of cells and whole organisms. This cause has been tremendously aided by the recent introduction of the CRISPR/Cas9 system-a versatile tool that allows researchers to manipulate the genome and transcriptome in order to, among other things, knock out, knock down, or knock in genes in a targeted manner. For the purpose of knocking out a gene, CRISPR/Cas9-mediated double-strand breaks recruit the non-homologous end-joining DNA repair pathway to introduce the frameshift-causing insertion or deletion of nucleotides at the break site. However, an individual guide RNA may cause undesirable off-target effects, and to rule these out, the use of multiple guide RNAs is necessary. This multiplicity of targets also means that a high-volume screening of clones is required, which in turn begs the use of an efficient high-throughput technique to genotype the knockout clones. Current genotyping techniques either suffer from inherent limitations or incur high cost, hence rendering them unsuitable for high-throughput purposes. Here, we detail the protocol for using fluorescent PCR, which uses genomic DNA from crude cell lysate as a template, and then resolving the PCR fragments via capillary gel electrophoresis. This technique is accurate enough to differentiate one base-pair difference between fragments and hence is adequate in indicating the presence or absence of a frameshift in the coding sequence of the targeted gene. This precise knowledge effectively precludes the need for a confirmatory sequencing step and allows users to save time and cost in the process. Moreover, this technique has proven to be versatile in genotyping various mammalian cells of various tissue origins targeted by guide RNAs against numerous genes, as shown here and elsewhere.

SeGRAm - A practical and versatile tool for spacecraft trajectory optimization

NASA Technical Reports Server (NTRS)

Rishikof, Brian H.; Mccormick, Bernell R.; Pritchard, Robert E.; Sponaugle, Steven J.

1991-01-01

An implementation of the Sequential Gradient/Restoration Algorithm, SeGRAm, is presented along with selected examples. This spacecraft trajectory optimization and simulation program uses variational calculus to solve problems of spacecraft flying under the influence of one or more gravitational bodies. It produces a series of feasible solutions to problems involving a wide range of vehicles, environments and optimization functions, until an optimal solution is found. The examples included highlight the various capabilities of the program and emphasize in particular its versatility over a wide spectrum of applications from ascent to interplanetary trajectories.

Synthesis of PLGA-Lipid Hybrid Nanoparticles for siRNA Delivery Using the Emulsion Method PLGA-PEG-Lipid Nanoparticles for siRNA Delivery.

PubMed

Wang, Lei; Griffel, Benjamin; Xu, Xiaoyang

2017-01-01

The effective delivery of small interfering RNA (siRNA) to tumor cells remains a challenge for applications in cancer therapy. The development of polymeric nanoparticles with high siRNA loading efficacy has shown great potential for cancer targets. Double emulsion solvent evaporation technique is a useful tool for encapsulation of hydrophilic molecules (e.g., siRNA). Here we describe a versatile platform for siRNA delivery based on PLGA-PEG-cationic lipid nanoparticles by using the double emulsion method. The resulting nanoparticles show high encapsulation efficiency for siRNA (up to 90%) and demonstrate effective downregulation of the target genes in vitro and vivo.

Precise Spatiotemporal Control of Optogenetic Activation Using an Acousto-Optic Device

PubMed Central

Guo, Yanmeng; Song, Peipei; Zhang, Xiaohui; Zeng, Shaoqun; Wang, Zuoren

2011-01-01

Light activation and inactivation of neurons by optogenetic techniques has emerged as an important tool for studying neural circuit function. To achieve a high resolution, new methods are being developed to selectively manipulate the activity of individual neurons. Here, we report that the combination of an acousto-optic device (AOD) and single-photon laser was used to achieve rapid and precise spatiotemporal control of light stimulation at multiple points in a neural circuit with millisecond time resolution. The performance of this system in activating ChIEF expressed on HEK 293 cells as well as cultured neurons was first evaluated, and the laser stimulation patterns were optimized. Next, the spatiotemporally selective manipulation of multiple neurons was achieved in a precise manner. Finally, we demonstrated the versatility of this high-resolution method in dissecting neural circuits both in the mouse cortical slice and the Drosophila brain in vivo. Taken together, our results show that the combination of AOD-assisted laser stimulation and optogenetic tools provides a flexible solution for manipulating neuronal activity at high efficiency and with high temporal precision. PMID:22174813

DLR MiroSurge: a versatile system for research in endoscopic telesurgery.

PubMed

Hagn, Ulrich; Konietschke, R; Tobergte, A; Nickl, M; Jörg, S; Kübler, B; Passig, G; Gröger, M; Fröhlich, F; Seibold, U; Le-Tien, L; Albu-Schäffer, A; Nothhelfer, A; Hacker, F; Grebenstein, M; Hirzinger, G

2010-03-01

Research on surgical robotics demands systems for evaluating scientific approaches. Such systems can be divided into dedicated and versatile systems. Dedicated systems are designed for a single surgical task or technique, whereas versatile systems are designed to be expandable and useful in multiple surgical applications. Versatile systems are often based on industrial robots, though, and because of this, are hardly suitable for close contact with humans. To achieve a high degree of versatility the Miro robotic surgery platform (MRSP) consists of versatile components, dedicated front-ends towards surgery and configurable interfaces for the surgeon. This paper presents MiroSurge, a configuration of the MRSP that allows for bimanual endoscopic telesurgery with force feedback. While the components of the MiroSurge system are shown to fulfil the rigid design requirements for robotic telesurgery with force feedback, the system remains versatile, which is supposed to be a key issue for the further development and optimisation.

Marine Rare Actinobacteria: Isolation, Characterization, and Strategies for Harnessing Bioactive Compounds

PubMed Central

Dhakal, Dipesh; Pokhrel, Anaya Raj; Shrestha, Biplav; Sohng, Jae Kyung

2017-01-01

Actinobacteria are prolific producers of thousands of biologically active natural compounds with diverse activities. More than half of these bioactive compounds have been isolated from members belonging to actinobacteria. Recently, rare actinobacteria existing at different environmental settings such as high altitudes, volcanic areas, and marine environment have attracted attention. It has been speculated that physiological or biochemical pressures under such harsh environmental conditions can lead to the production of diversified natural compounds. Hence, marine environment has been focused for the discovery of novel natural products with biological potency. Many novel and promising bioactive compounds with versatile medicinal, industrial, or agricultural uses have been isolated and characterized. The natural compounds cannot be directly used as drug or other purposes, so they are structurally modified and diversified to ameliorate their biological or chemical properties. Versatile synthetic biological tools, metabolic engineering techniques, and chemical synthesis platform can be used to assist such structural modification. This review summarizes the latest studies on marine rare actinobacteria and their natural products with focus on recent approaches for structural and functional diversification of such microbial chemicals for attaining better applications. PMID:28663748

Human-scale interaction for virtual model displays: a clear case for real tools

NASA Astrophysics Data System (ADS)

Williams, George C.; McDowall, Ian E.; Bolas, Mark T.

1998-04-01

We describe a hand-held user interface for interacting with virtual environments displayed on a Virtual Model Display. The tool, constructed entirely of transparent materials, is see-through. We render a graphical counterpart of the tool on the display and map it one-to-one with the real tool. This feature, combined with a capability for touch- sensitive, discrete input, results in a useful spatial input device that is visually versatile. We discuss the tool's design and interaction techniques it supports. Briefly, we look at the human factors issues and engineering challenges presented by this tool and, in general, by the class of hand-held user interfaces that are see-through.

Parameter Estimation for a Turbulent Buoyant Jet Using Approximate Bayesian Computation

NASA Astrophysics Data System (ADS)

Christopher, Jason D.; Wimer, Nicholas T.; Hayden, Torrey R. S.; Lapointe, Caelan; Grooms, Ian; Rieker, Gregory B.; Hamlington, Peter E.

2016-11-01

Approximate Bayesian Computation (ABC) is a powerful tool that allows sparse experimental or other "truth" data to be used for the prediction of unknown model parameters in numerical simulations of real-world engineering systems. In this presentation, we introduce the ABC approach and then use ABC to predict unknown inflow conditions in simulations of a two-dimensional (2D) turbulent, high-temperature buoyant jet. For this test case, truth data are obtained from a simulation with known boundary conditions and problem parameters. Using spatially-sparse temperature statistics from the 2D buoyant jet truth simulation, we show that the ABC method provides accurate predictions of the true jet inflow temperature. The success of the ABC approach in the present test suggests that ABC is a useful and versatile tool for engineering fluid dynamics research.

Total analysis systems with Thermochromic Etching Discs technology.

PubMed

Avella-Oliver, Miquel; Morais, Sergi; Carrascosa, Javier; Puchades, Rosa; Maquieira, Ángel

2014-12-16

A new analytical system based on Thermochromic Etching Discs (TED) technology is presented. TED comprises a number of attractive features such as track independency, selective irradiation, a high power laser, and the capability to create useful assay platforms. The analytical versatility of this tool opens up a wide range of possibilities to design new compact disc-based total analysis systems applicable in chemistry and life sciences. In this paper, TED analytical implementation is described and discussed, and their analytical potential is supported by several applications. Microarray immunoassay, immunofiltration assay, solution measurement, and cell culture approaches are herein addressed in order to demonstrate the practical capacity of this system. The analytical usefulness of TED technology is herein demonstrated, describing how to exploit this tool for developing truly integrated analytical systems that provide solutions within the point of care framework.

A versatile genetic tool for post-translational control of gene expression in Drosophila melanogaster

PubMed Central

Sethi, Sachin

2017-01-01

Several techniques have been developed to manipulate gene expression temporally in intact neural circuits. However, the applicability of current tools developed for in vivo studies in Drosophila is limited by their incompatibility with existing GAL4 lines and side effects on physiology and behavior. To circumvent these limitations, we adopted a strategy to reversibly regulate protein degradation with a small molecule by using a destabilizing domain (DD). We show that this system is effective across different tissues and developmental stages. We further show that this system can be used to control in vivo gene expression levels with low background, large dynamic range, and in a reversible manner without detectable side effects on the lifespan or behavior of the animal. Additionally, we engineered tools for chemically controlling gene expression (GAL80-DD) and recombination (FLP-DD). We demonstrate the applicability of this technology in manipulating neuronal activity and for high-efficiency sparse labeling of neuronal populations. PMID:29140243

CRISPR-enabled tools for engineering microbial genomes and phenotypes.

PubMed

Tarasava, Katia; Oh, Eun Joong; Eckert, Carrie A; Gill, Ryan T

2018-06-19

In recent years CRISPR-Cas technologies have revolutionized microbial engineering approaches. Genome editing and non-editing applications of various CRISPR-Cas systems have expanded the throughput and scale of engineering efforts, as well as opened up new avenues for manipulating genomes of non-model organisms. As we expand the range of organisms used for biotechnological applications, we need to develop better, more versatile tools for manipulation of these systems. Here we summarize the current advances in microbial gene editing using CRISPR-Cas based tools, and highlight state-of-the-art methods for high-throughput, efficient genome-scale engineering in model organisms Escherichia coli and Saccharomyces cerevisiae. We also review non-editing CRISPR-Cas applications available for gene expression manipulation, epigenetic remodeling, RNA editing, labeling and synthetic gene circuit design. Finally, we point out the areas of research that need further development in order to expand the range of applications and increase the utility of these new methods. This article is protected by copyright. All rights reserved.

Remote Control and Data Acquisition: A Case Study

NASA Technical Reports Server (NTRS)

DeGennaro, Alfred J.; Wilkinson, R. Allen

2000-01-01

This paper details software tools developed to remotely command experimental apparatus, and to acquire and visualize the associated data in soft real time. The work was undertaken because commercial products failed to meet the needs. This work has identified six key factors intrinsic to development of quality research laboratory software. Capabilities include access to all new instrument functions without any programming or dependence on others to write drivers or virtual instruments, simple full screen text-based experiment configuration and control user interface, months of continuous experiment run-times, order of 1% CPU load for condensed matter physics experiment described here, very little imposition of software tool choices on remote users, and total remote control from anywhere in the world over the Internet or from home on a 56 Kb modem as if the user is sitting in the laboratory. This work yielded a set of simple robust tools that are highly reliable, resource conserving, extensible, and versatile, with a uniform simple interface.

Highly efficient in vitro and in vivo delivery of functional RNAs using new versatile MS2-chimeric retrovirus-like particles

PubMed Central

Prel, Anne; Caval, Vincent; Gayon, Régis; Ravassard, Philippe; Duthoit, Christine; Payen, Emmanuel; Maouche-Chretien, Leila; Creneguy, Alison; Nguyen, Tuan Huy; Martin, Nicolas; Piver, Eric; Sevrain, Raphaël; Lamouroux, Lucille; Leboulch, Philippe; Deschaseaux, Frédéric; Bouillé, Pascale; Sensébé, Luc; Pagès, Jean-Christophe

2015-01-01

RNA delivery is an attractive strategy to achieve transient gene expression in research projects and in cell- or gene-based therapies. Despite significant efforts investigating vector-directed RNA transfer, there is still a requirement for better efficiency of delivery to primary cells and in vivo. Retroviral platforms drive RNA delivery, yet retrovirus RNA-packaging constraints limit gene transfer to two genome-molecules per viral particle. To improve retroviral transfer, we designed a dimerization-independent MS2-driven RNA packaging system using MS2-Coat-retrovirus chimeras. The engineered chimeric particles promoted effective packaging of several types of RNAs and enabled efficient transfer of biologically active RNAs in various cell types, including human CD34+ and iPS cells. Systemic injection of high-titer particles led to gene expression in mouse liver and transferring Cre-recombinase mRNA in muscle permitted widespread editing at the ROSA26 locus. We could further show that the VLPs were able to activate an osteoblast differentiation pathway by delivering RUNX2- or DLX5-mRNA into primary human bone-marrow mesenchymal-stem cells. Thus, the novel chimeric MS2-lentiviral particles are a versatile tool for a wide range of applications including cellular-programming or genome-editing. PMID:26528487

Tuning the Thermochemical Properties of Oxonol Dyes for Digital Versatile Disc Recordable: Reduction of Thermal Interference in High-Speed Recording

NASA Astrophysics Data System (ADS)

Morishima, Shin-Ichi; Wariishi, Koji; Mikoshiba, Hisashi; Inagaki, Yoshio; Shibata, Michihiro; Hashimoto, Hirokazu; Kubo, Hiroshi

To reduce thermal interference between adjacent recording marks on a recordable digital versatile disc, we examined the thermochemical behavior of oxonol dyes for digital versatile disc recordable (DVD-R). We found that oxonol dyes with Meldrum's acid skeleton exhibited an abrupt reduction in weight with increasing temperature without generating excessive heat that is the fundamental cause of thermal interference. DVD-R with the oxonol dyes suppressed fluctuation in the shapes of recorded marks, thereby attaining compatibility with high-speed recording.

Adding tools to the open source toolbox: The Internet

NASA Technical Reports Server (NTRS)

Porth, Tricia

1994-01-01

The Internet offers researchers additional sources of information not easily available from traditional sources such as print volumes or commercial data bases. Internet tools such as e-mail and file transfer protocol (ftp) speed up the way researchers communicate and transmit data. Mosaic, one of the newest additions to the Internet toolbox, allows users to combine tools such as ftp, gopher, wide area information server, and the world wide web with multimedia capabilities. Mosaic has quickly become a popular means of making information available on the Internet because it is versatile and easily customizable.

Assessment of neuropsychiatric symptoms in dementia: toward improving accuracy

PubMed Central

Stella, Florindo

2013-01-01

The issue of this article concerned the discussion about tools frequently used tools for assessing neuropsychiatric symptoms of patients with dementia, particularly Alzheimer's disease. The aims were to discuss the main tools for evaluating behavioral disturbances, and particularly the accuracy of the Neuropsychiatric Inventory – Clinician Rating Scale (NPI-C). The clinical approach to and diagnosis of neuropsychiatric syndromes in dementia require suitable accuracy. Advances in the recognition and early accurate diagnosis of psychopathological symptoms help guide appropriate pharmacological and non-pharmacological interventions. In addition, recommended standardized and validated measurements contribute to both scientific research and clinical practice. Emotional distress, caregiver burden, and cognitive impairment often experienced by elderly caregivers, may affect the quality of caregiver reports. The clinician rating approach helps attenuate these misinterpretations. In this scenario, the NPI-C is a promising and versatile tool for assessing neuropsychiatric syndromes in dementia, offering good accuracy and high reliability, mainly based on the diagnostic impression of the clinician. This tool can provide both strategies: a comprehensive assessment of neuropsychiatric symptoms in dementia or the investigation of specific psychopathological syndromes such as agitation, depression, anxiety, apathy, sleep disorders, and aberrant motor disorders, among others. PMID:29213846

Advances in nanopatterned and nanostructured supported lipid membranes and their applications.

PubMed

Reimhult, Erik; Baumann, Martina; Kaufmann, Stefan; Kumar, Karthik; Spycher, Philipp

2010-01-01

Lipid membranes are versatile and convenient alternatives to study the properties of natural cell membranes. Self-assembled, artificial, substrate-supported lipid membranes have taken a central role in membrane research due to a combination of factors such as ease of creation, control over complexity, stability and the applicability of a large range of different analytical techniques. While supported lipid bilayers have been investigated for several decades, recent advances in the understanding of the assembly of such membranes from liposomes have spawned a renaissance in the field. Supported lipid bilayers are a highly promising tool to study transmembrane proteins in their native state, an application that could have tremendous impact on, e.g. drug discovery, development of biointerfaces and as platforms for glycomics and probing of multivalent binding which requires ligand mobility. Parallel advances in microfluidics, biosensor design, micro- and nanofabrication have converged to bring self-assembled supported lipid bilayers closer to a versatile and easy to use research tool as well as closer to industrial applications. The field of supported lipid bilayer research and application is thus rapidly expanding and diversifying with new platforms continuously being proposed and developed. In order to use supported lipid bilayers for such applications several advances have to be made: decoupling of the membrane from the support while maintaining it close to the surface, making use of biologically relevant lipid compositions, patterning of lipid membranes into arrays, and application to nanostructured substrates and sensors. This review summarizes recent advances in the field which addresses these challenges.

User manual for two simple postscript output FORTRAN plotting routines

NASA Technical Reports Server (NTRS)

Nguyen, T. X.

1991-01-01

Graphics is one of the important tools in engineering analysis and design. However, plotting routines that generate output on high quality laser printers normally come in graphics packages, which tend to be expensive and system dependent. These factors become important for small computer systems or desktop computers, especially when only some form of a simple plotting routine is sufficient. With the Postscript language becoming popular, there are more and more Postscript laser printers now available. Simple, versatile, low cost plotting routines that can generate output on high quality laser printers are needed and standard FORTRAN language plotting routines using output in Postscript language seems logical. The purpose here is to explain two simple FORTRAN plotting routines that generate output in Postscript language.

Preparing and probing many-body correlated systems in a Quantum Gas Microscope by engineering arbitrary landscape potentials

NASA Astrophysics Data System (ADS)

Rispoli, Matthew; Lukin, Alexander; Ma, Ruichao; Preiss, Philipp; Tai, M. Eric; Islam, Rajibul; Greiner, Markus

2015-05-01

Ultracold atoms in optical lattices provide a versatile tool box for observing the emergence of strongly correlated physics in quantum systems. Dynamic control of optical potentials on the single-site level allows us to prepare and probe many-body quantum states through local Hamiltonian engineering. We achieve these high precision levels of optical control through spatial light modulation with a DMD (digital micro-mirror device). This allows for both arbitrary beam shaping and aberration compensation in our imaging system to produce high fidelity optical potentials. We use these techniques to control state initialization, Hamiltonian dynamics, and measurement in experiments investigating low-dimensional many-body physics - from one-dimensional correlated quantum walks to characterizing entanglement.

Heterocyclic Compounds: Effective α-Amylase and α-Glucosidase Inhibitors.

PubMed

Saeedi, Mina; Hadjiakhondi, Abbas; Nabavi, Seyed Mohammad; Manayi, Azadeh

2017-01-01

Diabetes Mellitus (DM) is a metabolic disease characterized by high blood sugar levels. Recently, it has emerged as an important and global health problem with long-term complications and high economic burden. α-Amylase (α-Amy) and α-glucosidase (α-Gls) are two enzymes which are involved in the hydrolysis of starch into sugars and disaccharides leading to the increase of blood glucose level. Hence, inhibition of α-amylase and α-glucosidase plays key role in the treatment of type 2 diabetes. Heterocyclic compounds -both synthetic and naturally occurring derivatives- possess efficient biological properties. At this juncture, they have demonstrated potent inhibitory activity against α-Amy and α-Gls and were found to be versatile tools for the development of novel anti-diabetic agents.

A comparison between ultraviolet disinfection and copper alginate beads within a vortex bioreactor for the deactivation of bacteria in simulated waste streams with high levels of colour, humic acid and suspended solids.

PubMed

Thomas, Simon F; Rooks, Paul; Rudin, Fabian; Atkinson, Sov; Goddard, Paul; Bransgrove, Rachel M; Mason, Paul T; Allen, Michael J

2014-01-01

We show in this study that the combination of a swirl flow reactor and an antimicrobial agent (in this case copper alginate beads) is a promising technique for the remediation of contaminated water in waste streams recalcitrant to UV-C treatment. This is demonstrated by comparing the viability of both common and UV-C resistant organisms in operating conditions where UV-C proves ineffective - notably high levels of solids and compounds which deflect UV-C. The swirl flow reactor is easy to construct from commonly available plumbing parts and may prove a versatile and powerful tool in waste water treatment in developing countries.

Versatile tissue lasers based on high-Q Fabry-Pérot microcavities.

PubMed

Chen, Yu-Cheng; Chen, Qiushu; Zhang, Tingting; Wang, Wenjie; Fan, Xudong

2017-01-31

Biolasers are an emerging technology for next generation biochemical detection and clinical applications. Progress has recently been made to achieve lasing from biomolecules and single living cells. Tissues, which consist of cells embedded in an extracellular matrix, mimic more closely the actual complex biological environment in a living body and therefore are of more practical significance. Here, we developed a highly versatile tissue laser platform, in which tissues stained with fluorophores are sandwiched in a high-Q Fabry-Pérot microcavity. Distinct lasing emissions from muscle and adipose tissues stained respectively with fluorescein isothiocyanate (FITC) and boron-dipyrromethene (BODIPY), and hybrid muscle/adipose tissue with dual staining were achieved with a threshold of only ∼10 μJ mm -2 . Additionally, we investigated how the tissue structure/geometry, tissue thickness, and staining dye concentration affect the tissue laser. Lasing emission from FITC conjugates (FITC-phalloidin) that specifically target F-actin in muscle tissues was also realized. It is further found that, despite the large fluorescence spectral overlap between FITC and BODIPY in tissues, their lasing emissions could be clearly distinguished and controlled due to their narrow lasing bands and different lasing thresholds, thus enabling highly multiplexed detection. Our tissue laser platform can be broadly applicable to various types of tissues/diseases. It provides a new tool for a wide range of biological and biomedical applications, such as diagnostics/screening of tissues and identification/monitoring of biological transformations in tissue engineering.

Modular, Semantics-Based Composition of Biosimulation Models

ERIC Educational Resources Information Center

Neal, Maxwell Lewis

2010-01-01

Biosimulation models are valuable, versatile tools used for hypothesis generation and testing, codification of biological theory, education, and patient-specific modeling. Driven by recent advances in computational power and the accumulation of systems-level experimental data, modelers today are creating models with an unprecedented level of…

Fiber-enhanced Raman multigas spectroscopy: a versatile tool for environmental gas sensing and breath analysis.

PubMed

Hanf, Stefan; Keiner, Robert; Yan, Di; Popp, Jürgen; Frosch, Torsten

2014-06-03

Versatile multigas analysis bears high potential for environmental sensing of climate relevant gases and noninvasive early stage diagnosis of disease states in human breath. In this contribution, a fiber-enhanced Raman spectroscopic (FERS) analysis of a suite of climate relevant atmospheric gases is presented, which allowed for reliable quantification of CH4, CO2, and N2O alongside N2 and O2 with just one single measurement. A highly improved analytical sensitivity was achieved, down to a sub-parts per million limit of detection with a high dynamic range of 6 orders of magnitude and within a second measurement time. The high potential of FERS for the detection of disease markers was demonstrated with the analysis of 27 nL of exhaled human breath. The natural isotopes (13)CO2 and (14)N(15)N were quantified at low levels, simultaneously with the major breath components N2, O2, and (12)CO2. The natural abundances of (13)CO2 and (14)N(15)N were experimentally quantified in very good agreement to theoretical values. A fiber adapter assembly and gas filling setup was designed for rapid and automated analysis of multigas compositions and their fluctuations within seconds and without the need for optical readjustment of the sensor arrangement. On the basis of the abilities of such miniaturized FERS system, we expect high potential for the diagnosis of clinically administered (13)C-labeled CO2 in human breath and also foresee high impact for disease detection via biologically vital nitrogen compounds.

Magrit: a new thematic cartography tool

NASA Astrophysics Data System (ADS)

Viry, Matthieu; Giraud, Timothée; Lambert, Nicolas

2018-05-01

The article provides an overview of the features of the Magrit web application: a free online thematic mapping tool, presenting a strong pedagogical dimension and making possible to mobilize all the elements necessary for the realization of a thematic map. In this tool, several simple modes of representation are proposed such as proportional maps or choropleth maps. Other, more complex modes are also available such as smoothed maps and cartograms. Each map can be finalized thanks to layout and customization features (projection, scale, orientation, toponyms, etc.) and exported in vector format. Magrit is therefore a complete, light and versatile tool particularly adapted to cartography teaching at the university.

An inexpensive, multipurpose physical pendulum

NASA Astrophysics Data System (ADS)

Schultz, David

2012-10-01

The pendulum is a highly versatile tool for teaching physics. Many special purpose pendula for student experiments have been described.1-4 In this paper, I describe an inexpensive, multipurpose physical pendulum that can function as both a variable gravity and ballistic pendulum. I designed the apparatus for use in a rotational dynamics unit of the AP Physics C mechanics course. The use of a bike wheel hub pivot allows for low-friction, rugged operation that yields results commensurate with those obtained with much more expensive pendula available on the market (typically 500 per unit5), placing these types of experiments within reach of the teacher on a restricted budget.

High-Speed Lateral Flow Strategy for a Fast Biosensing with an Improved Selectivity and Binding Affinity.

PubMed

Cho, Dong Guk; Yoo, Haneul; Lee, Haein; Choi, Yeol Kyo; Lee, Minju; Ahn, Dong June; Hong, Seunghun

2018-05-10

We report a high-speed lateral flow strategy for a fast biosensing with an improved selectivity and binding affinity even under harsh conditions. In this strategy, biosensors were fixed at a location away from the center of a round shape disk, and the disk was rotated to create the lateral flow of a target solution on the biosensors during the sensing measurements. Experimental results using the strategy showed high reaction speeds, high binding affinity, and low nonspecific adsorptions of target molecules to biosensors. Furthermore, binding affinity between target molecules and sensing molecules was enhanced even in harsh conditions such as low pH and low ionic strength conditions. These results show that the strategy can improve the performance of conventional biosensors by generating high-speed lateral flows on a biosensor surface. Therefore, our strategy can be utilized as a simple but powerful tool for versatile bio and medical applications.

Nanobody-derived nanobiotechnology tool kits for diverse biomedical and biotechnology applications.

PubMed

Wang, Yongzhong; Fan, Zhen; Shao, Lei; Kong, Xiaowei; Hou, Xianjuan; Tian, Dongrui; Sun, Ying; Xiao, Yazhong; Yu, Li

2016-01-01

Owing to peculiar properties of nanobody, including nanoscale size, robust structure, stable and soluble behaviors in aqueous solution, reversible refolding, high affinity and specificity for only one cognate target, superior cryptic cleft accessibility, and deep tissue penetration, as well as a sustainable source, it has been an ideal research tool for the development of sophisticated nanobiotechnologies. Currently, the nanobody has been evolved into versatile research and application tool kits for diverse biomedical and biotechnology applications. Various nanobody-derived formats, including the nanobody itself, the radionuclide or fluorescent-labeled nanobodies, nanobody homo- or heteromultimers, nanobody-coated nanoparticles, and nanobody-displayed bacteriophages, have been successfully demonstrated as powerful nanobiotechnological tool kits for basic biomedical research, targeting drug delivery and therapy, disease diagnosis, bioimaging, and agricultural and plant protection. These applications indicate a special advantage of these nanobody-derived technologies, already surpassing the "me-too" products of other equivalent binders, such as the full-length antibodies, single-chain variable fragments, antigen-binding fragments, targeting peptides, and DNA-based aptamers. In this review, we summarize the current state of the art in nanobody research, focusing on the nanobody structural features, nanobody production approach, nanobody-derived nanobiotechnology tool kits, and the potentially diverse applications in biomedicine and biotechnology. The future trends, challenges, and limitations of the nanobody-derived nanobiotechnology tool kits are also discussed.

Film Canister Science

ERIC Educational Resources Information Center

Ferstl, Andrew; Schneider, Jamie L.

2007-01-01

Opaque film canisters are readily available, cheap, and useful for scientific inquiry in the classroom. They can also be surprisingly versatile and useful as a tool for stimulating scientific inquiry. In this article, the authors describe inquiry activities using film canisters for preservice teachers, including a "black box" activity and several…

Cross-amplified microsatellites in the European cherry fly, Rhagoletis cerasi: medium polymorphic-highly informative markers.

PubMed

Augustinos, A A; Asimakopoulou, A K; Papadopoulos, N T; Bourtzis, K

2011-02-01

The European cherry fruit fly, Rhagoletis cerasi (Diptera: Tephritidae), is a major pest of cherries in Europe and parts of Asia. Despite its big economic significance, there is a lack of studies on the genetic structure of its natural populations. Knowledge about an insect pest on molecular, genetic and population levels facilitates the development of environmentally friendly control methods. In this study, we present the development of 13 microsatellite markers for R. cerasi, through cross-species amplification. These markers have been used for the genotyping of 130 individuals from five different sampling sites in Greece. Our results indicate that (i) cross-species amplification is a versatile and rapid tool for developing microsatellite markers in Rhagoletis spp., (ii) the microsatellite markers presented here constitute an important tool for population studies on this pest, and (iii) there is clear structuring of natural European cherry fly populations.

The application of CRISPR-Cas9 genome editing tool in cancer immunotherapy.

PubMed

Wu, Hong-Yan; Cao, Chun-Yu

2018-03-22

Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system was originally discovered in prokaryotes functioned as a part of the adaptive immune system. Because of its high efficiency and easy operability, CRISPR-Cas9 system has been developed to be a powerful and versatile gene editing tool shortly after its discovery. Given that multiple genetic alterations are the main factors that drive genesis and development of tumor, CRISPR-Cas9 system has been applied to correct cancer-causing gene mutations and deletions and to engineer immune cells, such as chimeric antigen receptor T (CAR T) cells, for cancer immunotherapeutic applications. Recently, CRISPR-Cas9-based CAR T-cell preparation has been an important breakthrough in antitumor therapy. Here, we summarize the mechanism, delivery and the application of CRISPR-Cas9 in gene editing, and discuss the challenges and future directions of CRISPR-Cas9 in cancer immunotherapy.

TRIUMF-ISAC Gamma-Ray Escape-Suppressed Spectrometer (TIGRESS): a versatile tool for radioactive beam physics

NASA Astrophysics Data System (ADS)

Ball, G. C.; Andreyev, A.; Austin, R. A. E.; Bandyopadhyay, D.; Becker, J. A.; Boston, A. J.; Boston, H. C.; Chen, A.; Churchman, R.; Cifarelli, F.; Cline, D.; Cooper, R. J.; Cross, D. S.; Dashdorj, D.; Demand, G.; Dimmock, M. R.; Drake, T. E.; Finlay, P.; Gagon-Moisan, F.; Gallant, A. T.; Garrett, P. E.; Green, K. L.; Grint, A. N.; Hackman, G.; Harkness, L. J.; Hayes, A. B.; Kanungo, R.; Leach, K. G.; Lee, G.; Maharaj, R.; Martin, J.-P.; Morton, A. C.; Mythili, S.; Nelson, L.; Newman, O.; Nolan, P. J.; Padilla-Rodal, E.; Pearson, C. J.; Phillips, A. A.; Porter-Peden, M.; Ressler, J. J.; Roy, R.; Ruiz, C.; Savajols, H.; Sarazin, F.; Schumaker, M. A.; Scraggs, D. P.; Svensson, C. E.; Waddington, J. C.; Wan, J. M.; Whitbeck, A.; Williams, S. J.; Wong, J.; Wu, C. Y.

2007-05-01

TIGRESS is a new generation γ-ray spectrometer designed for use with radioactive beams from ISAC. This paper gives an overview of the project and presents results from the first radioactive beam experiment with TIGRESS, the Coulomb excitation of 20,21Na.

An improved tri-tube cryogenic gravel sampler.

Treesearch

Fred H. Everest; Carl E. McLemore; John F. Ward

1980-01-01

The tri-tube cryogenic gravel sampler has been improved, and accessories have been developed that increase its reliability and safety of operation, reduce core extraction time, and allow accurate partitioning of cores into subsamples. The improved tri-tube sampler is one of the most versatile and efficient substrate sampling tools yet developed.

A New Approach to Teaching Mathematics

DTIC Science & Technology

1994-02-01

We propose a new approach to teaching discrete math : First, teach logic as a powerful and versatile tool for discovering and communicating truths...using logic in other areas of study. Our experiences in teaching discrete math at Cornell shows that such success is possible. Propositional logic, Predicate logic, Discrete mathematics.

NASA Tech Briefs, November/December 1986, Special Edition

NASA Technical Reports Server (NTRS)

1986-01-01

Topics: Computing: The View from NASA Headquarters; Earth Resources Laboratory Applications Software: Versatile Tool for Data Analysis; The Hypercube: Cost-Effective Supercomputing; Artificial Intelligence: Rendezvous with NASA; NASA's Ada Connection; COSMIC: NASA's Software Treasurehouse; Golden Oldies: Tried and True NASA Software; Computer Technical Briefs; NASA TU Services; Digital Fly-by-Wire.

Biotransformation of tryptophan by liquid medium culture of Psilocybe coprophila (Basidiomycetes).

PubMed

Alarcón, Julio; Foncea, Leyla; Aguila, Sergio; Alderete, Joel B

2006-01-01

Chemical reactions performed by fungi have been used as a modern tool in chemistry. In this work, we show the tryptophan biotransformation with Psilocybe coprophila on liquid culture medium. The results prove once more the versatility of fungi in performing a wide range of industrially attractive chemical reactions.

Modeling Spatial and Temporal Aspects of Visual Backward Masking

ERIC Educational Resources Information Center

Hermens, Frouke; Luksys, Gediminas; Gerstner, Wulfram; Herzog, Michael H.; Ernst, Udo

2008-01-01

Visual backward masking is a versatile tool for understanding principles and limitations of visual information processing in the human brain. However, the mechanisms underlying masking are still poorly understood. In the current contribution, the authors show that a structurally simple mathematical model can explain many spatial and temporal…

The Brain's Versatile Toolbox.

ERIC Educational Resources Information Center

Pinker, Steven

1997-01-01

Considers the role of evolution and natural selection in the functioning of the modern human brain. Natural selection equipped humans with a mental toolbox of intuitive theories about the world which were used to master rocks, tools, plants, animals, and one another. The same toolbox is used today to master the intellectual challenges of modern…

New Optical Sensing Materials for Application in Marine Research

NASA Astrophysics Data System (ADS)

Borisov, S.; Klimant, I.

2012-04-01

Optical chemosensors are versatile analytical tools which find application in numerous fields of science and technology. They proved to be a promising alternative to electrochemical methods and are applied increasingly often in marine research. However, not all state-of-the- art optical chemosensors are suitable for these demanding applications since they do not fully fulfil the requirements of high luminescence brightness, high chemical- and photochemical stability or their spectral properties are not adequate. Therefore, development of new advanced sensing materials is still of utmost importance. Here we present a set of novel optical sensing materials recently developed in the Institute of Analytical Chemistry and Food Chemistry which are optimized for marine applications. Particularly, we present new NIR indicators and sensors for oxygen and pH which feature high brightness and low level of autofluorescence. The oxygen sensors rely on highly photostable metal complexes of benzoporphyrins and azabenzoporphyrins and enable several important applications such as simultaneous monitoring of oxygen and chlorophyll or ultra-fast oxygen monitoring (Eddy correlation). We also developed ulta-sensitive oxygen optodes which enable monitoring in nM range and are primary designed for investigation of oxygen minimum zones. The dynamic range of our new NIR pH indicators based on aza-BODIPY dyes is optimized for the marine environment. A highly sensitive NIR luminescent phosphor (chromium(III) doped yttrium aluminium borate) can be used for non-invasive temperature measurements. Notably, the oxygen, pH sensors and temperature sensors are fully compatible with the commercially available fiber-optic readers (Firesting from PyroScience). An optical CO2 sensor for marine applications employs novel diketopyrrolopyrrol indicators and enables ratiometric imaging using a CCD camera. Oxygen, pH and temperature sensors suitable for lifetime and ratiometric imaging of analytes distribution are also realized. To enable versatility of applications we also obtained a range of nano- and microparticles suitable for intra- and extracellular imaging of the above analytes. Bright ratiometric 2-photon-excitable probes were also developed. Magnetic microparticles are demonstrated to be very promising tools for imaging of oxygen, temperature and other parameters in biofilms, corals etc. since they combine the sensing function with the possibility of external manipulation.

Apertureless near-field/far-field CW two-photon microscope for biological and material imaging and spectroscopic applications.

PubMed

Nowak, Derek B; Lawrence, A J; Sánchez, Erik J

2010-12-10

We present the development of a versatile spectroscopic imaging tool to allow for imaging with single-molecule sensitivity and high spatial resolution. The microscope allows for near-field and subdiffraction-limited far-field imaging by integrating a shear-force microscope on top of a custom inverted microscope design. The instrument has the ability to image in ambient conditions with optical resolutions on the order of tens of nanometers in the near field. A single low-cost computer controls the microscope with a field programmable gate array data acquisition card. High spatial resolution imaging is achieved with an inexpensive CW multiphoton excitation source, using an apertureless probe and simplified optical pathways. The high-resolution, combined with high collection efficiency and single-molecule sensitive optical capabilities of the microscope, are demonstrated with a low-cost CW laser source as well as a mode-locked laser source.

Recent Developments in the Design, Capabilities and Autonomous Operations of a Lightweight Surface Manipulation System and Test-bed

NASA Technical Reports Server (NTRS)

Dorsey, John T.; Jones, Thomas C.; Doggett, W. R.; Brady, Jeffrey S.; Berry, Felecia C.; Ganoe, George G.; Anderson, Eric; King, Bruce D.; Mercer, David C.

2011-01-01

The first generation of a versatile high performance device for performing payload handling and assembly operations on planetary surfaces, the Lightweight Surface Manipulation System (LSMS), has been designed and built. Over the course of its development, conventional crane type payload handling configurations and operations have been successfully demonstrated and the range of motion, types of operations and the versatility greatly expanded. This enhanced set of 1st generation LSMS hardware is now serving as a laboratory test-bed allowing the continuing development of end effectors, operational techniques and remotely controlled and automated operations. This paper describes the most recent LSMS and test-bed development activities, that have focused on two major efforts. The first effort was to complete a preliminary design of the 2nd generation LSMS that has the capability for limited mobility and can reposition itself between lander decks, mobility chassis, and fixed base locations. A major portion of this effort involved conducting a study to establish the feasibility of, and define, the specifications for a lightweight cable-drive waist joint. The second effort was to continue expanding the versatility and autonomy of large planetary surface manipulators using the 1st generation LSMS as a test-bed. This has been accomplished by increasing manipulator capabilities and efficiencies through both design changes and tool and end effector development. A software development effort has expanded the operational capabilities of the LSMS test-bed to include; autonomous operations based on stored paths, use of a vision system for target acquisition and tracking, and remote command and control over a communications bridge.

The Decoding Toolbox (TDT): a versatile software package for multivariate analyses of functional imaging data

PubMed Central

Hebart, Martin N.; Görgen, Kai; Haynes, John-Dylan

2015-01-01

The multivariate analysis of brain signals has recently sparked a great amount of interest, yet accessible and versatile tools to carry out decoding analyses are scarce. Here we introduce The Decoding Toolbox (TDT) which represents a user-friendly, powerful and flexible package for multivariate analysis of functional brain imaging data. TDT is written in Matlab and equipped with an interface to the widely used brain data analysis package SPM. The toolbox allows running fast whole-brain analyses, region-of-interest analyses and searchlight analyses, using machine learning classifiers, pattern correlation analysis, or representational similarity analysis. It offers automatic creation and visualization of diverse cross-validation schemes, feature scaling, nested parameter selection, a variety of feature selection methods, multiclass capabilities, and pattern reconstruction from classifier weights. While basic users can implement a generic analysis in one line of code, advanced users can extend the toolbox to their needs or exploit the structure to combine it with external high-performance classification toolboxes. The toolbox comes with an example data set which can be used to try out the various analysis methods. Taken together, TDT offers a promising option for researchers who want to employ multivariate analyses of brain activity patterns. PMID:25610393

4-Alkylated homoibotenic acid (HIBO) analogues: versatile pharmacological agents with diverse selectivity profiles towards metabotropic and ionotropic glutamate receptor subtypes.

PubMed

Madsen, Ulf; Pickering, Darryl S; Nielsen, Birgitte; Bräuner-Osborne, Hans

2005-01-01

4-Alkylated analogues of homoibotenic acid (HIBO) have previously shown high potency and selectivity at ionotropic and metabotropic glutamic acid receptor (iGluR and mGluR) subtypes. Compounds with different selectivity profiles are valuable pharmacological tools for neuropharmacological studies, and the series of 4-alkyl-HIBO analogues have been extended in this paper in the search for versatile agents. Pharmacological characterization of five new analogues, branched and unbranched 4-alkyl-HIBO analogues, have been carried out. The present compounds are all weak antagonists at Group I mGluRs (mGluR1 and 5) presenting only small differences in potencies (Ki values ranging from 89 to 670 microM). Affinities were studied at native and cloned iGluRs, and the compounds described show preference for the AMPA receptor subtypes GluR1 and 2 over GluR3 and 4. However, compared to previous 4-alkyl-HIBO analogues, these compounds show a remarkably high affinity for the Kain preferring subtype GluR5. The observed GluR5 affinities were either similar or higher compared to their GluR1 and 2 affinity. Isopropyl-HIBO showed the highest affinity for GluR5 (Ki=0.16 microM), and represents a unique compound with high affinity towards the three subtypes GluR1, 2 and 5. In general, these compounds represent new selectivity profiles compared to previously reported Glu receptor analogues.

Graphics processing unit (GPU) real-time infrared scene generation

NASA Astrophysics Data System (ADS)

Christie, Chad L.; Gouthas, Efthimios (Themie); Williams, Owen M.

2007-04-01

VIRSuite, the GPU-based suite of software tools developed at DSTO for real-time infrared scene generation, is described. The tools include the painting of scene objects with radiometrically-associated colours, translucent object generation, polar plot validation and versatile scene generation. Special features include radiometric scaling within the GPU and the presence of zoom anti-aliasing at the core of VIRSuite. Extension of the zoom anti-aliasing construct to cover target embedding and the treatment of translucent objects is described.

High-Throughput Sequencing, a Versatile Weapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology

PubMed Central

Caboche, Ségolène; Audebert, Christophe; Hot, David

2014-01-01

The recent progresses of high-throughput sequencing (HTS) technologies enable easy and cost-reduced access to whole genome sequencing (WGS) or re-sequencing. HTS associated with adapted, automatic and fast bioinformatics solutions for sequencing applications promises an accurate and timely identification and characterization of pathogenic agents. Many studies have demonstrated that data obtained from HTS analysis have allowed genome-based diagnosis, which has been consistent with phenotypic observations. These proofs of concept are probably the first steps toward the future of clinical microbiology. From concept to routine use, many parameters need to be considered to promote HTS as a powerful tool to help physicians and clinicians in microbiological investigations. This review highlights the milestones to be completed toward this purpose. PMID:25437800

Isolated and coupled superquadric loop antennas for mobile communications applications

NASA Technical Reports Server (NTRS)

Jensen, Michael A.; Rahmat-Samii, Yahya

1993-01-01

This work provides an investigation of the performance of loop antennas for use in mobile communications applications. The analysis tools developed allow for high flexibility by representing the loop antenna as a superquadric curve, which includes the case of circular, elliptical, and rectangular loops. The antenna may be in an isolated environment, located above an infinite ground plane, or placed near a finite conducting plate or box. In cases where coupled loops are used, the two loops may have arbitrary relative positions and orientations. Several design examples are included to illustrate the versatility of the analysis capabilities. The performance of coupled loops arranged in a diversity scheme is also evaluated, and it is found that high diversity gain can be achieved even when the antennas are closely spaced.

A Comparison between Ultraviolet Disinfection and Copper Alginate Beads within a Vortex Bioreactor for the Deactivation of Bacteria in Simulated Waste Streams with High Levels of Colour, Humic Acid and Suspended Solids

PubMed Central

Thomas, Simon F.; Rooks, Paul; Rudin, Fabian; Atkinson, Sov; Goddard, Paul; Bransgrove, Rachel M.; Mason, Paul T.; Allen, Michael J.

2014-01-01

We show in this study that the combination of a swirl flow reactor and an antimicrobial agent (in this case copper alginate beads) is a promising technique for the remediation of contaminated water in waste streams recalcitrant to UV-C treatment. This is demonstrated by comparing the viability of both common and UV-C resistant organisms in operating conditions where UV-C proves ineffective - notably high levels of solids and compounds which deflect UV-C. The swirl flow reactor is easy to construct from commonly available plumbing parts and may prove a versatile and powerful tool in waste water treatment in developing countries. PMID:25541706

A wireless remote high-power laser device for optogenetic experiments

NASA Astrophysics Data System (ADS)

Wang, Y.; Gong, Q.; Li, Y. Y.; Li, A. Z.; Zhang, Y. G.; Cao, C. F.; Xu, H. X.; Cui, J.; Gao, J. J.

2015-04-01

Optogenetics affords the ability to stimulate genetically targeted neurons in a relatively innocuous manner. Reliable and targetable tools have enabled versatile new classes of investigation in the study of neural systems. However, current hardware systems are generally limited to acute measurements or require external tethering of the system to the light source. Here we provide a low-cost, high-power, remotely controlled blue laser diode (LD) stimulator for the application of optogenetics in neuroscience, focusing on wearable and intelligent devices, which can be carried by monkeys, rats and any other animals under study. Compared with the conventional light emitting diode (LED) device, this LD stimulator has higher efficiency, output power, and stability. Our system is fully wirelessly controlled and suitable for experiments with a large number of animals.

CoCoNUT: an efficient system for the comparison and analysis of genomes

PubMed Central

2008-01-01

Background Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons. Results Most of the software tools available are tailored for one specific task. In contrast, we have developed a novel system CoCoNUT (Computational Comparative geNomics Utility Toolkit) that allows solving several different tasks in a unified framework: (1) finding regions of high similarity among multiple genomic sequences and aligning them, (2) comparing two draft or multi-chromosomal genomes, (3) locating large segmental duplications in large genomic sequences, and (4) mapping cDNA/EST to genomic sequences. Conclusion CoCoNUT is competitive with other software tools w.r.t. the quality of the results. The use of state of the art algorithms and data structures allows CoCoNUT to solve comparative genomics tasks more efficiently than previous tools. With the improved user interface (including an interactive visualization component), CoCoNUT provides a unified, versatile, and easy-to-use software tool for large scale studies in comparative genomics. PMID:19014477

TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization.

PubMed

Ollion, Jean; Cochennec, Julien; Loll, François; Escudé, Christophe; Boudier, Thomas

2013-07-15

The cell nucleus is a highly organized cellular organelle that contains the genetic material. The study of nuclear architecture has become an important field of cellular biology. Extracting quantitative data from 3D fluorescence imaging helps understand the functions of different nuclear compartments. However, such approaches are limited by the requirement for processing and analyzing large sets of images. Here, we describe Tools for Analysis of Nuclear Genome Organization (TANGO), an image analysis tool dedicated to the study of nuclear architecture. TANGO is a coherent framework allowing biologists to perform the complete analysis process of 3D fluorescence images by combining two environments: ImageJ (http://imagej.nih.gov/ij/) for image processing and quantitative analysis and R (http://cran.r-project.org) for statistical processing of measurement results. It includes an intuitive user interface providing the means to precisely build a segmentation procedure and set-up analyses, without possessing programming skills. TANGO is a versatile tool able to process large sets of images, allowing quantitative study of nuclear organization. TANGO is composed of two programs: (i) an ImageJ plug-in and (ii) a package (rtango) for R. They are both free and open source, available (http://biophysique.mnhn.fr/tango) for Linux, Microsoft Windows and Macintosh OSX. Distribution is under the GPL v.2 licence. thomas.boudier@snv.jussieu.fr Supplementary data are available at Bioinformatics online.

A Novel Chip for Cyclic Stretch and Intermittent Hypoxia Cell Exposures Mimicking Obstructive Sleep Apnea.

PubMed

Campillo, Noelia; Jorba, Ignasi; Schaedel, Laura; Casals, Blai; Gozal, David; Farré, Ramon; Almendros, Isaac; Navajas, Daniel

2016-01-01

Intermittent hypoxia (IH), a hallmark of obstructive sleep apnea (OSA), plays a critical role in the pathogenesis of OSA-associated morbidities, especially in the cardiovascular and respiratory systems. Oxidative stress and inflammation induced by IH are suggested as main contributors of end-organ dysfunction in OSA patients and animal models. Since the molecular mechanisms underlying these in vivo pathological responses remain poorly understood, implementation of experimental in vitro cell-based systems capable of inducing high-frequency IH would be highly desirable. Here, we describe the design, fabrication, and validation of a versatile chip for subjecting cultured cells to fast changes in gas partial pressure and to cyclic stretch. The chip is fabricated with polydimethylsiloxane (PDMS) and consists of a cylindrical well-covered by a thin membrane. Cells cultured on top of the membrane can be subjected to fast changes in oxygen concentration (equilibrium time ~6 s). Moreover, cells can be subjected to cyclic stretch at cardiac or respiratory frequencies independently or simultaneously. Rat bone marrow-derived mesenchymal stem cells (MSCs) exposed to IH mimicking OSA and cyclic stretch at cardiac frequencies revealed that hypoxia-inducible factor 1α (HIF-1α) expression was increased in response to both stimuli. Thus, the chip provides a versatile tool for the study of cellular responses to cyclical hypoxia and stretch.

Bioinspired production of magnetic laccase-biotitania particles for the removal of endocrine disrupting chemicals.

PubMed

Ardao, Inés; Magnin, Delphine; Agathos, Spiros N

2015-10-01

Microbial laccases are powerful enzymes capable of degrading lignin and other recalcitrant compounds including endocrine disrupting chemicals (EDCs). Efficient EDC removal on an industrial scale requires robust, stable, easy to handle and cost-effective immobilized biocatalysts. In this direction, magnetic biocatalysts are attractive due to their easy separation through an external magnetic field. Recently, a bioinspired immobilization technique that mimics the natural biomineralization reactions in diatoms has emerged as a fast and versatile tool for generating robust, cheap, and highly stable (nano) biocatalysts. In this work, bioinspired formation of a biotitania matrix is triggered on the surface of magnetic particles in the presence of laccase in order to produce laccase-biotitania (lac-bioTiO2 ) biocatalysts suitable for environmental applications using a novel, fast and versatile enzyme entrapment technique. Highly active lac-bioTiO2 particles have been produced and the effect of different parameters (enzyme loading, titania precursor concentration, pH, duration of the biotitania formation, and laccase adsorption steps) on the apparent activity yield of these biocatalysts were evaluated, the concentration of the titania precursor being the most influential. The lac-bioTiO2 particles were able to catalyze the removal of bisphenol A, 17α-ethinylestradiol and diclofenac in a mixture of six model EDCs and retained 90% of activity after five reaction cycles and 60% after 10 cycles. © 2015 Wiley Periodicals, Inc.

Investigation of the shape transferability of nanoscale multi-tip diamond tools in the diamond turning of nanostructures

NASA Astrophysics Data System (ADS)

Luo, Xichun; Tong, Zhen; Liang, Yingchun

2014-12-01

In this article, the shape transferability of using nanoscale multi-tip diamond tools in the diamond turning for scale-up manufacturing of nanostructures has been demonstrated. Atomistic multi-tip diamond tool models were built with different tool geometries in terms of the difference in the tip cross-sectional shape, tip angle, and the feature of tool tip configuration, to determine their effect on the applied forces and the machined nano-groove geometries. The quality of machined nanostructures was characterized by the thickness of the deformed layers and the dimensional accuracy achieved. Simulation results show that diamond turning using nanoscale multi-tip tools offers tremendous shape transferability in machining nanostructures. Both periodic and non-periodic nano-grooves with different cross-sectional shapes can be successfully fabricated using the multi-tip tools. A hypothesis of minimum designed ratio of tool tip distance to tip base width (L/Wf) of the nanoscale multi-tip diamond tool for the high precision machining of nanostructures was proposed based on the analytical study of the quality of the nanostructures fabricated using different types of the multi-tip tools. Nanometric cutting trials using nanoscale multi-tip diamond tools (different in L/Wf) fabricated by focused ion beam (FIB) were then conducted to verify the hypothesis. The investigations done in this work imply the potential of using the nanoscale multi-tip diamond tool for the deterministic fabrication of period and non-periodic nanostructures, which opens up the feasibility of using the process as a versatile manufacturing technique in nanotechnology.

CRISPR Mediated Genome Engineering and its Application in Industry.

PubMed

Kaboli, Saeed; Babazada, Hasan

2018-01-01

The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) method has been dramatically changing the field of genome engineering. It is a rapid, highly efficient and versatile tool for precise modification of genome that uses a guide RNA (gRNA) to target Cas9 to a specific sequence. This novel RNA-guided genome-editing technique has become a revolutionary tool in biomedical science and has many innovative applications in different fields. In this review, we briefly introduce the Cas9-mediated genome-editing tool, summarize the recent advances in CRISPR/Cas9 technology to engineer the genomes of a wide variety of organisms, and discuss their applications to treatment of fungal and viral disease. We also discuss advantageous of CRISPR/Cas9 technology to drug design, creation of animal model, and to food, agricultural and energy sciences. Adoption of the CRISPR/Cas9 technology in biomedical and biotechnological researches would create innovative applications of it not only for breeding of strains exhibiting desired traits for specific industrial and medical applications, but also for investigation of genome function.

Development of an Influenza virus protein array using Sortagging technology

PubMed Central

Sinisi, Antonia; Popp, Maximilian Wei-Lin; Antos, John M.; Pansegrau, Werner; Savino, Silvana; Nissum, Mikkel; Rappuoli, Rino; Ploegh, Hidde L.; Buti, Ludovico

2013-01-01

Protein array technology is an emerging tool that enables high throughput screening of protein-protein or protein-lipid interactions and identification of immunodominant antigens during the course of a bacterial or viral infection. In this work we developed an Influenza virus protein array using the sortase-mediated transpeptidation reaction known as “Sortagging”. LPETG-tagged Influenza virus proteins from bacterial and eukaryotic cellular extracts were immobilized at their carboxyl-termini onto a pre-activated amine-glass slide coated with a Gly3 linker. Immobilized proteins were revealed by specific antibodies and the newly generated Sortag-protein chip can be used as a device for antigen and/or antibody screening. The specificity of the Sortase A (SrtA) reaction avoids purification steps in array building and allows immobilization of proteins in an oriented fashion. Previously, this versatile technology has been successfully employed for protein labeling and protein conjugation. Here, the tool is implemented to covalently link proteins of a viral genome onto a solid support. The system could readily be scaled up to proteins of larger genomes in order to develop protein arrays for high throughput screening. PMID:22594688

Ticks and Tick-Borne Pathogens of the Caribbean: Current Understanding and Future Directions for More Comprehensive Surveillance.

PubMed

Gondard, Mathilde; Cabezas-Cruz, Alejandro; Charles, Roxanne A; Vayssier-Taussat, Muriel; Albina, Emmanuel; Moutailler, Sara

2017-01-01

Ticks are obligate hematophagous arthropods of significant importance to human and veterinary medicine. They transmit a vast array of pathogens, including bacteria, viruses, protozoa, and helminths. Most epidemiological data on ticks and tick-borne pathogens (TBPs) in the West Indies are limited to common livestock pathogens such as Ehrlichia ruminantium, Babesia spp. (i.e., B. bovis and B. bigemina ), and Anaplasma marginale , and less information is available on companion animal pathogens. Of note, human tick-borne diseases (TBDs) remain almost completely uncharacterized in the West Indies. Information on TBP presence in wildlife is also missing. Herein, we provide a comprehensive review of the ticks and TBPs affecting human and animal health in the Caribbean, and introduce the challenges associated with understanding TBD epidemiology and implementing successful TBD management in this region. In particular, we stress the need for innovative and versatile surveillance tools using high-throughput pathogen detection (e.g., high-throughput real-time microfluidic PCR). The use of such tools in large epidemiological surveys will likely improve TBD prevention and control programs in the Caribbean.

Mindtagger: A Demonstration of Data Labeling in Knowledge Base Construction.

PubMed

Shin, Jaeho; Ré, Christopher; Cafarella, Michael

2015-08-01

End-to-end knowledge base construction systems using statistical inference are enabling more people to automatically extract high-quality domain-specific information from unstructured data. As a result of deploying DeepDive framework across several domains, we found new challenges in debugging and improving such end-to-end systems to construct high-quality knowledge bases. DeepDive has an iterative development cycle in which users improve the data. To help our users, we needed to develop principles for analyzing the system's error as well as provide tooling for inspecting and labeling various data products of the system. We created guidelines for error analysis modeled after our colleagues' best practices, in which data labeling plays a critical role in every step of the analysis. To enable more productive and systematic data labeling, we created Mindtagger, a versatile tool that can be configured to support a wide range of tasks. In this demonstration, we show in detail what data labeling tasks are modeled in our error analysis guidelines and how each of them is performed using Mindtagger.

High content screening of defined chemical libraries using normal and glioma-derived neural stem cell lines.

PubMed

Danovi, Davide; Folarin, Amos A; Baranowski, Bart; Pollard, Steven M

2012-01-01

Small molecules with potent biological effects on the fate of normal and cancer-derived stem cells represent both useful research tools and new drug leads for regenerative medicine and oncology. Long-term expansion of mouse and human neural stem cells is possible using adherent monolayer culture. These cultures represent a useful cellular resource to carry out image-based high content screening of small chemical libraries. Improvements in automated microscopy, desktop computational power, and freely available image processing tools, now means that such chemical screens are realistic to undertake in individual academic laboratories. Here we outline a cost effective and versatile time lapse imaging strategy suitable for chemical screening. Protocols are described for the handling and screening of human fetal Neural Stem (NS) cell lines and their malignant counterparts, Glioblastoma-derived neural stem cells (GNS). We focus on identification of cytostatic and cytotoxic "hits" and discuss future possibilities and challenges for extending this approach to assay lineage commitment and differentiation. Copyright © 2012 Elsevier Inc. All rights reserved.

Quantification of differential gene expression by multiplexed targeted resequencing of cDNA

PubMed Central

Arts, Peer; van der Raadt, Jori; van Gestel, Sebastianus H.C.; Steehouwer, Marloes; Shendure, Jay; Hoischen, Alexander; Albers, Cornelis A.

2017-01-01

Whole-transcriptome or RNA sequencing (RNA-Seq) is a powerful and versatile tool for functional analysis of different types of RNA molecules, but sample reagent and sequencing cost can be prohibitive for hypothesis-driven studies where the aim is to quantify differential expression of a limited number of genes. Here we present an approach for quantification of differential mRNA expression by targeted resequencing of complementary DNA using single-molecule molecular inversion probes (cDNA-smMIPs) that enable highly multiplexed resequencing of cDNA target regions of ∼100 nucleotides and counting of individual molecules. We show that accurate estimates of differential expression can be obtained from molecule counts for hundreds of smMIPs per reaction and that smMIPs are also suitable for quantification of relative gene expression and allele-specific expression. Compared with low-coverage RNA-Seq and a hybridization-based targeted RNA-Seq method, cDNA-smMIPs are a cost-effective high-throughput tool for hypothesis-driven expression analysis in large numbers of genes (10 to 500) and samples (hundreds to thousands). PMID:28474677

Materials discovery at high pressures

NASA Astrophysics Data System (ADS)

Zhang, Lijun; Wang, Yanchao; Lv, Jian; Ma, Yanming

2017-02-01

Pressure is a fundamental thermodynamic variable that can be used to control the properties of materials, because it reduces interatomic distances and profoundly modifies electronic orbitals and bonding patterns. It is thus a versatile tool for the creation of exotic materials not accessible at ambient conditions. Recently developed static and dynamic high-pressure experimental techniques have led to the synthesis of many functional materials with excellent performance: for example, superconductors, superhard materials and high-energy-density materials. Some of these advances have been aided and accelerated by first-principles crystal-structure searching simulations. In this Review, we discuss recent progress in high-pressure materials discovery, placing particular emphasis on the record high-temperature superconductivity in hydrogen sulfide and on nanotwinned cubic boron nitride and diamond, the hardest known materials. Energy materials and exotic chemical materials obtained under high pressures are also discussed. The main drawback of high-pressure materials is their destabilization after pressure release; this problem and its possible solutions are surveyed in the conclusions, which also provide an outlook on the future developments in the field.

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 environments. This organizational principle is insensitive to the environments we consider and to the number of reactions in a metabolic network. Because we observe this principle not just in one or few biological networks, but in large random samples of networks, we propose that it may be a generic principle of metabolic network organization.

Blocks: A Versatile Learning Tool for Yesterday, Today, and Tomorrow

ERIC Educational Resources Information Center

Anderson, Charlotte

2010-01-01

In today's standards-driven climate, some teachers feel that incorporating content standards in the curriculum leads to a non-developmentally appropriate approach to working with young children. In her work as a preschool teacher trainer, the author shows students how something as common as blocks can guide them through each of the curriculum…

Using Specific Binding DNA Capture Elements to Direct Pulsed Power Killing of Biological Agents

DTIC Science & Technology

2003-06-01

Department of the Air Force position, policy, or decision unless so designated by other documentation. VI. REFERENCES [1] V. Majidi and M. R. Joseph...Spectroscopic applications of laser-induced plasmas,” Crit. Rev. Analyt. Chem. 23, 143-162, 1992. [2] V. Majidi , “Laser-induced plasmas: A versatile tool

Structural Order-Disorder Transformations Monitored by X-Ray Diffraction and Photoluminescence

ERIC Educational Resources Information Center

Lima, R. C.; Paris, E. C.; Leite, E. R.; Espinosa, J. W. M.; Souza, A. G.; Longo, E.

2007-01-01

A study was conducted to examine the structural order-disorder transformation promoted by controlled heat treatment using X-ray diffraction technique (XRD) and photoluminescence (PL) techniques as tools to monitor the degree of structural order. The experiment was observed to be versatile and easily achieved with low cost which allowed producing…

ecoSmart landscapes: a versatile SaaS platform for green infrastructure applications in urban environments

Treesearch

Greg McPherson; Qingfu Xiao; Joe Purohit; Mark Dietenberger; Charles (C.R.) Boardman; Jim Simpson; Paula Peper

2014-01-01

The urban environment offers significant opportunities to improve sustainability and optimize water resources. Historically, research and software applications have been focused on the built environment (buildings). Cost-effective, practical tools that can assess the impact of different landscape configurations and their interactions with buildings have not been widely...

Adventures with Cell Phones

ERIC Educational Resources Information Center

Kolb, Liz

2011-01-01

Teachers are finding creative ways to turn the basic cell phone from a digital distraction into a versatile learning tool. In this article, the author explains why cell phones are important in learning and suggests rather than banning them that they be integrated into learning. She presents activities that can be done on a basic cell phone with a…

Criticism and Assessment Applied to New Media Art

ERIC Educational Resources Information Center

Ursyn, Anna

2015-01-01

This text examines educational criticism and assessment with an emphasis on the new media arts. The article shares with readers the versatile, abridged to four points criteria, based on a research on assessment made by students, faculty, and non-art-related professionals, thus providing a preliminary tool for the use in the classroom environment.…

The aquamet Package for R: A Tool for Use with the National Rivers and Streams Assessment

EPA Science Inventory

The use of R software in environmental data analysis has become increasingly common because it is very powerful, versatile and available free of charge, with hundreds of contributed add-on packages available that perform almost every conceivable type of analysis or task. The Envi...

Two dimensional photoacoustic imaging using microfiber interferometric acoustic transducers

NASA Astrophysics Data System (ADS)

Wang, Xiu Xin; Li, Zhang Yong; Tian, Yin; Wang, Wei; Pang, Yu; Tam, Kin Yip

2018-07-01

Photoacoustic imaging transducer with a pair of wavelength-matched Bragg gratings (forming a Fabry-Perot cavity) inscribed on a short section of microfiber has been developed. A tunable laser with wavelength that matched to one of selected fringe slopes was used to transmit the acoustic induced wavelength. Interferometric fringes with high finesse in transmission significantly enhanced the sensitivity of the transducer even under very small acoustic perturbations. The performance of this novel transducer was evaluated through the imaging studies of human hairs (∼98 μm in diameter). The spatial resolution is 300 μm. We have demonstrated that the novel transducer developed in this study is a versatile tool for photoacoustic imaging study.

Transparent EuTiO3 films: a possible two-dimensional magneto-optical device

NASA Astrophysics Data System (ADS)

Bussmann-Holder, Annette; Roleder, Krystian; Stuhlhofer, Benjamin; Logvenov, Gennady; Lazar, Iwona; Soszyński, Andrzej; Koperski, Janusz; Simon, Arndt; Köhler, Jürgen

2017-01-01

The magneto-optical activity of high quality transparent thin films of insulating EuTiO3 (ETO) deposited on a thin SrTiO3 (STO) substrate, both being non-magnetic materials, are demonstrated to be a versatile tool for light modulation. The operating temperature is close to room temperature and allows for multiple device engineering. By using small magnetic fields birefringence of the samples can be switched off and on. Similarly, rotation of the sample in the field can modify its birefringence Δn. In addition, Δn can be increased by a factor of 4 in very modest fields with simultaneously enhancing the operating temperature by almost 100 K.

Click Chemistry, a Powerful Tool for Pharmaceutical Sciences

PubMed Central

Hein, Christopher D.; Liu, Xin-Ming; Wang, Dong

2008-01-01

Click chemistry refers to a group of reactions that are fast, simple to use, easy to purify, versatile, regiospecific, and give high product yields. While there are a number of reactions that fulfill the criteria, the Huisgen 1,3-dipolar cycloaddition of azides and terminal alkynes has emerged as the frontrunner. It has found applications in a wide variety of research areas, including materials sciences, polymer chemistry, and pharmaceutical sciences. In this manuscript, important aspects of the Huisgen cycloaddition will be reviewed, along with some of its many pharmaceutical applications. Bioconjugation, nanoparticle surface modification, and pharmaceutical-related polymer chemistry will all be covered. Limitations of the reaction will also be discussed. PMID:18509602

Pathway Design, Engineering, and Optimization.

PubMed

Garcia-Ruiz, Eva; HamediRad, Mohammad; Zhao, Huimin

The microbial metabolic versatility found in nature has inspired scientists to create microorganisms capable of producing value-added compounds. Many endeavors have been made to transfer and/or combine pathways, existing or even engineered enzymes with new function to tractable microorganisms to generate new metabolic routes for drug, biofuel, and specialty chemical production. However, the success of these pathways can be impeded by different complications from an inherent failure of the pathway to cell perturbations. Pursuing ways to overcome these shortcomings, a wide variety of strategies have been developed. This chapter will review the computational algorithms and experimental tools used to design efficient metabolic routes, and construct and optimize biochemical pathways to produce chemicals of high interest.

ADP-ribosyl-N₃: A Versatile Precursor for Divergent Syntheses of ADP-ribosylated Compounds.

PubMed

Li, Lingjun; Li, Qianqian; Ding, Shengqiang; Xin, Pengyang; Zhang, Yuqin; Huang, Shenlong; Zhang, Guisheng

2017-08-14

Adenosine diphosphate-ribose (ADP-ribose) and its derivatives play important roles in a series of complex physiological procedures. The design and synthesis of artificial ADP-ribosylated compounds is an efficient way to develop valuable chemical biology tools and discover new drug candidates. However, the synthesis of ADP-ribosylated compounds is currently difficult due to structural complexity, easily broken pyrophosphate bond and high hydrophilicity. In this paper, ADP-ribosyl-N₃ was designed and synthesized for the first time. With ADP-ribosyl-N₃ as the key precursor, a divergent post-modification strategy was developed to prepare structurally diverse ADP-ribosylated compounds including novel nucleotides and peptides bearing ADP-ribosyl moieties.

Fluorescent Arc/Arg3.1 indicator mice: a versatile tool to study brain activity changes in vitro and in vivo

PubMed Central

Grinevich, Valery; Kolleker, Alexander; Eliava, Marina; Takada, Naoki; Takuma, Hiroshi; Fukazawa, Yugo; Shigemoto, Ryuichi; Kuhl, Dietmar; Waters, Jack; Seeburg, Peter H.; Osten, Pavel

2014-01-01

The brain-specific immediate early gene Arc/Arg3.1 is induced in response to a variety of stimuli, including sensory and behavior-linked neural activity. Here we report the generation of transgenic mice, termed TgArc/Arg3.1-d4EGFP, expressing a 4-hour half-life form of enhanced green fluorescent protein (d4EGFP) under the control of the Arc/Arg3.1 promoter. We show that d4EGFP-mediated fluorescence faithfully reports Arc/Arg3.1 induction in response to physiological, pathological and pharmacological stimuli, and that this fluorescence permits electrical recording from activated neurons in the live mouse. Moreover, the fluorescent Arc/Arg3.1 indicator revealed activity changes in circumscribed brain areas in distinct modes of stress and in a mouse model of Alzheimer’s disease. These findings identify the TgArc/Arg3.1-d4EGFP mouse as a versatile tool to monitor Arc/Arg3.1 induction in neural circuits, both in vitro and in vivo. PMID:19628007

Versatile Genetic Tool Box for the Crenarchaeote Sulfolobus acidocaldarius

PubMed Central

Wagner, Michaela; van Wolferen, Marleen; Wagner, Alexander; Lassak, Kerstin; Meyer, Benjamin H.; Reimann, Julia; Albers, Sonja-Verena

2012-01-01

For reverse genetic approaches inactivation or selective modification of genes are required to elucidate their putative function. Sulfolobus acidocaldarius is a thermoacidophilic Crenarchaeon which grows optimally at 76°C and pH 3. As many antibiotics do not withstand these conditions the development of a genetic system in this organism is dependent on auxotrophies. Therefore we constructed a pyrE deletion mutant of S. acidocaldarius wild type strain DSM639 missing 322 bp called MW001. Using this strain as the starting point, we describe here different methods using single as well as double crossover events to obtain markerless deletion mutants, tag genes genomically and ectopically integrate foreign DNA into MW001. These methods enable us to construct single, double, and triple deletions strains that can still be complemented with the pRN1 based expression vector. Taken together we have developed a versatile and robust genetic tool box for the crenarchaeote S. acidocaldarius that will promote the study of unknown gene functions in this organism and makes it a suitable host for synthetic biology approaches. PMID:22707949

MINIVER upgrade for the AVID system. Volume 3: EXITS user's and input guide

NASA Technical Reports Server (NTRS)

Pond, J. E.; Schmitz, C. P.

1983-01-01

The successful design of thermal protection systems for vehicles operating in atmosphere and near-space environments requires accurate analyses of heating rate and temperature histories encountered along a trajectory. For preliminary design calculations, however, the requirement for accuracy must be tempered by the need for speed and versatility in computational tools used to determine thermal environments and structural thermal response. The MINIVER program was found to provide the proper balance between versatility, speed and accuracy for an aerothermal prediction tool. The advancement in computer aided design concepts at Langley Research Center (LaRC) in the past few years has made it desirable to incorporate the MINIVER program into the LaRC Advanced Vehicle Integrated Design, AVID, system. In order to effectively incorporate MINIVER into the AVID system, several changes to MINIVER were made. The thermal conduction options in MINIVER were removed and a new Explicit Interactive Thermal Structures (EXITS) code was developed. Many upgrades to the MINIVER code were made and a new Langley version of MINIVER called LANMIN was created.

MINIVER upgrade for the AVID system. Volume 1: LANMIN user's manual

NASA Technical Reports Server (NTRS)

Engel, C. D.; Praharaj, S. C.

1983-01-01

The successful design of thermal protection systems for vehicles operating in atmosphere and near space environments requires accurate analyses of heating rate and temperature histories encountered along a trajectory. For preliminary design calculations, however, the requirement for accuracy must be tempered by the need for speed and versatility in computational tools used to determine thermal environments and structural thermal response. The MINIVER program has been found to provide the proper balance between versatility, speed and accuracy for an aerothermal prediction tool. The advancement in computer aided design concepts at Langley Research Center (LaRC) in the past few years has made it desirable to incorporate the MINIVER program into the LaRC Advanced Vehicle Integrated Design, AVID, system. In order to effectively incorporate MINIVER into the AVID system, several changes to MINIVER were made. The thermal conduction options in MINIVER were removed and a new Explicit Interactive Thermal Structures (EXITS) code was developed. Many upgrades to the MINIVER code were made and a new Langley version of MINIVER called LANMIN was created. The theoretical methods and subroutine functions used in LANMIN are described.

RESPONSES OF MALE TROPICAL MOCKINGBIRDS TO VARIATION IN WITHIN-SONG AND BETWEEN-SONG VERSATILITY

PubMed Central

Botero, Carlos A.; Vehrencamp, Sandra L.

2007-01-01

Despite their large vocal repertoires and otherwise highly versatile singing style, male mockingbirds sometimes sing in a highly repetitive fashion. We conducted a playback experiment to determine the possible signal value of different syllable presentation patterns during simulated male intrusions in the Tropical Mockingbird (Mimus gilvus) testing the hypothesis that more repetitive singing represents a stronger threat and generates a stronger aggressive response. Responses were measured in terms of approach and singing behavior and were analyzed using McGregor’s (1992) multivariate method. We also introduce the use of survival analysis for analyzing response variables for which subjects do not perform the behavior in question in at least one of the replicates (known as ‘right-censored variables’ in the statistical literature). As predicted by theory, experimental subjects responded more aggressively to songs composed of a single note than to variable ones. However, versatility at the between-song level had an opposite effect as high song switching rates generated stronger responses than low ones. Given the lack of a statistical interaction between within-song versatility and switching rate, we conclude that these two parameters may serve independent purposes and possibly transmit different information. We discuss the possibility that the signal value of variation in vocal versatility lies in the mediation of territorial conflicts, the attraction of female partners and/or the mediation of conflicts over access to reproductive females. PMID:18509510

Design and Field Test of a Mass Efficient Crane for Lunar Payload Handling and Inspection: The Lunar Surface Manipulation System

NASA Technical Reports Server (NTRS)

Doggett, William R.; King, Bruce D.; Jones, Thomas Carno; Dorsey, John T.; Mikulas, Martin M.

2008-01-01

Devices for lifting, translating and precisely placing payloads are critical for efficient Earthbased construction operations. Both recent and past studies have demonstrated that devices with similar functionality will be needed to support lunar outpost operations. Lunar payloads include: a) prepackaged hardware and supplies which must be unloaded from landers and then accurately located at their operational site, b) sensor packages used for periodic inspection of landers, habitat surfaces, etc., and c) local materials such as regolith which require grading, excavation and placement. Although several designs have been developed for Earth based applications, these devices lack unique design characteristics necessary for transport to and use on the harsh lunar surface. These design characteristics include: a) composite components, b) compact packaging for launch, c) simple in-field reconfiguration and repair, and d) support for tele-operated or automated operations. Also, in contrast to Earth-based construction, where special purpose devices dominate a construction site, a lunar outpost will require versatile devices which provide operational benefit from initial construction through sustained operations. This paper will detail the design of a unique, high performance, versatile lifting device designed for operations on the lunar surface. The device is called the Lunar Surface Manipulation System to highlight the versatile nature of the device which supports conventional cable suspended crane operations as well as operations usually associated with a manipulator such as precise positioning where the payload is rigidly grappled by a tool attached to the tip of the device. A first generation test-bed to verify design methods and operational procedures is under development at the NASA Langley Research Center and recently completed field tests at Moses Lake Washington. The design relied on non-linear finite element analysis which is shown to correlate favorably with laboratory experiments. A key design objective, reviewed in this paper, is the device s simplicity, resulting from a focus on the minimum set of functions necessary to perform payload offload. Further development of the device has the potential for significant mass savings, with a high performance device incorporating composite elements estimated to have a mass less than 3% of the mass of the maximum lunar payload lifted at the tip. The paper will conclude with future plans for expanding the operational versatility of the device.

POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations

PubMed Central

Porollo, Aleksey; Meller, Jaroslaw

2010-01-01

Molecular simulations offer important mechanistic and functional clues in studies of proteins and other macromolecules. However, interpreting the results of such simulations increasingly requires tools that can combine information from multiple structural databases and other web resources, and provide highly integrated and versatile analysis tools. Here, we present a new web server that integrates high-quality animation of molecular motion (MM) with structural and functional analysis of macromolecules. The new tool, dubbed POLYVIEW-MM, enables animation of trajectories generated by molecular dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g. obtained as a result of protein structure prediction methods or small molecule docking. To facilitate structural analysis, POLYVIEW-MM combines interactive view and analysis of conformational changes using Jmol and its tailored extensions, publication quality animation using PyMol, and customizable 2D summary plots that provide an overview of MM, e.g. in terms of changes in secondary structure states and relative solvent accessibility of individual residues in proteins. Furthermore, POLYVIEW-MM integrates visualization with various structural annotations, including automated mapping of known inter-action sites from structural homologs, mapping of cavities and ligand binding sites, transmembrane regions and protein domains. URL: http://polyview.cchmc.org/conform.html. PMID:20504857

Two photon spectroscopy and microscopy of the fluorescent flavoprotein, iLOV.

PubMed

Homans, Rachael J; Khan, Raja U; Andrews, Michael B; Kjeldsen, Annemette E; Natrajan, Louise S; Marsden, Steven; McKenzie, Edward A; Christie, John M; Jones, Alex R

2018-06-06

LOV-domains are ubiquitous photosensory proteins that are commonly re-engineered to serve as powerful and versatile fluorescent proteins and optogenetic tools. The photoactive, flavin chromophore, however, is excited using short wavelengths of light in the blue and UV regions, which have limited penetration into biological samples and can cause photodamage. Here, we have used non-linear spectroscopy and microscopy of the fluorescent protein, iLOV, to reveal that functional variants of LOV can be activated to great effect by two non-resonant photons of lower energy, near infrared light, not only in solution but also in biological samples. The two photon cross section of iLOV has a significantly blue-shifted S0 → S1 transition compared with the one photon absorption spectrum, suggesting preferential population of excited vibronic states. It is highly likely, therefore, that the two photon absorption wavelength of engineered, LOV-based tools is tuneable. We also demonstrate for the first time two photon imaging using iLOV in human epithelial kidney cells. Consequently, two photon absorption by engineered, flavin-based bio-molecular tools can enable non-invasive activation with high depth resolution and the potential for not only improved image clarity but also enhanced spatiotemporal control for optogenetic applications.

Multilayer network decoding versatility and trust

NASA Astrophysics Data System (ADS)

Sarkar, Camellia; Yadav, Alok; Jalan, Sarika

2016-01-01

In the recent years, the multilayer networks have increasingly been realized as a more realistic framework to understand emergent physical phenomena in complex real-world systems. We analyze massive time-varying social data drawn from the largest film industry of the world under a multilayer network framework. The framework enables us to evaluate the versatility of actors, which turns out to be an intrinsic property of lead actors. Versatility in dimers suggests that working with different types of nodes are more beneficial than with similar ones. However, the triangles yield a different relation between type of co-actor and the success of lead nodes indicating the importance of higher-order motifs in understanding the properties of the underlying system. Furthermore, despite the degree-degree correlations of entire networks being neutral, multilayering picks up different values of correlation indicating positive connotations like trust, in the recent years. The analysis of weak ties of the industry uncovers nodes from a lower-degree regime being important in linking Bollywood clusters. The framework and the tools used herein may be used for unraveling the complexity of other real-world systems.

High-frequency ultrasonography (HFUS) as a useful tool in differentiating between plaque morphea and extragenital lichen sclerosus lesions

PubMed Central

Reszke, Radomir; Szepietowski, Jacek C.

2017-01-01

Introduction Morphea and lichen sclerosus (LS) are chronic inflammatory diseases that may pose a diagnostic challenge for a physician. High-frequency ultrasonography (HFUS) is a versatile diagnostic method utilized in dermatologic practice, allowing monitoring the course of the disease, treatment response and differentiation between certain skin disorders. Aim To prove the usefulness of HFUS in differentiating between plaque morphea and extragenital LS lesions. Material and methods We examined 16 patients with plaque morphea and 4 patients with extragenital LS using 20 MHz taberna pro medicum TM (Germany) device. Results Investigations revealed hyperechogenic entrance echo in both morphea and LS lesions, whereas a distinct polycyclic surface of the entrance echo was detected exclusively in LS. Conclusions High-frequency ultrasonography is a current diagnostic modality that may prove useful in differentiating between morphea and LS lesions. PMID:29507565

Nucleic Acid-Based Nanodevices in Biological Imaging.

PubMed

Chakraborty, Kasturi; Veetil, Aneesh T; Jaffrey, Samie R; Krishnan, Yamuna

2016-06-02

The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid-based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid-based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand.

The β-glucosidase secreted by Talaromyces amestolkiae under carbon starvation: a versatile catalyst for biofuel production from plant and algal biomass.

PubMed

Méndez-Líter, Juan Antonio; de Eugenio, Laura Isabel; Prieto, Alicia; Martínez, María Jesús

2018-01-01

In the last years, the most outstanding trend for obtaining high added-value components and second-generation (2G) biofuels consisted on exploitation of plant biomass. But recently, 3G biofuels, based in algae biomass, have emerged as a great alternative for production of energy. In this work, a versatile β-glucosidase from the ascomycete fungus Talaromyces amestolkiae has been purified, characterized, and heterologously expressed. The synthesis of this β-glucosidase (BGL-3) was not induced by cellulose, and the presence of a specific carbon source is not required for its production, which is uncommon for β-glucosidases. BGL-3, which was obtained from a basal medium with glucose as carbon source, was profusely secreted under carbon starvation conditions, which was corroborated by qRT-PCR assays. BGL-3 was purified from T. amestolkiae cultures in one step, and biochemically characterized. The enzyme showed high thermal stability, and very high efficiency on p NPG ( K m of 0.14 mM and V max of 381.1 U/mg), cellobiose ( K m of 0.48 mM and V max of 447.1 U/mg), and other cello-oligosaccharides. Surprisingly, it also showed remarkable ability to hydrolyze laminarin, a β-1,3-glucan present in algae. The recombinant enzyme, obtained in the yeast Pichia pastoris, exhibited kinetic and physicochemical properties similar to those found for the native protein. Enzyme efficiency was examined in wheat straw saccharification processes, in which BGL-3 worked better supplementing Celluclast 1.5L than the commercial cellulase cocktail N-50010. Besides, BGL-3 hydrolyzed laminarin more efficiently than a commercial laminarinase. A very efficient 1,4-β-glucosidase, which also showed activity over 1,3-β-glucose bonds, has been produced, purified, and characterized. This is the first report of such versatility in a 1,4-β-glucosidase. The application of this enzyme for saccharification of wheat straw and laminarin and its comparison with commercial enzymes suggest that it could be an interesting tool for the production of 2G and 3G biofuels.

Moving graphene devices from lab to market: advanced graphene-coated nanoprobes

NASA Astrophysics Data System (ADS)

Hui, Fei; Vajha, Pujashree; Shi, Yuanyuan; Ji, Yanfeng; Duan, Huiling; Padovani, Andrea; Larcher, Luca; Li, Xiao Rong; Xu, Jing Juan; Lanza, Mario

2016-04-01

After more than a decade working with graphene there is still a preoccupying lack of commercial devices based on this wonder material. Here we report the use of high-quality solution-processed graphene sheets to fabricate ultra-sharp probes with superior performance. Nanoprobes are versatile tools used in many fields of science, but they can wear fast after some experiments, reducing the quality and increasing the cost of the research. As the market of nanoprobes is huge, providing a solution for this problem should be a priority for the nanotechnology industry. Our graphene-coated nanoprobes not only show enhanced lifetime, but also additional unique properties of graphene, such as hydrophobicity. Moreover, we have functionalized the surface of graphene to provide piezoelectric capability, and have fabricated a nano relay. The simplicity and low cost of this method, which can be used to coat any kind of sharp tip, make it suitable for the industry, allowing production on demand.After more than a decade working with graphene there is still a preoccupying lack of commercial devices based on this wonder material. Here we report the use of high-quality solution-processed graphene sheets to fabricate ultra-sharp probes with superior performance. Nanoprobes are versatile tools used in many fields of science, but they can wear fast after some experiments, reducing the quality and increasing the cost of the research. As the market of nanoprobes is huge, providing a solution for this problem should be a priority for the nanotechnology industry. Our graphene-coated nanoprobes not only show enhanced lifetime, but also additional unique properties of graphene, such as hydrophobicity. Moreover, we have functionalized the surface of graphene to provide piezoelectric capability, and have fabricated a nano relay. The simplicity and low cost of this method, which can be used to coat any kind of sharp tip, make it suitable for the industry, allowing production on demand. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06235g

Programmable DNA-Guided Artificial Restriction Enzymes.

PubMed

Enghiad, Behnam; Zhao, Huimin

2017-05-19

Restriction enzymes are essential tools for recombinant DNA technology that have revolutionized modern biological research. However, they have limited sequence specificity and availability. Here we report a Pyrococcus furiosus Argonaute (PfAgo) based platform for generating artificial restriction enzymes (AREs) capable of recognizing and cleaving DNA sequences at virtually any arbitrary site and generating defined sticky ends of varying length. Short DNA guides are used to direct PfAgo to target sites for cleavage at high temperatures (>87 °C) followed by reannealing of the cleaved single stranded DNAs. We used this platform to generate over 18 AREs for DNA fingerprinting and molecular cloning of PCR-amplified or genomic DNAs. These AREs work as efficiently as their naturally occurring counterparts, and some of them even do not have any naturally occurring counterparts, demonstrating easy programmability, generality, versatility, and high efficiency for this new technology.

The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets.

PubMed

Droege, Marcus; Hill, Brendon

2008-08-31

The Genome Sequencer FLX System (GS FLX), powered by 454 Sequencing, is a next-generation DNA sequencing technology featuring a unique mix of long reads, exceptional accuracy, and ultra-high throughput. It has been proven to be the most versatile of all currently available next-generation sequencing technologies, supporting many high-profile studies in over seven applications categories. GS FLX users have pursued innovative research in de novo sequencing, re-sequencing of whole genomes and target DNA regions, metagenomics, and RNA analysis. 454 Sequencing is a powerful tool for human genetics research, having recently re-sequenced the genome of an individual human, currently re-sequencing the complete human exome and targeted genomic regions using the NimbleGen sequence capture process, and detected low-frequency somatic mutations linked to cancer.

Pushing the Limits of MALDI-TOF Mass Spectrometry: Beyond Fungal Species Identification

PubMed Central

Rizzato, Cosmeri; Lombardi, Lisa; Zoppo, Marina; Lupetti, Antonella; Tavanti, Arianna

2015-01-01

Matrix assisted laser desorption ionization time of flight (MALDI-TOF) is a powerful analytical tool that has revolutionized microbial identification. Routinely used for bacterial identification, MALDI-TOF has recently been applied to both yeast and filamentous fungi, confirming its pivotal role in the rapid and reliable diagnosis of infections. Subspecies-level identification holds an important role in epidemiological investigations aimed at tracing virulent or drug resistant clones. This review focuses on present and future applications of this versatile tool in the clinical mycology laboratory. PMID:29376916

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.

PubMed

Maere, Steven; Heymans, Karel; Kuiper, Martin

2005-08-15

The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape's versatile visualization environment to produce an intuitive and customizable visual representation of the results.

Illustrating the Concepts of Isotopes and Mass Spectrometry in Introductory Courses: A MALDI-TOF Mass Spectrometry Laboratory Experiment

ERIC Educational Resources Information Center

Dopke, Nancy Carter; Lovett, Timothy Neal

2007-01-01

Mass spectrometry is a widely used and versatile tool for scientists in many different fields. Soft ionization techniques such as matrix-assisted laser desorption/ionization (MALDI) allow for the analysis of biomolecules, polymers, and clusters. This article describes a MALDI mass spectrometry experiment designed for students in introductory…

Laboratory Exercise for Studying the Morphology of Heat-Denatured and Amyloid Aggregates of Lysozyme by Atomic Force Microscopy

ERIC Educational Resources Information Center

Gokalp, Sumeyra; Horton, William; Jónsdóttir-Lewis, Elfa B.; Foster, Michelle; Török, Marianna

2018-01-01

To facilitate learning advanced instrumental techniques, essential tools for visualizing biomaterials, a simple and versatile laboratory exercise demonstrating the use of Atomic Force Microscopy (AFM) in biomedical applications was developed. In this experiment, the morphology of heat-denatured and amyloid-type aggregates formed from a low-cost…

A Versatile Applet to Explore the Wave Behaviour of Particles

ERIC Educational Resources Information Center

Fernandez Palop, J. I.

2009-01-01

A pedagogical tool that consists of a Java applet has been developed so that undergraduate students in physics can explore the wave behaviour of particles. The applet executes a simulation in which a two-dimensional wave packet moves towards a slit and an obstacle with variable widths. By changing three parameters, slit width, obstacle width and…

Cost Effectiveness Ratio: Evaluation Tool for Comparing the Effectiveness of Similar Extension Programs

ERIC Educational Resources Information Center

Jayaratne, K. S. U.

2015-01-01

Extension educators have been challenged to be cost effective in their educational programming. The cost effectiveness ratio is a versatile evaluation indicator for Extension educators to compare the cost of achieving a unit of outcomes or educating a client in similar educational programs. This article describes the cost effectiveness ratio and…

Application of SWAT to assess the effects of land use change in the Murchison Bay catchment in Uganda

USDA-ARS?s Scientific Manuscript database

The Soil and Water Assessment Tool (SWAT) is a versatile model presently used worldwide to evaluate water quality and hydrological concerns under varying land use and environmental conditions. In this study, SWAT was used to simulate streamflow and to estimate sediment yield and nutrients loss from ...

SCANIT: centralized digitizing of forest resource maps or photographs

Treesearch

Elliot L. Amidon; E. Joyce Dye

1981-01-01

Spatial data on wildland resource maps and aerial photographs can be analyzed by computer after digitizing. SCANIT is a computerized system for encoding such data in digital form. The system, consisting of a collection of computer programs and subroutines, provides a powerful and versatile tool for a variety of resource analyses. SCANIT also may be converted easily to...

New Aspect of Technology Adoption: A Case Study of Students' Self-Made English-Learning Video

ERIC Educational Resources Information Center

Tai, Yaming; Ting, Yu-Liang

2016-01-01

Understanding how students perceive and adopt technology in their daily life is particularly relevant to today's Information and Communication Technology (ICT) environment, in which versatile ICT tools are becoming more and more pervasive, almost ubiquitous in our day-to-day activities. In the context of English as a foreign language, this study…

An Interactive, Versatile, Three-Dimensional Display, Manipulation and Plotting System for Biomedical Research

ERIC Educational Resources Information Center

Feldmann, Richard J.; And Others

1972-01-01

Computer graphics provides a valuable tool for the representation and a better understanding of structures, both small and large. Accurate and rapid construction, manipulation, and plotting of structures, such as macromolecules as complex as hemoglobin, are performed by a collection of computer programs and a time-sharing computer. (21 references)…

Posttraumatic eyebrow reconstruction with hair-bearing temporoparietal fascia flap

PubMed Central

Denadai, Rafael; Raposo-Amaral, Cassio Eduardo; Marques, Frederico Figueiredo; Raposo-Amaral, Cesar Augusto

2015-01-01

The temporoparietal fascia flap has been extensively used in craniofacial reconstructions. However, its use for eyebrow reconstruction has been sporadically reported. We describe a successfully repaired hair-bearing temporoparietal fascia flap after traumatic avulsion of eyebrow. Temporoparietal fascia flap is a versatile tool and should be considered as a therapeutic option by all plastic surgeons. PMID:25993077

Manipulating waves with LEGO bricks: A versatile experimental platform for metamaterial architectures

NASA Astrophysics Data System (ADS)

Celli, Paolo; Gonella, Stefano

2015-08-01

In this letter, we discuss a versatile, fully reconfigurable experimental platform for the investigation of phononic phenomena in metamaterial architectures. The approach revolves around the use of 3D laser vibrometry to reconstruct global and local wavefield features in specimens obtained through simple arrangements of LEGO® bricks on a thin baseplate. The agility by which it is possible to reconfigure the brick patterns into a nearly endless spectrum of topologies makes this an effective approach for rapid experimental proof of concept, as well as a powerful didactic tool, in the arena of phononic crystals and metamaterials engineering. We use our platform to provide a compelling visual illustration of important spatial wave manipulation effects (waveguiding and seismic isolation), and to elucidate fundamental dichotomies between Bragg-based and locally resonant bandgap mechanisms.

The Physics and Mathematics of MRI

NASA Astrophysics Data System (ADS)

Ansorge, Richard; Graves, Martin

2016-10-01

Magnetic Resonance Imaging is a very important clinical imaging tool. It combines different fields of physics and engineering in a uniquely complex way. MRI is also surprisingly versatile, `pulse sequences' can be designed to yield many different types of contrast. This versatility is unique to MRI. This short book gives both an in depth account of the methods used for the operation and construction of modern MRI systems and also the principles of sequence design and many examples of applications. An important additional feature of this book is the detailed discussion of the mathematical principles used in building optimal MRI systems and for sequence design. The mathematical discussion is very suitable for undergraduates attending medical physics courses. It is also more complete than usually found in alternative books for physical scientists or more clinically orientated works.

A versatile localization system for microscopic multiparametric analysis of cells.

PubMed

Thaw, H H; Rundquist, I; Johansson, U; Svensson, I; Collins, V P

1983-03-01

A new, simple and relatively inexpensive electronic digital position readout (DPRO) system which can be applied to the rapid localization and recovery of microscopic material is described. It is based upon a commercially available digital position readout system which is routinely utilized by industry for small machine tools and measuring equipment. This has been mounted onto the stage of various microscopic instrumentation to provide X and Y coordinates relative to an arbitrary reference point. The integration of small computers interfaced to scanning interferometric, microdensitometric and fluorescence microscopes were used to demonstrate the reliability, versatility and ease of application of this system to problems of multiparametric measurements and analysis of cultured cells. The system may be expanded and applied to clinical material to obtain automatized, multiparametric measurements of cells in haematology and clinical cytology.

Bayesian ISOLA: new tool for automated centroid moment tensor inversion

NASA Astrophysics Data System (ADS)

Vackář, Jiří; Burjánek, Jan; Gallovič, František; Zahradník, Jiří; Clinton, John

2017-08-01

We have developed a new, fully automated tool for the centroid moment tensor (CMT) inversion in a Bayesian framework. It includes automated data retrieval, data selection where station components with various instrumental disturbances are rejected and full-waveform inversion in a space-time grid around a provided hypocentre. A data covariance matrix calculated from pre-event noise yields an automated weighting of the station recordings according to their noise levels and also serves as an automated frequency filter suppressing noisy frequency ranges. The method is tested on synthetic and observed data. It is applied on a data set from the Swiss seismic network and the results are compared with the existing high-quality MT catalogue. The software package programmed in Python is designed to be as versatile as possible in order to be applicable in various networks ranging from local to regional. The method can be applied either to the everyday network data flow, or to process large pre-existing earthquake catalogues and data sets.

Parameter Estimation for a Pulsating Turbulent Buoyant Jet Using Approximate Bayesian Computation

NASA Astrophysics Data System (ADS)

Christopher, Jason; Wimer, Nicholas; Lapointe, Caelan; Hayden, Torrey; Grooms, Ian; Rieker, Greg; Hamlington, Peter

2017-11-01

Approximate Bayesian Computation (ABC) is a powerful tool that allows sparse experimental or other ``truth'' data to be used for the prediction of unknown parameters, such as flow properties and boundary conditions, in numerical simulations of real-world engineering systems. Here we introduce the ABC approach and then use ABC to predict unknown inflow conditions in simulations of a two-dimensional (2D) turbulent, high-temperature buoyant jet. For this test case, truth data are obtained from a direct numerical simulation (DNS) with known boundary conditions and problem parameters, while the ABC procedure utilizes lower fidelity large eddy simulations. Using spatially-sparse statistics from the 2D buoyant jet DNS, we show that the ABC method provides accurate predictions of true jet inflow parameters. The success of the ABC approach in the present test suggests that ABC is a useful and versatile tool for predicting flow information, such as boundary conditions, that can be difficult to determine experimentally.

Improving CRISPR-Cas specificity with chemical modifications in single-guide RNAs.

PubMed

Ryan, Daniel E; Taussig, David; Steinfeld, Israel; Phadnis, Smruti M; Lunstad, Benjamin D; Singh, Madhurima; Vuong, Xuan; Okochi, Kenji D; McCaffrey, Ryan; Olesiak, Magdalena; Roy, Subhadeep; Yung, Chong Wing; Curry, Bo; Sampson, Jeffrey R; Bruhn, Laurakay; Dellinger, Douglas J

2018-01-25

CRISPR systems have emerged as transformative tools for altering genomes in living cells with unprecedented ease, inspiring keen interest in increasing their specificity for perfectly matched targets. We have developed a novel approach for improving specificity by incorporating chemical modifications in guide RNAs (gRNAs) at specific sites in their DNA recognition sequence ('guide sequence') and systematically evaluating their on-target and off-target activities in biochemical DNA cleavage assays and cell-based assays. Our results show that a chemical modification (2'-O-methyl-3'-phosphonoacetate, or 'MP') incorporated at select sites in the ribose-phosphate backbone of gRNAs can dramatically reduce off-target cleavage activities while maintaining high on-target performance, as demonstrated in clinically relevant genes. These findings reveal a unique method for enhancing specificity by chemically modifying the guide sequence in gRNAs. Our approach introduces a versatile tool for augmenting the performance of CRISPR systems for research, industrial and therapeutic applications. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Improving CRISPR–Cas specificity with chemical modifications in single-guide RNAs

PubMed Central

Ryan, Daniel E; Taussig, David; Steinfeld, Israel; Phadnis, Smruti M; Lunstad, Benjamin D; Singh, Madhurima; Vuong, Xuan; Okochi, Kenji D; McCaffrey, Ryan; Olesiak, Magdalena; Roy, Subhadeep; Yung, Chong Wing; Curry, Bo; Sampson, Jeffrey R; Dellinger, Douglas J

2018-01-01

Abstract CRISPR systems have emerged as transformative tools for altering genomes in living cells with unprecedented ease, inspiring keen interest in increasing their specificity for perfectly matched targets. We have developed a novel approach for improving specificity by incorporating chemical modifications in guide RNAs (gRNAs) at specific sites in their DNA recognition sequence (‘guide sequence’) and systematically evaluating their on-target and off-target activities in biochemical DNA cleavage assays and cell-based assays. Our results show that a chemical modification (2′-O-methyl-3′-phosphonoacetate, or ‘MP’) incorporated at select sites in the ribose-phosphate backbone of gRNAs can dramatically reduce off-target cleavage activities while maintaining high on-target performance, as demonstrated in clinically relevant genes. These findings reveal a unique method for enhancing specificity by chemically modifying the guide sequence in gRNAs. Our approach introduces a versatile tool for augmenting the performance of CRISPR systems for research, industrial and therapeutic applications. PMID:29216382

Highly efficient, versatile, self-Q-switched, high-repetition-rate microchip laser generating Ince-Gaussian modes for optical trapping

NASA Astrophysics Data System (ADS)

Dong, Jun; He, Yu; Zhou, Xiao; Bai, Shengchuang

2016-03-01

Lasers operating in the Ince-Gaussian (IG) mode have potential applications for optical manipulation of microparticles and formation of optical vortices, as well as for optical trapping and optical tweezers. Versatile, self-Q-switched, high-peak-power, high-repetition-rate Cr, Nd:YAG microchip lasers operating in the IG mode are implemented under tilted, tightly focused laser-diode pumping. An average output power of over 2 W is obtained at an absorbed pump power of 6.4 W. The highest optical-to-optical efficiency of 33.2% is achieved at an absorbed pump power of 3.9 W. Laser pulses with a pulse energy of 7.5 μJ, pulse width of 3.5 ns and peak power of over 2 kW are obtained. A repetition rate up to 335 kHz is reached at an absorbed pump power of 5.8 W. Highly efficient, versatile, IG-mode lasers with a high repetition rate and a high peak power ensure a better flexibility in particle manipulation and optical trapping.

Highly efficient, versatile, self-Q-switched, high-repetition-rate microchip laser generating Ince–Gaussian modes for optical trapping

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

Jun Dong; Yu He; Xiao Zhou

2016-03-31

Lasers operating in the Ince-Gaussian (IG) mode have potential applications for optical manipulation of microparticles and formation of optical vortices, as well as for optical trapping and optical tweezers. Versatile, self-Q-switched, high-peak-power, high-repetition-rate Cr, Nd:YAG microchip lasers operating in the IG mode are implemented under tilted, tightly focused laser-diode pumping. An average output power of over 2 W is obtained at an absorbed pump power of 6.4 W. The highest optical-to-optical efficiency of 33.2% is achieved at an absorbed pump power of 3.9 W. Laser pulses with a pulse energy of 7.5 μJ, pulse width of 3.5 ns and peakmore » power of over 2 kW are obtained. A repetition rate up to 335 kHz is reached at an absorbed pump power of 5.8 W. Highly efficient, versatile, IG-mode lasers with a high repetition rate and a high peak power ensure a better flexibility in particle manipulation and optical trapping. (control of laser radiation parameters)« less

MicroMegascope.

PubMed

Canale, L; Laborieux, A; Mogane, A Aroul; Jubin, L; Comtet, J; Lainé, A; Bocquet, L; Siria, A; Niguès, A

2018-08-31

Atomic force microscopy (AFM) allows us to reconstruct the topography of surfaces with resolution in the nanometer range. The exceptional resolution attainable with the AFM makes this instrument a key tool in nanoscience and technology. The core of a standard AFM set-up relies on the detection of the change of the mechanical motion of a micro-oscillator when approaching the sample to image. This is despite the fact that AFM is nowadays a very common instrument for both fundamental and applied research. The fabrication of the micrometric scale mechanical oscillator is still a very complicated and expensive task requiring dedicated platforms. Being able to perform AFM with a macroscopic oscillator would make the instrument more versatile and accessible for an even larger spectrum of applications and audience. Here, we present atomic force imaging with a centimetric oscillator, an aluminum tuning fork of centimeter size as a sensor on which an accelerometer is glued on one prong to measure the oscillations. We show that it is possible to perform topographic images of nanometric resolution with a gram tuning fork. In addition to the stunning sensitivity, we show the high versatility of such an oscillator by imaging both in air and liquid. The set-up proposed here can be extended to numerous experiments where the probe has to be heavy and/or very complex, and so too the environment.

Versatile peroxidase as a valuable tool for generating new biomolecules by homogeneous and heterogeneous cross-linking.

PubMed

Salvachúa, Davinia; Prieto, Alicia; Mattinen, Maija-Liisa; Tamminen, Tarja; Liitiä, Tiina; Lille, Martina; Willför, Stefan; Martínez, Angel T; Martínez, María Jesús; Faulds, Craig B

2013-05-10

The modification and generation of new biomolecules intended to give higher molecular-mass species for biotechnological purposes, can be achieved by enzymatic cross-linking. The versatile peroxidase (VP) from Pleurotus eryngii is a high redox-potential enzyme with oxidative activity on a wide variety of substrates. In this study, VP was successfully used to catalyze the polymerization of low molecular mass compounds, such as lignans and peptides, as well as larger macromolecules, such as protein and complex polysaccharides. Different analytical, spectroscopic, and rheological techniques were used to determine structural changes and/or variations of the physicochemical properties of the reaction products. The lignans secoisolariciresinol and hydroxymatairesinol were condensed by VP forming up to 8 unit polymers in the presence of organic co-solvents and Mn(2+). Moreover, 11 unit of the peptides YIGSR and VYV were homogeneously cross-linked. The heterogeneous cross-linking of one unit of the peptide YIGSR and several lignan units was also achieved. VP could also induce gelation of feruloylated arabinoxylan and the polymerization of β-casein. These results demonstrate the efficacy of VP to catalyze homo- and hetero-condensation reactions, and reveal its potential exploitation for polymerizing different types of compounds. Copyright © 2013 Elsevier Inc. All rights reserved.

enoLOGOS: a versatile web tool for energy normalized sequence logos

PubMed Central

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

2005-01-01

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

PACOM: A Versatile Tool for Integrating, Filtering, Visualizing, and Comparing Multiple Large Mass Spectrometry Proteomics Data Sets.

PubMed

Martínez-Bartolomé, Salvador; Medina-Aunon, J Alberto; López-García, Miguel Ángel; González-Tejedo, Carmen; Prieto, Gorka; Navajas, Rosana; Salazar-Donate, Emilio; Fernández-Costa, Carolina; Yates, John R; Albar, Juan Pablo

2018-04-06

Mass-spectrometry-based proteomics has evolved into a high-throughput technology in which numerous large-scale data sets are generated from diverse analytical platforms. Furthermore, several scientific journals and funding agencies have emphasized the storage of proteomics data in public repositories to facilitate its evaluation, inspection, and reanalysis. (1) As a consequence, public proteomics data repositories are growing rapidly. However, tools are needed to integrate multiple proteomics data sets to compare different experimental features or to perform quality control analysis. Here, we present a new Java stand-alone tool, Proteomics Assay COMparator (PACOM), that is able to import, combine, and simultaneously compare numerous proteomics experiments to check the integrity of the proteomic data as well as verify data quality. With PACOM, the user can detect source of errors that may have been introduced in any step of a proteomics workflow and that influence the final results. Data sets can be easily compared and integrated, and data quality and reproducibility can be visually assessed through a rich set of graphical representations of proteomics data features as well as a wide variety of data filters. Its flexibility and easy-to-use interface make PACOM a unique tool for daily use in a proteomics laboratory. PACOM is available at https://github.com/smdb21/pacom .

High Efficiency Variable Speed Versatile Power Air Conditioning System

DTIC Science & Technology

2013-08-08

Design concept applicable for wide range of HVAC and refrigeration systems • One TXV size can be used for a wide range of cooling capacity...versatility, can run from AC and DC sources Cooling load adaptive, variable Speed Fully operable up to 140 degrees Fahrenheit 15. SUBJECT TERMS 16. SECURITY...ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 High Efficiency HVAC &R Technology

Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit

PubMed Central

2014-01-01

Background The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. Results We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Conclusions Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning. PMID:24708438

Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit.

PubMed

Hoefman, Sven; van der Ha, David; Boon, Nico; Vandamme, Peter; De Vos, Paul; Heylen, Kim

2014-04-04

The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning.

Four Chemical Trends Will Shape the Next Decade's Directions in Perfluoroalkyl and Polyfluoroalkyl Substances Research.

PubMed

Kotthoff, Matthias; Bücking, Mark

2018-01-01

Per- and polyfluoroalkyl substances (PFAS) represent a versatile group of ubiquitously occurring chemicals of increasing regulatory concern. The past years lead to an ever expanding portfolio of detected anthropogenic PFAS in numerous products encountered in daily life. Yet no clear picture of the full range of individual substance that comprise PFAS is available and this challenges analytical and engineering sciences. Authorities struggle to cope with uncertainties in managing risk of harm posed by PFAS. This is a result of an incomplete understanding of the range of compounds that they comprise in differing products. There are analytical uncertainties identifying PFAS and estimating the concentrations of the total PFAS load individual molecules remain unknown. There are four major trends from the chemical perspective that will shape PFAS research for the next decade. Mobility: A wide and dynamic distribution of short chain PFAS due to their high polarity, persistency and volatility.Substitution of regulated substances: The ban or restrictions of individual molecules will lead to a replacement with substitutes of similar concern.Increase in structural diversity of existing PFAS molecules: Introduction of e.g., hydrogens and chlorine atoms instead of fluorine, as well as branching and cross-linking lead to a high versatility of unknown target molecules.Unknown "Dark Matter": The amount, identity, formation pathways, and transformation dynamics of polymers and PFAS precursors are largely unknown. These directions require optimized analytical setups, especially multi-methods, and semi-specific tools to determine PFAS-sum parameters in any relevant matrix.

Four Chemical Trends Will Shape the Next Decade's Directions in Perfluoroalkyl and Polyfluoroalkyl Substances Research

PubMed Central

Kotthoff, Matthias; Bücking, Mark

2018-01-01

Per- and polyfluoroalkyl substances (PFAS) represent a versatile group of ubiquitously occurring chemicals of increasing regulatory concern. The past years lead to an ever expanding portfolio of detected anthropogenic PFAS in numerous products encountered in daily life. Yet no clear picture of the full range of individual substance that comprise PFAS is available and this challenges analytical and engineering sciences. Authorities struggle to cope with uncertainties in managing risk of harm posed by PFAS. This is a result of an incomplete understanding of the range of compounds that they comprise in differing products. There are analytical uncertainties identifying PFAS and estimating the concentrations of the total PFAS load individual molecules remain unknown. There are four major trends from the chemical perspective that will shape PFAS research for the next decade. Mobility: A wide and dynamic distribution of short chain PFAS due to their high polarity, persistency and volatility.Substitution of regulated substances: The ban or restrictions of individual molecules will lead to a replacement with substitutes of similar concern.Increase in structural diversity of existing PFAS molecules: Introduction of e.g., hydrogens and chlorine atoms instead of fluorine, as well as branching and cross-linking lead to a high versatility of unknown target molecules.Unknown “Dark Matter”: The amount, identity, formation pathways, and transformation dynamics of polymers and PFAS precursors are largely unknown. These directions require optimized analytical setups, especially multi-methods, and semi-specific tools to determine PFAS-sum parameters in any relevant matrix. PMID:29675408

Critically endangered blonde capuchins fish for termites and use new techniques to accomplish the task

PubMed Central

Souto, Antonio; Bione, Camila B. C.; Bastos, Monique; Bezerra, Bruna M.; Fragaszy, Dorothy; Schiel, Nicola

2011-01-01

We report the spontaneous modification and use of sticks to fish for termites, above the ground, in wild blonde capuchins (Cebus flavius). These critically endangered Neotropical primates inhabit remnants of the Atlantic Forest. They used two previously undescribed techniques to enhance their termite capture success: nest tapping and stick rotation. The current ecologically based explanation for tool use in wild capuchins (i.e. terrestrial habits and bipedalism) must be viewed cautiously. Instead, remarkable manual skills linked to a varied diet seem important in promoting tool use in different contexts. The repertoire of tool-using techniques employed by wild capuchins has been expanded, highlighting the behavioural versatility in this genus. PMID:21389018

Extrinsic Fluorescent Dyes as Tools for Protein Characterization

PubMed Central

Hawe, Andrea; Sutter, Marc

2008-01-01

Noncovalent, extrinsic fluorescent dyes are applied in various fields of protein analysis, e.g. to characterize folding intermediates, measure surface hydrophobicity, and detect aggregation or fibrillation. The main underlying mechanisms, which explain the fluorescence properties of many extrinsic dyes, are solvent relaxation processes and (twisted) intramolecular charge transfer reactions, which are affected by the environment and by interactions of the dyes with proteins. In recent time, the use of extrinsic fluorescent dyes such as ANS, Bis-ANS, Nile Red, Thioflavin T and others has increased, because of their versatility, sensitivity and suitability for high-throughput screening. The intention of this review is to give an overview of available extrinsic dyes, explain their spectral properties, and show illustrative examples of their various applications in protein characterization. PMID:18172579

The finite element method in low speed aerodynamics

NASA Technical Reports Server (NTRS)

Baker, A. J.; Manhardt, P. D.

1975-01-01

The finite element procedure is shown to be of significant impact in design of the 'computational wind tunnel' for low speed aerodynamics. The uniformity of the mathematical differential equation description, for viscous and/or inviscid, multi-dimensional subsonic flows about practical aerodynamic system configurations, is utilized to establish the general form of the finite element algorithm. Numerical results for inviscid flow analysis, as well as viscous boundary layer, parabolic, and full Navier Stokes flow descriptions verify the capabilities and overall versatility of the fundamental algorithm for aerodynamics. The proven mathematical basis, coupled with the distinct user-orientation features of the computer program embodiment, indicate near-term evolution of a highly useful analytical design tool to support computational configuration studies in low speed aerodynamics.

Gold glyconanoparticles: synthetic polyvalent ligands mimicking glycocalyx-like surfaces as tools for glycobiological studies.

PubMed

Barrientos, Africa G; de la Fuente, Jesús M; Rojas, Teresa C; Fernández, Asunción; Penadés, Soledad

2003-05-09

A simple and versatile methodology is described for tailoring sugar-functionalised gold nanoclusters (glyconanoparticles) that have 3D polyvalent carbohydrate display and globular shapes. This methodology allows the preparation of glyconanoparticles with biologically significant oligosaccharides as well as with differing carbohydrate density. Fluorescent glyconanoparticles have been also prepared for labelling cells in biological tests. The materials are water soluble, stable under physiological conditions and present an exceptional small core size. All of them have been characterised by (1)H NMR, UV and IR spectroscopy, TEM and elemental analysis. Their highly polyvalent network can mimic glycosphingolipid clustering and interactions at the plasma membrane, providing an controlled system for glycobiological studies. Furthermore, they are useful building blocks for the design of nanomaterials.

Direct Electrospray Ionization Mass Spectrometric Profiling of Real-World Samples via a Solid Sampling Probe

NASA Astrophysics Data System (ADS)

Yu, Zhan; Chen, Lee Chuin; Mandal, Mridul Kanti; Yoshimura, Kentaro; Takeda, Sen; Hiraoka, Kenzo

2013-10-01

This study presents a novel direct analysis strategy for rapid mass spectrometric profiling of biochemicals in real-world samples via a direct sampling probe (DSP) without sample pretreatments. Chemical modification is applied to a disposable stainless steel acupuncture needle to enhance its surface area and hydrophilicity. After insertion into real-world samples, biofluid can be attached on the DSP surface. With the presence of a high DC voltage and solvent vapor condensing on the tip of the DSP, analyte can be dissolved and electrosprayed. The simplicity in design, versatility in application aspects, and other advantages such as low cost and disposability make this new method a competitive tool for direct analysis of real-world samples.

Independent valine and leucine isotope labeling in Escherichia coli protein overexpression systems.

PubMed

Lichtenecker, Roman J; Weinhäupl, Katharina; Reuther, Lukas; Schörghuber, Julia; Schmid, Walther; Konrat, Robert

2013-11-01

The addition of labeled α-ketoisovalerate to the growth medium of a protein-expressing host organism has evolved into a versatile tool to achieve concomitant incorporation of specific isotopes into valine- and leucine- residues. The resulting target proteins represent excellent probes for protein NMR analysis. However, as the sidechain resonances of these residues emerge in a narrow spectral range, signal overlap represents a severe limitation in the case of high-molecular-weight NMR probes. We present a protocol to eliminate leucine labeling by supplying the medium with unlabeled α-ketoisocaproate. The resulting spectra of a model protein exclusively feature valine signals of increased intensity, confirming the method to be a first example of independent valine and leucine labeling employing α-ketoacid precursor compounds.

Soft X-ray spectroscopy of transition metal compounds: a theoretical perspective

NASA Astrophysics Data System (ADS)

Bokarev, S. I.; Hilal, R.; Aziz, S. G.; Kühn, O.

2017-01-01

To date, X-ray spectroscopy has become a routine tool that can reveal highly local and element-specific information on the electronic structure of atoms in complex environments. Here, we report on the development of an efficient and versatile theoretical methodology for the treatment of soft X-ray spectra of transition metal compounds based on the multi-configurational self-consistent field electronic structure theory. A special focus is put on the L-edge photon-in/photon-out and photon-in/electron-out processes, i.e. X-ray absorption, resonant inelastic scattering, partial fluorescence yield, and photoelectron spectroscopy, all treated on the same theoretical footing. The investigated systems range from small prototypical coordination compounds and catalysts to aggregates of biomolecules.

Lithium: a versatile tool for understanding renal physiology

PubMed Central

Ecelbarger, Carolyn M.

2013-01-01

By virtue of its unique interactions with kidney cells, lithium became an important research tool in renal physiology and pathophysiology. Investigators have uncovered the intricate relationships of lithium with the vasopressin and aldosterone systems, and the membrane channels or transporters regulated by them. While doing so, their work has also led to 1) questioning the role of adenylyl cyclase activity and prostaglandins in lithium-induced suppression of aquaporin-2 gene transcription; 2) unraveling the role of purinergic signaling in lithium-induced polyuria; and 3) highlighting the importance of the epithelial sodium channel (ENaC) in lithium-induced nephrogenic diabetes insipidus (NDI). Lithium-induced remodeling of the collecting duct has the potential to shed new light on collecting duct remodeling in disease conditions, such as diabetes insipidus. The finding that lithium inhibits glycogen synthase kinase-3β (GSK3β) has opened an avenue for studies on the role of GSK3β in urinary concentration, and GSK isoforms in renal development. Finally, proteomic and metabolomic profiling of the kidney and urine in rats treated with lithium is providing insights into how the kidney adapts its metabolism in conditions such as acquired NDI and the multifactorial nature of lithium-induced NDI. This review provides state-of-the-art knowledge of lithium as a versatile tool for understanding the molecular physiology of the kidney, and a comprehensive view of how this tool is challenging some of our long-standing concepts in renal physiology, often with paradigm shifts, and presenting paradoxical situations in renal pathophysiology. In addition, this review points to future directions in research where lithium can lead the renal community. PMID:23408166

Nanoporous hard data: optical encoding of information within nanoporous anodic alumina photonic crystals

NASA Astrophysics Data System (ADS)

Santos, Abel; Law, Cheryl Suwen; Pereira, Taj; Losic, Dusan

2016-04-01

Herein, we present a method for storing binary data within the spectral signature of nanoporous anodic alumina photonic crystals. A rationally designed multi-sinusoidal anodisation approach makes it possible to engineer the photonic stop band of nanoporous anodic alumina with precision. As a result, the transmission spectrum of these photonic nanostructures can be engineered to feature well-resolved and selectively positioned characteristic peaks across the UV-visible spectrum. Using this property, we implement an 8-bit binary code and assess the versatility and capability of this system by a series of experiments aiming to encode different information within the nanoporous anodic alumina photonic crystals. The obtained results reveal that the proposed nanosized platform is robust, chemically stable, versatile and has a set of unique properties for data storage, opening new opportunities for developing advanced nanophotonic tools for a wide range of applications, including sensing, photonic tagging, self-reporting drug releasing systems and secure encoding of information.Herein, we present a method for storing binary data within the spectral signature of nanoporous anodic alumina photonic crystals. A rationally designed multi-sinusoidal anodisation approach makes it possible to engineer the photonic stop band of nanoporous anodic alumina with precision. As a result, the transmission spectrum of these photonic nanostructures can be engineered to feature well-resolved and selectively positioned characteristic peaks across the UV-visible spectrum. Using this property, we implement an 8-bit binary code and assess the versatility and capability of this system by a series of experiments aiming to encode different information within the nanoporous anodic alumina photonic crystals. The obtained results reveal that the proposed nanosized platform is robust, chemically stable, versatile and has a set of unique properties for data storage, opening new opportunities for developing advanced nanophotonic tools for a wide range of applications, including sensing, photonic tagging, self-reporting drug releasing systems and secure encoding of information. Electronic supplementary information (ESI) available: Further details about anodisation profiles, SEM cross-section images, digital pictures, transmission spectra, photonic barcodes and ASCII codes of the different NAA photonic crystals fabricated and analysed in our study. See DOI: 10.1039/c6nr01068g

Radiesse: Advanced Techniques and Applications for a Unique and Versatile Implant.

PubMed

Eviatar, Joseph; Lo, Christopher; Kirszrot, James

2015-11-01

Radiesse is a well-tolerated facial injectable with unique filling and lifting capabilities. Although initially approved for facial volumizing in HIV-related lipodystrophy patients, it quickly gained wide acceptance for aesthetic facial rejuvenation. In the USA, the Food and Drug Administration has approved several new indications for its use. This synopsis presents the experience and injection techniques currently favored by the primary author after many years of use in thousands of patients. The anecdotal practice of an experienced injector is presented along with the current Food and Drug Administration-approved standards of Radiesse injection. Radiesse has many on- and off-label applications that can be thoughtfully incorporated into clinical practice. Its unique chemical composition allows for immediate lifting and filling with long-term collagen stimulation. The product can be reconstituted to increase its versatility and minimize adverse events. Injections can be performed in the supraperiosteal space and the subcutaneous layer and are best administered in small, calculated doses to prevent nodules or vascular occlusion. Various techniques for Radiesse injection in specific areas are discussed in detail. Radiesse is a versatile injectable implant and a valuable tool for short- and long-term cosmetic and reconstructive treatments. In addition to various off-label uses, this injectable is often used in conjunction with botox, other injectables, collagen stimulators and tightening devices. A customized reconstitution of product increases its versatility for natural appearing and long lasting results that are both economical and effective for full facial rejuvenation.

Issues around Creating a Reusable Learning Object to Support Statistics Teaching

ERIC Educational Resources Information Center

Gilchrist, Mollie

2007-01-01

Although our health professional students have some experience of simple charts, such as pie and bar, and some intuition of histograms, they do not appear to have much knowledge or understanding about box and whisker plots and their relation to the data they are describing or compared to histograms. The boxplot is a versatile charting tool, useful…

Laser And Microwave Induced Breakdown Spectroscopy: Basis for a New Detection Technique for Chemical and Biological Agents

DTIC Science & Technology

2001-06-01

Chem. , vol. 72, pp. 721A-776A, 2000. [2] V. Majidi and M. R. Joseph, “Spectroscopic applications of laser-induced plasmas,” Crit. Rev. Analyt...Chem., vol. 23, pp. 143-162, 1992. [3] V. Majidi , “Laser-induced plasmas: A versatile tool for chemical analysis,” Spectroscopy, vol. 8, pp. 16-24

Miniemulsion polymerization as a versatile tool for the synthesis of functionalized polymers

PubMed Central

Crespy, Daniel

2010-01-01

Summary The miniemulsion technique is a particular case in the family of heterophase polymerizations, which allows the formation of functionalized polymers by polymerization or modification of polymers in stable nanodroplets. We present here an overview of the different polymer syntheses within the miniemulsion droplets as reported in the literature, and of the current trends in the field. PMID:21160567

ETHNOS: A versatile electronic tool for the development and curation of national genetic databases

PubMed Central

2010-01-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation. PMID:20650823

ETHNOS : A versatile electronic tool for the development and curation of national genetic databases.

PubMed

van Baal, Sjozef; Zlotogora, Joël; Lagoumintzis, George; Gkantouna, Vassiliki; Tzimas, Ioannis; Poulas, Konstantinos; Tsakalidis, Athanassios; Romeo, Giovanni; Patrinos, George P

2010-06-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation.

MoKey: A versatile exergame creator for everyday usage.

PubMed

Eckert, Martina; López, Marcos; Lázaro, Carlos; Meneses, Juan

2017-11-27

Currently, virtual applications for physical exercises are highly appreciated as rehabilitation instruments. This article presents a middleware called "MoKey" (Motion Keyboard), which converts standard off-the-shelf software into exergames (exercise games). A configurable set of gestures, captured by a motion capture camera, is translated into the key strokes required by the chosen software. The present study assesses the tool regarding usability and viability on a heterogeneous group of 11 participants, aged 5 to 51, with moderate to severe disabilities, and mostly bound to a wheelchair. In comparison with FAAST (The Flexible Action and Articulated Skeleton Toolkit), MoKey achieved better results in terms of ease of use and computational load. The viability as an exergame creator tool was proven with help of four applications (PowerPoint®, e-book reader, Skype®, and Tetris). Success rates of up to 91% have been achieved, subjective perception was rated with 4.5 points (from 0-5). The middleware provides increased motivation due to the use of favorite software and the advantage of exploiting it for exercise. Used together with communication software or online games, social inclusion can be stimulated. The therapists can employ the tool to monitor the correctness and progress of the exercises.

DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration.

PubMed

Dryden, Michael D M; Wheeler, Aaron R

2015-01-01

Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as "black boxes," giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat's voltammetric measurements are much more sensitive than those of "CheapStat" (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial "black box" potentiostat. Likewise, in head-to-head tests, DStat's potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the "open source" movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools.

DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration

PubMed Central

Dryden, Michael D. M.; Wheeler, Aaron R.

2015-01-01

Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as “black boxes,” giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat’s voltammetric measurements are much more sensitive than those of “CheapStat” (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial “black box” potentiostat. Likewise, in head-to-head tests, DStat’s potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the “open source” movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools. PMID:26510100

High Efficiency Variable Speed Versatile Power Air Conditioning System for Military Vehicles

DTIC Science & Technology

2013-08-01

MOBILITY (P&M) MINI-SYMPOSIUM AUGUST 21-22, 2013 - TROY , MICHIGAN High efficiency variable speed versatile power air conditioning system for...power draw was measured using a calibrated Watt meter. The schematic of the setup is shown in Figure 5 and the setup is shown in Figure 6. Figure...Rocky Research environmental chamber. Cooling Capacity was directly measured in Btu/hr or Watts via measuring the Air flow velocity and the air

ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants.

PubMed

Klaften, Matthias; Hrabé de Angelis, Martin

2005-07-01

Genome-wide mapping in the identification of novel candidate genes has always been the standard method in genetics and genomics to correlate a clinically interesting phenotypic trait with a genotype. However, the performance of a mapping experiment using classical microsatellite approaches can be very time consuming. The high-throughput analysis of single-nucleotide polymorphisms (SNPs) has the potential of being the successor of microsatellite analysis routinely used for these mapping approaches, where one of the major obstacles is the design of the appropriate SNP marker set itself. Here we report on ARTS, an advanced retrieval tool for SNPs, which allows researchers to comb freely the public mouse dbSNP database for multiple reference and test strains. Several filters can be applied in order to improve the sensitivity and the specificity of the search results. By employing the panel generator function of this program, it is possible to abbreviate the extraction of reliable sequence data for a large marker panel including several different mouse strains from days to minutes. The concept of ARTS is easily adaptable to other species for which SNP databases are available, making it a versatile tool for the use of SNPs as markers for genotyping. The web interface is accessible at http://andromeda.gsf.de/arts.

MIPS: curated databases and comprehensive secondary data resources in 2010.

PubMed

Mewes, H Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F X; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de).

MIPS: curated databases and comprehensive secondary data resources in 2010

PubMed Central

Mewes, H. Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F.X.; Stümpflen, Volker; Antonov, Alexey

2011-01-01

The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38 000 000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de). PMID:21109531

iBodies: Modular Synthetic Antibody Mimetics Based on Hydrophilic Polymers Decorated with Functional Moieties.

PubMed

Šácha, Pavel; Knedlík, Tomáš; Schimer, Jiří; Tykvart, Jan; Parolek, Jan; Navrátil, Václav; Dvořáková, Petra; Sedlák, František; Ulbrich, Karel; Strohalm, Jiří; Majer, Pavel; Šubr, Vladimír; Konvalinka, Jan

2016-02-12

Antibodies are indispensable tools for biomedicine and anticancer therapy. Nevertheless, their use is compromised by high production costs, limited stability, and difficulty of chemical modification. The design and preparation of synthetic polymer conjugates capable of replacing antibodies in biomedical applications such as ELISA, flow cytometry, immunocytochemistry, and immunoprecipitation is reported. The conjugates, named "iBodies", consist of an HPMA copolymer decorated with low-molecular-weight compounds that function as targeting ligands, affinity anchors, and imaging probes. We prepared specific conjugates targeting several proteins with known ligands and used these iBodies for enzyme inhibition, protein isolation, immobilization, quantification, and live-cell imaging. Our data indicate that this highly modular and versatile polymer system can be used to produce inexpensive and stable antibody substitutes directed toward virtually any protein of interest with a known ligand. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

iBodies: Modular Synthetic Antibody Mimetics Based on Hydrophilic Polymers Decorated with Functional Moieties

PubMed Central

Šácha, Pavel; Knedlík, Tomáš; Schimer, Jiří; Tykvart, Jan; Parolek, Jan; Navrátil, Václav; Dvořáková, Petra; Sedlák, František; Ulbrich, Karel; Strohalm, Jiří; Majer, Pavel

2016-01-01

Abstract Antibodies are indispensable tools for biomedicine and anticancer therapy. Nevertheless, their use is compromised by high production costs, limited stability, and difficulty of chemical modification. The design and preparation of synthetic polymer conjugates capable of replacing antibodies in biomedical applications such as ELISA, flow cytometry, immunocytochemistry, and immunoprecipitation is reported. The conjugates, named “iBodies”, consist of an HPMA copolymer decorated with low‐molecular‐weight compounds that function as targeting ligands, affinity anchors, and imaging probes. We prepared specific conjugates targeting several proteins with known ligands and used these iBodies for enzyme inhibition, protein isolation, immobilization, quantification, and live‐cell imaging. Our data indicate that this highly modular and versatile polymer system can be used to produce inexpensive and stable antibody substitutes directed toward virtually any protein of interest with a known ligand. PMID:26749427

Nanostructured poly(benzimidazole): from mesoporous networks to nanofibers.

PubMed

Weber, Jens

2010-02-22

Poly(benzimidazole)s (PBIs) are a class of high-performance polymers which have been receiving increasing interest during the last years due to their high potential as constituents of membrane materials in proton-exchange membrane fuel cells (PEMFCs). In addition to the importance of PBI in fuel-cell technology, there are a number of other applications (e.g., catalysis) that make use of the special properties of this material. The scope of this Minireview is to first give a short overview about the use of nanostructured, mesoporous PBI as a proton conductor. Secondly, the use of spirobifluorene derivatives as new monomers, which allow the synthesis of hierarchically structured PBI, is presented. Limitations of traditional synthetic methods will be discussed, and an ionothermal scheme towards PBI will be presented as a versatile tool for the synthesis of plain and spirobifluorene-based PBIs. Finally, the use of electrospinning as a powerful processing technique for PBI will be presented briefly.

Towards on-chip time-resolved thermal mapping with micro-/nanosensor arrays

PubMed Central

2012-01-01

In recent years, thin-film thermocouple (TFTC) array emerged as a versatile candidate in micro-/nanoscale local temperature sensing for its high resolution, passive working mode, and easy fabrication. However, some key issues need to be taken into consideration before real instrumentation and industrial applications of TFTC array. In this work, we will demonstrate that TFTC array can be highly scalable from micrometers to nanometers and that there are potential applications of TFTC array in integrated circuits, including time-resolvable two-dimensional thermal mapping and tracing the heat source of a device. Some potential problems and relevant solutions from a view of industrial applications will be discussed in terms of material selection, multiplexer reading, pattern designing, and cold-junction compensation. We show that the TFTC array is a powerful tool for research fields such as chip thermal management, lab-on-a-chip, and other novel electrical, optical, or thermal devices. PMID:22931306

CRISPR/Cas9 Based Genome Editing of Penicillium chrysogenum.

PubMed

Pohl, C; Kiel, J A K W; Driessen, A J M; Bovenberg, R A L; Nygård, Y

2016-07-15

CRISPR/Cas9 based systems have emerged as versatile platforms for precision genome editing in a wide range of organisms. Here we have developed powerful CRISPR/Cas9 tools for marker-based and marker-free genome modifications in Penicillium chrysogenum, a model filamentous fungus and industrially relevant cell factory. The developed CRISPR/Cas9 toolbox is highly flexible and allows editing of new targets with minimal cloning efforts. The Cas9 protein and the sgRNA can be either delivered during transformation, as preassembled CRISPR-Cas9 ribonucleoproteins (RNPs) or expressed from an AMA1 based plasmid within the cell. The direct delivery of the Cas9 protein with in vitro synthesized sgRNA to the cells allows for a transient method for genome engineering that may rapidly be applicable for other filamentous fungi. The expression of Cas9 from an AMA1 based vector was shown to be highly efficient for marker-free gene deletions.

Atomic force microscopy and spectroscopy to probe single membrane proteins in lipid bilayers.

PubMed

Sapra, K Tanuj

2013-01-01

The atomic force microscope (AFM) has opened vast avenues hitherto inaccessible to the biological scientist. The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever stylus is aptly termed as a "lab on a tip" owing to its versatility as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples assert that the AFM can be used to study the mechanical properties and monitor processes of single proteins and single cells, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of membrane proteins. Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theoretical, and practical skills.

Long distance measurement with a femtosecond laser based frequency comb

NASA Astrophysics Data System (ADS)

Bhattacharya, N.; Cui, M.; Zeitouny, M. G.; Urbach, H. P.; van den Berg, S. A.

2017-11-01

Recent advances in the field of ultra-short pulse lasers have led to the development of reliable sources of carrier envelope phase stabilized femtosecond pulses. The pulse train generated by such a source has a frequency spectrum that consists of discrete, regularly spaced lines known as a frequency comb. In this case both the frequency repetition and the carrier-envelope-offset frequency are referenced to a frequency standard, like an atomic clock. As a result the accuracy of the frequency standard is transferred to the optical domain, with the frequency comb as transfer oscillator. These unique properties allow the frequency comb to be applied as a versatile tool, not only for time and frequency metrology, but also in fundamental physics, high-precision spectroscopy, and laser noise characterization. The pulse-to-pulse phase relationship of the light emitted by the frequency comb has opened up new directions for long range highly accurate distance measurement.

3D-Printed Graphene/Polylactic Acid Electrodes Promise High Sensitivity in Electroanalysis.

PubMed

Manzanares Palenzuela, C Lorena; Novotný, Filip; Krupička, Petr; Sofer, Zdeněk; Pumera, Martin

2018-05-01

Additive manufacturing provides a unique tool for prototyping structures toward electrochemical sensing, due to its ability to produce highly versatile, tailored-shaped devices in a low-cost and fast way with minimized waste. Here we present 3D-printed graphene electrodes for electrochemical sensing. Ring- and disc-shaped electrodes were 3D-printed with a Fused Deposition Modeling printer and characterized using cyclic voltammetry and scanning electron microscopy. Different redox probes K 3 Fe(CN) 6 :K 4 Fe(CN) 6 , FeCl 3 , ascorbic acid, Ru(NH 3 ) 6 Cl 3 , and ferrocene monocarboxylic acid) were used to assess the electrochemical performance of these devices. Finally, the electrochemical detection of picric acid and ascorbic acid was carried out as proof-of-concept analytes for sensing applications. Such customizable platforms represent promising alternatives to conventional electrodes for a wide range of sensing applications.

Advances in LEDs for automotive applications

NASA Astrophysics Data System (ADS)

Bhardwaj, Jy; Peddada, Rao; Spinger, Benno

2016-03-01

High power LEDs were introduced in automotive headlights in 2006-2007, for example as full LED headlights in the Audi R8 or low beam in Lexus. Since then, LED headlighting has become established in premium and volume automotive segments and beginning to enable new compact form factors such as distributed low beam and new functions such as adaptive driving beam. New generations of highly versatile high power LEDs are emerging to meet these application needs. In this paper, we will detail ongoing advances in LED technology that enable revolutionary styling, performance and adaptive control in automotive headlights. As the standards which govern the necessary lumens on the road are well established, increasing luminance enables not only more design freedom but also headlight cost reduction with space and weight saving through more compact optics. Adaptive headlighting is based on LED pixelation and requires high contrast, high luminance, smaller LEDs with high-packing density for pixelated Matrix Lighting sources. Matrix applications require an extremely tight tolerance on not only the X, Y placement accuracy, but also on the Z height of the LEDs given the precision optics used to image the LEDs onto the road. A new generation of chip scale packaged (CSP) LEDs based on Wafer Level Packaging (WLP) have been developed to meet these needs, offering a form factor less than 20% increase over the LED emitter surface footprint. These miniature LEDs are surface mount devices compatible with automated tools for L2 board direct attach (without the need for an interposer or L1 substrate), meeting the high position accuracy as well as the optical and thermal performance. To illustrate the versatility of the CSP LEDs, we will show the results of, firstly, a reflector-based distributed low beam using multiple individual cavities each with only 20mm height and secondly 3x4 to 3x28 Matrix arrays for adaptive full beam. Also a few key trends in rear lighting and impact on LED light source technology are discussed.

Simulation of magnetic active polymers for versatile microfluidic devices

NASA Astrophysics Data System (ADS)

Gusenbauer, Markus; Özelt, Harald; Fischbacher, Johann; Reichel, Franz; Exl, Lukas; Bance, Simon; Kataeva, Nadezhda; Binder, Claudia; Brückl, Hubert; Schrefl, Thomas

2013-01-01

We propose to use a compound of magnetic nanoparticles (20-100 nm) embedded in a flexible polymer (Polydimethylsiloxane PDMS) to filter circulating tumor cells (CTCs). The analysis of CTCs is an emerging tool for cancer biology research and clinical cancer management including the detection, diagnosis and monitoring of cancer. The combination of experiments and simulations lead to a versatile microfluidic lab-on-chip device. Simulations are essential to understand the influence of the embedded nanoparticles in the elastic PDMS when applying a magnetic gradient field. It combines finite element calculations of the polymer, magnetic simulations of the embedded nanoparticles and the fluid dynamic calculations of blood plasma and blood cells. With the use of magnetic active polymers a wide range of tunable microfluidic structures can be created. The method can help to increase the yield of needed isolated CTCs.

Manipulating waves with LEGO{sup ®} bricks: A versatile experimental platform for metamaterial architectures

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

Celli, Paolo, E-mail: pcelli@umn.edu; Gonella, Stefano, E-mail: sgonella@umn.edu

2015-08-24

In this letter, we discuss a versatile, fully reconfigurable experimental platform for the investigation of phononic phenomena in metamaterial architectures. The approach revolves around the use of 3D laser vibrometry to reconstruct global and local wavefield features in specimens obtained through simple arrangements of LEGO{sup ®} bricks on a thin baseplate. The agility by which it is possible to reconfigure the brick patterns into a nearly endless spectrum of topologies makes this an effective approach for rapid experimental proof of concept, as well as a powerful didactic tool, in the arena of phononic crystals and metamaterials engineering. We use ourmore » platform to provide a compelling visual illustration of important spatial wave manipulation effects (waveguiding and seismic isolation), and to elucidate fundamental dichotomies between Bragg-based and locally resonant bandgap mechanisms.« less

Modular magnetic tweezers for single-molecule characterizations of helicases.

PubMed

Kemmerich, Felix E; Kasaciunaite, Kristina; Seidel, Ralf

2016-10-01

Magnetic tweezers provide a versatile toolkit supporting the mechanistic investigation of helicases. In the present article, we show that custom magnetic tweezers setups are straightforward to construct and can easily be extended to provide adaptable platforms, capable of addressing a multitude of enquiries regarding the functions of these fascinating molecular machines. We first address the fundamental components of a basic magnetic tweezers scheme and review some previous results to demonstrate the versatility of this instrument. We then elaborate on several extensions to the basic magnetic tweezers scheme, and demonstrate their applications with data from ongoing research. As our methodological overview illustrates, magnetic tweezers are an extremely useful tool for the characterization of helicases and a custom built instrument can be specifically tailored to suit the experimenter's needs. Copyright © 2016 Elsevier Inc. All rights reserved.

Peptide-mediated vectorization of metal complexes: conjugation strategies and biomedical applications.

PubMed

Soler, Marta; Feliu, Lidia; Planas, Marta; Ribas, Xavi; Costas, Miquel

2016-08-16

The rich chemical and structural versatility of transition metal complexes provides numerous novel paths to be pursued in the design of molecules that exert particular chemical or physicochemical effects that could operate over specific biological targets. However, the poor cell permeability of metallodrugs represents an important barrier for their therapeutic use. The conjugation between metal complexes and a functional peptide vector can be regarded as a versatile and potential strategy to improve their bioavailability and accumulation inside cells, and the site selectivity of their effect. This perspective lies in reviewing the recent advances in the design of metallopeptide conjugates for biomedical applications. Additionally, we highlight the studies where this approach has been directed towards the incorporation of redox active metal centers into living organisms for modulating the cellular redox balance, as a tool with application in anticancer therapy.

A low-cost and versatile system for projecting wide-field visual stimuli within fMRI scanners

PubMed Central

Greco, V.; Frijia, F.; Mikellidou, K.; Montanaro, D.; Farini, A.; D’Uva, M.; Poggi, P.; Pucci, M.; Sordini, A.; Morrone, M. C.; Burr, D. C.

2016-01-01

We have constructed and tested a custom-made magnetic-imaging-compatible visual projection system designed to project on a very wide visual field (~80°). A standard projector was modified with a coupling lens, projecting images into the termination of an image fiber. The other termination of the fiber was placed in the 3-T scanner room with a projection lens, which projected the images relayed by the fiber onto a screen over the head coil, viewed by a participant wearing magnifying goggles. To validate the system, wide-field stimuli were presented in order to identify retinotopic visual areas. The results showed that this low-cost and versatile optical system may be a valuable tool to map visual areas in the brain that process peripheral receptive fields. PMID:26092392

Numerical model of tapered fiber Bragg gratings for comprehensive analysis and optimization of their sensing and strain-induced tunable dispersion properties.

PubMed

Osuch, Tomasz; Markowski, Konrad; Jędrzejewski, Kazimierz

2015-06-10

A versatile numerical model for spectral transmission/reflection, group delay characteristic analysis, and design of tapered fiber Bragg gratings (TFBGs) is presented. This approach ensures flexibility with defining both distribution of refractive index change of the gratings (including apodization) and shape of the taper profile. Additionally, sensing and tunable dispersion properties of the TFBGs were fully examined, considering strain-induced effects. The presented numerical approach, together with Pareto optimization, were also used to design the best tanh apodization profiles of the TFBG in terms of maximizing its spectral width with simultaneous minimization of the group delay oscillations. Experimental verification of the model confirms its correctness. The combination of model versatility and possibility to define the other objective functions of Pareto optimization creates a universal tool for TFBG analysis and design.

IgSimulator: a versatile immunosequencing simulator.

PubMed

Safonova, Yana; Lapidus, Alla; Lill, Jennie

2015-10-01

The recent introduction of next-generation sequencing technologies to antibody studies have resulted in a growing number of immunoinformatics tools for antibody repertoire analysis. However, benchmarking these newly emerging tools remains problematic since the gold standard datasets that are needed to validate these tools are typically not available. Since simulating antibody repertoires is often the only feasible way to benchmark new immunoinformatics tools, we developed the IgSimulator tool that addresses various complications in generating realistic antibody repertoires. IgSimulator's code has modular structure and can be easily adapted to new requirements to simulation. IgSimulator is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from yana-safonova.github.io/ig_simulator. safonova.yana@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

PubMed Central

Prigent, Sylvain; Frioux, Clémence; Dittami, Simon M.; Larhlimi, Abdelhalim; Collet, Guillaume; Gutknecht, Fabien; Got, Jeanne; Eveillard, Damien; Bourdon, Jérémie; Plewniak, Frédéric; Tonon, Thierry; Siegel, Anne

2017-01-01

Increasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system. PMID:28129330

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks.

PubMed

Prigent, Sylvain; Frioux, Clémence; Dittami, Simon M; Thiele, Sven; Larhlimi, Abdelhalim; Collet, Guillaume; Gutknecht, Fabien; Got, Jeanne; Eveillard, Damien; Bourdon, Jérémie; Plewniak, Frédéric; Tonon, Thierry; Siegel, Anne

2017-01-01

Increasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system.

3D Chemical Patterning of Micromaterials for Encoded Functionality.

PubMed

Ceylan, Hakan; Yasa, Immihan Ceren; Sitti, Metin

2017-03-01

Programming local chemical properties of microscale soft materials with 3D complex shapes is indispensable for creating sophisticated functionalities, which has not yet been possible with existing methods. Precise spatiotemporal control of two-photon crosslinking is employed as an enabling tool for 3D patterning of microprinted structures for encoding versatile chemical moieties. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exploring the Reasons for Using Electric Books and Technologic Pedagogical and Content Knowledge of Taiwanese Elementary Mathematics and Science Teachers

ERIC Educational Resources Information Center

Chen, Ho-Yuan; Jang, Syh-Jong

2013-01-01

This study highlights trends and features of E-books and their versatility of this tool in elementary educational settings. There has been little quantitative research employed to examine teachers' reasons for using or not using E-books. The purpose of this study was to examine elementary school mathematics and science teachers' reasons for using…

Finding the Effective Mass and Spring Constant of a Force Probe from Simple Harmonic Motion

ERIC Educational Resources Information Center

Greene, Nathaniel R.; Gill, Tom; Eyerly, Stephen

2016-01-01

Force probes are versatile tools in the physics lab, but their internal workings can introduce artifacts when measuring rapidly changing forces. The Dual-Range Force Sensor by Vernier uses strain gage technology to measure force, based on the bending of a beam. Strain gages along the length of the beam change resistance as the beam bends. The…

A versatile Escherichia coli strain for identification of biotin transporters and for biotin quantification

PubMed Central

Finkenwirth, Friedrich; Kirsch, Franziska; Eitinger, Thomas

2014-01-01

Biotin is an essential cofactor of carboxylase enzymes in all kingdoms of life. The vitamin is produced by many prokaryotes, certain fungi, and plants. Animals depend on biotin uptake from their diet and in humans lack of the vitamin is associated with serious disorders. Many aspects of biotin metabolism, uptake, and intracellular transport remain to be elucidated. In order to characterize the activity of novel biotin transporters by a sensitive assay, an Escherichia coli strain lacking both biotin synthesis and its endogenous high-affinity biotin importer was constructed. This strain requires artificially high biotin concentrations for growth. When only trace levels of biotin are available, it is viable only if equipped with a heterologous high-affinity biotin transporter. This feature was used to ascribe transport activity to members of the BioY protein family in previous work. Here we show that this strain together with its parent is also useful as a diagnostic tool for wide-concentration-range bioassays. PMID:24256712

MALDI mass spectrometry imaging, from its origins up to today: the state of the art.

PubMed

Francese, Simona; Dani, Francesca R; Traldi, Pietro; Mastrobuoni, Guido; Pieraccini, Giuseppe; Moneti, Gloriano

2009-02-01

Mass Spectrometry (MS) has a number of features namely sensitivity, high dynamic range, high resolution, and versatility which make it a very powerful analytical tool for a wide spectrum of applications spanning all the life science fields. Among all the MS techniques, MALDI Imaging mass spectrometry (MALDI MSI) is currently one of the most exciting both for its rapid technological improvements, and for its great potential in high impact bioscience fields. Here, MALDI MSI general principles are described along with technical and instrumental details as well as application examples. Imaging MS instruments and imaging mass spectrometric techniques other than MALDI, are presented along with examples of their use. As well as reporting MSI successes in several bioscience fields, an attempt is made to take stock of what has been achieved so far with this technology and to discuss the analytical and technological advances required for MSI to be applied as a routine technique in clinical diagnostics, clinical monitoring and in drug discovery.

Under the Microscope: Single-Domain Antibodies for Live-Cell Imaging and Super-Resolution Microscopy.

PubMed

Traenkle, Bjoern; Rothbauer, Ulrich

2017-01-01

Single-domain antibodies (sdAbs) have substantially expanded the possibilities of advanced cellular imaging such as live-cell or super-resolution microscopy to visualize cellular antigens and their dynamics. In addition to their unique properties including small size, high stability, and solubility in many environments, sdAbs can be efficiently functionalized according to the needs of the respective imaging approach. Genetically encoded intrabodies fused to fluorescent proteins (chromobodies) have become versatile tools to study dynamics of endogenous proteins in living cells. Additionally, sdAbs conjugated to organic dyes were shown to label cellular structures with high density and minimal fluorophore displacement making them highly attractive probes for super-resolution microscopy. Here, we review recent advances of the chromobody technology to visualize localization and dynamics of cellular targets and the application of chromobody-based cell models for compound screening. Acknowledging the emerging importance of super-resolution microscopy in cell biology, we further discuss advantages and challenges of sdAbs for this technology.

Constructing, connecting and soldering nanostructures by environmental electron beam deposition

NASA Astrophysics Data System (ADS)

Mølhave, Kristian; Nørgaard Madsen, Dorte; Dohn, Søren; Bøggild, Peter

2004-08-01

Highly conductive nanoscale deposits with solid gold cores can be made by electron beam deposition in an environmental scanning electron microscope (ESEM), suggesting the method to be used for constructing, connecting and soldering nanostructures. This paper presents a feasibility study for such applications. We identify several issues related to contamination and unwanted deposition, relevant for deposition in both vacuum (EBD) and environmental conditions (EEBD). We study relations between scan rate, deposition rate, angle and line width for three-dimensional structures. Furthermore, we measure the conductivity of deposits containing gold cores, and find these structures to be highly conductive, approaching the conductivity of solid gold and capable of carrying high current densities. Finally, we study the use of the technique for soldering nanostructures such as carbon nanotubes. Based on the presented results we are able to estimate limits for the applicability of the method for the various applications, but also demonstrate that it is a versatile and powerful tool for nanotechnology within these limits.

A Highly Specific Gold Nanoprobe for Live-Cell Single-Molecule Imaging

NASA Astrophysics Data System (ADS)

Leduc, Cécile; Si, Satyabrata; Gautier, Jérémie; Soto-Ribeiro, Martinho; Wehrle-Haller, Bernhard; Gautreau, Alexis; Giannone, Grégory; Cognet, Laurent; Lounis, Brahim

2013-04-01

Single molecule tracking in live cells is the ultimate tool to study subcellular protein dynamics, but it is often limited by the probe size and photostability. Due to these issues, long-term tracking of proteins in confined and crowded environments, such as intracellular spaces, remains challenging. We have developed a novel optical probe consisting of 5-nm gold nanoparticles functionalized with a small fragment of camelid antibodies that recognize widely used GFPs with a very high affinity, which we call GFP-nanobodies. These small gold nanoparticles can be detected and tracked using photothermal imaging for arbitrarily long periods of time. Surface and intracellular GFP-proteins were effectively labeled even in very crowded environments such as adhesion sites and cytoskeletal structures both in vitro and in live cell cultures. These nanobody-coated gold nanoparticles are probes with unparalleled capabilities; small size, perfect photostability, high specificity, and versatility afforded by combination with the vast existing library of GFP-tagged proteins.

SiC-Based Schottky Diode Gas Sensors

NASA Technical Reports Server (NTRS)

Hunter, Gary W.; Neudeck, Philip G.; Chen, Liang-Yu; Knight, Dak; Liu, Chung-Chiun; Wu, Quing-Hai

1997-01-01

Silicon carbide based Schottky diode gas sensors are being developed for high temperature applications such as emission measurements. Two different types of gas sensitive diodes will be discussed in this paper. By varying the structure of the diode, one can affect the diode stability as well as the diode sensitivity to various gases. It is concluded that the ability of SiC to operate as a high temperature semiconductor significantly enhances the versatility of the Schottky diode gas sensing structure and will potentially allow the fabrication of a SiC-based gas sensor arrays for versatile high temperature gas sensing applications.

VAC: Versatile Advection Code

NASA Astrophysics Data System (ADS)

Tóth, Gábor; Keppens, Rony

2012-07-01

The Versatile Advection Code (VAC) is a freely available general hydrodynamic and magnetohydrodynamic simulation software that works in 1, 2 or 3 dimensions on Cartesian and logically Cartesian grids. VAC runs on any Unix/Linux system with a Fortran 90 (or 77) compiler and Perl interpreter. VAC can run on parallel machines using either the Message Passing Interface (MPI) library or a High Performance Fortran (HPF) compiler.

Machine learning for neuroimaging with scikit-learn.

PubMed

Abraham, Alexandre; Pedregosa, Fabian; Eickenberg, Michael; Gervais, Philippe; Mueller, Andreas; Kossaifi, Jean; Gramfort, Alexandre; Thirion, Bertrand; Varoquaux, Gaël

2014-01-01

Statistical machine learning methods are increasingly used for neuroimaging data analysis. Their main virtue is their ability to model high-dimensional datasets, e.g., multivariate analysis of activation images or resting-state time series. Supervised learning is typically used in decoding or encoding settings to relate brain images to behavioral or clinical observations, while unsupervised learning can uncover hidden structures in sets of images (e.g., resting state functional MRI) or find sub-populations in large cohorts. By considering different functional neuroimaging applications, we illustrate how scikit-learn, a Python machine learning library, can be used to perform some key analysis steps. Scikit-learn contains a very large set of statistical learning algorithms, both supervised and unsupervised, and its application to neuroimaging data provides a versatile tool to study the brain.

Machine learning for neuroimaging with scikit-learn

PubMed Central

Abraham, Alexandre; Pedregosa, Fabian; Eickenberg, Michael; Gervais, Philippe; Mueller, Andreas; Kossaifi, Jean; Gramfort, Alexandre; Thirion, Bertrand; Varoquaux, Gaël

2014-01-01

Statistical machine learning methods are increasingly used for neuroimaging data analysis. Their main virtue is their ability to model high-dimensional datasets, e.g., multivariate analysis of activation images or resting-state time series. Supervised learning is typically used in decoding or encoding settings to relate brain images to behavioral or clinical observations, while unsupervised learning can uncover hidden structures in sets of images (e.g., resting state functional MRI) or find sub-populations in large cohorts. By considering different functional neuroimaging applications, we illustrate how scikit-learn, a Python machine learning library, can be used to perform some key analysis steps. Scikit-learn contains a very large set of statistical learning algorithms, both supervised and unsupervised, and its application to neuroimaging data provides a versatile tool to study the brain. PMID:24600388

Overview of artificial neural networks.

PubMed

Zou, Jinming; Han, Yi; So, Sung-Sau

2008-01-01

The artificial neural network (ANN), or simply neural network, is a machine learning method evolved from the idea of simulating the human brain. The data explosion in modem drug discovery research requires sophisticated analysis methods to uncover the hidden causal relationships between single or multiple responses and a large set of properties. The ANN is one of many versatile tools to meet the demand in drug discovery modeling. Compared to a traditional regression approach, the ANN is capable of modeling complex nonlinear relationships. The ANN also has excellent fault tolerance and is fast and highly scalable with parallel processing. This chapter introduces the background of ANN development and outlines the basic concepts crucially important for understanding more sophisticated ANN. Several commonly used learning methods and network setups are discussed briefly at the end of the chapter.

Transitions between superstatistical regimes: Validity, breakdown and applications

NASA Astrophysics Data System (ADS)

Jizba, Petr; Korbel, Jan; Lavička, Hynek; Prokš, Martin; Svoboda, Václav; Beck, Christian

2018-03-01

Superstatistics is a widely employed tool of non-equilibrium statistical physics which plays an important rôle in analysis of hierarchical complex dynamical systems. Yet, its "canonical" formulation in terms of a single nuisance parameter is often too restrictive when applied to complex empirical data. Here we show that a multi-scale generalization of the superstatistics paradigm is more versatile, allowing to address such pertinent issues as transmutation of statistics or inter-scale stochastic behavior. To put some flesh on the bare bones, we provide a numerical evidence for a transition between two superstatistics regimes, by analyzing high-frequency (minute-tick) data for share-price returns of seven selected companies. Salient issues, such as breakdown of superstatistics in fractional diffusion processes or connection with Brownian subordination are also briefly discussed.

Atlas of susceptibility to pollution in marinas. Application to the Spanish coast.

PubMed

Gómez, Aina G; Ondiviela, Bárbara; Fernández, María; Juanes, José A

2017-01-15

An atlas of susceptibility to pollution of 320 Spanish marinas is provided. Susceptibility is assessed through a simple, fast and low cost empirical method estimating the flushing capacity of marinas. The Complexity Tidal Range Index (CTRI) was selected among eleven empirical methods. The CTRI method was selected by means of statistical analyses because: it contributes to explain the system's variance; it is highly correlated to numerical model results; and, it is sensitive to marinas' location and typology. The process of implementation to the Spanish coast confirmed its usefulness, versatility and adaptability as a tool for the environmental management of marinas worldwide. The atlas of susceptibility, assessed through CTRI values, is an appropriate instrument to prioritize environmental and planning strategies at a regional scale. Copyright © 2016 Elsevier Ltd. All rights reserved.

Superresolution microscopy with transient binding.

PubMed

Molle, Julia; Raab, Mario; Holzmeister, Susanne; Schmitt-Monreal, Daniel; Grohmann, Dina; He, Zhike; Tinnefeld, Philip

2016-06-01

For single-molecule localization based superresolution, the concentration of fluorescent labels has to be thinned out. This is commonly achieved by photophysically or photochemically deactivating subsets of molecules. Alternatively, apparent switching of molecules can be achieved by transient binding of fluorescent labels. Here, a diffusing dye yields bright fluorescent spots when binding to the structure of interest. As the binding interaction is weak, the labeling is reversible and the dye ligand construct diffuses back into solution. This approach of achieving superresolution by transient binding (STB) is reviewed in this manuscript. Different realizations of STB are discussed and compared to other localization-based superresolution modalities. We propose the development of labeling strategies that will make STB a highly versatile tool for superresolution microscopy at highest resolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array.

PubMed

Devault, Alison M; McLoughlin, Kevin; Jaing, Crystal; Gardner, Shea; Porter, Teresita M; Enk, Jacob M; Thissen, James; Allen, Jonathan; Borucki, Monica; DeWitte, Sharon N; Dhody, Anna N; Poinar, Hendrik N

2014-03-06

Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering a rapid, affordable, and highly informative snapshot of microbial diversity in complex samples without the lengthy analysis and/or high cost associated with high-throughput sequencing. Their versatility is well established for modern clinical specimens, but they have yet to be applied to ancient remains. Here we report bacterial profiles of archaeological and historical human remains using the Lawrence Livermore Microbial Detection Array (LLMDA). The array successfully identified previously-verified bacterial human pathogens, including Vibrio cholerae (cholera) in a 19th century intestinal specimen and Yersinia pestis ("Black Death" plague) in a medieval tooth, which represented only minute fractions (0.03% and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA content. This demonstrates that the LLMDA can identify primary and/or co-infecting bacterial pathogens in ancient samples, thereby serving as a rapid and inexpensive paleopathological screening tool to study health across both space and time.

Development of a versatile tool for the simultaneous differential detection of Pseudomonas savastanoi pathovars by End Point and Real-Time PCR

PubMed Central

2010-01-01

Background Pseudomonas savastanoi pv. savastanoi is the causal agent of olive knot disease. The strains isolated from oleander and ash belong to the pathovars nerii and fraxini, respectively. When artificially inoculated, pv. savastanoi causes disease also on ash, and pv. nerii attacks also olive and ash. Surprisingly nothing is known yet about their distribution in nature on these hosts and if spontaneous cross-infections occur. On the other hand sanitary certification programs for olive plants, also including P. savastanoi, were launched in many countries. The aim of this work was to develop several PCR-based tools for the rapid, simultaneous, differential and quantitative detection of these P. savastanoi pathovars, in multiplex and in planta. Results Specific PCR primers and probes for the pathovars savastanoi, nerii and fraxini of P. savastanoi were designed to be used in End Point and Real-Time PCR, both with SYBR® Green or TaqMan® chemistries. The specificity of all these assays was 100%, as assessed by testing forty-four P. savastanoi strains, belonging to the three pathovars and having different geographical origins. For comparison strains from the pathovars phaseolicola and glycinea of P. savastanoi and bacterial epiphytes from P. savastanoi host plants were also assayed, and all of them tested always negative. The analytical detection limits were about 5 - 0.5 pg of pure genomic DNA and about 102 genome equivalents per reaction. Similar analytical thresholds were achieved in Multiplex Real-Time PCR experiments, even on artificially inoculated olive plants. Conclusions Here for the first time a complex of PCR-based assays were developed for the simultaneous discrimination and detection of P. savastanoi pv. savastanoi, pv. nerii and pv. fraxini. These tests were shown to be highly reliable, pathovar-specific, sensitive, rapid and able to quantify these pathogens, both in multiplex reactions and in vivo. Compared with the other methods already available for P. savastanoi, the identification procedures here reported provide a versatile tool both for epidemiological and ecological studies on these pathovars, and for diagnostic procedures monitoring the asymptomatic presence of P. savastanoi on olive and oleander propagation materials. PMID:20509893

Four chemical trends will shape the next decade's directions in Perfluoroalkyl and Polyfluoroalkyl substances research

NASA Astrophysics Data System (ADS)

Kotthoff, Matthias; Bücking, Mark

2018-04-01

Per- and polyfluoroalkyl substances (PFAS) represent a versatile group of ubiquitously occurring chemicals of increasing regulatory concern. The past years lead to an ever expanding portfolio of detected anthropogenic PFAS in numerous products encountered in daily life. Yet no clear picture of the full range of individual substance that comprise PFAS is available and this challenges analytical and engineering sciences. Authorities struggle to cope with uncertainties in managing risk of harm posed by PFAS.This is a result of an incomplete understanding of the range of compounds that they comprise in differing products. There are analytical uncertainties identifying PFAS and estimating the concentrations of the total PFAS loadindividual molecules remain unknown. There are four major trends from the chemical perspective that will shape PFAS research for the next decade. 1.Mobility: A wide and dynamic distribution of short chain PFAS due to their high polarity, persistency and volatility. 2.Substitution of regulated substances: The ban or restrictions of individual molecules will lead to a replacement with substitutes of similar concern. 3.Increase in structural diversity of existing PFAS molecules: Introduction of e.g. hydrogens and chlorine atoms instead of fluorine, as well as branching and cross-linking lead to a high versatility of unknown target molecules. 4. Unknown “Dark Matter”: The amount, identity, formation pathways, and transformation dynamics of polymers and PFAS precursors are largely unknown. These directions require optimized analytical setups, especially multi-methods, and semi-specific tools to determine PFAS-sum parameters in any relevant matrix.

SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis.

PubMed

Aguirre-Gamboa, Raul; Gomez-Rueda, Hugo; Martínez-Ledesma, Emmanuel; Martínez-Torteya, Antonio; Chacolla-Huaringa, Rafael; Rodriguez-Barrientos, Alberto; Tamez-Peña, José G; Treviño, Victor

2013-01-01

Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R.

SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis

PubMed Central

Aguirre-Gamboa, Raul; Gomez-Rueda, Hugo; Martínez-Ledesma, Emmanuel; Martínez-Torteya, Antonio; Chacolla-Huaringa, Rafael; Rodriguez-Barrientos, Alberto; Tamez-Peña, José G.; Treviño, Victor

2013-01-01

Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R. PMID:24066126

Robust and versatile ionic liquid microarrays achieved by microcontact printing

NASA Astrophysics Data System (ADS)

Gunawan, Christian A.; Ge, Mengchen; Zhao, Chuan

2014-04-01

Lab-on-a-chip and miniaturized systems have gained significant popularity motivated by marked differences in material performance at the micro-to-nano-scale realm. However, to fully exploit micro-to-nano-scale chemistry, solvent volatility and lack of reproducibility need to be overcome. Here, we combine the non-volatile and versatile nature of ionic liquids with microcontact printing in an attempt to establish a facile protocol for high throughput fabrication of open microreactors and microfluidics. The micropatterned ionic liquid droplets have been demonstrated as electrochemical cells and reactors for microfabrication of metals and charge transfer complexes, substrates for immobilization of proteins and as membrane-free high-performance amperometric gas sensor arrays. The results suggest that miniaturized ionic liquid systems can be used to solve the problems of solvent volatility and slow mass transport in viscous ionic liquids in lab-on-a-chip devices, thus providing a versatile platform for a diverse number of applications.

Melvin Calvin award lecture, Isotopic chemistry: the most varied of careers…with tritium and deuterium the most versatile of the isotopes.

PubMed

Lockley, William J S

2013-01-01

Isotopic chemistry offers the opportunity for organic chemists to explore a surprisingly large variety of scientific avenues. It lends itself naturally to multidisciplinary research projects and provides the sophisticated tools with which the most complex of processes can be investigated. This Melvin Calvin Award lecture will keep to a broadly chronological theme and will give examples of how the remarkable versatility of the two heavy hydrogen isotopes has been utilised during collaborative studies in areas as varied as plant and insect biochemistry, drug metabolism and pharmacokinetics, structure determination, NMR spectroscopy, reaction mechanisms, molecular energetics and novel catalyst development. Few other careers can provide the opportunity to study such varied and fundamental subjects and still provide challenges that are as compelling and exciting some 4 decades later. Copyright © 2013 John Wiley & Sons, Ltd.

Microscale Symmetrical Electroporator Array as a Versatile Molecular Delivery System

NASA Astrophysics Data System (ADS)

Ouyang, Mengxing; Hill, Winfield; Lee, Jung Hyun; Hur, Soojung Claire

2017-03-01

Successful developments of new therapeutic strategies often rely on the ability to deliver exogenous molecules into cytosol. We have developed a versatile on-chip vortex-assisted electroporation system, engineered to conduct sequential intracellular delivery of multiple molecules into various cell types at low voltage in a dosage-controlled manner. Micro-patterned planar electrodes permit substantial reduction in operational voltages and seamless integration with an existing microfluidic technology. Equipped with real-time process visualization functionality, the system enables on-chip optimization of electroporation parameters for cells with varying properties. Moreover, the system’s dosage control and multi-molecular delivery capabilities facilitate intracellular delivery of various molecules as a single agent or in combination and its utility in biological research has been demonstrated by conducting RNA interference assays. We envision the system to be a powerful tool, aiding a wide range of applications, requiring single-cell level co-administrations of multiple molecules with controlled dosages.

Midlevel Maternity Providers' Preferences of a Childbirth Monitoring Tool in Low-Income Health Units in Uganda.

PubMed

Balikuddembe, Michael S; Wakholi, Peter K; Tumwesigye, Nazarius M; Tylleskär, Thorkild

2018-01-01

A third of women in childbirth are inadequately monitored, partly due to the tools used. Some stakeholders assert that the current labour monitoring tools are not efficient and need improvement to become more relevant to childbirth attendants. The study objective was to explore the expectations of maternity service providers for a mobile childbirth monitoring tool in maternity facilities in a low-income country like Uganda. Semi-structured interviews of purposively selected midwives and doctors in rural-urban childbirth facilities in Uganda were conducted before thematic data analysis. The childbirth providers expected a tool that enabled fast and secure childbirth record storage and sharing. They desired a tool that would automatically and conveniently register patient clinical findings, and actively provide interactive clinical decision support on a busy ward. The tool ought to support agreed upon standards for good pregnancy outcomes but also adaptable to the patient and their difficult working conditions. The tool functionality should include clinical data management and real-time decision support to the midwives, while the non-functional attributes include versatility and security.

EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens.

PubMed

Peng, Duo; Tarleton, Rick

2015-10-01

Recent development of CRISPR-Cas9 genome editing has enabled highly efficient and versatile manipulation of a variety of organisms and adaptation of the CRISPR-Cas9 system to eukaryotic pathogens has opened new avenues for studying these otherwise hard to manipulate organisms. Here we describe a webtool, Eukaryotic Pathogen gRNA Design Tool (EuPaGDT; available at http://grna.ctegd.uga.edu), which identifies guide RNA (gRNA) in input gene(s) to guide users in arriving at well-informed and appropriate gRNA design for many eukaryotic pathogens. Flexibility in gRNA design, accommodating unique eukaryotic pathogen (gene and genome) attributes and high-throughput gRNA design are the main features that distinguish EuPaGDT from other gRNA design tools. In addition to employing an array of known principles to score and rank gRNAs, EuPaGDT implements an effective on-target search algorithm to identify gRNA targeting multi-gene families, which are highly represented in these pathogens and play important roles in host-pathogen interactions. EuPaGDT also identifies and scores microhomology sequences flanking each gRNA targeted cut-site; these sites are often essential for the microhomology-mediated end joining process used for double-stranded break repair in these organisms. EuPaGDT also assists users in designing single-stranded oligonucleotides for homology directed repair. In batch processing mode, EuPaGDT is able to process genome-scale sequences, enabling preparation of gRNA libraries for large-scale screening projects.

Novel versatile smart phone based Microplate readers for on-site diagnoses.

PubMed

Fu, Qiangqiang; Wu, Ze; Li, Xiuqing; Yao, Cuize; Yu, Shiting; Xiao, Wei; Tang, Yong

2016-07-15

Microplate readers are important diagnostic instruments, used intensively for various readout test kits (biochemical analysis kits and ELISA kits). However, due to their expensive and non-portability, commercial microplate readers are unavailable for home testing, community and rural hospitals, especially in developing countries. In this study, to provide a field-portable, cost-effective and versatile diagnostic tool, we reported a novel smart phone based microplate reader. The basic principle of this devise relies on a smart phone's optical sensor that measures transmitted light intensities of liquid samples. To prove the validity of these devises, developed smart phone based microplate readers were applied to readout results of various analytical targets. These targets included analanine aminotransferase (ALT; limit of detection (LOD) was 17.54 U/L), alkaline phosphatase (AKP; LOD was 15.56 U/L), creatinine (LOD was 1.35μM), bovine serum albumin (BSA; LOD was 0.0041mg/mL), prostate specific antigen (PSA; LOD was 0.76pg/mL), and ractopamine (Rac; LOD was 0.31ng/mL). The developed smart phone based microplate readers are versatile, portable, and inexpensive; they are unique because of their ability to perform under circumstances where resources and expertize are limited. Copyright © 2016 Elsevier B.V. All rights reserved.

Ketenimines Generated from Ynamides: Versatile Building Blocks for Nitrogen-Containing Scaffolds.

PubMed

Dodd, Robert H; Cariou, Kevin

2018-02-16

Using ynamides as readily available starting materials, a single step can generate highly reactive ketenimines, which can then undergo a variety of transformations. The choice of the method for generating the ketenimine dictates the outcome of the reaction that can, moreover, be precisely steered through minor variations of the starting material. This Concept gives an overview of the different existing methodologies for this objective, showcasing the diverse nitrogen-containing frameworks that can be obtained by this highly versatile strategy. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Note: Versatile sample stick for neutron scattering experiments in high electric fields

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

Bartkowiak, M., E-mail: marek.bartkowiak@psi.ch; White, J. S.; Laboratory for Quantum Magnetism, Ecole Polytechnique Fédérale de Lausanne

2014-02-15

We present a versatile high voltage sample stick that fits into all cryomagnets and standard cryostats at the Swiss Spallation Neutron Source, Paul Scherrer Institut, and which provides a low effort route to neutron scattering experiments that combine electric field with low temperature and magnetic field. The stick allows for voltages up to 5 kV and can be easily adapted for different scattering geometries. We discuss the design consideration and thermal behavior of the stick, and give one example to showcase the abilities of the device.

Versatile, High Quality and Scalable Continuous Flow Production of Metal-Organic Frameworks

PubMed Central

Rubio-Martinez, Marta; Batten, Michael P.; Polyzos, Anastasios; Carey, Keri-Constanti; Mardel, James I.; Lim, Kok-Seng; Hill, Matthew R.

2014-01-01

Further deployment of Metal-Organic Frameworks in applied settings requires their ready preparation at scale. Expansion of typical batch processes can lead to unsuccessful or low quality synthesis for some systems. Here we report how continuous flow chemistry can be adapted as a versatile route to a range of MOFs, by emulating conditions of lab-scale batch synthesis. This delivers ready synthesis of three different MOFs, with surface areas that closely match theoretical maxima, with production rates of 60 g/h at extremely high space-time yields. PMID:24962145

Acoustic prediction methods for the NASA generalized advanced propeller analysis system (GAPAS)

NASA Technical Reports Server (NTRS)

Padula, S. L.; Block, P. J. W.

1984-01-01

Classical methods of propeller performance analysis are coupled with state-of-the-art Aircraft Noise Prediction Program (ANOPP:) techniques to yield a versatile design tool, the NASA Generalized Advanced Propeller Analysis System (GAPAS) for the novel quiet and efficient propellers. ANOPP is a collection of modular specialized programs. GAPAS as a whole addresses blade geometry and aerodynamics, rotor performance and loading, and subsonic propeller noise.

RNA splicing process analysis for identifying antisense oligonucleotide inhibitors with padlock probe-based isothermal amplification.

PubMed

Ren, Xiaojun; Deng, Ruijie; Wang, Lida; Zhang, Kaixiang; Li, Jinghong

2017-08-01

RNA splicing, which mainly involves two transesterification steps, is a fundamental process of gene expression and its abnormal regulation contributes to serious genetic diseases. Antisense oligonucleotides (ASOs) are genetic control tools that can be used to specifically control genes through alteration of the RNA splicing pathway. Despite intensive research, how ASOs or various other factors influence the multiple processes of RNA splicing still remains obscure. This is largely due to an inability to analyze the splicing efficiency of each step in the RNA splicing process with high sensitivity. We addressed this limitation by introducing a padlock probe-based isothermal amplification assay to achieve quantification of the specific products in different splicing steps. With this amplified assay, the roles that ASOs play in RNA splicing inhibition in the first and second steps could be distinguished. We identified that 5'-ASO could block RNA splicing by inhibiting the first step, while 3'-ASO could block RNA splicing by inhibiting the second step. This method provides a versatile tool for assisting efficient ASO design and discovering new splicing modulators and therapeutic drugs.

Technical Review: Microscopy and Image Processing Tools to Analyze Plant Chromatin: Practical Considerations.

PubMed

Baroux, Célia; Schubert, Veit

2018-01-01

In situ nucleus and chromatin analyses rely on microscopy imaging that benefits from versatile, efficient fluorescent probes and proteins for static or live imaging. Yet the broad choice in imaging instruments offered to the user poses orientation problems. Which imaging instrument should be used for which purpose? What are the main caveats and what are the considerations to best exploit each instrument's ability to obtain informative and high-quality images? How to infer quantitative information on chromatin or nuclear organization from microscopy images? In this review, we present an overview of common, fluorescence-based microscopy systems and discuss recently developed super-resolution microscopy systems, which are able to bridge the resolution gap between common fluorescence microscopy and electron microscopy. We briefly present their basic principles and discuss their possible applications in the field, while providing experience-based recommendations to guide the user toward best-possible imaging. In addition to raw data acquisition methods, we discuss commercial and noncommercial processing tools required for optimal image presentation and signal evaluation in two and three dimensions.

Using computer graphics to enhance astronaut and systems safety

NASA Technical Reports Server (NTRS)

Brown, J. W.

1985-01-01

Computer graphics is being employed at the NASA Johnson Space Center as a tool to perform rapid, efficient and economical analyses for man-machine integration, flight operations development and systems engineering. The Operator Station Design System (OSDS), a computer-based facility featuring a highly flexible and versatile interactive software package, PLAID, is described. This unique evaluation tool, with its expanding data base of Space Shuttle elements, various payloads, experiments, crew equipment and man models, supports a multitude of technical evaluations, including spacecraft and workstation layout, definition of astronaut visual access, flight techniques development, cargo integration and crew training. As OSDS is being applied to the Space Shuttle, Orbiter payloads (including the European Space Agency's Spacelab) and future space vehicles and stations, astronaut and systems safety are being enhanced. Typical OSDS examples are presented. By performing physical and operational evaluations during early conceptual phases. supporting systems verification for flight readiness, and applying its capabilities to real-time mission support, the OSDS provides the wherewithal to satisfy a growing need of the current and future space programs for efficient, economical analyses.

Enantioselective Brønsted Acid Catalysis as a Tool for the Synthesis of Natural Products and Pharmaceuticals.

PubMed

Merad, Jérémy; Lalli, Claudia; Bernadat, Guillaume; Maury, Julien; Masson, Géraldine

2018-03-15

Synthesis of biologically active molecules (whether at laboratory or industrial scale) remains a highly appealing area of modern organic chemistry. Nowadays, the need to access original bioactive scaffolds goes together with the desire to improve synthetic efficiency, while reducing the environmental footprint of chemical activities. Long neglected in the field of total synthesis, enantioselective organocatalysis has recently emerged as an environmentally friendly and indispensable tool for the construction of relevant bioactive molecules. Notably, enantioselective Brønsted acid catalysis has offered new opportunities in terms of both retrosynthetic disconnections and controlling stereoselectivity. The present report attempts to provide an overview of enantioselective total or formal syntheses designed around Brønsted acid-catalyzed transformations. To demonstrate the versatility of the reactions promoted and the diversity of the accessible motifs, this Minireview draws a systematic parallel between methods and retrosynthetic analysis. The manuscript is organized according to the main reaction types and the nature of newly-formed bonds. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synchronous Bioimaging of Intracellular pH and Chloride Based on LSS Fluorescent Protein.

PubMed

Paredes, Jose M; Idilli, Aurora I; Mariotti, Letizia; Losi, Gabriele; Arslanbaeva, Lyaysan R; Sato, Sebastian Sulis; Artoni, Pietro; Szczurkowska, Joanna; Cancedda, Laura; Ratto, Gian Michele; Carmignoto, Giorgio; Arosio, Daniele

2016-06-17

Ion homeostasis regulates critical physiological processes in the living cell. Intracellular chloride concentration not only contributes in setting the membrane potential of quiescent cells but it also plays a role in modulating the dynamic voltage changes during network activity. Dynamic chloride imaging demands new tools, allowing faster acquisition rates and correct accounting of concomitant pH changes. Joining a long-Stokes-shift red-fluorescent protein to a GFP variant with high sensitivity to pH and chloride, we obtained LSSmClopHensor, a genetically encoded fluorescent biosensor optimized for the simultaneous chloride and pH imaging and requiring only two excitation wavelengths (458 and 488 nm). LSSmClopHensor allowed us to monitor the dynamic changes of intracellular pH and chloride concentration during seizure like discharges in neocortical brain slices. Only cells with tightly controlled resting potential revealed a narrow distribution of chloride concentration peaking at about 5 and 8 mM, in neocortical neurons and SK-N-SH cells, respectively. We thus showed that LSSmClopHensor represents a new versatile tool for studying the dynamics of chloride and proton concentration in living systems.

λ5-Phosphorus-Containing α-Diazo Compounds: A Valuable Tool for Accessing Phosphorus-Functionalized Molecules.

PubMed

Marinozzi, Maura; Pertusati, Fabrizio; Serpi, Michaela

2016-11-23

The compounds characterized by the presence of a λ 5 -phosphorus functionality at the α-position with respect to the diazo moiety, here referred to as λ 5 -phosphorus-containing α-diazo compounds (PCDCs), represent a vast class of extremely versatile reagents in organic chemistry and are particularly useful in the preparation of phosphonate- and phosphinoxide-functionalized molecules. Indeed, thanks to the high reactivity of the diazo moiety, PCDCs can be induced to undergo a wide variety of chemical transformations. Among them are carbon-hydrogen, as well as heteroatom-hydrogen insertion reactions, cyclopropanation, ylide formation, Wolff rearrangement, and cycloaddition reactions. PCDCs can be easily prepared from readily accessible precursors by a variety of different methods, such as diazotization, Bamford-Stevens-type elimination, and diazo transfer reactions. This evidence along with their relative stability and manageability make them appealing tools in organic synthesis. This Review aims to demonstrate the ongoing utility of PCDCs in the modern preparation of different classes of phosphorus-containing compounds, phosphonates, in particular. Furthermore, to address the lack of precedent collective papers, this Review also summarizes the methods for PCDCs preparation.

Aeroelastic analysis of versatile thermal insulation (VTI) panels with pinched boundary conditions

NASA Astrophysics Data System (ADS)

Carrera, Erasmo; Zappino, Enrico; Patočka, Karel; Komarek, Martin; Ferrarese, Adriano; Montabone, Mauro; Kotzias, Bernhard; Huermann, Brian; Schwane, Richard

2014-03-01

Launch vehicle design and analysis is a crucial problem in space engineering. The large range of external conditions and the complexity of space vehicles make the solution of the problem really challenging. The problem considered in the present work deals with the versatile thermal insulation (VTI) panel. This thermal protection system is designed to reduce heat fluxes on the LH2 tank during the long coasting phases. Because of the unconventional boundary conditions and the large-scale geometry of the panel, the aeroelastic behaviour of VTI is investigated in the present work. Known available results from literature related to similar problem, are reviewed by considering the effect of various Mach regimes, including boundary layer thickness effects, in-plane mechanical and thermal loads, non-linear effects and amplitude of limit cycle oscillations. A dedicated finite element model is developed for the supersonic regime. The models used for coupling the orthotropic layered structural model with Piston Theory aerodynamic models allow the calculations of flutter conditions in case of curved panels supported in a discrete number of points. An advanced computational aeroelasticity tool is developed using various dedicated commercial softwares (CFX, ZAERO, EDGE). A wind tunnel test campaign is carried out to assess the computational tool in the analysis of this type of problem.

AccuRT: A versatile tool for radiative transfer simulations in the coupled atmosphere-ocean system

NASA Astrophysics Data System (ADS)

Hamre, Børge; Stamnes, Snorre; Stamnes, Knut; Stamnes, Jakob

2017-02-01

Reliable, accurate, and efficient modeling of the transport of electromagnetic radiation in turbid media has important applications in the study of the Earth's climate by remote sensing. For example, such modeling is needed to develop forward-inverse methods used to quantify types and concentrations of aerosol and cloud particles in the atmosphere, the dissolved organic and particulate biogeochemical matter in lakes, rivers, coastal, and open-ocean waters. It is also needed to simulate the performance of remote sensing detectors deployed on aircraft, balloons, and satellites as well as radiometric detectors deployed on buoys, gliders and other aquatic observing systems. Accurate radiative transfer modeling is also required to compute irradiances and scalar irradiances that are used to compute warming/cooling and photolysis rates in the atmosphere and primary production and warming/cooling rates in the water column. AccuRT is a radiative transfer model for the coupled atmosphere-water system that is designed to be a versatile tool for researchers in the ocean optics and remote sensing communities. It addresses the needs of researchers interested in analyzing irradiance and radiance measurements in the field and laboratory as well as those interested in making simulations of the top-of-the-atmosphere radiance in support of remote sensing algorithm development.

Label-free NIR reflectance imaging as a complimentary tool for two-photon fluorescence microscopy: multimodal investigation of stroke (Conference Presentation)

NASA Astrophysics Data System (ADS)

Allegra Mascaro, Anna Letizia; Costantini, Irene; Margoni, Emilia; Iannello, Giulio; Bria, Alessandro; Sacconi, Leonardo; Pavone, Francesco S.

2016-03-01

Two-photon imaging combined with targeted fluorescent indicators is extensively used for visualizing critical features of brain functionality and structural plasticity. Back-scattered photons from the NIR laser provide complimentary information without introducing any exogenous labelling. Here, we describe a versatile approach that, by collecting the reflected NIR light, provides structural details on the myelinated axons and blood vessels in the brain, both in fixed samples and in live animals. Indeed, by combining NIR reflectance and two-photon imaging of a slice of hippocampus from Thy1-GFPm mice, we show the presence of randomly oriented axons intermingled with sparsely fluorescent neuronal processes. The back-scattered photons guide the contextualization of the fluorescence structure within brain atlas thanks to the recognition of characteristic hippocampal structures. Label-free detection of axonal elongations over the layer 2/3 of mouse cortex under a cranial window was also possible in live brain. Finally, blood flow could be measured in vivo, thus validating label free NIR reflectance as a tool for monitoring hemodynamic fluctuations. The prospective versatility of this label-free technique complimentary to two-photon fluorescence microscopy is demonstrated in a mouse model of photothrombotic stroke in which the axonal degeneration and blood flow remodeling can be investigated simultaneously.

Frontal affinity chromatography: A unique research tool for biospecific interaction that promotes glycobiology

PubMed Central

KASAI, Kenichi

2014-01-01

Combination of bioaffinity and chromatography gave birth to affinity chromatography. A further combination with frontal analysis resulted in creation of frontal affinity chromatography (FAC). This new versatile research tool enabled detailed analysis of weak interactions that play essential roles in living systems, especially those between complex saccharides and saccharide-binding proteins. FAC now becomes the best method for the investigation of saccharide-binding proteins (lectins) from viewpoints of sensitivity, accuracy, and efficiency, and is contributing greatly to the development of glycobiology. It opened a door leading to deeper understanding of the significance of saccharide recognition in life. The theory is also concisely described. PMID:25169774

Current and future prospects for CRISPR-based tools in bacteria

PubMed Central

Luo, Michelle L.; Leenay, Ryan T.; Beisel, Chase L.

2015-01-01

CRISPR-Cas systems have rapidly transitioned from intriguing prokaryotic defense systems to powerful and versatile biomolecular tools. This article reviews how these systems have been translated into technologies to manipulate bacterial genetics, physiology, and communities. Recent applications in bacteria have centered on multiplexed genome editing, programmable gene regulation, and sequence-specific antimicrobials, while future applications can build on advances in eukaryotes, the rich natural diversity of CRISPR-Cas systems, and the untapped potential of CRISPR-based DNA acquisition. Overall, these systems have formed the basis of an ever-expanding genetic toolbox and hold tremendous potential for our future understanding and engineering of the bacterial world. PMID:26460902

Innovative methods and tools for professionals working in supported living services for intellectually disabled persons.

PubMed

Gruiz, Katalin

2015-01-01

Autonomy of mid-seriously and seriously intellectually disabled persons is encouraged both by legislations on human rights and the modern social care and services. The process leading to the maximum possible autonomy is illustrated by a developmental spiral in our model. Specialty of the development is that the personal educational projects are realized during everyday activities. The process requires conscious professionals with an empowering and motivating attitude, with adult relationship to the intellectually disabled persons and versatile skills and tools. In this educational relationship the social professional and the supported person are equal partners moving together along the spiral of human development. An innovative tool-battery has been developed aiding support-staff in the 'pedagogical' task embedded into everyday social services. The tool-battery and its first application in supported living services of the Hungarian Down Foundation are introduced in this paper.

A Format for Phylogenetic Placements

PubMed Central

Matsen, Frederick A.; Hoffman, Noah G.; Gallagher, Aaron; Stamatakis, Alexandros

2012-01-01

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement. PMID:22383988

A format for phylogenetic placements.

PubMed

Matsen, Frederick A; Hoffman, Noah G; Gallagher, Aaron; Stamatakis, Alexandros

2012-01-01

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.

Innovative and Advanced Coupled Neutron Transport and Thermal Hydraulic Method (Tool) for the Design, Analysis and Optimization of VHTR/NGNP Prismatic Reactors

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

Rahnema, Farzad; Garimeela, Srinivas; Ougouag, Abderrafi

2013-11-29

This project will develop a 3D, advanced coarse mesh transport method (COMET-Hex) for steady- state and transient analyses in advanced very high-temperature reactors (VHTRs). The project will lead to a coupled neutronics and thermal hydraulic (T/H) core simulation tool with fuel depletion capability. The computational tool will be developed in hexagonal geometry, based solely on transport theory without (spatial) homogenization in complicated 3D geometries. In addition to the hexagonal geometry extension, collaborators will concurrently develop three additional capabilities to increase the code’s versatility as an advanced and robust core simulator for VHTRs. First, the project team will develop and implementmore » a depletion method within the core simulator. Second, the team will develop an elementary (proof-of-concept) 1D time-dependent transport method for efficient transient analyses. The third capability will be a thermal hydraulic method coupled to the neutronics transport module for VHTRs. Current advancements in reactor core design are pushing VHTRs toward greater core and fuel heterogeneity to pursue higher burn-ups, efficiently transmute used fuel, maximize energy production, and improve plant economics and safety. As a result, an accurate and efficient neutron transport, with capabilities to treat heterogeneous burnable poison effects, is highly desirable for predicting VHTR neutronics performance. This research project’s primary objective is to advance the state of the art for reactor analysis.« less

Sma3s: a three-step modular annotator for large sequence datasets.

PubMed

Muñoz-Mérida, Antonio; Viguera, Enrique; Claros, M Gonzalo; Trelles, Oswaldo; Pérez-Pulido, Antonio J

2014-08-01

Automatic sequence annotation is an essential component of modern 'omics' studies, which aim to extract information from large collections of sequence data. Most existing tools use sequence homology to establish evolutionary relationships and assign putative functions to sequences. However, it can be difficult to define a similarity threshold that achieves sufficient coverage without sacrificing annotation quality. Defining the correct configuration is critical and can be challenging for non-specialist users. Thus, the development of robust automatic annotation techniques that generate high-quality annotations without needing expert knowledge would be very valuable for the research community. We present Sma3s, a tool for automatically annotating very large collections of biological sequences from any kind of gene library or genome. Sma3s is composed of three modules that progressively annotate query sequences using either: (i) very similar homologues, (ii) orthologous sequences or (iii) terms enriched in groups of homologous sequences. We trained the system using several random sets of known sequences, demonstrating average sensitivity and specificity values of ~85%. In conclusion, Sma3s is a versatile tool for high-throughput annotation of a wide variety of sequence datasets that outperforms the accuracy of other well-established annotation algorithms, and it can enrich existing database annotations and uncover previously hidden features. Importantly, Sma3s has already been used in the functional annotation of two published transcriptomes. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

High-Sensitivity Nuclear Magnetic Resonance at Giga-Pascal Pressures: A New Tool for Probing Electronic and Chemical Properties of Condensed Matter under Extreme Conditions

PubMed Central

Meier, Thomas; Haase, Jürgen

2014-01-01

Nuclear Magnetic Resonance (NMR) is one of the most important techniques for the study of condensed matter systems, their chemical structure, and their electronic properties. The application of high pressure enables one to synthesize new materials, but the response of known materials to high pressure is a very useful tool for studying their electronic structure and developing theories. For example, high-pressure synthesis might be at the origin of life; and understanding the behavior of small molecules under extreme pressure will tell us more about fundamental processes in our universe. It is no wonder that there has always been great interest in having NMR available at high pressures. Unfortunately, the desired pressures are often well into the Giga-Pascal (GPa) range and require special anvil cell devices where only very small, secluded volumes are available. This has restricted the use of NMR almost entirely in the past, and only recently, a new approach to high-sensitivity GPa NMR, which has a resonating micro-coil inside the sample chamber, was put forward. This approach enables us to achieve high sensitivity with experiments that bring the power of NMR to Giga-Pascal pressure condensed matter research. First applications, the detection of a topological electronic transition in ordinary aluminum metal and the closing of the pseudo-gap in high-temperature superconductivity, show the power of such an approach. Meanwhile, the range of achievable pressures was increased tremendously with a new generation of anvil cells (up to 10.1 GPa), that fit standard-bore NMR magnets. This approach might become a new, important tool for the investigation of many condensed matter systems, in chemistry, geochemistry, and in physics, since we can now watch structural changes with the eyes of a very versatile probe. PMID:25350694

High-sensitivity nuclear magnetic resonance at Giga-Pascal pressures: a new tool for probing electronic and chemical properties of condensed matter under extreme conditions.

PubMed

Meier, Thomas; Haase, Jürgen

2014-10-10

Nuclear Magnetic Resonance (NMR) is one of the most important techniques for the study of condensed matter systems, their chemical structure, and their electronic properties. The application of high pressure enables one to synthesize new materials, but the response of known materials to high pressure is a very useful tool for studying their electronic structure and developing theories. For example, high-pressure synthesis might be at the origin of life; and understanding the behavior of small molecules under extreme pressure will tell us more about fundamental processes in our universe. It is no wonder that there has always been great interest in having NMR available at high pressures. Unfortunately, the desired pressures are often well into the Giga-Pascal (GPa) range and require special anvil cell devices where only very small, secluded volumes are available. This has restricted the use of NMR almost entirely in the past, and only recently, a new approach to high-sensitivity GPa NMR, which has a resonating micro-coil inside the sample chamber, was put forward. This approach enables us to achieve high sensitivity with experiments that bring the power of NMR to Giga-Pascal pressure condensed matter research. First applications, the detection of a topological electronic transition in ordinary aluminum metal and the closing of the pseudo-gap in high-temperature superconductivity, show the power of such an approach. Meanwhile, the range of achievable pressures was increased tremendously with a new generation of anvil cells (up to 10.1 GPa), that fit standard-bore NMR magnets. This approach might become a new, important tool for the investigation of many condensed matter systems, in chemistry, geochemistry, and in physics, since we can now watch structural changes with the eyes of a very versatile probe.

High hydrostatic pressure specifically affects molecular dynamics and shape of low-density lipoprotein particles

PubMed Central

Golub, M.; Lehofer, B.; Martinez, N.; Ollivier, J.; Kohlbrecher, J.; Prassl, R.; Peters, J.

2017-01-01

Lipid composition of human low-density lipoprotein (LDL) and its physicochemical characteristics are relevant for proper functioning of lipid transport in the blood circulation. To explore dynamical and structural features of LDL particles with either a normal or a triglyceride-rich lipid composition we combined coherent and incoherent neutron scattering methods. The investigations were carried out under high hydrostatic pressure (HHP), which is a versatile tool to study the physicochemical behavior of biomolecules in solution at a molecular level. Within both neutron techniques we applied HHP to probe the shape and degree of freedom of the possible motions (within the time windows of 15 and 100 ps) and consequently the flexibility of LDL particles. We found that HHP does not change the types of motion in LDL, but influences the portion of motions participating. Contrary to our assumption that lipoprotein particles, like membranes, are highly sensitive to pressure we determined that LDL copes surprisingly well with high pressure conditions, although the lipid composition, particularly the triglyceride content of the particles, impacts the molecular dynamics and shape arrangement of LDL under pressure. PMID:28382948

A new ultra-high-accuracy angle generator: current status and future direction

NASA Astrophysics Data System (ADS)

Guertin, Christian F.; Geckeler, Ralf D.

2017-09-01

Lack of an extreme high-accuracy angular positioning device available in the United States has left a gap in industrial and scientific efforts conducted there, requiring certain user groups to undertake time-consuming work with overseas laboratories. Specifically, in x-ray mirror metrology the global research community is advancing the state-of-the-art to unprecedented levels. We aim to fill this U.S. gap by developing a versatile high-accuracy angle generator as a part of the national metrology tool set for x-ray mirror metrology and other important industries. Using an established calibration technique to measure the errors of the encoder scale graduations for full-rotation rotary encoders, we implemented an optimized arrangement of sensors positioned to minimize propagation of calibration errors. Our initial feasibility research shows that upon scaling to a full prototype and including additional calibration techniques we can expect to achieve uncertainties at the level of 0.01 arcsec (50 nrad) or better and offer the immense advantage of a highly automatable and customizable product to the commercial market.

High hydrostatic pressure specifically affects molecular dynamics and shape of low-density lipoprotein particles

NASA Astrophysics Data System (ADS)

Golub, M.; Lehofer, B.; Martinez, N.; Ollivier, J.; Kohlbrecher, J.; Prassl, R.; Peters, J.

2017-04-01

Lipid composition of human low-density lipoprotein (LDL) and its physicochemical characteristics are relevant for proper functioning of lipid transport in the blood circulation. To explore dynamical and structural features of LDL particles with either a normal or a triglyceride-rich lipid composition we combined coherent and incoherent neutron scattering methods. The investigations were carried out under high hydrostatic pressure (HHP), which is a versatile tool to study the physicochemical behavior of biomolecules in solution at a molecular level. Within both neutron techniques we applied HHP to probe the shape and degree of freedom of the possible motions (within the time windows of 15 and 100 ps) and consequently the flexibility of LDL particles. We found that HHP does not change the types of motion in LDL, but influences the portion of motions participating. Contrary to our assumption that lipoprotein particles, like membranes, are highly sensitive to pressure we determined that LDL copes surprisingly well with high pressure conditions, although the lipid composition, particularly the triglyceride content of the particles, impacts the molecular dynamics and shape arrangement of LDL under pressure.

Dispensing of very low volumes of ultra high viscosity alginate gels: a new tool for encapsulation of adherent cells and rapid prototyping of scaffolds and implants.

PubMed

Gepp, Michael M; Ehrhart, Friederike; Shirley, Stephen G; Howitz, Steffen; Zimmermann, Heiko

2009-01-01

We present a tool for dispensing very low volumes (20 nL or more) of ultra high viscosity (UHV) medical-grade alginate hydrogels. It uses a modified piezo-driven micrometering valve, integrated into a versatile system that allows fast prototyping of encapsulation procedures and scaffold production. Valves show excellent dispensing properties for UHV alginate in concentrations of 0.4% and 0.7% and also for aqueous liquids. An optimized process flow provides excellent handling of biological samples under sterile conditions. This technique allows the encapsulation of adherent cells and structuring of substrates for biotechnology and regenerative medicine. A variety of cell lines showed at least 70% viability after encapsulation (including cell lines that are relevant in regenerative medicine like Hep G2), and time-lapse analysis revealed cells proliferating and showing limited motility under alginate spots. Cells show metabolic activity, gene product expression, and physiological function. Encapsulated cells have contact with the substrate and can exchange metabolites while being isolated from macromolecules in the environment. Contactless dispensing allows structuring of substrates with alginate, isolation and transfer of cell-alginate complexes, and the dispensing of biological active hydrogels like extracellular matrix-derived gels.

Targeted disruption of sp7 and myostatin with CRISPR-Cas9 results in severe bone defects and more muscular cells in common carp

PubMed Central

Zhong, Zhaomin; Niu, Pengfei; Wang, Mingyong; Huang, Guodong; Xu, Shuhao; Sun, Yi; Xu, Xiaona; Hou, Yi; Sun, Xiaowen; Yan, Yilin; Wang, Han

2016-01-01

The common carp (Cyprinus carpio) as one of the most important aquaculture fishes produces over 3 million metric tones annually, approximately 10% the annual production of the all farmed freshwater fish worldwide. However, the tetraploidy genome and long generation-time of the common carp have made its breeding and genetic studies extremely difficult. Here, TALEN and CRISPR-Cas9, two versatile genome-editing tools, are employed to target common carp bone-related genes sp7, runx2, bmp2a, spp1, opg, and muscle suppressor gene mstn. TALEN were shown to induce mutations in the target coding sites of sp7, runx2, spp1 and mstn. With CRISPR-Cas9, the two common carp sp7 genes, sp7a and sp7b, were mutated individually, all resulting in severe bone defects; while mstnba mutated fish have grown significantly more muscle cells. We also employed CRISPR-Cas9 to generate double mutant fish of sp7a;mstnba with high efficiencies in a single step. These results demonstrate that both TALEN and CRISPR-Cas9 are highly efficient tools for modifying the common carp genome, and open avenues for facilitating common carp genetic studies and breeding. PMID:26976234

Multiscale dispersion-state characterization of nanocomposites using optical coherence tomography

PubMed Central

Schneider, Simon; Eppler, Florian; Weber, Marco; Olowojoba, Ganiu; Weiss, Patrick; Hübner, Christof; Mikonsaari, Irma; Freude, Wolfgang; Koos, Christian

2016-01-01

Nanocomposite materials represent a success story of nanotechnology. However, development of nanomaterial fabrication still suffers from the lack of adequate analysis tools. In particular, achieving and maintaining well-dispersed particle distributions is a key challenge, both in material development and industrial production. Conventional methods like optical or electron microscopy need laborious, costly sample preparation and do not permit fast extraction of nanoscale structural information from statistically relevant sample volumes. Here we show that optical coherence tomography (OCT) represents a versatile tool for nanomaterial characterization, both in a laboratory and in a production environment. The technique does not require sample preparation and is applicable to a wide range of solid and liquid material systems. Large particle agglomerates can be directly found by OCT imaging, whereas dispersed nanoparticles are detected by model-based analysis of depth-dependent backscattering. Using a model system of polystyrene nanoparticles, we demonstrate nanoparticle sizing with high accuracy. We further prove the viability of the approach by characterizing highly relevant material systems based on nanoclays or carbon nanotubes. The technique is perfectly suited for in-line metrology in a production environment, which is demonstrated using a state-of-the-art compounding extruder. These experiments represent the first demonstration of multiscale nanomaterial characterization using OCT. PMID:27557544

Multiscale dispersion-state characterization of nanocomposites using optical coherence tomography.

PubMed

Schneider, Simon; Eppler, Florian; Weber, Marco; Olowojoba, Ganiu; Weiss, Patrick; Hübner, Christof; Mikonsaari, Irma; Freude, Wolfgang; Koos, Christian

2016-08-25

Nanocomposite materials represent a success story of nanotechnology. However, development of nanomaterial fabrication still suffers from the lack of adequate analysis tools. In particular, achieving and maintaining well-dispersed particle distributions is a key challenge, both in material development and industrial production. Conventional methods like optical or electron microscopy need laborious, costly sample preparation and do not permit fast extraction of nanoscale structural information from statistically relevant sample volumes. Here we show that optical coherence tomography (OCT) represents a versatile tool for nanomaterial characterization, both in a laboratory and in a production environment. The technique does not require sample preparation and is applicable to a wide range of solid and liquid material systems. Large particle agglomerates can be directly found by OCT imaging, whereas dispersed nanoparticles are detected by model-based analysis of depth-dependent backscattering. Using a model system of polystyrene nanoparticles, we demonstrate nanoparticle sizing with high accuracy. We further prove the viability of the approach by characterizing highly relevant material systems based on nanoclays or carbon nanotubes. The technique is perfectly suited for in-line metrology in a production environment, which is demonstrated using a state-of-the-art compounding extruder. These experiments represent the first demonstration of multiscale nanomaterial characterization using OCT.

Light weight, high-speed, and self-powered wireless fiber optic sensor (WiFOS) structural health monitor system for avionics and aerospace environments

NASA Astrophysics Data System (ADS)

Mendoza, Edgar A.; Kempen, Cornelia; Sun, Sunjian; Esterkin, Yan

2014-09-01

This paper describes recent progress towards the development of an innovative light weight, high-speed, and selfpowered wireless fiber optic sensor (WiFOS™) structural health monitor system suitable for the onboard and in-flight unattended detection, localization, and classification of load, fatigue, and structural damage in advanced composite materials commonly used in avionics and aerospace systems. The WiFOS™ system is based on ROI's advancements on monolithic photonic integrated circuit microchip technology, integrated with smart power management, on-board data processing, wireless data transmission optoelectronics, and self-power using energy harvesting tools such as solar, vibration, thermoelectric, and magneto-electric. The self-powered, wireless WiFOS™ system offers a versatile and powerful SHM tool to enhance the reliability and safety of avionics platforms, jet fighters, helicopters, commercial aircraft that use lightweight composite material structures, by providing comprehensive information about the structural integrity of the structure from a large number of locations. Immediate SHM applications are found in rotorcraft and aircraft, ships, submarines, and in next generation weapon systems, and in commercial oil and petrochemical, aerospace industries, civil structures, power utilities, portable medical devices, and biotechnology, homeland security and a wide spectrum of other applications.

Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks

PubMed Central

2011-01-01

Background Protein domains are globular structures of independently folded polypeptides that exert catalytic or binding activities. Their sequences are recognized as evolutionary units that, through genome recombination, constitute protein repertoires of linkage patterns. Via mutations, domains acquire modified functions that contribute to the fitness of cells and organisms. Recent studies have addressed the evolutionary selection that may have shaped the functions of individual domains and the emergence of particular domain combinations, which led to new cellular functions in multi-cellular animals. This study focuses on modeling domain linkage globally and investigates evolutionary implications that may be revealed by novel computational analysis. Results A survey of 77 completely sequenced eukaryotic genomes implies a potential hierarchical and modular organization of biological functions in most living organisms. Domains in a genome or multiple genomes are modeled as a network of hetero-duplex covalent linkages, termed bigrams. A novel computational technique is introduced to decompose such networks, whereby the notion of domain "networking versatility" is derived and measured. The most and least "versatile" domains (termed "core domains" and "peripheral domains" respectively) are examined both computationally via sequence conservation measures and experimentally using selected domains. Our study suggests that such a versatility measure extracted from the bigram networks correlates with the adaptivity of domains during evolution, where the network core domains are highly adaptive, significantly contrasting the network peripheral domains. Conclusions Domain recombination has played a major part in the evolution of eukaryotes attributing to genome complexity. From a system point of view, as the results of selection and constant refinement, networks of domain linkage are structured in a hierarchical modular fashion. Domains with high degree of networking versatility appear to be evolutionary adaptive, potentially through functional innovations. Domain bigram networks are informative as a model of biological functions. The networking versatility indices extracted from such networks for individual domains reflect the strength of evolutionary selection that the domains have experienced. PMID:21849086

Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks.

PubMed

Xie, Xueying; Jin, Jing; Mao, Yongyi

2011-08-18

Protein domains are globular structures of independently folded polypeptides that exert catalytic or binding activities. Their sequences are recognized as evolutionary units that, through genome recombination, constitute protein repertoires of linkage patterns. Via mutations, domains acquire modified functions that contribute to the fitness of cells and organisms. Recent studies have addressed the evolutionary selection that may have shaped the functions of individual domains and the emergence of particular domain combinations, which led to new cellular functions in multi-cellular animals. This study focuses on modeling domain linkage globally and investigates evolutionary implications that may be revealed by novel computational analysis. A survey of 77 completely sequenced eukaryotic genomes implies a potential hierarchical and modular organization of biological functions in most living organisms. Domains in a genome or multiple genomes are modeled as a network of hetero-duplex covalent linkages, termed bigrams. A novel computational technique is introduced to decompose such networks, whereby the notion of domain "networking versatility" is derived and measured. The most and least "versatile" domains (termed "core domains" and "peripheral domains" respectively) are examined both computationally via sequence conservation measures and experimentally using selected domains. Our study suggests that such a versatility measure extracted from the bigram networks correlates with the adaptivity of domains during evolution, where the network core domains are highly adaptive, significantly contrasting the network peripheral domains. Domain recombination has played a major part in the evolution of eukaryotes attributing to genome complexity. From a system point of view, as the results of selection and constant refinement, networks of domain linkage are structured in a hierarchical modular fashion. Domains with high degree of networking versatility appear to be evolutionary adaptive, potentially through functional innovations. Domain bigram networks are informative as a model of biological functions. The networking versatility indices extracted from such networks for individual domains reflect the strength of evolutionary selection that the domains have experienced.

Development and characterization of hollow microprobe array as a potential tool for versatile and massively parallel manipulation of single cells.

PubMed

Nagai, Moeto; Oohara, Kiyotaka; Kato, Keita; Kawashima, Takahiro; Shibata, Takayuki

2015-04-01

Parallel manipulation of single cells is important for reconstructing in vivo cellular microenvironments and studying cell functions. To manipulate single cells and reconstruct their environments, development of a versatile manipulation tool is necessary. In this study, we developed an array of hollow probes using microelectromechanical systems fabrication technology and demonstrated the manipulation of single cells. We conducted a cell aspiration experiment with a glass pipette and modeled a cell using a standard linear solid model, which provided information for designing hollow stepped probes for minimally invasive single-cell manipulation. We etched a silicon wafer on both sides and formed through holes with stepped structures. The inner diameters of the holes were reduced by SiO2 deposition of plasma-enhanced chemical vapor deposition to trap cells on the tips. This fabrication process makes it possible to control the wall thickness, inner diameter, and outer diameter of the probes. With the fabricated probes, single cells were manipulated and placed in microwells at a single-cell level in a parallel manner. We studied the capture, release, and survival rates of cells at different suction and release pressures and found that the cell trapping rate was directly proportional to the suction pressure, whereas the release rate and viability decreased with increasing the suction pressure. The proposed manipulation system makes it possible to place cells in a well array and observe the adherence, spreading, culture, and death of the cells. This system has potential as a tool for massively parallel manipulation and for three-dimensional hetero cellular assays.

Benchmarking a Visual-Basic based multi-component one-dimensional reactive transport modeling tool

NASA Astrophysics Data System (ADS)

Torlapati, Jagadish; Prabhakar Clement, T.

2013-01-01

We present the details of a comprehensive numerical modeling tool, RT1D, which can be used for simulating biochemical and geochemical reactive transport problems. The code can be run within the standard Microsoft EXCEL Visual Basic platform, and it does not require any additional software tools. The code can be easily adapted by others for simulating different types of laboratory-scale reactive transport experiments. We illustrate the capabilities of the tool by solving five benchmark problems with varying levels of reaction complexity. These literature-derived benchmarks are used to highlight the versatility of the code for solving a variety of practical reactive transport problems. The benchmarks are described in detail to provide a comprehensive database, which can be used by model developers to test other numerical codes. The VBA code presented in the study is a practical tool that can be used by laboratory researchers for analyzing both batch and column datasets within an EXCEL platform.

A Software Upgrade of the NASA Aeroheating Code "MINIVER"

NASA Technical Reports Server (NTRS)

Louderback, Pierce Mathew

2013-01-01

Computational Fluid Dynamics (CFD) is a powerful and versatile tool simulating fluid and thermal environments of launch and re-entry vehicles alike. Where it excels in power and accuracy, however, it lacks in speed. An alternative tool for this purpose is known as MINIVER, an aeroheating code widely used by NASA and within the aerospace industry. Capable of providing swift, reasonably accurate approximations of the fluid and thermal environment of launch vehicles, MINIVER is used where time is of the essence and accuracy need not be exact. However, MINIVER is an old, aging tool: running on a user-unfriendly, legacy command-line interface, it is difficult for it to keep pace with more modem software tools. Florida Institute of Technology was tasked with the construction of a new Graphical User Interface (GUI) that implemented the legacy version's capabilities and enhanced them with new tools and utilities. This thesis provides background to the legacy version of the program, the progression and final version of a modem user interface, and benchmarks to demonstrate its usefulness.

A versatile bio-based material for efficiently removing toxic dyes, heavy metal ions and emulsified oil droplets from water simultaneously.

PubMed

Li, Daikun; Li, Qing; Mao, Daoyong; Bai, Ningning; Dong, Hongzhou

2017-12-01

Developing versatile materials for effective water purification is significant for environment and water source protection. Herein, a versatile bio-based material (CH-PAA-T) was reported by simple thermal cross-linking chitosan and polyacrylic acid which exhibits excellent performances for removing insoluble oil, soluble toxic dyes and heavy metal ions from water, simultaneously. The adsorption capacities are 990.1mgg -1 for methylene blue (MB) and 135.9mgg -1 for Cu 2+ , which are higher than most of present advanced absorbents. The adsorption towards organic dyes possesses high selectivity which makes CH-PAA-T be able to efficiently separate dye mixtures. The stable superoleophobicity under water endows CH-PAA-T good performance to separate toluene-in-water emulsion stabilized by Tween 80. Moreover, CH-PAA-T can be recycled for 10 times with negligible reduction of efficiency. Such versatile bio-based material is a potential candidate for water purification. Copyright © 2017. Published by Elsevier Ltd.

Lessons Learned from Pit Viper System Deployment

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

Catalan, Michael A.; Alzheimer, James M.; Valdez, Patrick LJ

2002-04-11

Tele-operated and robotic systems operated in unstructured field environments pose unique challenges for tool design. Since field tasks are not always well defined and the robot work area usually cannot be designed for ease of operation, the tools must be versatile. It's important to carefully consider the orientation of the grip the robot takes on the tool, as it's not easily changed in the field. The stiffness of the robot and the possibility of robot positioning errors encourages the use of non-contact or minimal-contact tooling. While normal hand tools can usually be modified for use by the robot, this ismore » not always the most effective approach. It's desirable to have tooling that is relatively independent of the robot; in this case, the robot places the tool near the desired work location and the tool performs its task relatively independently. Here we consider the adaptation of a number of tools for cleanup of a radioactively contaminated piping junction and valve pit. The tasks to be considered are debris removal (small nuts and bolts and pipe up to 100 mm in diameter), size reduction, surface cleaning, and support of past practice crane-based methods for working in the pits.« less

A Versatile PDMS/Paper Hybrid Microfluidic Platform for Sensitive Infectious Disease Diagnosis

PubMed Central

2015-01-01

Bacterial meningitis is a serious health concern worldwide. Given that meningitis can be fatal and many meningitis cases occurred in high-poverty areas, a simple, low-cost, highly sensitive method is in great need for immediate and early diagnosis of meningitis. Herein, we report a versatile and cost-effective polydimethylsiloxane (PDMS)/paper hybrid microfluidic device integrated with loop-mediated isothermal amplification (LAMP) for the rapid, sensitive, and instrument-free detection of the main meningitis-causing bacteria, Neisseria meningitidis (N. meningitidis). The introduction of paper into the microfluidic device for LAMP reactions enables stable test results over a much longer period of time than a paper-free microfluidic system. This hybrid system also offers versatile functions, by providing not only on-site qualitative diagnostic analysis (i.e., a yes or no answer), but also confirmatory testing and quantitative analysis in laboratory settings. The limit of detection of N. meningitidis is about 3 copies per LAMP zone within 45 min, close to single-bacterium detection sensitivity. In addition, we have achieved simple pathogenic microorganism detection without a laborious sample preparation process and without the use of centrifuges. This low-cost hybrid microfluidic system provides a simple and highly sensitive approach for fast instrument-free diagnosis of N. meningitidis in resource-limited settings. This versatile PDMS/paper microfluidic platform has great potential for the point of care (POC) diagnosis of a wide range of infectious diseases, especially for developing nations. PMID:25019330

Integrated Design and Analysis Tools for Software-Based Control Systems

DTIC Science & Technology

2005-07-01

in understanding this space. Jini and Java Spaces To give us a versatile experimental platform in anticipation of the Boeing OCP, we developed a...This demonstration shows the network integration and publish-and- subscribe interactions working with Ptolemy II. Moreover, the demo used Jini , a...develop a better understanding of its role to help determine whether it should be incorporated later, and in what form. Pioneer and Jini Jie Liu and

Use of the rectus abdominis muscle flap to fill a retroperitoneal defect following blast injury.

PubMed

Talarczyk, Matthew R; Ricci, Michael A

2009-02-01

Wartime injuries from explosive devices have created the need for atypical responses to devastating and unusual injuries. We report a case of an explosive abdominal injury that produced a huge defect in the posterior abdominal wall which was ultimately repaired with a rectus abdominus flap, an usual use of this versatile muscle flap. The rectus abdominus muscle may be another tool available for the repair of wartime injuries.

Rolling circle amplification detection of RNA and DNA

DOEpatents

Christian, Allen T.; Pattee, Melissa S.; Attix, Cristina M.; Tucker, James D.

2004-08-31

Rolling circle amplification (RCA) has been useful for detecting point mutations in isolated nucleic acids, but its application in cytological preparations has been problematic. By pretreating cells with a combination of restriction enzymes and exonucleases, we demonstrate RCA in solution and in situ to detect gene copy number and single base mutations. It can also detect and quantify transcribed RNA in individual cells, making it a versatile tool for cell-based assays.

The Influence of Physical Body Traits and Masculinity on Anal Sex Roles in Gay and Bisexual Men

PubMed Central

Moskowitz, David A.; Hart, Trevor A.

2016-01-01

Sociological, psychological, and public health studies document that many gay and bisexual men may self-label by their anal penetrative role (i.e., bottom or exclusively receptive; top or exclusively insertive; or versatile, both receptive and insertive during anal intercourse). Yet, what orients men to think of themselves as tops, bottoms or versatiles is poorly understood. We surveyed 429 men engaging in same-sex anal intercourse to investigate the degree to which anal penetrative self-identity was concordant with actual penetrative behavior. Additionally, the roles of masculinity and physical body traits (e.g., penis size, muscularity, height, hairiness, and weight) were tested as correlates of anal penetrative identity and identity-behavior concordance. Tops and bottoms showed a high degree of concordance between identity and enacted behavior; however, only half of versatiles reported concordant identity and behavior (i.e., wanting to be versatile and actually reporting versatile behavior). Generally, tops reported larger penises than bottoms. They also reported being comparatively more masculine than bottoms. Versatiles fell somewhat between the tops and bottoms on these traits. Of the six independent variables, penis size and masculinity were the only two factors to influence concordance or discordance between identity and penetrative behavior. Our study suggests that the correlates of gay men’s sexual self-labels may depend on objective traits in addition to the subjective pleasure associated with receptive or insertive anal intercourse. PMID:21465269

Characterization of Nanocomposites by Thermal Analysis

PubMed Central

Corcione, Carola Esposito; Frigione, Mariaenrica

2012-01-01

In materials research, the development of polymer nanocomposites (PN) is rapidly emerging as a multidisciplinary research field with results that could broaden the applications of polymers to many different industries. PN are polymer matrices (thermoplastics, thermosets or elastomers) that have been reinforced with small quantities of nano-sized particles, preferably characterized by high aspect ratios, such as layered silicates and carbon nanotubes. Thermal analysis (TA) is a useful tool to investigate a wide variety of properties of polymers and it can be also applied to PN in order to gain further insight into their structure. This review illustrates the versatile applications of TA methods in the emerging field of polymer nanomaterial research, presenting some examples of applications of differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), dynamic mechanical thermal analysis (DMTA) and thermal mechanical analysis (TMA) for the characterization of nanocomposite materials.

Extrusomes in ciliates: diversification, distribution, and phylogenetic implications.

PubMed

Rosati, Giovanna; Modeo, Letizia

2003-01-01

Exocytosis is, in all likelihood, an important communication method among microbes. Ciliates are highly differentiated and specialized micro-organisms for which versatile and/or sophisticated exocytotic organelles may represent important adaptive tools. Thus, in ciliates, we find a broad range of different extrusomes, i.e ejectable membrane-bound organelles. Structurally simple extrusomes, like mucocysts and cortical granules, are widespread in different taxa within the phylum. They play the roles in each case required for the ecological needs of the organisms. Then, we find a number of more elaborate extrusomes, whose distribution within the phylum is more limited, and in some way related to phylogenetic affinities. Herein we provide a survey of literature and our data on selected extrusomes in ciliates. Their morphology, distribution, and possible function are discussed. The possible phylogenetic implications of their diversity are considered.

APPHi: Automated Photometry Pipeline for High Cadence Large Volume Data

NASA Astrophysics Data System (ADS)

Sánchez, E.; Castro, J.; Silva, J.; Hernández, J.; Reyes, M.; Hernández, B.; Alvarez, F.; García T.

2018-04-01

APPHi (Automated Photometry Pipeline) carries out aperture and differential photometry of TAOS-II project data. It is computationally efficient and can be used also with other astronomical wide-field image data. APPHi works with large volumes of data and handles both FITS and HDF5 formats. Due the large number of stars that the software has to handle in an enormous number of frames, it is optimized to automatically find the best value for parameters to carry out the photometry, such as mask size for aperture, size of window for extraction of a single star, and the number of counts for the threshold for detecting a faint star. Although intended to work with TAOS-II data, APPHi can analyze any set of astronomical images and is a robust and versatile tool to performing stellar aperture and differential photometry.

Aerodynamic shape optimization of a HSCT type configuration with improved surface definition

NASA Technical Reports Server (NTRS)

Thomas, Almuttil M.; Tiwari, Surendra N.

1994-01-01

Two distinct parametrization procedures of generating free-form surfaces to represent aerospace vehicles are presented. The first procedure is the representation using spline functions such as nonuniform rational b-splines (NURBS) and the second is a novel (geometrical) parametrization using solutions to a suitably chosen partial differential equation. The main idea is to develop a surface which is more versatile and can be used in an optimization process. Unstructured volume grid is generated by an advancing front algorithm and solutions obtained using an Euler solver. Grid sensitivity with respect to surface design parameters and aerodynamic sensitivity coefficients based on potential flow is obtained using an automatic differentiator precompiler software tool. Aerodynamic shape optimization of a complete aircraft with twenty four design variables is performed. High speed civil transport aircraft (HSCT) configurations are targeted to demonstrate the process.

From Playroom to Lab: Tough Stretchable Electronics Analyzed with a Tabletop Tensile Tester Made from Toy‐Bricks

PubMed Central

Kettlgruber, Gerald; Siket, Christian M.; Drack, Michael; Graz, Ingrid M.; Cakmak, Umut; Major, Zoltan; Kaltenbrunner, Martin; Bauer, Siegfried

2016-01-01

Toy bricks are an ideal platform for the cost‐effective rapid prototyping of a tabletop tensile tester with measurement accuracy on par with expensive, commercially available laboratory equipment. Here, a tester is presented that is not only a versatile demonstration device in mechanics, electronics, and physics education and an eye‐catcher on exhibitions, but also a powerful tool for stretchable electronics research. Following the “open‐source movement” the build‐up of the tester is described and all the details for easy reproduction are disclosed. A a new design of highly conformable all‐elastomer based graded rigid island printed circuit boards is developed. Tough bonded to this elastomer substrate are imperceptible electronic foils bearing conductors and off‐the‐shelf microelectronics, paving the way for next generation smart electronic appliances. PMID:27588259

Microjets and coated wheels: versatile tools for exploring collisions and reactions at gas-liquid interfaces.

PubMed

Faust, Jennifer A; Nathanson, Gilbert M

2016-07-07

This tutorial review describes experimental aspects of two techniques for investigating collisions and reactions at the surfaces of liquids in vacuum. These gas-liquid scattering experiments provide insights into the dynamics of interfacial processes while minimizing interference from vapor-phase collisions. We begin with a historical survey and then compare attributes of the microjet and coated-wheel techniques, developed by Manfred Faubel and John Fenn, respectively, for studies of high- and low-vapor pressure liquids in vacuum. Our objective is to highlight the strengths and shortcomings of each technique and summarize lessons we have learned in using them for scattering and evaporation experiments. We conclude by describing recent microjet studies of energy transfer between O2 and liquid hydrocarbons, HCl dissociation in salty water, and super-Maxwellian helium evaporation.

Towards effective interactive three-dimensional colour postprocessing

NASA Technical Reports Server (NTRS)

Bailey, B. C.; Hajjar, J. F.; Abel, J. F.

1986-01-01

Recommendations for the development of effective three-dimensional, graphical color postprocessing are made. First, the evaluation of large, complex numerical models demands that a postprocessor be highly interactive. A menu of available functions should be provided and these operations should be performed quickly so that a sense of continuity and spontaneity exists during the post-processing session. Second, an agenda for three-dimensional color postprocessing is proposed. A postprocessor must be versatile with respect to application and basic algorithms must be designed so that they are flexible. A complete selection of tools is necessary to allow arbitrary specification of views, extraction of qualitative information, and access to detailed quantitative and problem information. Finally, full use of advanced display hardware is necessary if interactivity is to be maximized and effective postprocessing of today's numerical simulations is to be achieved.

Formation of Wear Resistant Steel Surfaces by Plasma Immersion Ion Implantation

NASA Astrophysics Data System (ADS)

Mändl, S.; Rauschenbach, B.

2003-08-01

Plasma immersion ion implantation (PIII) is a versatile and fast method for implanting energetic ions into large and complex shaped three-dimensional objects where the ions are accelerated by applying negative high voltage pulses to a substrate immersed in a plasma. As the line-of-sight restrictions of conventional implanters are circumvented, it results in a fast and cost-effective technology. Implantation of nitrogen at 30 - 40 keV at moderate temperatures of 200 - 400 °C into steel circumvents the diminishing thermal nitrogen activation encountered, e.g., in plasma nitriding in this temperature regime, thus enabling nitriding of additional steel grades. Nitride formation and improvement of the mechanical properties after PIII are presented for several steel grades, including AISI 316Ti (food industry), AISI D2 (used for bending tools) and AISI 1095 (with applications in the textile industry).

Dense Plasma Focus - From Alternative Fusion Source to Versatile High Energy Density Plasma Source for Plasma Nanotechnology

NASA Astrophysics Data System (ADS)

Rawat, R. S.

2015-03-01

The dense plasma focus (DPF), a coaxial plasma gun, utilizes pulsed high current electrical discharge to heat and compress the plasma to very high density and temperature with energy densities in the range of 1-10 × 1010 J/m3. The DPF device has always been in the company of several alternative magnetic fusion devices as it produces intense fusion neutrons. Several experiments conducted on many different DPF devices ranging over several order of storage energy have demonstrated that at higher storage energy the neutron production does not follow I4 scaling laws and deteriorate significantly raising concern about the device's capability and relevance for fusion energy. On the other hand, the high energy density pinch plasma in DPF device makes it a multiple radiation source of ions, electron, soft and hard x-rays, and neutrons, making it useful for several applications in many different fields such as lithography, radiography, imaging, activation analysis, radioisotopes production etc. Being a source of hot dense plasma, strong shockwave, intense energetic beams and radiation, etc, the DPF device, additionally, shows tremendous potential for applications in plasma nanoscience and plasma nanotechnology. In the present paper, the key features of plasma focus device are critically discussed to understand the novelties and opportunities that this device offers in processing and synthesis of nanophase materials using, both, the top-down and bottom-up approach. The results of recent key experimental investigations performed on (i) the processing and modification of bulk target substrates for phase change, surface reconstruction and nanostructurization, (ii) the nanostructurization of PLD grown magnetic thin films, and (iii) direct synthesis of nanostructured (nanowire, nanosheets and nanoflowers) materials using anode target material ablation, ablated plasma and background reactive gas based synthesis and purely gas phase synthesis of various different types of nanostructured materials using DPF device will discussed to establish this device as versatile tool for plasma nanotechnology.

Solution-Phase Photochemical Nanopatterning Enabled by High-Refractive-Index Beam Pen Arrays.

PubMed

Xie, Zhuang; Gordiichuk, Pavlo; Lin, Qing-Yuan; Meckes, Brian; Chen, Peng-Cheng; Sun, Lin; Du, Jingshan S; Zhu, Jinghan; Liu, Yuan; Dravid, Vinayak P; Mirkin, Chad A

2017-08-22

A high-throughput, solution-based, scanning-probe photochemical nanopatterning approach, which does not require the use of probes with subwavelength apertures, is reported. Specifically, pyramid arrays made from high-refractive-index polymeric materials were constructed and studied as patterning tools in a conventional liquid-phase beam pen lithography experiment. Two versions of the arrays were explored with either metal-coated or metal-free tips. Importantly, light can be channeled through both types of tips and the appropriate solution phase (e.g., H 2 O or CH 3 OH) and focused on subwavelength regions of a substrate to effect a photoreaction in solution that results in localized patterning of a self-assembled monolayer (SAM)-coated Au thin film substrate. Arrays with as many as 4500 pyramid-shaped probes were used to simultaneously initiate thousands of localized free-radical photoreactions (decomposition of a lithium acylphosphinate photoinitiator in an aqueous solution) that result in oxidative removal of the SAM. The technique is attractive since it allows one to rapidly generate features less than 200 nm in diameter, and the metal-free tips afford more than 10-fold higher intensity than the tips with nanoapertures over a micrometer propagation length. In principle, this mask-free method can be utilized as a versatile tool for performing a wide variety of photochemistries across multiple scales that may be important in high-throughput combinatorial screening applications related to chemistry, biology, and materials science.

Highly versatile heteroditopic ligand scaffolds for accommodating group 8, 9 & 11 heterobimetallic complexes.

PubMed

Gatus, Mark R D; Bhadbhade, Mohan; Messerle, Barbara A

2017-10-24

Two highly versatile xanthene scaffolds containing pairs of heteroditopic ligands were found to be capable of accommodating a range of transition metal ions, including Au(i), Ir(i), Ir(iii), Rh(i), and Ru(ii) to generate an array of heterobimetallic complexes. The metal complexes were fully characterised and proved to be stable in the solid and solution state, with no observed metal-metal scrambling. Heterobimetallic complexes containing the Rh(i)/Ir(i) combinations were tested as catalysts for the two-step dihydroalkoxylation reaction of alkynediols and sequential hydroamination/hydrosilylation reaction of alkynamines.

Surface plasmon resonance-enabled antibacterial digital versatile discs

NASA Astrophysics Data System (ADS)

Dou, Xuan; Chung, Pei-Yu; Jiang, Peng; Dai, Jianli

2012-02-01

We report the achievement of effective sterilization of exemplary bacteria including Escherichia coli and Geobacillus stearothermophilus spores on a digital versatile disc (DVD). The spiral arrangement of aluminum-covered pits generates strong surface plasmon resonance (SPR) absorption of near-infrared light, leading to high surface temperature that could even damage the DVD plastics. Localized protein denaturation and high sterilization efficiency have been demonstrated by using a fluorescence microscope and cell cultures. Numerical simulations have also been conducted to model the SPR properties and the surface temperature distribution of DVDs under laser illumination. The theoretical predictions agree reasonably well with the experimental results.

Versatile module for experiments with focussing neutron guides

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

Adams, T.; Pfleiderer, C.; Böni, P.

2014-09-22

We report the development of a versatile module that permits fast and reliable use of focussing neutron guides under varying scattering angles. A simple procedure for setting up the module and neutron guides is illustrated by typical intensity patterns to highlight operational aspects as well as typical parasitic artefacts. Combining a high-precision alignment table with separate housings for the neutron guides on kinematic mounts, the change-over between neutron guides with different focussing characteristics requires no readjustments of the experimental setup. Exploiting substantial gain factors, we demonstrate the performance of this versatile neutron scattering module in a study of the effectsmore » of uniaxial stress on the domain populations in the transverse spin density wave phase of single crystal Cr.« less

Tandem SUMO fusion vectors for improving soluble protein expression and purification.

PubMed

Guerrero, Fernando; Ciragan, Annika; Iwaï, Hideo

2015-12-01

Availability of highly purified proteins in quantity is crucial for detailed biochemical and structural investigations. Fusion tags are versatile tools to facilitate efficient protein purification and to improve soluble overexpression of proteins. Various purification and fusion tags have been widely used for overexpression in Escherichia coli. However, these tags might interfere with biological functions and/or structural investigations of the protein of interest. Therefore, an additional purification step to remove fusion tags by proteolytic digestion might be required. Here, we describe a set of new vectors in which yeast SUMO (SMT3) was used as the highly specific recognition sequence of ubiquitin-like protease 1, together with other commonly used solubility enhancing proteins, such as glutathione S-transferase, maltose binding protein, thioredoxin and trigger factor for optimizing soluble expression of protein of interest. This tandem SUMO (T-SUMO) fusion system was tested for soluble expression of the C-terminal domain of TonB from different organisms and for the antiviral protein scytovirin. Copyright © 2015 Elsevier Inc. All rights reserved.

Flow Cytometric Methods for Circulating Tumor Cell Isolation and Molecular Analysis.

PubMed

Bhagwat, Neha; Carpenter, Erica L

2017-01-01

Circulating tumor cells provide a non-invasive source of tumor material that can be valuable at all stages of disease management, including screening and early diagnosis, monitoring response to therapy, identifying therapeutic targets, and assessing development of drug resistance. Cells isolated from the blood of cancer patients can be used for phenotypic analysis, tumor genotyping, transcriptional profiling, as well as for ex vivo culture of isolated cells. There are a variety of novel technologies currently being developed for the detection and analysis of rare cells in circulation of cancer patients. Flow cytometry is a powerful cell analysis platform that is increasingly being used in this field of study due to its relatively high throughput and versatility with respect to the large number of commercially available antibodies and fluorescent probes available to translational and clinical researchers. More importantly, it offers the ability to easily recover viable cells with high purity that are suitable for downstream molecular analysis, thus making it an attractive technology for cancer research and as a diagnostic tool.

Programming Light-Harvesting Efficiency Using DNA Origami

PubMed Central

2016-01-01

The remarkable performance and quantum efficiency of biological light-harvesting complexes has prompted a multidisciplinary interest in engineering biologically inspired antenna systems as a possible route to novel solar cell technologies. Key to the effectiveness of biological “nanomachines” in light capture and energy transport is their highly ordered nanoscale architecture of photoactive molecules. Recently, DNA origami has emerged as a powerful tool for organizing multiple chromophores with base-pair accuracy and full geometric freedom. Here, we present a programmable antenna array on a DNA origami platform that enables the implementation of rationally designed antenna structures. We systematically analyze the light-harvesting efficiency with respect to number of donors and interdye distances of a ring-like antenna using ensemble and single-molecule fluorescence spectroscopy and detailed Förster modeling. This comprehensive study demonstrates exquisite and reliable structural control over multichromophoric geometries and points to DNA origami as highly versatile platform for testing design concepts in artificial light-harvesting networks. PMID:26906456

Single-shot velocity-map imaging of attosecond light-field control at kilohertz rate.

PubMed

Süssmann, F; Zherebtsov, S; Plenge, J; Johnson, Nora G; Kübel, M; Sayler, A M; Mondes, V; Graf, C; Rühl, E; Paulus, G G; Schmischke, D; Swrschek, P; Kling, M F

2011-09-01

High-speed, single-shot velocity-map imaging (VMI) is combined with carrier-envelope phase (CEP) tagging by a single-shot stereographic above-threshold ionization (ATI) phase-meter. The experimental setup provides a versatile tool for angle-resolved studies of the attosecond control of electrons in atoms, molecules, and nanostructures. Single-shot VMI at kHz repetition rate is realized with a highly sensitive megapixel complementary metal-oxide semiconductor camera omitting the need for additional image intensifiers. The developed camera software allows for efficient background suppression and the storage of up to 1024 events for each image in real time. The approach is demonstrated by measuring the CEP-dependence of the electron emission from ATI of Xe in strong (≈10(13) W/cm(2)) near single-cycle (4 fs) laser fields. Efficient background signal suppression with the system is illustrated for the electron emission from SiO(2) nanospheres. © 2011 American Institute of Physics

Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes.

PubMed

Thestrup, Thomas; Litzlbauer, Julia; Bartholomäus, Ingo; Mues, Marsilius; Russo, Luigi; Dana, Hod; Kovalchuk, Yuri; Liang, Yajie; Kalamakis, Georgios; Laukat, Yvonne; Becker, Stefan; Witte, Gregor; Geiger, Anselm; Allen, Taylor; Rome, Lawrence C; Chen, Tsai-Wen; Kim, Douglas S; Garaschuk, Olga; Griesinger, Christian; Griesbeck, Oliver

2014-02-01

The quality of genetically encoded calcium indicators (GECIs) has improved dramatically in recent years, but high-performing ratiometric indicators are still rare. Here we describe a series of fluorescence resonance energy transfer (FRET)-based calcium biosensors with a reduced number of calcium binding sites per sensor. These 'Twitch' sensors are based on the C-terminal domain of Opsanus troponin C. Their FRET responses were optimized by a large-scale functional screen in bacterial colonies, refined by a secondary screen in rat hippocampal neuron cultures. We tested the in vivo performance of the most sensitive variants in the brain and lymph nodes of mice. The sensitivity of the Twitch sensors matched that of synthetic calcium dyes and allowed visualization of tonic action potential firing in neurons and high resolution functional tracking of T lymphocytes. Given their ratiometric readout, their brightness, large dynamic range and linear response properties, Twitch sensors represent versatile tools for neuroscience and immunology.

Nanoimprint of a 3D structure on an optical fiber for light wavefront manipulation.

PubMed

Calafiore, Giuseppe; Koshelev, Alexander; Allen, Frances I; Dhuey, Scott; Sassolini, Simone; Wong, Edward; Lum, Paul; Munechika, Keiko; Cabrini, Stefano

2016-09-16

Integration of complex photonic structures onto optical fiber facets enables powerful platforms with unprecedented optical functionalities. Conventional nanofabrication technologies, however, do not permit viable integration of complex photonic devices onto optical fibers owing to their low throughput and high cost. In this paper we report the fabrication of a three-dimensional structure achieved by direct nanoimprint lithography on the facet of an optical fiber. Nanoimprint processes and tools were specifically developed to enable a high lithographic accuracy and coaxial alignment of the optical device with respect to the fiber core. To demonstrate the capability of this new approach, a 3D beam splitter has been designed, imprinted and optically characterized. Scanning electron microscopy and optical measurements confirmed the good lithographic capabilities of the proposed approach as well as the desired optical performance of the imprinted structure. The inexpensive solution presented here should enable advancements in areas such as integrated optics and sensing, achieving enhanced portability and versatility of fiber optic components.

384 hanging drop arrays give excellent Z-factors and allow versatile formation of co-culture spheroids.

PubMed

Hsiao, Amy Y; Tung, Yi-Chung; Qu, Xianggui; Patel, Lalit R; Pienta, Kenneth J; Takayama, Shuichi

2012-05-01

We previously reported the development of a simple, user-friendly, and versatile 384 hanging drop array plate for 3D spheroid culture and the importance of utilizing 3D cellular models in anti-cancer drug sensitivity testing. The 384 hanging drop array plate allows for high-throughput capabilities and offers significant improvements over existing 3D spheroid culture methods. To allow for practical 3D cell-based high-throughput screening and enable broader use of the plate, we characterize the robustness of the 384 hanging drop array plate in terms of assay performance and demonstrate the versatility of the plate. We find that the 384 hanging drop array plate performance is robust in fluorescence- and colorimetric-based assays through Z-factor calculations. Finally, we demonstrate different plate capabilities and applications, including: spheroid transfer and retrieval for Janus spheroid formation, sequential addition of cells for concentric layer patterning of different cell types, and culture of a wide variety of cell types. Copyright © 2011 Wiley Periodicals, Inc.

384 Hanging Drop Arrays Give Excellent Z-factors and Allow Versatile Formation of Co-culture Spheroids

PubMed Central

Hsiao, Amy Y.; Tung, Yi-Chung; Qu, Xianggui; Patel, Lalit R.; Pienta, Kenneth J.; Takayama, Shuichi

2012-01-01

We previously reported the development of a simple, user-friendly, and versatile 384 hanging drop array plate for 3D spheroid culture and the importance of utilizing 3D cellular models in anti-cancer drug sensitivity testing. The 384 hanging drop array plate allows for high-throughput capabilities and offers significant improvements over existing 3D spheroid culture methods. To allow for practical 3D cell-based high-throughput screening and enable broader use of the plate, we characterize the robustness of the 384 hanging drop array plate in terms of assay performance and demonstrate the versatility of the plate. We find that the 384 hanging drop array plate performance is robust in fluorescence- and colorimetric-based assays through z-factor calculations. Finally, we demonstrate different plate capabilities and applications, including: spheroid transfer and retrieval for Janus spheroid formation, sequential addition of cells for concentric layer patterning of different cell types, and culture of a wide variety of cell types. PMID:22161651

A fluid-filled soft robot that exhibits spontaneous switching among versatile spatiotemporal oscillatory patterns inspired by the true slime mold.

PubMed

Umedachi, Takuya; Idei, Ryo; Ito, Kentaro; Ishiguro, Akio

2013-01-01

Behavioral diversity is an essential feature of living systems, enabling them to exhibit adaptive behavior in hostile and dynamically changing environments. However, traditional engineering approaches strive to avoid, or suppress, the behavioral diversity in artificial systems to achieve high performance in specific environments for given tasks. The goals of this research include understanding how living systems exhibit behavioral diversity and using these findings to build lifelike robots that exhibit truly adaptive behaviors. To this end, we have focused on one of the most primitive forms of intelligence concerning behavioral diversity, namely, a plasmodium of true slime mold. The plasmodium is a large amoeba-like unicellular organism that does not possess any nervous system or specialized organs. However, it exhibits versatile spatiotemporal oscillatory patterns and switches spontaneously between these. Inspired by the plasmodium, we built a mathematical model that exhibits versatile oscillatory patterns and spontaneously transitions between these patterns. This model demonstrates that, in contrast to coupled nonlinear oscillators with a well-designed complex diffusion network, physically interacting mechanosensory oscillators are capable of generating versatile oscillatory patterns without changing any parameters. Thus, the results are expected to shed new light on the design scheme for lifelike robots that exhibit amazingly versatile and adaptive behaviors.

Tools for controlling protein interactions with light

PubMed Central

Tucker, Chandra L.; Vrana, Justin D.; Kennedy, Matthew J.

2014-01-01

Genetically-encoded actuators that allow control of protein-protein interactions with light, termed ‘optical dimerizers’, are emerging as new tools for experimental biology. In recent years, numerous new and versatile dimerizer systems have been developed. Here we discuss the design of optical dimerizer experiments, including choice of a dimerizer system, photoexcitation sources, and coordinate use of imaging reporters. We provide detailed protocols for experiments using two dimerization systems we previously developed, CRY2/CIB and UVR8/UVR8, for use controlling transcription, protein localization, and protein secretion with light. Additionally, we provide instructions and software for constructing a pulse-controlled LED light device for use in experiments requiring extended light treatments. PMID:25181301

Infrared Spectroscopy as a Versatile Analytical Tool for the Quantitative Determination of Antioxidants in Agricultural Products, Foods and Plants

PubMed Central

Cozzolino, Daniel

2015-01-01

Spectroscopic methods provide with very useful qualitative and quantitative information about the biochemistry and chemistry of antioxidants. Near infrared (NIR) and mid infrared (MIR) spectroscopy are considered as powerful, fast, accurate and non-destructive analytical tools that can be considered as a replacement of traditional chemical analysis. In recent years, several reports can be found in the literature demonstrating the usefulness of these methods in the analysis of antioxidants in different organic matrices. This article reviews recent applications of infrared (NIR and MIR) spectroscopy in the analysis of antioxidant compounds in a wide range of samples such as agricultural products, foods and plants. PMID:26783838

Current and future prospects for CRISPR-based tools in bacteria.

PubMed

Luo, Michelle L; Leenay, Ryan T; Beisel, Chase L

2016-05-01

CRISPR-Cas systems have rapidly transitioned from intriguing prokaryotic defense systems to powerful and versatile biomolecular tools. This article reviews how these systems have been translated into technologies to manipulate bacterial genetics, physiology, and communities. Recent applications in bacteria have centered on multiplexed genome editing, programmable gene regulation, and sequence-specific antimicrobials, while future applications can build on advances in eukaryotes, the rich natural diversity of CRISPR-Cas systems, and the untapped potential of CRISPR-based DNA acquisition. Overall, these systems have formed the basis of an ever-expanding genetic toolbox and hold tremendous potential for our future understanding and engineering of the bacterial world. © 2015 Wiley Periodicals, Inc.

Scheduling Observations of Celestial Objects for Earth Observing Sensor Calibration

NASA Technical Reports Server (NTRS)

Wilson, Truman; Xiong, Xiaoxiong

2016-01-01

Radiometric calibration of Earth-observing satellite sensors is critical for tracking on-orbit gain changes through- out the satellite's mission. The Moon, being a stable, well-characterized radiometric target, has been used effectively for tracking the relative gain changes of the reflective solar bands for the Moderate Resolution Imaging Spectroradiometer (MODIS) on board EOS AM-1 (Terra) and PM-1 (Aqua). The Moon is viewed through the MODIS space-view port, and the relative phase of the Moon is restricted to within 0.5 degrees of a chosen target phase to increase the accuracy of the calibration. These geometric restrictions require spacecraft maneuvers in order to bring space-view port into proper alignment with the position of the Moon when the phase requirement is met. In this paper, we describe a versatile tool for scheduling such maneuvers based on the required geometry and lunar phase restrictions for a general spacecraft bound instrument. The results of the scheduling tool have been verified using lunar images from Aqua and Terra MODIS after a scheduled roll maneuver was performed. This tool has also been tested for the Visible Infrared Imaging Radiometer Suite (VIIRS) and the Advanced Technology Microwave Sounder on-board the Suomi-NPP spacecraft. As an extension of this work, we have also developed a tool for scheduling views of bright stars. These stars provide another well-characterized radiometric source that can be used for sensor calibration. This tool has been implemented to determine the times in which a chosen star can be viewed by the high gain stages of the day/night band for the VIIRS instrument.

New Applications for Phage Integrases

PubMed Central

Fogg, Paul C.M.; Colloms, Sean; Rosser, Susan; Stark, Marshall; Smith, Margaret C.M.

2014-01-01

Within the last 25 years, bacteriophage integrases have rapidly risen to prominence as genetic tools for a wide range of applications from basic cloning to genome engineering. Serine integrases such as that from ϕC31 and its relatives have found an especially wide range of applications within diverse micro-organisms right through to multi-cellular eukaryotes. Here, we review the mechanisms of the two major families of integrases, the tyrosine and serine integrases, and the advantages and disadvantages of each type as they are applied in genome engineering and synthetic biology. In particular, we focus on the new areas of metabolic pathway construction and optimization, biocomputing, heterologous expression and multiplexed assembly techniques. Integrases are versatile and efficient tools that can be used in conjunction with the various extant molecular biology tools to streamline the synthetic biology production line. PMID:24857859

Ion mobility-mass spectrometry as a tool to investigate protein-ligand interactions.

PubMed

Göth, Melanie; Pagel, Kevin

2017-07-01

Ion mobility-mass spectrometry (IM-MS) is a powerful tool for the simultaneous analysis of mass, charge, size, and shape of ionic species. It allows the characterization of even low-abundant species in complex samples and is therefore particularly suitable for the analysis of proteins and their assemblies. In the last few years even complex and intractable species have been investigated successfully with IM-MS and the number of publications in this field is steadily growing. This trend article highlights recent advances in which IM-MS was used to study protein-ligand complexes and in particular focuses on the catch and release (CaR) strategy and collision-induced unfolding (CIU). Graphical Abstract Native mass spectrometry and ion mobility-mass spectrometry are versatile tools to follow the stoichiometry, energetics, and structural impact of protein-ligand binding.

Scanning electrochemical microscopy (SECM) as a tool in biosensor research.

PubMed

Stoica, Leonard; Neugebauer, Sebastian; Schuhmann, Wolfgang

2008-01-01

Scanning electrochemical microscopy (SECM) is discussed as a versatile tool to provide localized (electro)chemical information in the context of biosensor research. Advantages of localized electrochemical measurements will be discussed and a brief introduction to SECM and its operation modes will be given. Experimental challenges of the different detection modes of SECM and its applicability for different fields in biosensor research are discussed. Among these are the evaluation of immobilization techniques by probing the local distribution of biological activity, the visualization of diffusion profiles of reactants, cofactors, mediators, and products, and the elucidation of (local) kinetic parameters. The combination of SECM with other scanning-probe techniques allows to maximize the information on a given biosensing system. The potential of SECM as a tool in micro-fabrication aiming for the fabrication of microstructured biosensors will be shortly discussed.

Coupled Solid Rocket Motor Ballistics and Trajectory Modeling for Higher Fidelity Launch Vehicle Design

NASA Technical Reports Server (NTRS)

Ables, Brett

2014-01-01

Multi-stage launch vehicles with solid rocket motors (SRMs) face design optimization challenges, especially when the mission scope changes frequently. Significant performance benefits can be realized if the solid rocket motors are optimized to the changing requirements. While SRMs represent a fixed performance at launch, rapid design iterations enable flexibility at design time, yielding significant performance gains. The streamlining and integration of SRM design and analysis can be achieved with improved analysis tools. While powerful and versatile, the Solid Performance Program (SPP) is not conducive to rapid design iteration. Performing a design iteration with SPP and a trajectory solver is a labor intensive process. To enable a better workflow, SPP, the Program to Optimize Simulated Trajectories (POST), and the interfaces between them have been improved and automated, and a graphical user interface (GUI) has been developed. The GUI enables real-time visual feedback of grain and nozzle design inputs, enforces parameter dependencies, removes redundancies, and simplifies manipulation of SPP and POST's numerous options. Automating the analysis also simplifies batch analyses and trade studies. Finally, the GUI provides post-processing, visualization, and comparison of results. Wrapping legacy high-fidelity analysis codes with modern software provides the improved interface necessary to enable rapid coupled SRM ballistics and vehicle trajectory analysis. Low cost trade studies demonstrate the sensitivities of flight performance metrics to propulsion characteristics. Incorporating high fidelity analysis from SPP into vehicle design reduces performance margins and improves reliability. By flying an SRM designed with the same assumptions as the rest of the vehicle, accurate comparisons can be made between competing architectures. In summary, this flexible workflow is a critical component to designing a versatile launch vehicle model that can accommodate a volatile mission scope.

FlexED8: the first member of a fast and flexible sample-changer family for macromolecular crystallography.

PubMed

Papp, Gergely; Felisaz, Franck; Sorez, Clement; Lopez-Marrero, Marcos; Janocha, Robert; Manjasetty, Babu; Gobbo, Alexandre; Belrhali, Hassan; Bowler, Matthew W; Cipriani, Florent

2017-10-01

Automated sample changers are now standard equipment for modern macromolecular crystallography synchrotron beamlines. Nevertheless, most are only compatible with a single type of sample holder and puck. Recent work aimed at reducing sample-handling efforts and crystal-alignment times at beamlines has resulted in a new generation of compact and precise sample holders for cryocrystallography: miniSPINE and NewPin [see the companion paper by Papp et al. (2017, Acta Cryst., D73, 829-840)]. With full data collection now possible within seconds at most advanced beamlines, and future fourth-generation synchrotron sources promising to extract data in a few tens of milliseconds, the time taken to mount and centre a sample is rate-limiting. In this context, a versatile and fast sample changer, FlexED8, has been developed that is compatible with the highly successful SPINE sample holder and with the miniSPINE and NewPin sample holders. Based on a six-axis industrial robot, FlexED8 is equipped with a tool changer and includes a novel open sample-storage dewar with a built-in ice-filtering system. With seven versatile puck slots, it can hold up to 112 SPINE sample holders in uni-pucks, or 252 miniSPINE or NewPin sample holders, with 36 samples per puck. Additionally, a double gripper, compatible with the SPINE sample holders and uni-pucks, allows a reduction in the sample-exchange time from 40 s, the typical time with a standard single gripper, to less than 5 s. Computer vision-based sample-transfer monitoring, sophisticated error handling and automatic error-recovery procedures ensure high reliability. The FlexED8 sample changer has been successfully tested under real conditions on a beamline.

Recent Advances in Genome Editing Using CRISPR/Cas9.

PubMed

Ding, Yuduan; Li, Hong; Chen, Ling-Ling; Xie, Kabin

2016-01-01

The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system is a versatile tool for genome engineering that uses a guide RNA (gRNA) to target Cas9 to a specific sequence. This simple RNA-guided genome-editing technology has become a revolutionary tool in biology and has many innovative applications in different fields. In this review, we briefly introduce the Cas9-mediated genome-editing method, summarize the recent advances in CRISPR/Cas9 technology, and discuss their implications for plant research. To date, targeted gene knockout using the Cas9/gRNA system has been established in many plant species, and the targeting efficiency and capacity of Cas9 has been improved by optimizing its expression and that of its gRNA. The CRISPR/Cas9 system can also be used for sequence-specific mutagenesis/integration and transcriptional control of target genes. We also discuss off-target effects and the constraint that the protospacer-adjacent motif (PAM) puts on CRISPR/Cas9 genome engineering. To address these problems, a number of bioinformatic tools are available to help design specific gRNAs, and new Cas9 variants and orthologs with high fidelity and alternative PAM specificities have been engineered. Owing to these recent efforts, the CRISPR/Cas9 system is becoming a revolutionary and flexible tool for genome engineering. Adoption of the CRISPR/Cas9 technology in plant research would enable the investigation of plant biology at an unprecedented depth and create innovative applications in precise crop breeding.

Dose Control System in the Optima XE Single Wafer High Energy Ion Implanter

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

Satoh, Shu; Yoon, Jongyoon; David, Jonathan

2011-01-07

Photoresist outgassing can significantly compromise accurate dosimetry of high energy implants. High energy implant even at a modest beam current produces high beam powers which create significantly worse outgassing than low and medium energy implants and the outgassing continues throughout the implant due to the low dose in typical high energy implant recipes. In the previous generation of high energy implanters, dose correction by monitoring of process chamber pressure during photoresist outgassing has been used. However, as applications diversify and requirements change, the need arises for a more versatile photoresist correction system to match the versatility of a single wafermore » high energy ion implanter. We have successfully developed a new dosimetry system for the Optima XE single wafer high energy ion implanter which does not require any form of compensation due to the implant conditions. This paper describes the principles and performance of this new dose system.« less

High-throughput screening and small animal models, where are we?

PubMed Central

Giacomotto, Jean; Ségalat, Laurent

2010-01-01

Current high-throughput screening methods for drug discovery rely on the existence of targets. Moreover, most of the hits generated during screenings turn out to be invalid after further testing in animal models. To by-pass these limitations, efforts are now being made to screen chemical libraries on whole animals. One of the most commonly used animal model in biology is the murine model Mus musculus. However, its cost limit its use in large-scale therapeutic screening. In contrast, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the fish Danio rerio are gaining momentum as screening tools. These organisms combine genetic amenability, low cost and culture conditions that are compatible with large-scale screens. Their main advantage is to allow high-throughput screening in a whole-animal context. Moreover, their use is not dependent on the prior identification of a target and permits the selection of compounds with an improved safety profile. This review surveys the versatility of these animal models for drug discovery and discuss the options available at this day. PMID:20423335

A versatile and efficient high-throughput cloning tool for structural biology.

PubMed

Geertsma, Eric R; Dutzler, Raimund

2011-04-19

Methods for the cloning of large numbers of open reading frames into expression vectors are of critical importance for challenging structural biology projects. Here we describe a system termed fragment exchange (FX) cloning that facilitates the high-throughput generation of expression constructs. The method is based on a class IIS restriction enzyme and negative selection markers. FX cloning combines attractive features of established recombination- and ligation-independent cloning methods: It allows the straightforward transfer of an open reading frame into a variety of expression vectors and is highly efficient and very economic in its use. In addition, FX cloning avoids the common but undesirable feature of significantly extending target open reading frames with cloning related sequences, as it leaves a minimal seam of only a single extra amino acid to either side of the protein. The method has proven to be very robust and suitable for all common pro- and eukaryotic expression systems. It considerably speeds up the generation of expression constructs compared to traditional methods and thus facilitates a broader expression screening.

Novel Strategy to Evaluate Infectious Salmon Anemia Virus Variants by High Resolution Melting

PubMed Central

Sepúlveda, Dagoberto; Cárdenas, Constanza; Carmona, Marisela; Marshall, Sergio H.

2012-01-01

Genetic variability is a key problem in the prevention and therapy of RNA-based virus infections. Infectious Salmon Anemia virus (ISAv) is an RNA virus which aggressively attacks salmon producing farms worldwide and in particular in Chile. Just as with most of the Orthomyxovirus, ISAv displays high variability in its genome which is reflected by a wider infection potential, thus hampering management and prevention of the disease. Although a number of widely validated detection procedures exist, in this case there is a need of a more complex approach to the characterization of virus variability. We have adapted a procedure of High Resolution Melting (HRM) as a fine-tuning technique to fully differentiate viral variants detected in Chile and projected to other infective variants reported elsewhere. Out of the eight viral coding segments, the technique was adapted using natural Chilean variants for two of them, namely segments 5 and 6, recognized as virulence-associated factors. Our work demonstrates the versatility of the technique as well as its superior resolution capacity compared with standard techniques currently in use as key diagnostic tools. PMID:22719837

20-W 1952-nm tandem hybrid single and double clad TDFA

NASA Astrophysics Data System (ADS)

Romano, Clément; Tench, Robert E.; Delavaux, Jean-Marc

2018-02-01

A simple engineering design is important for achieving high Thulium-doped amplifier (TDFA) performance such as good power conversion, low noise figure (NF), scalable output power, high gain, and stable operation over a large dynamic range. In this paper we report the design, performance, and simulation of two stage high-power 1952 nm hybrid single and double clad TDFAs. The first stage of our hybrid amplifier is a single clad design, and the second stage is a double clad design. We demonstrate TDFAs with an output power greater than 20 W with single-frequency narrow linewidth (i.e. MHz) input signals at both 1952 and 2004 nm. An optical 10 dB bandwidth of 80 nm is derived from the ASE spectrum. The power stage is constructed with 10 μm core active fibers showing a maximum optical slope efficiency greater than 50 %. The experimental results lead to a 1 dB agreement with our simulation tool developed for single clad and double clad TDFAs. Overall this hybrid amplifier offers versatile features with the potential of much higher output power.

Selection and use of crystallization inhibitors for matrix-type transdermal drug-delivery systems containing sex steroids.

PubMed

Lipp, R

1998-12-01

The purpose of this study was to stabilize transdermal drug-delivery systems (TDDS) highly loaded with sex steroids against recrystallization of drugs during storage. To facilitate the selection of potential crystallization inhibitors a drug-excipient interaction test was also established. Analysis of the thermal behaviour of 1:1 steroid-excipient mixtures by differential scanning calorimetry (DSC) revealed that oestradiol and gestodene interact strongly with silicone dioxide and povidones, e.g. povidone K12. The addition of povidone K12 to polyacrylate-based matrix TDDS containing either 3% oestradiol or 2% gestodene resulted in stable systems which did not recrystallize during storage at 25 degrees C for more than 5 years. Significant recrystallization was, on the other hand, observed in non-stabilized reference patches even after 1 to 2 months storage. The DSC screening model proved very effective for selection of inhibitors of the crystallization of sex steroids in matrix TDDS. The crystallization inhibitor approach is a highly versatile stabilization tool for matrix patches containing high concentrations of sex steroids.

Digital Imprinting of RNA Recognition and Processing on a Self-Assembled Nucleic Acid Matrix

NASA Astrophysics Data System (ADS)

Redhu, Shiv K.; Castronovo, Matteo; Nicholson, Allen W.

2013-08-01

The accelerating progress of research in nanomedicine and nanobiotechnology has included initiatives to develop highly-sensitive, high-throughput methods to detect biomarkers at the single-cell level. Current sensing approaches, however, typically involve integrative instrumentation that necessarily must balance sensitivity with rapidity in optimizing biomarker detection quality. We show here that laterally-confined, self-assembled monolayers of a short, double-stranded(ds)[RNA-DNA] chimera enable permanent digital detection of dsRNA-specific inputs. The action of ribonuclease III and the binding of an inactive, dsRNA-binding mutant can be permanently recorded by the input-responsive action of a restriction endonuclease that cleaves an ancillary reporter site within the dsDNA segment. The resulting irreversible height change of the arrayed ds[RNA-DNA], as measured by atomic force microscopy, provides a distinct digital output for each dsRNA-specific input. These findings provide the basis for developing imprinting-based bio-nanosensors, and reveal the versatility of AFM as a tool for characterizing the behaviour of highly-crowded biomolecules at the nanoscale.

Three Hundred Patients Treated with Ultrapulsed 980 nm Diode Laser for Skin Disorders

PubMed Central

Wollina, Uwe

2016-01-01

The use of lasers in skin diseases is quite common. In contrast to other laser types, medical literature about 980 nm ultrapulsed diode laser is sparse in dermatology. Herein, we report the use of ultrapulsed diode 980 nm laser in 300 patients with vascular lesions, cysts and pseudocysts, infectious disease, and malignant tumors. This laser is a versatile tool with excellent safety and efficacy in the hands of the experienced user. PMID:27688445

A Tetrazine-Labile Vinyl Ether Benzyloxycarbonyl Protecting Group (VeZ): An Orthogonal Tool for Solid-Phase Peptide Chemistry.

PubMed

Staderini, Matteo; Gambardella, Alessia; Lilienkampf, Annamaria; Bradley, Mark

2018-06-01

The vinyl ether benzyloxycarbonyl (VeZ) protecting group is selectively cleaved by treatment with tetrazines via an inverse electron-demand Diels-Alder reaction. This represents a new orthogonal protecting group for solid-phase peptide synthesis, with Fmoc-Lys(VeZ)-OH as a versatile alternative to Fmoc-Lys(Alloc)-OH and Fmoc-Lys(Dde)-OH, as demonstrated by the synthesis of two biologically relevant cyclic peptides.

Chronopotentiometry of refractory metals, actinides and oxyanions in molten salts: A review

NASA Technical Reports Server (NTRS)

Bansal, Narottam P.

1992-01-01

The applications of chronopotentiometry to the study of electrochemical behavior of three technologically important areas of refractory metals, actinides, and oxyanions in molten salts are critically reviewed. Chronopotentiometry is a very versatile diagnostic tool to understand the reaction mechanism of the electrode processes for the electrochemical reduction/oxidation of these electroactive species in molten salt solutions. Well adherent, compact, and uniformly thick coatings of refractory metals may be electrodeposited from their solutions in molten salts.

A nanoparticle-based epigenetic modulator for efficient gene modulation

NASA Astrophysics Data System (ADS)

Pongkulapa, Thanapat

Modulation of gene expression through chromatin remodeling involves epigenetic mechanisms, such as histone acetylation. Acetylation is tightly regulated by two classes of enzymes, histone acetyltransferases (HATs) and histone deacetylases (HDACs). Molecules that can regulate these enzymes by altering (activating or inhibiting) their functions have become a valuable tool for understanding cell development and diseases. HAT activators, i.e. N-(4-Chloro-(3-trifluoromethyl)phenyl)-2-ethoxybenzamide (CTB), have shown a therapeutic potential for many diseases, including cancer and neurodegeneration. However, these compounds encounter a solubility and a membrane permeability issue, which restricts their full potential for practical usage, especially for in vivo applications. To address this issue, in this work, we developed a nanoparticle-based HAT activator CTB, named Au-CTB, by incorporating a new CTB analogue onto gold nanoparticles (AuNPs) along with a poly(ethylene glycol) moiety and a nuclear localization signal (NLS) peptide to assist with solubility and membrane permeability. We found that our new CTB analogue and Au-CTB could activate HAT activity. Significantly, an increase in potency to activate HAT activity by Au-CTB proved the effectiveness of using the nanoparticle delivery platform. In addition, the versatility of Au-CTB platform permits the attachment of multiple ligands with tunable ratios on the nanoparticle surface via facile surface functionalization of gold nanoparticles. Due to its high delivery efficiency and versatility, Au-CTB can be a powerful platform for applications in epigenetic regulation of gene expression.

Eye-safe digital 3-D sensing for space applications

NASA Astrophysics Data System (ADS)

Beraldin, J.-Angelo; Blais, Francois; Rioux, Marc; Cournoyer, Luc; Laurin, Denis G.; MacLean, Steve G.

2000-01-01

This paper focuses on the characteristics and performance of an eye-safe laser range scanner (LARS) with short- and medium-range 3D sensing capabilities for space applications. This versatile LARS is a precision measurement tool that will complement the current Canadian Space Vision System. The major advantages of the LARS over conventional video- based imaging are its ability to operate with sunlight shining directly into the scanner and its immunity to spurious reflections and shadows, which occur frequently in space. Because the LARS is equipped with two high-speed galvanometers to steer the laser beam, any spatial location within the field of view of the camera can be addressed. This versatility enables the LARS to operate in two basis scan pattern modes: (1) variable-scan-resolution mode and (2) raster-scan mode. In the variable-resolution mode, the LARS can search and track targets and geometrical features on objects located within a field of view of 30 by 30 deg and with corresponding range from about 0.5 to 2000 m. The tracking mode can reach a refresh rate of up to 130 Hz. The raster mode is used primarily for the measurement of registered range and intensity information on large stationary objects. It allows, among other things, target- based measurements, feature-based measurements, and surface- reflectance monitoring. The digitizing and modeling of human subjects, cargo payloads, and environments are also possible with the LARS. Examples illustrating its capabilities are presented.

DataHigh: Graphical user interface for visualizing and interacting with high-dimensional neural activity

PubMed Central

Cowley, Benjamin R.; Kaufman, Matthew T.; Butler, Zachary S.; Churchland, Mark M.; Ryu, Stephen I.; Shenoy, Krishna V.; Yu, Byron M.

2014-01-01

Objective Analyzing and interpreting the activity of a heterogeneous population of neurons can be challenging, especially as the number of neurons, experimental trials, and experimental conditions increases. One approach is to extract a set of latent variables that succinctly captures the prominent co-fluctuation patterns across the neural population. A key problem is that the number of latent variables needed to adequately describe the population activity is often greater than three, thereby preventing direct visualization of the latent space. By visualizing a small number of 2-d projections of the latent space or each latent variable individually, it is easy to miss salient features of the population activity. Approach To address this limitation, we developed a Matlab graphical user interface (called DataHigh) that allows the user to quickly and smoothly navigate through a continuum of different 2-d projections of the latent space. We also implemented a suite of additional visualization tools (including playing out population activity timecourses as a movie and displaying summary statistics, such as covariance ellipses and average timecourses) and an optional tool for performing dimensionality reduction. Main results To demonstrate the utility and versatility of DataHigh, we used it to analyze single-trial spike count and single-trial timecourse population activity recorded using a multi-electrode array, as well as trial-averaged population activity recorded using single electrodes. Significance DataHigh was developed to fulfill a need for visualization in exploratory neural data analysis, which can provide intuition that is critical for building scientific hypotheses and models of population activity. PMID:24216250

DataHigh: graphical user interface for visualizing and interacting with high-dimensional neural activity

NASA Astrophysics Data System (ADS)

Cowley, Benjamin R.; Kaufman, Matthew T.; Butler, Zachary S.; Churchland, Mark M.; Ryu, Stephen I.; Shenoy, Krishna V.; Yu, Byron M.

2013-12-01

Objective. Analyzing and interpreting the activity of a heterogeneous population of neurons can be challenging, especially as the number of neurons, experimental trials, and experimental conditions increases. One approach is to extract a set of latent variables that succinctly captures the prominent co-fluctuation patterns across the neural population. A key problem is that the number of latent variables needed to adequately describe the population activity is often greater than 3, thereby preventing direct visualization of the latent space. By visualizing a small number of 2-d projections of the latent space or each latent variable individually, it is easy to miss salient features of the population activity. Approach. To address this limitation, we developed a Matlab graphical user interface (called DataHigh) that allows the user to quickly and smoothly navigate through a continuum of different 2-d projections of the latent space. We also implemented a suite of additional visualization tools (including playing out population activity timecourses as a movie and displaying summary statistics, such as covariance ellipses and average timecourses) and an optional tool for performing dimensionality reduction. Main results. To demonstrate the utility and versatility of DataHigh, we used it to analyze single-trial spike count and single-trial timecourse population activity recorded using a multi-electrode array, as well as trial-averaged population activity recorded using single electrodes. Significance. DataHigh was developed to fulfil a need for visualization in exploratory neural data analysis, which can provide intuition that is critical for building scientific hypotheses and models of population activity.

DataHigh: graphical user interface for visualizing and interacting with high-dimensional neural activity.

PubMed

Cowley, Benjamin R; Kaufman, Matthew T; Butler, Zachary S; Churchland, Mark M; Ryu, Stephen I; Shenoy, Krishna V; Yu, Byron M

2013-12-01

Analyzing and interpreting the activity of a heterogeneous population of neurons can be challenging, especially as the number of neurons, experimental trials, and experimental conditions increases. One approach is to extract a set of latent variables that succinctly captures the prominent co-fluctuation patterns across the neural population. A key problem is that the number of latent variables needed to adequately describe the population activity is often greater than 3, thereby preventing direct visualization of the latent space. By visualizing a small number of 2-d projections of the latent space or each latent variable individually, it is easy to miss salient features of the population activity. To address this limitation, we developed a Matlab graphical user interface (called DataHigh) that allows the user to quickly and smoothly navigate through a continuum of different 2-d projections of the latent space. We also implemented a suite of additional visualization tools (including playing out population activity timecourses as a movie and displaying summary statistics, such as covariance ellipses and average timecourses) and an optional tool for performing dimensionality reduction. To demonstrate the utility and versatility of DataHigh, we used it to analyze single-trial spike count and single-trial timecourse population activity recorded using a multi-electrode array, as well as trial-averaged population activity recorded using single electrodes. DataHigh was developed to fulfil a need for visualization in exploratory neural data analysis, which can provide intuition that is critical for building scientific hypotheses and models of population activity.

Diverse Application of Magnetic Resonance Imaging for Mouse Phenotyping

PubMed Central

Wu, Yijen L.; Lo, Cecilia W.

2017-01-01

Small animal models, particularly mouse models, of human diseases are becoming an indispensable tool for biomedical research. Studies in animal models have provided important insights into the etiology of diseases and accelerated the development of therapeutic strategies. Detailed phenotypic characterization is essential, both for the development of such animal models and mechanistic studies into disease pathogenesis and testing the efficacy of experimental therapeutics. Magnetic Resonance Imaging (MRI) is a versatile and non-invasive imaging modality with excellent penetration depth, tissue coverage, and soft tissue contrast. MRI, being a multi-modal imaging modality, together with proven imaging protocols and availability of good contrast agents, is ideally suited for phenotyping mutant mouse models. Here we describe the applications of MRI for phenotyping structural birth defects involving the brain, heart, and kidney in mice. The versatility of MRI and its ease of use are well suited to meet the rapidly increasing demands for mouse phenotyping in the coming age of functional genomics. PMID:28544650

Steric antisense inhibition of AMPA receptor Q/R editing reveals tight coupling to intronic editing sites and splicing

PubMed Central

Penn, Andrew C.; Balik, Ales; Greger, Ingo H.

2013-01-01

Adenosine-to-Inosine (A-to-I) RNA editing is a post-transcriptional mechanism, evolved to diversify the transcriptome in metazoa. In addition to wide-spread editing in non-coding regions protein recoding by RNA editing allows for fine tuning of protein function. Functional consequences are only known for some editing sites and the combinatorial effect between multiple sites (functional epistasis) is currently unclear. Similarly, the interplay between RNA editing and splicing, which impacts on post-transcriptional gene regulation, has not been resolved. Here, we describe a versatile antisense approach, which will aid resolving these open questions. We have developed and characterized morpholino oligos targeting the most efficiently edited site—the AMPA receptor GluA2 Q/R site. We show that inhibition of editing closely correlates with intronic editing efficiency, which is linked to splicing efficiency. In addition to providing a versatile tool our data underscore the unique efficiency of a physiologically pivotal editing site. PMID:23172291

BioPhotonics workstation: A versatile setup for simultaneous optical manipulation, heat stress, and intracellular pH measurements of a live yeast cell

NASA Astrophysics Data System (ADS)

Aabo, Thomas; Banás, Andrew Raphael; Glückstad, Jesper; Siegumfeldt, Henrik; Arneborg, Nils

2011-08-01

In this study we have modified the BioPhotonics workstation (BWS), which allows for using long working distance objective for optical trapping, to include traditional epi-fluorescence microscopy, using the trapping objectives. We have also added temperature regulation of sample stage, allowing for fast temperature variations while trapping. Using this modified BWS setup, we investigated the internal pH (pHi) response and membrane integrity of an optically trapped Saccharomyces cerevisiae cell at 5 mW subject to increasing temperatures. The pHi of the cell is obtained from the emission of 5-(and-6)-carboxyfluorescein diacetate, succinimidyl ester, at 435 and 485 nm wavelengths, while the permeability is indicated by the fluorescence of propidium iodide. We present images mapping the pHi and permeability of the cell at different temperatures and with enough spatial resolution to localize these attributes within the cell. The combined capability of optical trapping, fluorescence microscopy and temperature regulation offers a versatile tool for biological research.

Tattoo-Paper Transfer as a Versatile Platform for All-Printed Organic Edible Electronics.

PubMed

Bonacchini, Giorgio E; Bossio, Caterina; Greco, Francesco; Mattoli, Virgilio; Kim, Yun-Hi; Lanzani, Guglielmo; Caironi, Mario

2018-04-01

The use of natural or bioinspired materials to develop edible electronic devices is a potentially disruptive technology that can boost point-of-care testing. The technology exploits devices that can be safely ingested, along with pills or even food, and operated from within the gastrointestinal tract. Ingestible electronics can potentially target a significant number of biomedical applications, both as therapeutic and diagnostic tool, and this technology may also impact the food industry, by providing ingestible or food-compatible electronic tags that can "smart" track goods and monitor their quality along the distribution chain. Temporary tattoo-paper is hereby proposed as a simple and versatile platform for the integration of electronics onto food and pharmaceutical capsules. In particular, the fabrication of all-printed organic field-effect transistors on untreated commercial tattoo-paper, and their subsequent transfer and operation on edible substrates with a complex nonplanar geometry is demonstrated. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

GO2OGS 1.0: a versatile workflow to integrate complex geological information with fault data into numerical simulation models

NASA Astrophysics Data System (ADS)

Fischer, T.; Naumov, D.; Sattler, S.; Kolditz, O.; Walther, M.

2015-11-01

We offer a versatile workflow to convert geological models built with the ParadigmTM GOCAD© (Geological Object Computer Aided Design) software into the open-source VTU (Visualization Toolkit unstructured grid) format for usage in numerical simulation models. Tackling relevant scientific questions or engineering tasks often involves multidisciplinary approaches. Conversion workflows are needed as a way of communication between the diverse tools of the various disciplines. Our approach offers an open-source, platform-independent, robust, and comprehensible method that is potentially useful for a multitude of environmental studies. With two application examples in the Thuringian Syncline, we show how a heterogeneous geological GOCAD model including multiple layers and faults can be used for numerical groundwater flow modeling, in our case employing the OpenGeoSys open-source numerical toolbox for groundwater flow simulations. The presented workflow offers the chance to incorporate increasingly detailed data, utilizing the growing availability of computational power to simulate numerical models.

Octanol-assisted liposome assembly on chip

PubMed Central

Deshpande, Siddharth; Caspi, Yaron; Meijering, Anna E. C.; Dekker, Cees

2016-01-01

Liposomes are versatile supramolecular assemblies widely used in basic and applied sciences. Here we present a novel microfluidics-based method, octanol-assisted liposome assembly (OLA), to form monodisperse, cell-sized (5–20 μm), unilamellar liposomes with excellent encapsulation efficiency. Akin to bubble blowing, an inner aqueous phase and a surrounding lipid-carrying 1-octanol phase is pinched off by outer fluid streams. Such hydrodynamic flow focusing results in double-emulsion droplets that spontaneously develop a side-connected 1-octanol pocket. Owing to interfacial energy minimization, the pocket splits off to yield fully assembled solvent-free liposomes within minutes. This solves the long-standing fundamental problem of prolonged presence of residual oil in the liposome bilayer. We demonstrate the unilamellarity of liposomes with functional α-haemolysin protein pores in the membrane and validate the biocompatibility by inner leaflet localization of bacterial divisome proteins (FtsZ and ZipA). OLA offers a versatile platform for future analytical tools, delivery systems, nanoreactors and synthetic cells. PMID:26794442

Octanol-assisted liposome assembly on chip.

PubMed

Deshpande, Siddharth; Caspi, Yaron; Meijering, Anna E C; Dekker, Cees

2016-01-22

Liposomes are versatile supramolecular assemblies widely used in basic and applied sciences. Here we present a novel microfluidics-based method, octanol-assisted liposome assembly (OLA), to form monodisperse, cell-sized (5-20 μm), unilamellar liposomes with excellent encapsulation efficiency. Akin to bubble blowing, an inner aqueous phase and a surrounding lipid-carrying 1-octanol phase is pinched off by outer fluid streams. Such hydrodynamic flow focusing results in double-emulsion droplets that spontaneously develop a side-connected 1-octanol pocket. Owing to interfacial energy minimization, the pocket splits off to yield fully assembled solvent-free liposomes within minutes. This solves the long-standing fundamental problem of prolonged presence of residual oil in the liposome bilayer. We demonstrate the unilamellarity of liposomes with functional α-haemolysin protein pores in the membrane and validate the biocompatibility by inner leaflet localization of bacterial divisome proteins (FtsZ and ZipA). OLA offers a versatile platform for future analytical tools, delivery systems, nanoreactors and synthetic cells.

Octanol-assisted liposome assembly on chip

NASA Astrophysics Data System (ADS)

Deshpande, Siddharth; Caspi, Yaron; Meijering, Anna E. C.; Dekker, Cees

2016-01-01

Liposomes are versatile supramolecular assemblies widely used in basic and applied sciences. Here we present a novel microfluidics-based method, octanol-assisted liposome assembly (OLA), to form monodisperse, cell-sized (5-20 μm), unilamellar liposomes with excellent encapsulation efficiency. Akin to bubble blowing, an inner aqueous phase and a surrounding lipid-carrying 1-octanol phase is pinched off by outer fluid streams. Such hydrodynamic flow focusing results in double-emulsion droplets that spontaneously develop a side-connected 1-octanol pocket. Owing to interfacial energy minimization, the pocket splits off to yield fully assembled solvent-free liposomes within minutes. This solves the long-standing fundamental problem of prolonged presence of residual oil in the liposome bilayer. We demonstrate the unilamellarity of liposomes with functional α-haemolysin protein pores in the membrane and validate the biocompatibility by inner leaflet localization of bacterial divisome proteins (FtsZ and ZipA). OLA offers a versatile platform for future analytical tools, delivery systems, nanoreactors and synthetic cells.

Nanoporous hard data: optical encoding of information within nanoporous anodic alumina photonic crystals.

PubMed

Santos, Abel; Law, Cheryl Suwen; Pereira, Taj; Losic, Dusan

2016-04-21

Herein, we present a method for storing binary data within the spectral signature of nanoporous anodic alumina photonic crystals. A rationally designed multi-sinusoidal anodisation approach makes it possible to engineer the photonic stop band of nanoporous anodic alumina with precision. As a result, the transmission spectrum of these photonic nanostructures can be engineered to feature well-resolved and selectively positioned characteristic peaks across the UV-visible spectrum. Using this property, we implement an 8-bit binary code and assess the versatility and capability of this system by a series of experiments aiming to encode different information within the nanoporous anodic alumina photonic crystals. The obtained results reveal that the proposed nanosized platform is robust, chemically stable, versatile and has a set of unique properties for data storage, opening new opportunities for developing advanced nanophotonic tools for a wide range of applications, including sensing, photonic tagging, self-reporting drug releasing systems and secure encoding of information.

BAMS2 Workspace: a comprehensive and versatile neuroinformatic platform for collating and processing neuroanatomical connections

PubMed Central

Bota, Mihail; Talpalaru, Ştefan; Hintiryan, Houri; Dong, Hong-Wei; Swanson, Larry W.

2014-01-01

We present in this paper a novel neuroinformatic platform, the BAMS2 Workspace (http://brancusi1.usc.edu), designed for storing and processing information about gray matter region axonal connections. This de novo constructed module allows registered users to directly collate their data by using a simple and versatile visual interface. It also allows construction and analysis of sets of connections associated with gray matter region nomenclatures from any designated species. The Workspace includes a set of tools allowing the display of data in matrix and networks formats, and the uploading of processed information in visual, PDF, CSV, and Excel formats. Finally, the Workspace can be accessed anonymously by third party systems to create individualized connectivity networks. All features of the BAMS2 Workspace are described in detail, and are demonstrated with connectivity reports collated in BAMS and associated with the rat sensory-motor cortex, medial frontal cortex, and amygdalar regions. PMID:24668342

Point-of-care diagnostic assay for the detection of Zika virus using the recombinase polymerase amplification method.

PubMed

Vasileva Wand, Nadina I; Bonney, Laura C; Watson, Robert J; Graham, Victoria; Hewson, Roger

2018-06-13

The sudden and explosive expansion of Zika virus (ZIKV) from the African continent through Oceania and culminating in the outbreak in South America has highlighted the importance of new rapid point-of-care diagnostic tools for the control and prevention of transmission. ZIKV infection has devastating consequences, such as neurological congenital malformations in infants born to infected mothers and Guillain-Barré syndrome in adults. Additionally, its potential for transmission through vector bites, as well as from person to person through blood transfusions and sexual contact, are important considerations for prompt diagnosis. Recombinase polymerase amplification (RPA), an isothermal method, was developed as an alternative field-applicable assay to PCR. Here we report the development of a novel ZIKV real-time reverse transcriptase RPA (RT-RPA) assay capable of detecting a range of different ZIKV strains from a variety of geographical locations. The ZIKV RT-RPA was shown to be highly sensitive, being capable of detecting as few as five copies of target nucleic acid per reaction, and suitable for use with a battery-operated portable device. The ZIKV RT-RPA demonstrated 100 % specificity and 83 % sensitivity in clinical samples. Furthermore, we determined that the ZIKV RT-RPA is a versatile assay that can be applied to crude samples, such as saliva and serum, and can be used as a vector surveillance tool on crude mosquito homogenates. Therefore, the developed ZIKV RT-RPA is a useful diagnostic tool that can be transferred to a resource-limited location, eliminating the need for a specialized and sophisticated laboratory environment and highly trained staff.

DUK - A Fast and Efficient Kmer Based Sequence Matching Tool

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

Li, Mingkun; Copeland, Alex; Han, James

2011-03-21

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

Chromatibody, a novel non-invasive molecular tool to explore and manipulate chromatin in living cells

PubMed Central

Jullien, Denis; Vignard, Julien; Fedor, Yoann; Béry, Nicolas; Olichon, Aurélien; Crozatier, Michèle; Erard, Monique; Cassard, Hervé; Ducommun, Bernard; Salles, Bernard

2016-01-01

ABSTRACT Chromatin function is involved in many cellular processes, its visualization or modification being essential in many developmental or cellular studies. Here, we present the characterization of chromatibody, a chromatin-binding single-domain, and explore its use in living cells. This non-intercalating tool specifically binds the heterodimer of H2A–H2B histones and displays a versatile reactivity, specifically labeling chromatin from yeast to mammals. We show that this genetically encoded probe, when fused to fluorescent proteins, allows non-invasive real-time chromatin imaging. Chromatibody is a dynamic chromatin probe that can be modulated. Finally, chromatibody is an efficient tool to target an enzymatic activity to the nucleosome, such as the DNA damage-dependent H2A ubiquitylation, which can modify this epigenetic mark at the scale of the genome and result in DNA damage signaling and repair defects. Taken together, these results identify chromatibody as a universal non-invasive tool for either in vivo chromatin imaging or to manipulate the chromatin landscape. PMID:27206857

Use of software tools in the development of real time software systems

NASA Technical Reports Server (NTRS)

Garvey, R. C.

1981-01-01

The transformation of a preexisting software system into a larger and more versatile system with different mission requirements is discussed. The history of this transformation is used to illustrate the use of structured real time programming techniques and tools to produce maintainable and somewhat transportable systems. The predecessor system is a single ground diagnostic system; its purpose is to exercise a computer controlled hardware set prior to its deployment in its functional environment, as well as test the equipment set by supplying certain well known stimulas. The successor system (FTE) is required to perform certain testing and control functions while this hardware set is in its functional environment. Both systems must deal with heavy user input/output loads and a new I/O requirement is included in the design of the FTF system. Human factors are enhanced by adding an improved console interface and special function keyboard handler. The additional features require the inclusion of much new software to the original set from which FTF was developed. As a result, it is necessary to split the system into a duel programming configuration with high rates of interground communications. A generalized information routing mechanism is used to support this configuration.

Measuring fish and their physical habitats: Versatile 2D and 3D video techniques with user-friendly software

USGS Publications Warehouse

Neuswanger, Jason R.; Wipfli, Mark S.; Rosenberger, Amanda E.; Hughes, Nicholas F.

2017-01-01

Applications of video in fisheries research range from simple biodiversity surveys to three-dimensional (3D) measurement of complex swimming, schooling, feeding, and territorial behaviors. However, researchers lack a transparently developed, easy-to-use, general purpose tool for 3D video measurement and event logging. Thus, we developed a new measurement system, with freely available, user-friendly software, easily obtained hardware, and flexible underlying mathematical methods capable of high precision and accuracy. The software, VidSync, allows users to efficiently record, organize, and navigate complex 2D or 3D measurements of fish and their physical habitats. Laboratory tests showed submillimetre accuracy in length measurements of 50.8 mm targets at close range, with increasing errors (mostly <1%) at longer range and for longer targets. A field test on juvenile Chinook salmon (Oncorhynchus tshawytscha) feeding behavior in Alaska streams found that individuals within aggregations avoided the immediate proximity of their competitors, out to a distance of 1.0 to 2.9 body lengths. This system makes 3D video measurement a practical tool for laboratory and field studies of aquatic or terrestrial animal behavior and ecology.

The CRISPR/Cas Genome-Editing Tool: Application in Improvement of Crops

PubMed Central

Khatodia, Surender; Bhatotia, Kirti; Passricha, Nishat; Khurana, S. M. P.; Tuteja, Narendra

2016-01-01

The Clustered Regularly Interspaced Short Palindromic Repeats associated Cas9/sgRNA system is a novel targeted genome-editing technique derived from bacterial immune system. It is an inexpensive, easy, most user friendly and rapidly adopted genome editing tool transforming to revolutionary paradigm. This technique enables precise genomic modifications in many different organisms and tissues. Cas9 protein is an RNA guided endonuclease utilized for creating targeted double-stranded breaks with only a short RNA sequence to confer recognition of the target in animals and plants. Development of genetically edited (GE) crops similar to those developed by conventional or mutation breeding using this potential technique makes it a promising and extremely versatile tool for providing sustainable productive agriculture for better feeding of rapidly growing population in a changing climate. The emerging areas of research for the genome editing in plants include interrogating gene function, rewiring the regulatory signaling networks and sgRNA library for high-throughput loss-of-function screening. In this review, we have described the broad applicability of the Cas9 nuclease mediated targeted plant genome editing for development of designer crops. The regulatory uncertainty and social acceptance of plant breeding by Cas9 genome editing have also been described. With this powerful and innovative technique the designer GE non-GM plants could further advance climate resilient and sustainable agriculture in the future and maximizing yield by combating abiotic and biotic stresses. PMID:27148329

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

PubMed Central

Jaeger, Sébastien; Thieffry, Denis

2017-01-01

Abstract Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. PMID:28591841

Chipster: user-friendly analysis software for microarray and other high-throughput data.

PubMed

Kallio, M Aleksi; Tuimala, Jarno T; Hupponen, Taavi; Klemelä, Petri; Gentile, Massimiliano; Scheinin, Ilari; Koski, Mikko; Käki, Janne; Korpelainen, Eija I

2011-10-14

The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available.

Multicellular tumor spheroids as an in vivo-like tumor model for three-dimensional imaging of chemotherapeutic and nano material cellular penetration.

PubMed

Ma, Hui-li; Jiang, Qiao; Han, Siyuan; Wu, Yan; Cui Tomshine, Jin; Wang, Dongliang; Gan, Yaling; Zou, Guozhang; Liang, Xing-Jie

2012-01-01

We present a flexible and highly reproducible method using three-dimensional (3D) multicellular tumor spheroids to quantify chemotherapeutic and nanoparticle penetration properties in vitro. We generated HeLa cell-derived spheroids using the liquid overlay method. To properly characterize HeLa spheroids, scanning electron microscopy, transmission electron microscopy, and multiphoton microscopy were used to obtain high-resolution 3D images of HeLa spheroids. Next, pairing high-resolution optical characterization techniques with flow cytometry, we quantitatively compared the penetration of doxorubicin, quantum dots, and synthetic micelles into 3D HeLa spheroid versus HeLa cells grown in a traditional two-dimensional culturing system. Our data revealed that 3D cultured HeLa cells acquired several clinically relevant morphologic and cellular characteristics (such as resistance to chemotherapeutics) often found in human solid tumors. These characteristic, however, could not be captured using conventional two-dimensional cell culture techniques. This study demonstrated the remarkable versatility of HeLa spheroid 3D imaging. In addition, our results revealed the capability of HeLa spheroids to function as a screening tool for nanoparticles or synthetic micelles that, due to their inherent size, charge, and hydrophobicity, can penetrate into solid tumors and act as delivery vehicles for chemotherapeutics. The development of this image-based, reproducible, and quantifiable in vitro HeLa spheroid screening tool will greatly aid future exploration of chemotherapeutics and nanoparticle delivery into solid tumors.

Chipster: user-friendly analysis software for microarray and other high-throughput data

PubMed Central

2011-01-01

Background The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software. Results Chipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies. Conclusions Chipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available. PMID:21999641

TOPICAL REVIEW: Semiconductors for terahertz photonics applications

NASA Astrophysics Data System (ADS)

Krotkus, Arūnas

2010-07-01

Generation and measurement of ultrashort, subpicosecond pulses of electromagnetic radiation with their characteristic Fourier spectra that reach far into terahertz (THz) frequency range has recently become a versatile tool of far-infrared spectroscopy and imaging. This technique, THz time-domain spectroscopy, in addition to a femtosecond pulse laser, requires semiconductor components manufactured from materials with a short photoexcited carrier lifetime, high carrier mobility and large dark resistivity. Here we will review the most important developments in the field of investigation of such materials. The main characteristics of low-temperature-grown or ion-implanted GaAs and semiconducting compounds sensitive in the wavelength ranges around 1 µm and 1.5 µm will be surveyed. The second part of the paper is devoted to the effect of surface emission of THz transients from semiconductors illuminated by femtosecond laser pulses. The main physical mechanisms leading to this emission as well as their manifestation in various crystals will be described.

Solution Exchange Lithography: A Versatile Tool for Sequential Surface Engineering

NASA Astrophysics Data System (ADS)

Pester, Christian; Mattson, Kaila; Bothman, David; Klinger, Daniel; Lee, Kenneth; Discekici, Emre; Narupai, Benjaporn; Hawker, Craig

The covalent attachment of polymers has emerged as a viable strategy for the preparation of multi-functional surfaces. Patterned, surface-grafted polymer brushes provide spatial control over wetting, mechanical, biological or electronic properties, and allow fabrication of `intelligent' substrates which selectively adapt to their environment. However, the route towards patterned polymer brush surfaces often remains challenging, creating a demand for more efficient and less complicated fabrication strategies. We describe the design and application of a novel experimental setup to combine light-mediated and flow chemistry for the fabrication of hierarchical surface-grafted polymer brushes. Using light-mediated, surface initiated controlled radical polymerization and post-functionalization via well-established, and highly efficient chemistries, polymer brush films of previously unimaginable complexity are now shown to be accessible. This methodology allows full flexibility to exchange both lithographic photomasks and chemical environments in-situ, readily affording multidimensional thin film architectures, all from uniformly functionalized substrates.

Generation of genome-modified Drosophila cell lines using SwAP.

PubMed

Franz, Alexandra; Brunner, Erich; Basler, Konrad

2017-10-02

The ease of generating genetically modified animals and cell lines has been markedly increased by the recent development of the versatile CRISPR/Cas9 tool. However, while the isolation of isogenic cell populations is usually straightforward for mammalian cell lines, the generation of clonal Drosophila cell lines has remained a longstanding challenge, hampered by the difficulty of getting Drosophila cells to grow at low densities. Here, we describe a highly efficient workflow to generate clonal Cas9-engineered Drosophila cell lines using a combination of cell pools, limiting dilution in conditioned medium and PCR with allele-specific primers, enabling the efficient selection of a clonal cell line with a suitable mutation profile. We validate the protocol by documenting the isolation, selection and verification of eight independently Cas9-edited armadillo mutant Drosophila cell lines. Our method provides a powerful and simple workflow that improves the utility of Drosophila cells for genetic studies with CRISPR/Cas9.

Recent advances in applications of nanomaterials for sample preparation.

PubMed

Xu, Linnan; Qi, Xiaoyue; Li, Xianjiang; Bai, Yu; Liu, Huwei

2016-01-01

Sample preparation is a key step for qualitative and quantitative analysis of trace analytes in complicated matrix. Along with the rapid development of nanotechnology in material science, numerous nanomaterials have been developed with particularly useful applications in analytical chemistry. Benefitting from their high specific areas, increased surface activities, and unprecedented physical/chemical properties, the potentials of nanomaterials for rapid and efficient sample preparation have been exploited extensively. In this review, recent progress of novel nanomaterials applied in sample preparation has been summarized and discussed. Both nanoparticles and nanoporous materials are evaluated for their unusual performance in sample preparation. Various compositions and functionalizations extended the applications of nanomaterials in sample preparations, and distinct size and shape selectivity was generated from the diversified pore structures of nanoporous materials. Such great variety make nanomaterials a kind of versatile tools in sample preparation for almost all categories of analytes. Copyright © 2015 Elsevier B.V. All rights reserved.

Airborne mass spectrometers: four decades of atmospheric and space research at the Air Force research laboratory.

PubMed

Viggiano, A A; Hunton, D E

1999-11-01

Mass spectrometry is a versatile research tool that has proved to be extremely useful for exploring the fundamental nature of the earth's atmosphere and ionosphere and in helping to solve operational problems facing the Air Force and the Department of Defense. In the past 40 years, our research group at the Air Force Research Laboratory has flown quadrupole mass spectrometers of many designs on nearly 100 sounding rockets, nine satellites, three Space Shuttles and many missions of high-altitude research aircraft and balloons. We have also used our instruments in ground-based investigations of rocket and jet engine exhaust, combustion chemistry and microwave breakdown chemistry. This paper is a review of the instrumentation and techniques needed for space research, a summary of the results from many of the experiments, and an introduction to the broad field of atmospheric and space mass spectrometry in general. Copyright 1999 John Wiley & Sons, Ltd.

Determination of the Goos-Hanchen shift in dielectric waveguides via photo emission electron microscopy in the visible spectrum

DOE PAGES

Stenmark, Theodore; Word, R. C.; Konenkamp, R.

2016-02-16

Photoemission Electron Microscopy (PEEM) is a versatile tool that relies on the photoelectric effect to produce high-resolution images. Pulse lasers allow for multi-photon PEEM where multiple photons are required excite a single electron. This non-linear process can directly image the near field region of electromagnetic fields in materials. We use this ability here to analyze wave propagation in a linear dielectric waveguide with wavelengths of 410nm and 780nm. The propagation constant of the waveguide can be extracted from the interference pattern created by the coupled and incident light and shows distinct polarization dependence. Furthermore, the electromagnetic field interaction at themore » boundaries can then be deduced which is essential to understand power flow in wave guiding structures. These results match well with simulations using finite element techniques.« less

Magnetic nanomaterials and sensors for biological detection.

PubMed

Sobczak-Kupiec, Agnieszka; Venkatesan, Jayachandran; Alhathal AlAnezi, Adnan; Walczyk, Dorota; Farooqi, Ammad; Malina, Dagmara; Hosseini, Seyed Hossein; Tyliszczak, Bozena

2016-11-01

It is becoming progressively more understandable that sensitivity and versatility of magnetic biosensors provides unique platform for high performance diagnostics in clinical settings. Confluence of information suggested that magnetic biosensors required well-tailored magnetic particles as probes for detection that generate large and specific biological signal with minimum possible nonspecific binding. However, there are visible knowledge gaps in our understanding of the strategies to overcome existing challenges related to even smaller size of intracellular targets and lower signal-to-noise ratio than that in whole-cell studies, therefore tool designing and development for intracellular measurement and manipulation is problematic. In this review we describe magnetic nanoparticles, synthesis and sensing principles of magnetic nanoparticles as well as surface functionalization and modification and finally magnetic nanoparticles for medical diagnostics. This review gathers important and up-to-date information and may help to develop the method of obtaining magnetic materials especially for medical application. Copyright © 2016 Elsevier Inc. All rights reserved.

Reviews

NASA Astrophysics Data System (ADS)

2005-05-01

WE RECOMMEND Private Universe and Minds of Our Own This DVD for teachers addresses challenges faced in the classroom. EasySenseLink and EasySense Flash Logger These two dataloggers are fast, versatile and inexpensive. The Butthead Game, Space Rifle and Disc Shooter Together, these toys can be used to explain the photoelectric effect. Resistance and thickness boards These high-quality, value-for-money boards produce excellent results. WORTH A LOOK Einstein A to Z A useful and well researched text about EinsteinÂ's life and work. Einstein Alive Depending on how it is lit, this display can look concave or convex. Phyzzing Through Physics As PowerPoint presentations go, this one is useful and good value. HANDLE WITH CARE Pressure toadstools An overpriced tool that you could make yourself using dowelling. Parallel and series boards Easily damaged, these boards are best used in demonstrations only. WEB WATCH Educational websites that make electricity fun to learn. Applets website: an online gem for teachers.

Poly(2-vinyl pyridine)-block-poly(ethylene oxide) featuring a furan group at the block junction-synthesis and functionalization.

PubMed

Rudolph, Tobias; Barthel, Markus J; Kretschmer, Florian; Mansfeld, Ulrich; Hoeppener, Stephanie; Hager, Martin D; Schubert, Ulrich S; Schacher, Felix H

2014-05-01

Furfuryl glycidyl ether (FGE) represents a highly versatile monomer for the preparation of reversibly cross-linkable nanostructured materials via Diels-Alder reactions. Here, the use of FGE for the mid-chain functionalization of a P2VP-b-PEO diblock copolymer is reported. The material features one furan moiety at the block junction, P2VP68 -FGE-b-PEO390 , which can be subsequently addressed in Diels-Alder reactions using maleimide-functionalized counterparts. The presence of the FGE moiety enables the introduction of dyes as model labels or the formation of hetero-grafted brushes as shell on hybrid Au@Polymer nanoparticles. This renders P2VP68 -FGE-b-PEO390 , a powerful tool for selective functionalization reactions, including the modification of surfaces. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Placing and shaping liposomes with reconfigurable DNA nanocages

NASA Astrophysics Data System (ADS)

Zhang, Zhao; Yang, Yang; Pincet, Frederic; C. Llaguno, Marc; Lin, Chenxiang

2017-07-01

The diverse structure and regulated deformation of lipid bilayer membranes are among a cell's most fascinating features. Artificial membrane-bound vesicles, known as liposomes, are versatile tools for modelling biological membranes and delivering foreign objects to cells. To fully mimic the complexity of cell membranes and optimize the efficiency of delivery vesicles, controlling liposome shape (both statically and dynamically) is of utmost importance. Here we report the assembly, arrangement and remodelling of liposomes with designer geometry: all of which are exquisitely controlled by a set of modular, reconfigurable DNA nanocages. Tubular and toroid shapes, among others, are transcribed from DNA cages to liposomes with high fidelity, giving rise to membrane curvatures present in cells yet previously difficult to construct in vitro. Moreover, the conformational changes of DNA cages drive membrane fusion and bending with predictable outcomes, opening up opportunities for the systematic study of membrane mechanics.

Adeno-associated Virus as a Mammalian DNA Vector

PubMed Central

SALGANIK, MAX; HIRSCH, MATTHEW L.; SAMULSKI, RICHARD JUDE

2015-01-01

In the nearly five decades since its accidental discovery, adeno-associated virus (AAV) has emerged as a highly versatile vector system for both research and clinical applications. A broad range of natural serotypes, as well as an increasing number of capsid variants, has combined to produce a repertoire of vectors with different tissue tropisms, immunogenic profiles and transduction efficiencies. The story of AAV is one of continued progress and surprising discoveries in a viral system that, at first glance, is deceptively simple. This apparent simplicity has enabled the advancement of AAV into the clinic, where despite some challenges it has provided hope for patients and a promising new tool for physicians. Although a great deal of work remains to be done, both in studying the basic biology of AAV and in optimizing its clinical application, AAV vectors are currently the safest and most efficient platform for gene transfer in mammalian cells. PMID:26350320

Functional Smiles: Tools for Love, Sympathy, and War.

PubMed

Rychlowska, Magdalena; Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G; Martin, Jared D; Niedenthal, Paula M

2017-09-01

A smile is the most frequent facial expression, but not all smiles are equal. A social-functional account holds that smiles of reward, affiliation, and dominance serve basic social functions, including rewarding behavior, bonding socially, and negotiating hierarchy. Here, we characterize the facial-expression patterns associated with these three types of smiles. Specifically, we modeled the facial expressions using a data-driven approach and showed that reward smiles are symmetrical and accompanied by eyebrow raising, affiliative smiles involve lip pressing, and dominance smiles are asymmetrical and contain nose wrinkling and upper-lip raising. A Bayesian-classifier analysis and a detection task revealed that the three smile types are highly distinct. Finally, social judgments made by a separate participant group showed that the different smile types convey different social messages. Our results provide the first detailed description of the physical form and social messages conveyed by these three types of functional smiles and document the versatility of these facial expressions.

Self-organizing maps: a versatile tool for the automatic analysis of untargeted imaging datasets.

PubMed

Franceschi, Pietro; Wehrens, Ron

2014-04-01

MS-based imaging approaches allow for location-specific identification of chemical components in biological samples, opening up possibilities of much more detailed understanding of biological processes and mechanisms. Data analysis, however, is challenging, mainly because of the sheer size of such datasets. This article presents a novel approach based on self-organizing maps, extending previous work in order to be able to handle the large number of variables present in high-resolution mass spectra. The key idea is to generate prototype images, representing spatial distributions of ions, rather than prototypical mass spectra. This allows for a two-stage approach, first generating typical spatial distributions and associated m/z bins, and later analyzing the interesting bins in more detail using accurate masses. The possibilities and advantages of the new approach are illustrated on an in-house dataset of apple slices. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advanced Nanoindentation Testing for Studying Strain-Rate Sensitivity and Activation Volume

NASA Astrophysics Data System (ADS)

Maier-Kiener, Verena; Durst, Karsten

2017-11-01

Nanoindentation became a versatile tool for testing local mechanical properties beyond hardness and modulus. By adapting standard nanoindentation test methods, simple protocols capable of probing thermally activated deformation processes can be accomplished. Abrupt strain-rate changes within one indentation allow determining the strain-rate dependency of hardness at various indentation depths. For probing lower strain-rates and excluding thermal drift influences, long-term creep experiments can be performed by using the dynamic contact stiffness for determining the true contact area. From both procedures hardness and strain-rate, and consequently strain-rate sensitivity and activation volume can be reliably deducted within one indentation, permitting information on the locally acting thermally activated deformation mechanism. This review will first discuss various testing protocols including possible challenges and improvements. Second, it will focus on different examples showing the direct influence of crystal structure and/or microstructure on the underlying deformation behavior in pure and highly alloyed material systems.

Placing and shaping liposomes with reconfigurable DNA nanocages.

PubMed

Zhang, Zhao; Yang, Yang; Pincet, Frederic; Llaguno, Marc C; Lin, Chenxiang

2017-06-23

The diverse structure and regulated deformation of lipid bilayer membranes are among a cell's most fascinating features. Artificial membrane-bound vesicles, known as liposomes, are versatile tools for modelling biological membranes and delivering foreign objects to cells. To fully mimic the complexity of cell membranes and optimize the efficiency of delivery vesicles, controlling liposome shape (both statically and dynamically) is of utmost importance. Here we report the assembly, arrangement and remodelling of liposomes with designer geometry: all of which are exquisitely controlled by a set of modular, reconfigurable DNA nanocages. Tubular and toroid shapes, among others, are transcribed from DNA cages to liposomes with high fidelity, giving rise to membrane curvatures present in cells yet previously difficult to construct in vitro. Moreover, the conformational changes of DNA cages drive membrane fusion and bending with predictable outcomes, opening up opportunities for the systematic study of membrane mechanics.

The Role of Affordable, Point-of-Care Technologies for Cancer Care in Low- and Middle-Income Countries: A Review and Commentary.

PubMed

Haney, Karen; Tandon, Pushpa; Divi, Rao; Ossandon, Miguel R; Baker, Houston; Pearlman, Paul C

2017-01-01

As the burden of non-communicable diseases such as cancer continues to rise in low- and middle-income countries (LMICs), it is essential to identify and invest in promising solutions for cancer control and treatment. Point-of-care technologies (POCTs) have played critical roles in curbing infectious disease epidemics in both high- and low-income settings, and their successes can serve as a model for transforming cancer care in LMICs, where access to traditional clinical resources is often limited. The versatility, cost-effectiveness, and simplicity of POCTs warrant attention for their potential to revolutionize cancer detection, diagnosis, and treatment. This paper reviews the landscape of affordable POCTs for cancer care in LMICs with a focus on imaging tools, in vitro diagnostics, and treatment technologies and aspires to encourage innovation and further investment in this space.

The Role of Affordable, Point-of-Care Technologies for Cancer Care in Low- and Middle-Income Countries: A Review and Commentary

PubMed Central

Tandon, Pushpa; Divi, Rao; Ossandon, Miguel R.; Baker, Houston; Pearlman, Paul C.

2017-01-01

As the burden of non-communicable diseases such as cancer continues to rise in low- and middle-income countries (LMICs), it is essential to identify and invest in promising solutions for cancer control and treatment. Point-of-care technologies (POCTs) have played critical roles in curbing infectious disease epidemics in both high- and low-income settings, and their successes can serve as a model for transforming cancer care in LMICs, where access to traditional clinical resources is often limited. The versatility, cost-effectiveness, and simplicity of POCTs warrant attention for their potential to revolutionize cancer detection, diagnosis, and treatment. This paper reviews the landscape of affordable POCTs for cancer care in LMICs with a focus on imaging tools, in vitro diagnostics, and treatment technologies and aspires to encourage innovation and further investment in this space. PMID:29204328

Investigation of selected imagery from SKYLAB/EREP S190 system for medium and small scale mapping

NASA Technical Reports Server (NTRS)

Stewart, R. A.

1975-01-01

Satellite photography provided by the Skylab mission was investigated as a tool in planimetric mapping at medium and small scales over land surface in Canada. The main interest involved the potential usage of Skylab imagery for new and revision line mapping, photomapping possibilities, and the application of this photography as control for conventional high altitude aerial surveys. The results of six independent investigations clearly indicate that certain selected sets of this photography are adequate for planimetric mapping purposes at scales of 1:250,000 and smaller. In limited cases, the NATO planimetric accuracy requirements for Class B 1:50,000 scale mapping were also achieved. Of the S190A photography system, the camera containing the Pan X Aerial Black and White film offers the greatest potential to mapping at small scales. However, the S190B system continually proved to offer more versatility throughout the entire investigation.

Recent Progress on Transition Metal Catalyst Separation and Recycling in ATRP.

PubMed

Ding, Mingqiang; Jiang, Xiaowu; Zhang, Lifen; Cheng, Zhenping; Zhu, Xiulin

2015-10-01

Atom transfer radical polymerization (ATRP) is a versatile and robust tool to synthesize a wide spectrum of monomers with various designable structures. However, it usually needs large amounts of transition metal as the catalyst to mediate the equilibrium between the dormant and propagating species. Unfortunately, the catalyst residue may contaminate or color the resultant polymers, which limits its application, especially in biomedical and electronic materials. How to efficiently and economically remove or reduce the catalyst residue from its products is a challenging and encouraging task. Herein, recent advances in catalyst separation and recycling are highlighted with a focus on (1) highly active ppm level transition metal or metal free catalyzed ATRP; (2) post-purification method; (3) various soluble, insoluble, immobilized/soluble, and reversible supported catalyst systems; and (4) liquid-liquid biphasic catalyzed systems, especially thermo-regulated catalysis systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Versatile, modular 3D microelectrode arrays for neuronal ensemble recordings: from design to fabrication, assembly, and functional validation in non-human primates.

PubMed

Barz, F; Livi, A; Lanzilotto, M; Maranesi, M; Bonini, L; Paul, O; Ruther, P

2017-06-01

Application-specific designs of electrode arrays offer an improved effectiveness for providing access to targeted brain regions in neuroscientific research and brain machine interfaces. The simultaneous and stable recording of neuronal ensembles is the main goal in the design of advanced neural interfaces. Here, we describe the development and assembly of highly customizable 3D microelectrode arrays and demonstrate their recording performance in chronic applications in non-human primates. System assembly relies on a microfabricated stacking component that is combined with Michigan-style silicon-based electrode arrays interfacing highly flexible polyimide cables. Based on the novel stacking component, the lead time for implementing prototypes with altered electrode pitches is minimal. Once the fabrication and assembly accuracy of the stacked probes have been characterized, their recording performance is assessed during in vivo chronic experiments in awake rhesus macaques (Macaca mulatta) trained to execute reaching-grasping motor tasks. Using a single set of fabrication tools, we implemented three variants of the stacking component for electrode distances of 250, 300 and 350 µm in the stacking direction. We assembled neural probes with up to 96 channels and an electrode density of 98 electrodes mm -2 . Furthermore, we demonstrate that the shank alignment is accurate to a few µm at an angular alignment better than 1°. Three 64-channel probes were chronically implanted in two monkeys providing single-unit activity on more than 60% of all channels and excellent recording stability. Histological tissue sections, obtained 52 d after implantation from one of the monkeys, showed minimal tissue damage, in accordance with the high quality and stability of the recorded neural activity. The versatility of our fabrication and assembly approach should significantly support the development of ideal interface geometries for a broad spectrum of applications. With the demonstrated performance, these probes are suitable for both semi-chronic and chronic applications.

Versatile, modular 3D microelectrode arrays for neuronal ensemble recordings: from design to fabrication, assembly, and functional validation in non-human primates

NASA Astrophysics Data System (ADS)

Barz, F.; Livi, A.; Lanzilotto, M.; Maranesi, M.; Bonini, L.; Paul, O.; Ruther, P.

2017-06-01

Objective. Application-specific designs of electrode arrays offer an improved effectiveness for providing access to targeted brain regions in neuroscientific research and brain machine interfaces. The simultaneous and stable recording of neuronal ensembles is the main goal in the design of advanced neural interfaces. Here, we describe the development and assembly of highly customizable 3D microelectrode arrays and demonstrate their recording performance in chronic applications in non-human primates. Approach. System assembly relies on a microfabricated stacking component that is combined with Michigan-style silicon-based electrode arrays interfacing highly flexible polyimide cables. Based on the novel stacking component, the lead time for implementing prototypes with altered electrode pitches is minimal. Once the fabrication and assembly accuracy of the stacked probes have been characterized, their recording performance is assessed during in vivo chronic experiments in awake rhesus macaques (Macaca mulatta) trained to execute reaching-grasping motor tasks. Main results. Using a single set of fabrication tools, we implemented three variants of the stacking component for electrode distances of 250, 300 and 350 µm in the stacking direction. We assembled neural probes with up to 96 channels and an electrode density of 98 electrodes mm-2. Furthermore, we demonstrate that the shank alignment is accurate to a few µm at an angular alignment better than 1°. Three 64-channel probes were chronically implanted in two monkeys providing single-unit activity on more than 60% of all channels and excellent recording stability. Histological tissue sections, obtained 52 d after implantation from one of the monkeys, showed minimal tissue damage, in accordance with the high quality and stability of the recorded neural activity. Significance. The versatility of our fabrication and assembly approach should significantly support the development of ideal interface geometries for a broad spectrum of applications. With the demonstrated performance, these probes are suitable for both semi-chronic and chronic applications.

PENTrack - a versatile Monte Carlo tool for ultracold neutron sources and experiments

NASA Astrophysics Data System (ADS)

Picker, Ruediger; Chahal, Sanmeet; Christopher, Nicolas; Losekamm, Martin; Marcellin, James; Paul, Stephan; Schreyer, Wolfgang; Yapa, Pramodh

2016-09-01

Ultracold neutrons have energies in the hundred nano eV region. They can be stored in traps for hundreds of seconds. This makes them the ideal tool to study the neutron itself. Measurements of neutron decay correlations, lifetime or electric dipole moment are ideally suited for ultracold neutrons, as well as experiments probing the neutron's gravitational levels in the earth's field. We have developed a Monte Carlo simulation tool that can serve to design and optimize these experiments, and possibly correct results: PENTrack is a C++ based simulation code that tracks neutrons, protons and electrons or atoms, as well as their spins, in gravitational and electromagnetic fields. In addition wall interactions of neutrons due to strong interaction are modeled with a Fermi-potential formalism and take surface roughness into account. The presentation will introduce the physics behind the simulation and provide examples of its application.

PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.

PubMed

Gore, Swanand P; Burke, David F; Blundell, Tom L

2005-08-01

Voronoi tessellation has proved to be a useful tool in protein structure analysis. We have developed PROVAT, a versatile public domain software that enables computation and visualization of Voronoi tessellations of proteins and protein complexes. It is a set of Python scripts that integrate freely available specialized software (Qhull, Pymol etc.) into a pipeline. The calculation component of the tool computes Voronoi tessellation of a given protein system in a way described by a user-supplied XML recipe and stores resulting neighbourhood information as text files with various styles. The Python pickle file generated in the process is used by the visualization component, a Pymol plug-in, that offers a GUI to explore the tessellation visually. PROVAT source code can be downloaded from http://raven.bioc.cam.ac.uk/~swanand/Provat1, which also provides a webserver for its calculation component, documentation and examples.

Giving students the run of sprinting models

NASA Astrophysics Data System (ADS)

Heck, André; Ellermeijer, Ton

2009-11-01

A biomechanical study of sprinting is an interesting task for students who have a background in mechanics and calculus. These students can work with real data and do practical investigations similar to the way sports scientists do research. Student research activities are viable when the students are familiar with tools to collect and work with data from sensors and video recordings and with modeling tools for comparing simulation and experimental results. This article describes a multipurpose system, named COACH, that offers a versatile integrated set of tools for learning, doing, and teaching mathematics and science in a computer-based inquiry approach. Automated tracking of reference points and correction of perspective distortion in videos, state-of-the-art algorithms for data smoothing and numerical differentiation, and graphical system dynamics based modeling are some of the built-in techniques that are suitable for motion analysis. Their implementation and their application in student activities involving models of running are discussed.

DNA microarrays: a powerful genomic tool for biomedical and clinical research

PubMed Central

Trevino, Victor; Falciani, Francesco; Barrera-Saldaña, Hugo A.

2007-01-01

Among the many benefits of the Human Genome Project are new and powerful tools such as the genome-wide hybridization devices referred as microarrays. Initially designed to measure gene transcriptional levels, microarray technologies are now used for comparing other genome features among individuals and their tissues and cells. Results provide valuable information on disease subcategories, disease prognosis, and treatment outcome. Likewise, reveal differences in genetic makeup, regulatory mechanisms and subtle variations are approaching the era of personalized medicine. To understand this powerful tool, its versatility and how it is dramatically changing the molecular approach to biomedical and clinical research, this review describes the technology, its applications, a didactic step-by-step review of a typical microarray protocol, and a real experiment. Finally, it calls the attention of the medical community to integrate multidisciplinary teams, to take advantage of this technology and its expanding applications that in a slide reveals our genetic inheritance and destiny. PMID:17660860

BFPTool: a software tool for analysis of Biomembrane Force Probe experiments.

PubMed

Šmít, Daniel; Fouquet, Coralie; Doulazmi, Mohamed; Pincet, Frédéric; Trembleau, Alain; Zapotocky, Martin

2017-01-01

The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of forces from 0.1 pN to 1000 pN. Experiments are typically repeated many times, conditions are often not optimal, the captured video can be unstable and lose focus; this makes efficient analysis challenging, while out-of-the-box non-proprietary solutions are not freely available. This dedicated tool was developed to integrate and simplify the image processing and analysis of videomicroscopy recordings from BFP experiments. A novel processing feature, allowing the tracking of the pipette, was incorporated to address a limitation of preceding methods. Emphasis was placed on versatility and comprehensible user interface implemented in a graphical form. An integrated analytical tool was implemented to provide a faster, simpler and more convenient way to process and analyse BFP experiments.

DNA marker technology for wildlife conservation

PubMed Central

Arif, Ibrahim A.; Khan, Haseeb A.; Bahkali, Ali H.; Al Homaidan, Ali A.; Al Farhan, Ahmad H.; Al Sadoon, Mohammad; Shobrak, Mohammad

2011-01-01

Use of molecular markers for identification of protected species offers a greater promise in the field of conservation biology. The information on genetic diversity of wildlife is necessary to ascertain the genetically deteriorated populations so that better management plans can be established for their conservation. Accurate classification of these threatened species allows understanding of the species biology and identification of distinct populations that should be managed with utmost care. Molecular markers are versatile tools for identification of populations with genetic crisis by comparing genetic diversities that in turn helps to resolve taxonomic uncertainties and to establish management units within species. The genetic marker analysis also provides sensitive and useful tools for prevention of illegal hunting and poaching and for more effective implementation of the laws for protection of the endangered species. This review summarizes various tools of DNA markers technology for application in molecular diversity analysis with special emphasis on wildlife conservation. PMID:23961128

Citrate-Based Biomaterials and Their Applications in Regenerative Engineering

PubMed Central

Tran, Richard T.; Yang, Jian; Ameer, Guillermo A.

2015-01-01

Advances in biomaterials science and engineering are crucial to translating regenerative engineering, an emerging field that aims to recreate complex tissues, into clinical practice. In this regard, citrate-based biomaterials have become an important tool owing to their versatile material and biological characteristics including unique antioxidant, antimicrobial, adhesive, and fluorescent properties. This review discusses fundamental design considerations, strategies to incorporate unique functionality, and examples of how citrate-based biomaterials can be an enabling technology for regenerative engineering. PMID:27004046

Measuring Intracranial Pressure and Correlation with Severity of Blast Traumatic Brain Injury

DTIC Science & Technology

2011-10-01

cannula was then filled with a sterile saline solution. The cannula cap was filled with petroleum jelly and a fiber optic pressure sensor (FOP-MIV, FISO...petroleum jelly and the fiber optic pressure sensor (FOP-MIV, Fiso Inc.) was inserted into the cannula and threaded onto the cannula pedestal. Figure 1b...neurological consequences of explosives. J. Neurol. Sci. 249:63–67, 2006. 9Henshall, B. Shock tube–versatile tool of aerodynamic research. J. Royal

Anti-Hassle Chip

NASA Technical Reports Server (NTRS)

1998-01-01

With assistance from NASA's Ames Research Center, the iTV Corporation has developed a full custom microprocessor that enables access to the Internet through a $49 device. The microprocessor is supported with a compliment of design tools for customization and adaptation as either a licensable core or as a complete microprocessor. Other uses include cell phones, DVD (digital versatile disk) players, cable modems, video conferencing equipment, digital cameras, wireless LANs (Local Area Network) and WANs (Wide Area Network). iTV continues to design new, low-cost consumer products.

Miniature penetrator (MinPen) acceleration recorder development test

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

Franco, R.J.; Platzbecker, M.R.

1998-08-01

The Telemetry Technology Development Department at Sandia National Laboratories actively develops and tests acceleration recorders for penetrating weapons. This new acceleration recorder (MinPen) utilizes a microprocessor-based architecture for operational flexibility while maintaining electronics and packaging techniques developed over years of penetrator testing. MinPen has been demonstrated to function in shock environments up to 20,000 Gs. The MinPen instrumentation development has resulted in a rugged, versatile, miniature acceleration recorder and is a valuable tool for penetrator testing in a wide range of applications.

Understanding carbohydrate-carbohydrate interactions by means of glyconanotechnology.

PubMed

de la Fuente, Jesus M; Penadés, Soledad

2004-01-01

Carbohydrate-carbohydrate interaction is a reliable and versatile mechanism for cell adhesion and recognition. Glycosphingolipid (GSL) clusters at the cell membrane are mainly involved in this interaction. To investigate carbohydrate-carbohydrate interaction an integrated strategy (Glyconanotechnology) was developed. This strategy includes polyvalent tools (gold glyconanoparticles) mimicking GSL clustering at the cell membrane as well as analytical techniques such as AFM, TEM, and SPR to evaluate the interactions. The results obtained by means of this strategy and current status are presented.

An Easily Constructed and Versatile Molecular Model

NASA Astrophysics Data System (ADS)

Hernandez, Sandra A.; Rodriguez, Nora M.; Quinzani, Oscar

1996-08-01

Three-dimensional molecular models are powerful tools used in basic courses of general and organic chemistry when the students must visualize the spatial distributions of atoms in molecules and relate them to the physical and chemical properties of such molecules. This article discusses inexpensive, easily carried, and semipermanent molecular models that the students may build by themselves. These models are based upon two different types of arrays of thin flexible wires, like telephone hook-up wires, which may be bent easily but keep their shapes.

Closed-loop ARS mode for scanning ion conductance microscopy with improved speed and stability for live cell imaging applications.

PubMed

Jung, Goo-Eun; Noh, Hanaul; Shin, Yong Kyun; Kahng, Se-Jong; Baik, Ku Youn; Kim, Hong-Bae; Cho, Nam-Joon; Cho, Sang-Joon

2015-07-07

Scanning ion conductance microscopy (SICM) is an increasingly useful nanotechnology tool for non-contact, high resolution imaging of live biological specimens such as cellular membranes. In particular, approach-retract-scanning (ARS) mode enables fast probing of delicate biological structures by rapid and repeated approach/retraction of a nano-pipette tip. For optimal performance, accurate control of the tip position is a critical issue. Herein, we present a novel closed-loop control strategy for the ARS mode that achieves higher operating speeds with increased stability. The algorithm differs from that of most conventional (i.e., constant velocity) approach schemes as it includes a deceleration phase near the sample surface, which is intended to minimize the possibility of contact with the surface. Analysis of the ion current and tip position demonstrates that the new mode is able to operate at approach speeds of up to 250 μm s(-1). As a result of the improved stability, SICM imaging with the new approach scheme enables significantly improved, high resolution imaging of subtle features of fixed and live cells (e.g., filamentous structures & membrane edges). Taken together, the results suggest that optimization of the tip approach speed can substantially improve SICM imaging performance, further enabling SICM to become widely adopted as a general and versatile research tool for biological studies at the nanoscale level.

SAM/SAH Analogs as Versatile Tools for SAM-Dependent Methyltransferases.

PubMed

Zhang, Jing; Zheng, Yujun George

2016-03-18

S-Adenosyl-L-methionine (SAM) is a sulfonium molecule with a structural hybrid of methionine and adenosine. As the second largest cofactor in the human body, its major function is to serve as methyl donor for SAM-dependent methyltransferases (MTases). The resultant transmethylation of biomolecules constitutes a significant biochemical mechanism in epigenetic regulation, cellular signaling, and metabolite degradation. Recently, numerous SAM analogs have been developed as synthetic cofactors to transfer the activated groups on MTase substrates for downstream ligation and identification. Meanwhile, new compounds built upon or derived from the SAM scaffold have been designed and tested as selective inhibitors for important MTase targets. Here, we summarized the recent development and application of SAM analogs as chemical biology tools for MTases.

CRISPR/Cas9 Immune System as a Tool for Genome Engineering.

PubMed

Hryhorowicz, Magdalena; Lipiński, Daniel; Zeyland, Joanna; Słomski, Ryszard

2017-06-01

CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) adaptive immune systems constitute a bacterial defence against invading nucleic acids derived from bacteriophages or plasmids. This prokaryotic system was adapted in molecular biology and became one of the most powerful and versatile platforms for genome engineering. CRISPR/Cas9 is a simple and rapid tool which enables the efficient modification of endogenous genes in various species and cell types. Moreover, a modified version of the CRISPR/Cas9 system with transcriptional repressors or activators allows robust transcription repression or activation of target genes. The simplicity of CRISPR/Cas9 has resulted in the widespread use of this technology in many fields, including basic research, biotechnology and biomedicine.

CIFOG: Cosmological Ionization Fields frOm Galaxies

NASA Astrophysics Data System (ADS)

Hutter, Anne

2018-03-01

CIFOG is a versatile MPI-parallelised semi-numerical tool to perform simulations of the Epoch of Reionization. From a set of evolving cosmological gas density and ionizing emissivity fields, it computes the time and spatially dependent ionization of neutral hydrogen (HI), neutral (HeI) and singly ionized helium (HeII) in the intergalactic medium (IGM). The code accounts for HII, HeII, HeIII recombinations, and provides different descriptions for the photoionization rate that are used to calculate the residual HI fraction in ionized regions. This tool has been designed to be coupled to semi-analytic galaxy formation models or hydrodynamical simulations. The modular fashion of the code allows the user to easily introduce new descriptions for recombinations and the photoionization rate.

Accuracy Improvement of Multi-Axis Systems Based on Laser Correction of Volumetric Geometric Errors

NASA Astrophysics Data System (ADS)

Teleshevsky, V. I.; Sokolov, V. A.; Pimushkin, Ya I.

2018-04-01

The article describes a volumetric geometric errors correction method for CNC- controlled multi-axis systems (machine-tools, CMMs etc.). The Kalman’s concept of “Control and Observation” is used. A versatile multi-function laser interferometer is used as Observer in order to measure machine’s error functions. A systematic error map of machine’s workspace is produced based on error functions measurements. The error map results into error correction strategy. The article proposes a new method of error correction strategy forming. The method is based on error distribution within machine’s workspace and a CNC-program postprocessor. The postprocessor provides minimal error values within maximal workspace zone. The results are confirmed by error correction of precision CNC machine-tools.

The value of the Semantic Web in the laboratory.

PubMed

Frey, Jeremy G

2009-06-01

The Semantic Web is beginning to impact on the wider chemical and physical sciences, beyond the earlier adopted bio-informatics. While useful in large-scale data driven science with automated processing, these technologies can also help integrate the work of smaller scale laboratories producing diverse data. The semantics aid the discovery, reliable re-use of data, provide improved provenance and facilitate automated processing by increased resilience to changes in presentation and reduced ambiguity. The Semantic Web, its tools and collections are not yet competitive with well-established solutions to current problems. It is in the reduced cost of instituting solutions to new problems that the versatility of Semantic Web-enabled data and resources will make their mark once the more general-purpose tools are more available.

A quantitative image cytometry technique for time series or population analyses of signaling networks.

PubMed

Ozaki, Yu-ichi; Uda, Shinsuke; Saito, Takeshi H; Chung, Jaehoon; Kubota, Hiroyuki; Kuroda, Shinya

2010-04-01

Modeling of cellular functions on the basis of experimental observation is increasingly common in the field of cellular signaling. However, such modeling requires a large amount of quantitative data of signaling events with high spatio-temporal resolution. A novel technique which allows us to obtain such data is needed for systems biology of cellular signaling. We developed a fully automatable assay technique, termed quantitative image cytometry (QIC), which integrates a quantitative immunostaining technique and a high precision image-processing algorithm for cell identification. With the aid of an automated sample preparation system, this device can quantify protein expression, phosphorylation and localization with subcellular resolution at one-minute intervals. The signaling activities quantified by the assay system showed good correlation with, as well as comparable reproducibility to, western blot analysis. Taking advantage of the high spatio-temporal resolution, we investigated the signaling dynamics of the ERK pathway in PC12 cells. The QIC technique appears as a highly quantitative and versatile technique, which can be a convenient replacement for the most conventional techniques including western blot, flow cytometry and live cell imaging. Thus, the QIC technique can be a powerful tool for investigating the systems biology of cellular signaling.

Lens-free shadow image based high-throughput continuous cell monitoring technique.

PubMed

Jin, Geonsoo; Yoo, In-Hwa; Pack, Seung Pil; Yang, Ji-Woon; Ha, Un-Hwan; Paek, Se-Hwan; Seo, Sungkyu

2012-01-01

A high-throughput continuous cell monitoring technique which does not require any labeling reagents or destruction of the specimen is demonstrated. More than 6000 human alveolar epithelial A549 cells are monitored for up to 72 h simultaneously and continuously with a single digital image within a cost and space effective lens-free shadow imaging platform. In an experiment performed within a custom built incubator integrated with the lens-free shadow imaging platform, the cell nucleus division process could be successfully characterized by calculating the signal-to-noise ratios (SNRs) and the shadow diameters (SDs) of the cell shadow patterns. The versatile nature of this platform also enabled a single cell viability test followed by live cell counting. This study firstly shows that the lens-free shadow imaging technique can provide a continuous cell monitoring without any staining/labeling reagent and destruction of the specimen. This high-throughput continuous cell monitoring technique based on lens-free shadow imaging may be widely utilized as a compact, low-cost, and high-throughput cell monitoring tool in the fields of drug and food screening or cell proliferation and viability testing. Copyright © 2012 Elsevier B.V. All rights reserved.

Advanced Differential Radar Interferometry (A-DInSAR) as integrative tool for a structural geological analysis

NASA Astrophysics Data System (ADS)

Crippa, B.; Calcagni, L.; Rossi, G.; Sternai, P.

2009-04-01

Advanced Differential SAR interferometry (A-DInSAR) is a technique monitoring large-coverage surface deformations using a stack of interferograms generated from several complex SLC SAR images, acquired over the same target area at different times. In this work are described the results of a procedure to calculate terrain motion velocity on highly correlated pixels (E. Biescas, M. Crosetto, M. Agudo, O. Monserrat e B. Crippa: Two Radar Interferometric Approaches to Monitor Slow and Fast Land Deformation, 2007) in two area Gemona - Friuli, Northern Italy, Pollino - Calabria, Southern Italy, and, furthermore, are presented some consideration, based on successful examples of the present analysis. The choice of these pixels whose displacement velocity is calculated depends on the dispersion index value (DA) or using coherence values along the stack interferograms. A-DInSAR technique allows to obtain highly reliable velocity values of the vertical displacement. These values concern the movement of minimum surfaces of about 80m2 at the maximum resolution and the minimum velocity that can be recognized is of the order of mm/y. Because of the high versatility of the technology, because of the large dimensions of the area that can be analyzed (of about 10000Km2) and because of the high precision and reliability of the results obtained, we think it is possible to exploit radar interferometry to obtain some important information about the structural context of the studied area, otherwise very difficult to recognize. Therefore we propose radar interferometry as a valid investigation tool whose results must be considered as an important integration of the data collected in fieldworks.

Towards early software reliability prediction for computer forensic tools (case study).

PubMed

Abu Talib, Manar

2016-01-01

Versatility, flexibility and robustness are essential requirements for software forensic tools. Researchers and practitioners need to put more effort into assessing this type of tool. A Markov model is a robust means for analyzing and anticipating the functioning of an advanced component based system. It is used, for instance, to analyze the reliability of the state machines of real time reactive systems. This research extends the architecture-based software reliability prediction model for computer forensic tools, which is based on Markov chains and COSMIC-FFP. Basically, every part of the computer forensic tool is linked to a discrete time Markov chain. If this can be done, then a probabilistic analysis by Markov chains can be performed to analyze the reliability of the components and of the whole tool. The purposes of the proposed reliability assessment method are to evaluate the tool's reliability in the early phases of its development, to improve the reliability assessment process for large computer forensic tools over time, and to compare alternative tool designs. The reliability analysis can assist designers in choosing the most reliable topology for the components, which can maximize the reliability of the tool and meet the expected reliability level specified by the end-user. The approach of assessing component-based tool reliability in the COSMIC-FFP context is illustrated with the Forensic Toolkit Imager case study.

Highly versatile in-reflection photonic crystal fibre interferometer

NASA Astrophysics Data System (ADS)

Jha, Rajan; Villatoro, Joel; Kreuzer, Mark; Finazzi, Vittoria; Pruneri, Valerio

2009-10-01

We report a simple and highly versatile photonic crystal fiber (PCF) interferometer that operates in reflection mode. The device consists of a short section of PCF fusion spliced at the distal end of a standard single mode fiber. The air-holes of the PCF are intentionally collapsed over a microscopic region around the splice. The collapsed region broadens the propagating mode because of diffraction. This allows the coupling and recombination of two PCF modes. Depending on the PCF structure two core modes or a core and a cladding mode can be excited. In either case the devices exhibit sinusoidal interference patterns with fringe spacing depending on the PCF length. The interferometers are highly stable over time and can operate at high temperatures with minimal degradation. The interferometers are suitable for highresolution sensing of strain, refractive index (biosensing), gases, volatile organic compounds, etc.

Integrated Kerr comb-based reconfigurable transversal differentiator for microwave photonic signal processing

NASA Astrophysics Data System (ADS)

Xu, Xingyuan; Wu, Jiayang; Shoeiby, Mehrdad; Nguyen, Thach G.; Chu, Sai T.; Little, Brent E.; Morandotti, Roberto; Mitchell, Arnan; Moss, David J.

2018-01-01

An arbitrary-order intensity differentiator for high-order microwave signal differentiation is proposed and experimentally demonstrated on a versatile transversal microwave photonic signal processing platform based on integrated Kerr combs. With a CMOS-compatible nonlinear micro-ring resonator, high quality Kerr combs with broad bandwidth and large frequency spacings are generated, enabling a larger number of taps and an increased Nyquist zone. By programming and shaping individual comb lines' power, calculated tap weights are realized, thus achieving a versatile microwave photonic signal processing platform. Arbitrary-order intensity differentiation is demonstrated on the platform. The RF responses are experimentally characterized, and systems demonstrations for Gaussian input signals are also performed.

Fabrication of versatile cladding light strippers and fiber end-caps with CO2 laser radiation

NASA Astrophysics Data System (ADS)

Steinke, M.; Theeg, T.; Wysmolek, M.; Ottenhues, C.; Pulzer, T.; Neumann, J.; Kracht, D.

2018-02-01

We report on novel fabrication schemes of versatile cladding light strippers and end-caps via CO2 laser radiation. We integrated cladding light strippers in SMA-like connectors for reliable and stable fiber-coupling of high-power laser diodes. Moreover, the application of cladding light strippers in typical fiber geometries for high-power fiber lasers was evaluated. In addition, we also developed processes to fuse end-caps to fiber end faces via CO2 laser radiation and inscribe the fibers with cladding light strippers near the end-cap. Corresponding results indicate the great potential of such devices as a monolithic and low-cost alternative to SMA connectors.

Unmanned Aerial Systems as Versatile Tools for Atmospheric and Environmental Research

NASA Astrophysics Data System (ADS)

Lange, Manfred; Argyrides, Marios; Ioannou, Stelios; Keleshis, Christos; Levin, Zev

2013-04-01

Unmanned Aerial Systems (UASs) are increasingly recognized as versatile tools for different earth-sciences applications providing chiefly a link between in-situ ground based measurements and satellite remote sensing observations. Based on the Autonomous Flying Platforms for Atmospheric and Earth Surface Observations project (APAESO) of the Energy, Environment and Water Research Center (EEWRC) at the Cyprus Institute (APAESO is co-financed by the European Development Fund and the Republic of Cyprus through the Cyprus Research Promotion Foundation: ΝΕΑ ΥΠΟΔΟΜΗ/ΝΕΚΥΠ/0308/09), we have acquired four CRUISERS (ET-Air, Slovakia) as UAS platforms and a substantial range of scientific instruments to be employed on these platforms. The APAESO platforms are aimed at the dual purpose of carrying out atmospheric and earth-surface observations in the (Eastern) Mediterranean They will enable 3D measurements for determining physical, chemical and radiative atmospheric properties, aerosol and dust concentrations and atmospheric dynamics as well as 2D investigations into land management practices, vegetation and agricultural mapping, contaminant detection and the monitoring and assessment of hydrological parameters and processes of a given region at high spatial resolution. Currently, we are building up an Unmanned Airplane Facility at CyI. In the process of reaching full operational capacity, we have initiated and carried out first test missions involving highly specialized and specifically adapted instrumentation for atmospheric investigations. The first scientific mission involves the employment of a DOAS-system (Differential Optical Absorption Spectroscopy) in cooperation with colleagues from Heidelberg and Mainz, Germany and has been successfully completed. More recently, we started work on a new collaborative project aimed at measuring vertical profiles of aerosols in the Eastern Mediterranean. The project involves colleagues from the University of Frankfurt, Germany as well as from the University of Tel Aviv and the Weizmann Institute, both in Israel. For this project, a specially designed multi-stage electrostatic aerosol collector is being placed on one of the APAESO UAS. Simultaneously, atmospheric aerosols size and concentrations will be measured with an optical aerosol spectrometer, mounted on the same platform. The collected samples will be divided into two parts for analysis in both the University of Frankfurt and the Weizmann Institute

Recent Advances in Genome Editing Using CRISPR/Cas9

PubMed Central

Ding, Yuduan; Li, Hong; Chen, Ling-Ling; Xie, Kabin

2016-01-01

The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system is a versatile tool for genome engineering that uses a guide RNA (gRNA) to target Cas9 to a specific sequence. This simple RNA-guided genome-editing technology has become a revolutionary tool in biology and has many innovative applications in different fields. In this review, we briefly introduce the Cas9-mediated genome-editing method, summarize the recent advances in CRISPR/Cas9 technology, and discuss their implications for plant research. To date, targeted gene knockout using the Cas9/gRNA system has been established in many plant species, and the targeting efficiency and capacity of Cas9 has been improved by optimizing its expression and that of its gRNA. The CRISPR/Cas9 system can also be used for sequence-specific mutagenesis/integration and transcriptional control of target genes. We also discuss off-target effects and the constraint that the protospacer-adjacent motif (PAM) puts on CRISPR/Cas9 genome engineering. To address these problems, a number of bioinformatic tools are available to help design specific gRNAs, and new Cas9 variants and orthologs with high fidelity and alternative PAM specificities have been engineered. Owing to these recent efforts, the CRISPR/Cas9 system is becoming a revolutionary and flexible tool for genome engineering. Adoption of the CRISPR/Cas9 technology in plant research would enable the investigation of plant biology at an unprecedented depth and create innovative applications in precise crop breeding. PMID:27252719

Insights into the unique functionality of inorganic micro/nanoparticles for versatile ultrasound theranostics.

PubMed

Qian, Xiaoqin; Han, Xiaoxia; Chen, Yu

2017-10-01

The clinical ultrasound (US)-based theranostic biomedicine suffers from the critical issue that traditional microbubbles (MBs) have lots of drawbacks such as low stability, large particle size, difficult structural control, etc. The unique composition, structure and functionality of inorganic micro/nanoplatforms have shown their great prospect for solving these critical issues and drawbacks of traditional organic MBs. This review summarizes and discusses the state-of-art development on exploring inorganic micro/nanoparticles for versatile US-based biomedical applications, ranging from US imaging, photoacoustic imaging, sonodynamic therapy, high intensity-focused US ablation and US-triggered chemotherapy. These inorganic micro/nanoplatforms include silica-based particles, Au, carbon nanotubes, TiO 2 , manganese oxide, iron oxide, Prussian blue, inorganic gas-generating nanoparticles and their versatile composite micro/nanosystems. Especially, their unique structure/composition-functionality relationships and biocompatibility/biosafety in US-based theranostics have been discussed and revealed in detail. Their facing challenges and future developments are finally discussed to promote their further clinical translations. It is highly expected that these inorganic micro/nanoplatforms will enter the clinical stage to benefit the personalized theranostics biomedicine based on their unique functionalities and high performance as necessarily required in US-based theranostics. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Versatile Ion Injector at KACST

NASA Astrophysics Data System (ADS)

El Ghazaly, M. O. A.; Behery, S. A.; Almuqhim, A. A.; Papash, A. I.; Welsch, C. P.

2011-10-01

A versatile ion-beam injector is presently being constructed at the National Centre for Mathematics and Physics (NCMP) at the King Abdul-Aziz City for Science and Technology (KACST), Saudi Arabia. This versatile injector will provide an electrostatic storage ring with high-quality ion beams of energies up to 30 keV per charge q. It will also allow for crossed-beams experiments in single-pass setups. The injector has been designed to include beams from two different ion sources, switched by a 90° deflection setup, and to allow for matching of the beam parameters to the Twiss parameters of the ring. The injector is equipped with two crossed beam-lines (inlets), with duplicated beam extraction and acceleration systems. As part of the initial setup, a simple electric discharge ion source has been developed for commissioning of the whole injector. In this paper, we report on the ion optics layout and the design parameters of the injector.

Versatility and addiction in gaming: the number of video-game genres played is associated with pathological gaming in male adolescents.

PubMed

Donati, Maria Anna; Chiesi, Francesca; Ammannato, Giulio; Primi, Caterina

2015-02-01

This study tested the predictive power of gaming versatility (i.e., the number of video game genres engaged in) on game addiction in male adolescents, controlling for time spent on gaming. Participants were 701 male adolescents attending high school (Mage=15.6 years). Analyses showed that pathological gaming was predicted not only by higher time spent on gaming, but also by participation in a greater number of video game genres. Specifically, the wider the array of video game genres played, the higher were the negative consequences caused by gaming. Findings show that versatility can be considered as one of the behavioral risk factors related to gaming addiction, which may be characterized by a composite and diversified experience with video games. This study suggests that educational efforts designed to prevent gaming addiction among youth may also be focused on adolescents' engagement in different video games.

ICAN: A versatile code for predicting composite properties

NASA Technical Reports Server (NTRS)

Ginty, C. A.; Chamis, C. C.

1986-01-01

The Integrated Composites ANalyzer (ICAN), a stand-alone computer code, incorporates micromechanics equations and laminate theory to analyze/design multilayered fiber composite structures. Procedures for both the implementation of new data in ICAN and the selection of appropriate measured data are summarized for: (1) composite systems subject to severe thermal environments; (2) woven fabric/cloth composites; and (3) the selection of new composite systems including those made from high strain-to-fracture fibers. The comparisons demonstrate the versatility of ICAN as a reliable method for determining composite properties suitable for preliminary design.

Versatile, low-cost, computer-controlled, sample positioning system for vacuum applications

NASA Technical Reports Server (NTRS)

Vargas-Aburto, Carlos; Liff, Dale R.

1991-01-01

A versatile, low-cost, easy to implement, microprocessor-based motorized positioning system (MPS) suitable for accurate sample manipulation in a Second Ion Mass Spectrometry (SIMS) system, and for other ultra-high vacuum (UHV) applications was designed and built at NASA LeRC. The system can be operated manually or under computer control. In the latter case, local, as well as remote operation is possible via the IEEE-488 bus. The position of the sample can be controlled in three linear orthogonal and one angular coordinates.

Tunable two-dimensional arrays of single Rydberg atoms for realizing quantum Ising models

NASA Astrophysics Data System (ADS)

Labuhn, Henning; Barredo, Daniel; Ravets, Sylvain; de Léséleuc, Sylvain; Macrì, Tommaso; Lahaye, Thierry; Browaeys, Antoine

2016-06-01

Spin models are the prime example of simplified many-body Hamiltonians used to model complex, strongly correlated real-world materials. However, despite the simplified character of such models, their dynamics often cannot be simulated exactly on classical computers when the number of particles exceeds a few tens. For this reason, quantum simulation of spin Hamiltonians using the tools of atomic and molecular physics has become a very active field over the past years, using ultracold atoms or molecules in optical lattices, or trapped ions. All of these approaches have their own strengths and limitations. Here we report an alternative platform for the study of spin systems, using individual atoms trapped in tunable two-dimensional arrays of optical microtraps with arbitrary geometries, where filling fractions range from 60 to 100 per cent. When excited to high-energy Rydberg D states, the atoms undergo strong interactions whose anisotropic character opens the way to simulating exotic matter. We illustrate the versatility of our system by studying the dynamics of a quantum Ising-like spin-1/2 system in a transverse field with up to 30 spins, for a variety of geometries in one and two dimensions, and for a wide range of interaction strengths. For geometries where the anisotropy is expected to have small effects on the dynamics, we find excellent agreement with ab initio simulations of the spin-1/2 system, while for strongly anisotropic situations the multilevel structure of the D states has a measurable influence. Our findings establish arrays of single Rydberg atoms as a versatile platform for the study of quantum magnetism.

GRIFFIN: A versatile methodology for optimization of protein-lipid interfaces for membrane protein simulations

PubMed Central

Staritzbichler, René; Anselmi, Claudio; Forrest, Lucy R.; Faraldo-Gómez, José D.

2014-01-01

As new atomic structures of membrane proteins are resolved, they reveal increasingly complex transmembrane topologies, and highly irregular surfaces with crevices and pores. In many cases, specific interactions formed with the lipid membrane are functionally crucial, as is the overall lipid composition. Compounded with increasing protein size, these characteristics pose a challenge for the construction of simulation models of membrane proteins in lipid environments; clearly, that these models are sufficiently realistic bears upon the reliability of simulation-based studies of these systems. Here, we introduce GRIFFIN, which uses a versatile framework to automate and improve a widely-used membrane-embedding protocol. Initially, GRIFFIN carves out lipid and water molecules from a volume equivalent to that of the protein, so as to conserve the system density. In the subsequent optimization phase GRIFFIN adds an implicit grid-based protein force-field to a molecular dynamics simulation of the pre-carved membrane. In this force-field, atoms inside the implicit protein volume experience an outward force that will expel them from that volume, whereas those outside are subject to electrostatic and van-der-Waals interactions with the implicit protein. At each step of the simulation, these forces are updated by GRIFFIN and combined with the intermolecular forces of the explicit lipid-water system. This procedure enables the construction of realistic and reproducible starting configurations of the protein-membrane interface within a reasonable timeframe and with minimal intervention. GRIFFIN is a standalone tool designed to work alongside any existing molecular dynamics package, such as NAMD or GROMACS. PMID:24707227

Ultra-High Throughput Synthesis of Nanoparticles with Homogeneous Size Distribution Using a Coaxial Turbulent Jet Mixer

PubMed Central

2015-01-01

High-throughput production of nanoparticles (NPs) with controlled quality is critical for their clinical translation into effective nanomedicines for diagnostics and therapeutics. Here we report a simple and versatile coaxial turbulent jet mixer that can synthesize a variety of NPs at high throughput up to 3 kg/d, while maintaining the advantages of homogeneity, reproducibility, and tunability that are normally accessible only in specialized microscale mixing devices. The device fabrication does not require specialized machining and is easy to operate. As one example, we show reproducible, high-throughput formulation of siRNA-polyelectrolyte polyplex NPs that exhibit effective gene knockdown but exhibit significant dependence on batch size when formulated using conventional methods. The coaxial turbulent jet mixer can accelerate the development of nanomedicines by providing a robust and versatile platform for preparation of NPs at throughputs suitable for in vivo studies, clinical trials, and industrial-scale production. PMID:24824296

Ultrastable Photoelectrodes for Solar Water Splitting Based on Organic Metal Halide Perovskite Fabricated by Lift-Off Process.

PubMed

Nam, SeongSik; Mai, Cuc Thi Kim; Oh, Ilwhan

2018-05-02

Herein, we report an integrated photoelectrolysis of water employing organic metal halide (OMH) perovskite material. As generic OMH perovskite material and device architecture are highly susceptible to degradation by aqueous electrolytes, we have developed a versatile mold-cast and lift-off process to fabricate and assemble multipurpose metal encapsulation onto perovskite devices. With the metal encapsulation effectively protecting the perovskite cell and also functioning as electrocatalyst, the high-performance perovskite photoelectrodes exhibit high photovoltage and photocurrent that are effectively inherited from the original solid-state solar cell. More importantly, thus-fabricated perovskite photoelectrode demonstrates record-long unprecedented stability even at highly oxidizing potential in strong alkaline electrolyte. We expect that this versatile lift-off process can be adapted in a wide variety of photoelectrochemical devices to protect the material surfaces from corroding electrolyte and facilitate various electrochemical reactions.

Visualizing substructure of Ca2+ waves by total internal reflection fluorescence microscopy

NASA Astrophysics Data System (ADS)

Bai, Yongqiang; Tang, Aihui; Wang, Shiqiang; Zhu, Xing

2005-02-01

Total internal reflection fluorescence microscope is a new optical microscopic system based on near-field optical theory. Its character of illumination by evanescent wave, together with the great signal-to-noise ratio and temporal resolution achieved by high quality CCD, allows us to analyze the spatiotemporal details of local Ca2+ dynamics within the nanoscale microdomain surrounding different Ca2+ channels. We have recently constructed a versatile objective TIRFM equipped with a high numerical aperture (NA=1.45) objective. Using fluo-4 as the Ca2+ indicator, we visualized the near-membrane profiles of Ca2+ waves and elementary Ca2+ sparks generated by Ca2+ release channels in rat ventricular myocytes. Different from those detected using conventional and confocal microscopy, Ca2+ waves observed with TIRFM exhibited fine inhomogenous substructures composed of fluctuating Ca2+ sparks. The anfractuous routes of spark recruitment suggested that the propagation of Ca2+ waves is much more complicated than previously imagined. We believe that TIRFM will provide a unique tool for dissecting the microscopic mechanisms of intracellular Ca2+ signaling.

Widespread occurrence of low levels of alternariol in apple and tomato products, as determined by comparative immunochemical assessment using monoclonal and polyclonal antibodies.

PubMed

Ackermann, Yvonne; Curtui, Valeriu; Dietrich, Richard; Gross, Madeleine; Latif, Hadri; Märtlbauer, Erwin; Usleber, Ewald

2011-06-22

This study investigated the production of polyclonal (pAB) antibodies and the first time production of monoclonal (mAB) antibodies against the mycotoxin alternariol, and their implementation in enzyme immunoassay (EIA) for the rapid determination of alternariol in foods. Both EIAs were highly sensitive, with detection limits (IC₂₀) of 35 ± 6.9 pg/mL (mAb EIA) and 59 ± 16 pg/mL (pAb EIA). Food products (n = 109; apple and tomato products, white wine) from German retail shops were analyzed. At a detection limit of 1-2 μg/kg, alternariol at 1-13 μg/kg was found with high frequency in apple (67%) and tomato (93%) products. Tomatoes with visible signs of Alternaria infection, stored at room temperature for up to 4 weeks, contained alternariol at levels up to 50 mg/kg, as determined by EIA and HPLC-FLD. It is concluded that the alternariol immunoassays present a versatile screening tool which could facilitate food control for Alternaria toxins.

Highly active and efficient catalysts for alkoxycarbonylation of alkenes

PubMed Central

Dong, Kaiwu; Fang, Xianjie; Gülak, Samet; Franke, Robert; Spannenberg, Anke; Neumann, Helfried; Jackstell, Ralf; Beller, Matthias

2017-01-01

Carbonylation reactions of alkenes constitute the most important industrial processes in homogeneous catalysis. Despite the tremendous progress in this transformation, the development of advanced catalyst systems to improve their activity and widen the range of feedstocks continues to be essential for new practical applications. Herein a palladium catalyst based on 1,2-bis((tert-butyl(pyridin-2-yl)phosphanyl)methyl)benzene L3 (pytbpx) is rationally designed and synthesized. Application of this system allows a general alkoxycarbonylation of sterically hindered and demanding olefins including all kinds of tetra-, tri- and 1,1-disubstituted alkenes as well as natural products and pharmaceuticals to the desired esters in excellent yield. Industrially relevant bulk ethylene is functionalized with high activity (TON: >1,425,000; TOF: 44,000 h−1 for initial 18 h) and selectivity (>99%). Given its generality and efficiency, we expect this catalytic system to immediately impact both the chemical industry and research laboratories by providing a practical synthetic tool for the transformation of nearly any alkene into a versatile ester product. PMID:28120947

Self-contained microfluidic systems: a review.

PubMed

Boyd-Moss, Mitchell; Baratchi, Sara; Di Venere, Martina; Khoshmanesh, Khashayar

2016-08-16

Microfluidic systems enable rapid diagnosis, screening and monitoring of diseases and health conditions using small amounts of biological samples and reagents. Despite these remarkable features, conventional microfluidic systems rely on bulky expensive external equipment, which hinders their utility as powerful analysis tools outside of research laboratories. 'Self-contained' microfluidic systems, which contain all necessary components to facilitate a complete assay, have been developed to address this limitation. In this review, we provide an in-depth overview of self-contained microfluidic systems. We categorise these systems based on their operating mechanisms into three major groups: passive, hand-powered and active. Several examples are provided to discuss the structure, capabilities and shortcomings of each group. In particular, we discuss the self-contained microfluidic systems enabled by active mechanisms, due to their unique capability for running multi-step and highly controllable diagnostic assays. Integration of self-contained microfluidic systems with the image acquisition and processing capabilities of smartphones, especially those equipped with accessory optical components, enables highly sensitive and quantitative assays, which are discussed. Finally, the future trends and possible solutions to expand the versatility of self-contained, stand-alone microfluidic platforms are outlined.

GATG dendrimers and PEGylated block copolymers: from synthesis to bioapplications.

PubMed

Sousa-Herves, Ana; Novoa-Carballal, Ramon; Riguera, Ricardo; Fernandez-Megia, Eduardo

2014-09-01

Dendrimers are synthetic macromolecules composed of repetitive layers of branching units that emerge from a central core. They are characterized by a tunable size and precise number of peripheral groups which determine their physicochemical properties and function. Their high multivalency, functional surface, and globular architecture with diameters in the nanometer scale makes them ideal candidates for a wide range of applications. Gallic acid-triethylene glycol (GATG) dendrimers have attracted our attention as a promising platform in the biomedical field because of their high tunability and versatility. The presence of terminal azides in GATG dendrimers and poly(ethylene glycol) (PEG)-dendritic block copolymers allows their efficient functionalization with a variety of ligands of biomedical relevance including anionic and cationic groups, carbohydrates, peptides, or imaging agents. The resulting functionalized dendrimers have found application in drug and gene delivery, as antiviral agents and for the treatment of neurodegenerative diseases, in diagnosis and as tools to study multivalent carbohydrate recognition and dendrimer dynamics. Herein, we present an account on the preparation and recent applications of GATG dendrimers in these fields.

Two-dimensional magneto-optical light modulation in EuTiO3

NASA Astrophysics Data System (ADS)

Bussmann-Holder, Annette; Roleder, Krystian; Stuhlhofer, Benjamin; Logvenov, Gennady; Simon, Arndt; KöHler, Jürgen

EuTiO3 is antiferromagnetic at low temperature, namely below TN = 5.7K. In the high temperature paramagnetic phase the strongly nonlinear coupling between the lattice and the nomnially silent Eu 4f7 spins induces magnetic correlations which become apparent in muon spin rotation experiments and more recently in birefringence measurments in an external magnetic field. It is shown here, that high quality films of insulating EuTiO3 deposited on a thin SrTiO3 substrate are versatile tools for light modulation. The operating temperature is close to room temperature and admits multiple device engineering. By using small magnetic fields the birefringence of the samples can be switched off and on. Similarly, rotation of the sample in the field can modify its birefringence Δn. In addition, Δn can be increased by a factor of 4 in very modest fields with simultaneously enhancing the operating temperature by almost 100K. The results can be understood in terms of paramagnon phonon interaction where spin activity is achieved via the local spin-phonon double-well potential.

Aeolian transport of Icelandic dust: a look from Space

NASA Astrophysics Data System (ADS)

Smejda, Ladislav; Dagsson Waldhauserova, Pavla; Hejcman, Michal

2017-04-01

Iceland represents a unique type of Arctic environment where glaciers capture the precipitation, consequently forming large deserts on the leeward side. Deserts are subject to strong winds and dust is reported to be suspended at least 135 days a year. Icelandic dust has seven major dust sources in extensive deserts, consisting mainly of volcanic glass. In this paper, we address a new approach to the question of the island's contribution to atmospheric dust transport in the North Atlantic and Arctic Oceans. We explore the strengths and limitations of satellite imagery for the study of high altitude dust storm phenomenon, and more specifically the potential of freely available set of tools for remote sensing and spatial data analysis, the Earth Engine provided by Google. This cloud-based geospatial processing platform requires only a web browser on the side of a user, and it allows writing powerful and versatile algorithms for scientific analysis of spatial data. We demonstrate how this approach can be applied to mapping of Icelandic dust sources and studying the wind erosion and transport of particles in the atmosphere in high latitudes.

Phosphate deficiency promotes coral bleaching and is reflected by the ultrastructure of symbiotic dinoflagellates.

PubMed

Rosset, Sabrina; Wiedenmann, Jörg; Reed, Adam J; D'Angelo, Cecilia

2017-05-15

Enrichment of reef environments with dissolved inorganic nutrients is considered a major threat to the survival of corals living in symbiosis with dinoflagellates (Symbiodinium sp.). We argue, however, that the direct negative effects on the symbiosis are not necessarily caused by the nutrient enrichment itself but by the phosphorus starvation of the algal symbionts that can be caused by skewed nitrogen (N) to phosphorus (P) ratios. We exposed corals to imbalanced N:P ratios in long-term experiments and found that the undersupply of phosphate severely disturbed the symbiosis, indicated by the loss of coral biomass, malfunctioning of algal photosynthesis and bleaching of the corals. In contrast, the corals tolerated an undersupply with nitrogen at high phosphate concentrations without negative effects on symbiont photosynthesis, suggesting a better adaptation to nitrogen limitation. Transmission electron microscopy analysis revealed that the signatures of ultrastructural biomarkers represent versatile tools for the classification of nutrient stress in symbiotic algae. Notably, high N:P ratios in the water were clearly identified by the accumulation of uric acid crystals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

ZnO-Based Microfluidic pH Sensor: A Versatile Approach for Quick Recognition of Circulating Tumor Cells in Blood.

PubMed

Mani, Ganesh Kumar; Morohoshi, Madoka; Yasoda, Yutaka; Yokoyama, Sho; Kimura, Hiroshi; Tsuchiya, Kazuyoshi

2017-02-15

The present study is concerned about the development of highly sensitive and stable microfluidic pH sensor for possible identification of circulating tumor cells (CTCs) in blood. The precise pH measurements between silver-silver chloride (Ag/AgCl) reference electrode and zinc oxide (ZnO) working electrode have been investigated in the microfluidic device. Since there is a direct link between pH and cancer cells, the developed device is one of the valuable tools to examine circulating tumor cells (CTCs) in blood. The ZnO-based working electrode was deposited by radio frequency (rf) sputtering technique. The potential voltage difference between the working and reference electrodes (Ag/AgCl) is evaluated on the microfluidic device. The ideal Nernstian response of -43.71165 mV/pH was achieved along with high stability and quick response time. Finally, to evaluate the real time capability of the developed microfluidic device, in vitro testing was done with A549, A7r5, and MDCK cells.

Strategies in Ebola virus disease (EVD) diagnostics at the point of care.

PubMed

Coarsey, Chad T; Esiobu, Nwadiuto; Narayanan, Ramswamy; Pavlovic, Mirjana; Shafiee, Hadi; Asghar, Waseem

2017-11-01

Ebola virus disease (EVD) is a devastating, highly infectious illness with a high mortality rate. The disease is endemic to regions of Central and West Africa, where there is limited laboratory infrastructure and trained staff. The recent 2014 West African EVD outbreak has been unprecedented in case numbers and fatalities, and has proven that such regional outbreaks can become a potential threat to global public health, as it became the source for the subsequent transmission events in Spain and the USA. The urgent need for rapid and affordable means of detecting Ebola is crucial to control the spread of EVD and prevent devastating fatalities. Current diagnostic techniques include molecular diagnostics and other serological and antigen detection assays; which can be time-consuming, laboratory-based, often require trained personnel and specialized equipment. In this review, we discuss the various Ebola detection techniques currently in use, and highlight the potential future directions pertinent to the development and adoption of novel point-of-care diagnostic tools. Finally, a case is made for the need to develop novel microfluidic technologies and versatile rapid detection platforms for early detection of EVD.

A novel optical-fiber based surface plasmon resonance sensing architecture and its application to gastric cancer diagnostics

NASA Astrophysics Data System (ADS)

Francois, Alexandre; Boehm, Jonathan; Penno, Megan; Hoffmann, Peter; Monro, Tanya M.

2011-05-01

The management of threats such as pandemics and explosives, and of health and the environment requires the rapid deployment of highly sensitive detection tools. Sensors based on Surface Plasmon Resonance (SPR) allow rapid, labelfree, highly sensitive detection, and indeed this phenomenon underpins the only label-free optical biosensing technology that is available commercially. In these sensors, the existence of surface plasmons is inferred indirectly from absorption features that correspond to the coupling of light to the surface plasmon. Although SPR is not intrinsically a radiative process, under certain conditions the surface plasmon can itself couple to the local photon states, and emit light. Here we show for the first time that by collecting and characterising this re-emitted light, it is possible to realise new SPR sensing architectures that are more compact, versatile and robust than existing approaches. It is applicable to a range of SPR geometries, including optical fibres. As an example, this approach has been used to demonstrate the detection of a protein identified as a being a biomarker for cancer.

Probing the interaction between nanoparticles and lipid membranes by quartz crystal microbalance with dissipation monitoring

NASA Astrophysics Data System (ADS)

Yousefi, Nariman; Tufenkji, Nathalie

2016-12-01

There is increasing interest in using quartz crystal microbalance with dissipation monitoring (QCM-D) to investigate the interaction of nanoparticles (NPs) with model surfaces. The high sensitivity, ease of use and the ability to monitor interactions in real-time has made it a popular technique for colloid chemists, biologists, bioengineers and biophysicists. QCM-D has been recently used to probe the interaction of NPs with supported lipid bilayers (SLBs) as model cell membranes. The interaction of NPs with SLBs is highly influenced by the quality of the lipid bilayers. Unlike many surface sensitive techniques, using QCM-D, the quality of SLBs can be assessed in real-time, hence QCM-D studies on SLB-NP interactions are less prone to the artefacts arising from bilayers that are not well formed. The ease of use and commercial availability of a wide range of sensor surfaces also have made QCM-D a versatile tool for studying NP interactions with lipid bilayers. In this review, we summarize the state-of-the-art on QCM-D based techniques for probing the interactions of NPs with lipid bilayers.

2013 R&D 100 Award: ‘Miniapps’ Bolster High Performance Computing

ScienceCinema

Belak, Jim; Richards, David

2018-06-12

Two Livermore computer scientists served on a Sandia National Laboratories-led team that developed Mantevo Suite 1.0, the first integrated suite of small software programs, also called "miniapps," to be made available to the high performance computing (HPC) community. These miniapps facilitate the development of new HPC systems and the applications that run on them. Miniapps (miniature applications) serve as stripped down surrogates for complex, full-scale applications that can require a great deal of time and effort to port to a new HPC system because they often consist of hundreds of thousands of lines of code. The miniapps are a prototype that contains some or all of the essentials of the real application but with many fewer lines of code, making the miniapp more versatile for experimentation. This allows researchers to more rapidly explore options and optimize system design, greatly improving the chances the full-scale application will perform successfully. These miniapps have become essential tools for exploring complex design spaces because they can reliably predict the performance of full applications.

Jet Noise Modeling for Supersonic Business Jet Application

NASA Technical Reports Server (NTRS)

Stone, James R.; Krejsa, Eugene A.; Clark, Bruce J.

2004-01-01

This document describes the development of an improved predictive model for coannular jet noise, including noise suppression modifications applicable to small supersonic-cruise aircraft such as the Supersonic Business Jet (SBJ), for NASA Langley Research Center (LaRC). For such aircraft a wide range of propulsion and integration options are under consideration. Thus there is a need for very versatile design tools, including a noise prediction model. The approach used is similar to that used with great success by the Modern Technologies Corporation (MTC) in developing a noise prediction model for two-dimensional mixer ejector (2DME) nozzles under the High Speed Research Program and in developing a more recent model for coannular nozzles over a wide range of conditions. If highly suppressed configurations are ultimately required, the 2DME model is expected to provide reasonable prediction for these smaller scales, although this has not been demonstrated. It is considered likely that more modest suppression approaches, such as dual stream nozzles featuring chevron or chute suppressors, perhaps in conjunction with inverted velocity profiles (IVP), will be sufficient for the SBJ.

Lab-on-a-chip in vitro compartmentalization technologies for protein studies.

PubMed

Zhu, Yonggang; Power, Barbara E

2008-01-01

In vitro compartmentalization (IVC) is a powerful tool for studying protein-protein reactions, due to its high capacity and the versatility of droplet technologies. IVC bridges the gap between chemistry and biology as it enables the incorporation of unnatural amino acids with modifications into biological systems, through protein transcription and translation reactions, in a cell-like microdrop environment. The quest for the ultimate chip for protein studies using IVC is the drive for the development of various microfluidic droplet technologies to enable these unusual biochemical reactions to occur. These techniques have been shown to generate precise microdrops with a controlled size. Various chemical and physical phenomena have been utilized for on-chip manipulation to allow the droplets to be generated, fused, and split. Coupled with detection techniques, droplets can be sorted and selected. These capabilities allow directed protein evolution to be carried out on a microchip. With further technological development of the detection module, factors such as addressable storage, transport and interfacing technologies, could be integrated and thus provide platforms for protein studies with high efficiency and accuracy that conventional laboratories cannot achieve.

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.

PubMed

Althammer, Sonja; González-Vallinas, Juan; Ballaré, Cecilia; Beato, Miguel; Eyras, Eduardo

2011-12-15

High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein-DNA and protein-RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing. We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics. Open-source software, with tutorials and protocol files, is available at http://regulatorygenomics.upf.edu/pyicos or as a Galaxy server at http://regulatorygenomics.upf.edu/galaxy eduardo.eyras@upf.edu Supplementary data are available at Bioinformatics online.

Manufacturing and advanced characterization of sub-25nm diameter CD-AFM probes with sub-10nm tip edges radius

NASA Astrophysics Data System (ADS)

Foucher, Johann; Filippov, Pavel; Penzkofer, Christian; Irmer, Bernd; Schmidt, Sebastian W.

2013-04-01

Atomic force microscopy (AFM) is increasingly used in the semiconductor industry as a versatile monitoring tool for highly critical lithography and etching process steps. Applications range from the inspection of the surface roughness of new materials, over accurate depth measurements to the determination of critical dimension structures. The aim to address the rapidly growing demands on measurement uncertainty and throughput more and more shifts the focus of attention to the AFM tip, which represents the crucial link between AFM tool and the sample to be monitored. Consequently, in order to reach the AFM tool's full potential, the performance of the AFM tip has to be considered as a determining parameter. Currently available AFM tips made from silicon are generally limited by their diameter, radius, and sharpness, considerably restricting the AFM measurement capabilities on sub-30nm spaces. In addition to that, there's lack of adequate characterization structures to accurately characterize sub-25nm tip diameters. Here, we present and discuss a recently introduced AFM tip design (T-shape like design) with precise tip diameters down to 15nm and tip radii down to 5nm fabricated from amorphous, high density diamond-like carbon (HDC/DLC) using electron beam induced processing (EBIP). In addition to that advanced design, we propose a new characterizer structure, which allows for accurate characterization and design control of sub-25nm tip diameters and sub-10nm tip edges radii. We demonstrate the potential advantages of combining a small tip shape design, i.e. tip diameter and tip edge radius, and an advanced tip characterizer for the semiconductor industry by the measurement of advanced lithography patterns.

Targeted Gene Manipulation in Plants Using the CRISPR/Cas Technology.

PubMed

Zhang, Dandan; Li, Zhenxiang; Li, Jian-Feng

2016-05-20

The CRISPR/Cas technology is emerging as a revolutionary genome editing tool in diverse organisms including plants, and has quickly evolved into a suite of versatile tools for sequence-specific gene manipulations beyond genome editing. Here, we review the most recent applications of the CRISPR/Cas toolkit in plants and also discuss key factors for improving CRISPR/Cas performance and strategies for reducing the off-target effects. Novel technical breakthroughs in mammalian research regarding the CRISPR/Cas toolkit will also be incorporated into this review in hope to stimulate prospective users from the plant research community to fully explore the potential of these technologies. Copyright © 2016 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Development of CCSDS DCT to Support Spacecraft Dynamic Events

NASA Technical Reports Server (NTRS)

Sidhwa, Anahita F

2011-01-01

This report discusses the development of Consultative Committee for Space Data Systems (CCSDS) Design Control Table (DCT) to support spacecraft dynamic events. The Consultative Committee for Space Data Systems (CCSDS) Design Control Table (DCT) is a versatile link calculation tool to analyze different kinds of radio frequency links. It started out as an Excel-based program, and is now being evolved into a Mathematica-based link analysis tool. The Mathematica platform offers a rich set of advanced analysis capabilities, and can be easily extended to a web-based architecture. Last year the CCSDS DCT's for the uplink, downlink, two-way, and ranging models were developed as well as the corresponding input and output interfaces. Another significant accomplishment is the integration of the NAIF SPICE library into the Mathematica computation platform.

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

PubMed Central

Rampp, Markus; Soddemann, Thomas; Lederer, Hermann

2006-01-01

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at (click ‘Start Toolkit’). PMID:16844980

Exploiting CRISPR/Cas: Interference Mechanisms and Applications

PubMed Central

Richter, Hagen; Randau, Lennart; Plagens, André

2013-01-01

The discovery of biological concepts can often provide a framework for the development of novel molecular tools, which can help us to further understand and manipulate life. One recent example is the elucidation of the prokaryotic adaptive immune system, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) that protects bacteria and archaea against viruses or conjugative plasmids. The immunity is based on small RNA molecules that are incorporated into versatile multi-domain proteins or protein complexes and specifically target viral nucleic acids via base complementarity. CRISPR/Cas interference machines are utilized to develop novel genome editing tools for different organisms. Here, we will review the latest progress in the elucidation and application of prokaryotic CRISPR/Cas systems and discuss possible future approaches to exploit the potential of these interference machineries. PMID:23857052

A Molecular Toolbox to Engineer Site-Specific DNA Replication Perturbation.

PubMed

Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

2018-01-01

Site-specific arrest of DNA replication is a useful tool for analyzing cellular responses to DNA replication perturbation. The E. coli Tus-Ter replication barrier can be reconstituted in eukaryotic cells as a system to engineer an unscheduled collision between a replication fork and an "alien" impediment to DNA replication. To further develop this system as a versatile tool, we describe a set of reagents and a detailed protocol that can be used to engineer Tus-Ter barriers into any locus in the budding yeast genome. Because the Tus-Ter complex is a bipartite system with intrinsic DNA replication-blocking activity, the reagents and protocols developed and validated in yeast could also be optimized to engineer site-specific replication fork barriers into other eukaryotic cell types.

Exploiting CRISPR/Cas: interference mechanisms and applications.

PubMed

Richter, Hagen; Randau, Lennart; Plagens, André

2013-07-12

The discovery of biological concepts can often provide a framework for the development of novel molecular tools, which can help us to further understand and manipulate life. One recent example is the elucidation of the prokaryotic adaptive immune system, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) that protects bacteria and archaea against viruses or conjugative plasmids. The immunity is based on small RNA molecules that are incorporated into versatile multi-domain proteins or protein complexes and specifically target viral nucleic acids via base complementarity. CRISPR/Cas interference machines are utilized to develop novel genome editing tools for different organisms. Here, we will review the latest progress in the elucidation and application of prokaryotic CRISPR/Cas systems and discuss possible future approaches to exploit the potential of these interference machineries.

Restricted numerical range: A versatile tool in the theory of quantum information

NASA Astrophysics Data System (ADS)

Gawron, Piotr; Puchała, Zbigniew; Miszczak, Jarosław Adam; Skowronek, Łukasz; Życzkowski, Karol

2010-10-01

Numerical range of a Hermitian operator X is defined as the set of all possible expectation values of this observable among a normalized quantum state. We analyze a modification of this definition in which the expectation value is taken among a certain subset of the set of all quantum states. One considers, for instance, the set of real states, the set of product states, separable states, or the set of maximally entangled states. We show exemplary applications of these algebraic tools in the theory of quantum information: analysis of k-positive maps and entanglement witnesses, as well as study of the minimal output entropy of a quantum channel. Product numerical range of a unitary operator is used to solve the problem of local distinguishability of a family of two unitary gates.

Analytical formulation of directly modulated OOFDM signals transmitted over an IM/DD dispersive link.

PubMed

Sánchez, C; Ortega, B; Wei, J L; Tang, J; Capmany, J

2013-03-25

We provide an analytical study on the propagation effects of a directly modulated OOFDM signal through a dispersive fiber and subsequent photo-detection. The analysis includes the effects of the laser operation point and the interplay between chromatic dispersion and laser chirp. The final expression allows to understand the physics behind the transmission of a multi-carrier signal in the presence of residual frequency modulation and the description of the induced intermodulation distortion gives us a detailed insight into the diferent intermodulation products which impair the recovered signal at the receiver-end side. Numerical comparisons between transmission simulations results and those provided by evaluating the expression obtained are carried out for different laser operation points. Results obtained by changing the fiber length, laser parameters and using single mode fiber with negative and positive dispersion are calculated in order to demonstrate the validity and versatility of the theory provided in this paper. Therefore, a novel analytical formulation is presented as a versatile tool for the description and study of IM/DD OOFDM systems with variable design parameters.

Organic nanofiber nanosensors

NASA Astrophysics Data System (ADS)

Madsen, M.; Schiek, M.; Thomsen, P.; Andersen, N. L.; Lützen, A.; Rubahn, H.-G.

2007-09-01

A new way of developing optical nanosensors is presented. Organic nanofibers serve as key elements in these new types of devices, which exploit both the smallness and brightness of the nanoaggregates to make new compact and sensitive optical nanosensors. On the basis of bottom up technology, we functionalize individual molecules, which are then intrinsically sensitive to specific agents. These molecules are used as building blocks for controlled growth of larger nanoscaled aggregates. The aggregates in turn can be used as sensing elements on the meso-scale in the size range from hundred nanometers to a few hundred microns. The organic nanofibers thereby might become a versatile tool within nanosensor technology, allowing sensing on the basis of individual molecules over small aggregates to large assemblies. First experiments of Bovine Serum Albumin (BSA) coupling to para-hexaphenyl (p-6P) nanofibers are presented, which could lead towards a new type of protein sensors. Besides large versatility and sensitivity, the nanofibers benefit from the fact that they can be integrated in devices, either in liquids by the use of microfluidic cavities or all in parallel.

A Robust Kalman Framework with Resampling and Optimal Smoothing

PubMed Central

Kautz, Thomas; Eskofier, Bjoern M.

2015-01-01

The Kalman filter (KF) is an extremely powerful and versatile tool for signal processing that has been applied extensively in various fields. We introduce a novel Kalman-based analysis procedure that encompasses robustness towards outliers, Kalman smoothing and real-time conversion from non-uniformly sampled inputs to a constant output rate. These features have been mostly treated independently, so that not all of their benefits could be exploited at the same time. Here, we present a coherent analysis procedure that combines the aforementioned features and their benefits. To facilitate utilization of the proposed methodology and to ensure optimal performance, we also introduce a procedure to calculate all necessary parameters. Thereby, we substantially expand the versatility of one of the most widely-used filtering approaches, taking full advantage of its most prevalent extensions. The applicability and superior performance of the proposed methods are demonstrated using simulated and real data. The possible areas of applications for the presented analysis procedure range from movement analysis over medical imaging, brain-computer interfaces to robot navigation or meteorological studies. PMID:25734647

A versatile transfection assay system to evaluate the biological effects of diverse industrial chemicals.

PubMed

Koizumi, Shinji; Ohno, Shotaro; Otsuka, Fuminori

2012-01-01

Gene expression processes are now recognized as important targets of the toxic effects exerted by industrial chemicals. The transient transfection assay is a powerful tool to evaluate such effects. Thus, we developed a versatile assay system by constructing a basic reporter plasmid in which the regulatory DNA sequence to be studied can easily be substituted. To verify the performance of this system, reporter plasmids carrying any of the three distinct regulatory sequences, estrogen responsive element (ERE), glucocorticoid responsive element (GRE) and xenobiotic responsive element (XRE) were constructed. After transfection of human cells, these plasmids successfully expressed the relevant reporter genes in response to specific inducers, β-estradiol, dexamethasone and 3-methylcholanthrene, respectively. Several industrial chemicals were assayed using these reporter plasmids, and the ability of p-dimethylaminoazobenzene to elevate GRE- and XRE-mediated transcription was detected. α-Naphthylamine and o-tolidine were also observed to increase the XRE-mediated response. The transfection assay system established here will be useful to evaluate the effects of a wide variety of industrial chemicals.

Strain-Induced Alignment in Collagen Gels

PubMed Central

Vader, David; Kabla, Alexandre; Weitz, David; Mahadevan, Lakshminarayana

2009-01-01

Collagen is the most abundant extracellular-network-forming protein in animal biology and is important in both natural and artificial tissues, where it serves as a material of great mechanical versatility. This versatility arises from its almost unique ability to remodel under applied loads into anisotropic and inhomogeneous structures. To explore the origins of this property, we develop a set of analysis tools and a novel experimental setup that probes the mechanical response of fibrous networks in a geometry that mimics a typical deformation profile imposed by cells in vivo. We observe strong fiber alignment and densification as a function of applied strain for both uncrosslinked and crosslinked collagenous networks. This alignment is found to be irreversibly imprinted in uncrosslinked collagen networks, suggesting a simple mechanism for tissue organization at the microscale. However, crosslinked networks display similar fiber alignment and the same geometrical properties as uncrosslinked gels, but with full reversibility. Plasticity is therefore not required to align fibers. On the contrary, our data show that this effect is part of the fundamental non-linear properties of fibrous biological networks. PMID:19529768

A cryogen-free variable temperature scanning tunneling microscope capable for inelastic electron tunneling spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Shuai; Huang, Di; Wu, Shiwei

While low temperature scanning tunneling microscope (STM) has become an indispensable research tool in surface science, its versatility is yet limited by the shortage or high cost of liquid helium. The makeshifts include the use of alternative cryogen (such as liquid nitrogen) at higher temperature or the development of helium liquefier system usually at departmental or campus wide. The ultimate solution would be the direct integration of a cryogen-free cryocooler based on GM or pulse tube closed cycle in the STM itself. However, the nasty mechanical vibration at low frequency intrinsic to cryocoolers has set the biggest obstacle because of the known challenges in vibration isolation required to high performance of STM. In this talk, we will present the design and performance of our home-built cryogen-free variable temperature STM at Fudan University. This system can obtain atomically sharp STM images and high resolution dI/dV spectra comparable to state-of-the-art low temperature STMs, but with no limitation on running hours. Moreover, we demonstrated the inelastic tunneling spectroscopy (STM-IETS) on a single CO molecule with a cryogen-free STM for the first time.

Cardiovascular magnetic resonance imaging: clinical implications in the evaluation of connective tissue diseases

PubMed Central

Mavrogeni, Sophie; Markousis-Mavrogenis, George; Koutsogeorgopoulou, Loukia; Kolovou, Genovefa

2017-01-01

Cardiovascular magnetic resonance imaging is a recently developed noninvasive, nonradiating, operator-independent technique that has been successfully used for the evaluation of congenital heart disease, valvular and pericardial diseases, iron overload, cardiomyopathies, great and coronary vessel diseases, cardiac inflammation, stress–rest myocardial perfusion, and fibrosis. Rheumatoid arthritis and other spondyloarthropathies, systemic lupus erythematosus, inflammatory myopathies, mixed connective tissue diseases (CTDs), systemic sclerosis, vasculitis, and sarcoidosis are among CTDs with serious cardiovascular involvement; this is due to multiple causative factors such as myopericarditis, micro/macrovascular disease, coronary artery disease, myocardial fibrosis, pulmonary hypertension, and finally heart failure. The complicated pathophysiology and the high cardiovascular morbidity and mortality of CTDs demand a versatile, noninvasive, nonradiative diagnostic tool for early cardiovascular diagnosis, risk stratification, and treatment follow-up. Cardiovascular magnetic resonance imaging can detect early silent cardiovascular lesions, assess disease acuteness, and reliably evaluate the effect of both cardiac and rheumatic medication in the cardiovascular system, due to its capability to perform tissue characterization and its high spatial resolution. However, until now, high cost; lack of interaction between cardiologists, radiologists, and rheumatologists; lack of availability; and lack of experts in the field have limited its wider adoption in the clinical practice. PMID:28546762

Capillary electrophoresis: principles and applications in illicit drug analysis.

PubMed

Tagliaro, F; Turrina, S; Smith, F P

1996-02-09

Capillary electrophoresis, which appeared in the early 1980s, is now rapidly expanding into many scientific disciplines, including analytical chemistry, biotechnology and biomedical and pharmaceutical sciences. In capillary electrophoresis,electrokinetic separations are carried out in tiny capillaries at high voltages (10-30 kV), thus obtaining high efficiencies (N > 10(5)) and excellent mass sensitivities (down to 10(-18)-10(-20) moles). The main features of capillary electrophoresis are: versatility of application (from inorganic ions to large DNA fragments), use of different separation modes with different selectivity, extremely low demands on sample volume, negligible running costs, possibility of interfacing with different detection systems, ruggedness and simplicity of instrumentation. Capillary electrophoresis applications in forensic sciences have appeared only recently, but are now rapidly growing, particularly in forensic toxicology. The present paper briefly describes the basic principles of capillary electrophoresis, from both the instrumental and analytical points of view. Furthermore, the main applications in the analysis of illicit/controlled drugs in both illicit preparations and biological samples are presented and discussed (43 references). It is concluded that the particular separation mechanism and the high complementarity of this technique to chromatography makes capillary electrophoresis a new powerful tool of investigation in the hands of forensic toxicologists.

Hierarchical Micro-/Nanostructures from Human Hair for Biomedical Applications.

PubMed

Zheng, Di-Wei; Hong, Sheng; Xu, Lu; Li, Chu-Xin; Li, Ke; Cheng, Si-Xue; Zhang, Xian-Zheng

2018-05-21

With the prominent progress of biomedical engineering, materials with high biocompatibility and versatile functions are urgently needed. So far, hierarchical structures in nature have shed some light on the design of high performance materials both in concept and implementation. Inspired by these, the hierarchical micro-/nanostructures of human hair are explored and human hair is further broken into hierarchical microparticles (HMP) and hierarchical nanoparticles (HNP) with top-down procedures. Compared with commercialized carriers, such as liposomes or albumin nanoparticles, the obtained particles exhibit high hemocompatibility and negligible immunogenicity. Furthermore, these materials also display attentional abilities in the aspects of light absorption and free radical scavenging. It is found that HMP and HNP can prevent skin from UV-induced damage and relieve symptoms of cataract in vitro. Besides, both HMP and HNP show satisfactory photothermal conversion ability. By using microcomputed tomography and intravital fluorescence microscopy, it is found that warfarin-loaded HMP can rescue mice from vein thrombosis. In another aspect, HNP modified with tumor targeted aptamers exhibit dramatic antineoplastic effect, and suppress 96.8% of tumor growth in vivo. Thus, the multifaceted materials described here might provide a new tool for addressing biomedical challenges. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A versatile synthetic route for the preparation of titanium metal-organic frameworks

DOE PAGES

Zou, Lanfang; Feng, Dawei; Liu, Tian-Fu; ...

2016-02-01

Exploitation of new titanium metal–organic frameworks (Ti-MOFs) with high crystallinity has been attracting great attention due to their vast application potential in photocatalysis. Herein a versatile synthetic strategy, namely, High Valence Metathesis and Oxidation (HVMO), is developed to synthesize a series of Ti-MOFs with predesigned topologies and structures. The crystallinity of these Ti-MOFs was well maintained throughout, as confirmed by powder X-ray diffraction and gas adsorption measurements. Significantly, there were only a few examples of Ti-MOFs, not to mention a general synthetic strategy for various kinds of Ti-MOFs in the literature. This contribution also illustrates the intriguing potential of Ti-MOFmore » platforms in photocatalysis.« less

A versatile electrophoresis system for the analysis of high- and low-molecular-weight proteins

PubMed Central

Tastet, Christophe; Lescuyer, Pierre; Diemer, Hélène; Luche, Sylvie; van Dorsselaer, Alain; Rabilloud, Thierry

2003-01-01

A new, versatile, multiphasic buffer system for high resolution sodium dodecyl sulfatepolyacrylamide gel electrophoresis of proteins in the relative molecular weight Mw range of 300,000-3000 Da is described. The system, based on the theory of multiphasic zone electrophoresis, allows complete stacking and destacking of proteins in the above Mw range. The buffer system uses taurine and chloride as trailing and leading ion, respectively, and Tris, at a pH close to its pKa, as the buffering counter ion. Coupled with limited variation in the acrylamide concentration, this electrophoresis system allows to tailor the resolution in the 6–200 kDa Mw range, with minimal difficulties in the post electrophoretic identification processes. PMID:12783456

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud

PubMed Central

Afgan, Enis; Sloggett, Clare; Goonasekera, Nuwan; Makunin, Igor; Benson, Derek; Crowe, Mark; Gladman, Simon; Kowsar, Yousef; Pheasant, Michael; Horst, Ron; Lonie, Andrew

2015-01-01

Background Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s) enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise. Results We designed and implemented the Genomics Virtual Laboratory (GVL) as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook) or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au) and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic. Conclusions This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints, and explore the value added to the research community through the suite of services and resources provided by our implementation. PMID:26501966

InCHlib - interactive cluster heatmap for web applications.

PubMed

Skuta, Ctibor; Bartůněk, Petr; Svozil, Daniel

2014-12-01

Hierarchical clustering is an exploratory data analysis method that reveals the groups (clusters) of similar objects. The result of the hierarchical clustering is a tree structure called dendrogram that shows the arrangement of individual clusters. To investigate the row/column hierarchical cluster structure of a data matrix, a visualization tool called 'cluster heatmap' is commonly employed. In the cluster heatmap, the data matrix is displayed as a heatmap, a 2-dimensional array in which the colour of each element corresponds to its value. The rows/columns of the matrix are ordered such that similar rows/columns are near each other. The ordering is given by the dendrogram which is displayed on the side of the heatmap. We developed InCHlib (Interactive Cluster Heatmap Library), a highly interactive and lightweight JavaScript library for cluster heatmap visualization and exploration. InCHlib enables the user to select individual or clustered heatmap rows, to zoom in and out of clusters or to flexibly modify heatmap appearance. The cluster heatmap can be augmented with additional metadata displayed in a different colour scale. In addition, to further enhance the visualization, the cluster heatmap can be interconnected with external data sources or analysis tools. Data clustering and the preparation of the input file for InCHlib is facilitated by the Python utility script inchlib_clust . The cluster heatmap is one of the most popular visualizations of large chemical and biomedical data sets originating, e.g., in high-throughput screening, genomics or transcriptomics experiments. The presented JavaScript library InCHlib is a client-side solution for cluster heatmap exploration. InCHlib can be easily deployed into any modern web application and configured to cooperate with external tools and data sources. Though InCHlib is primarily intended for the analysis of chemical or biological data, it is a versatile tool which application domain is not limited to the life sciences only.

AHCODA-DB: a data repository with web-based mining tools for the analysis of automated high-content mouse phenomics data.

PubMed

Koopmans, Bastijn; Smit, August B; Verhage, Matthijs; Loos, Maarten

2017-04-04

Systematic, standardized and in-depth phenotyping and data analyses of rodent behaviour empowers gene-function studies, drug testing and therapy design. However, no data repositories are currently available for standardized quality control, data analysis and mining at the resolution of individual mice. Here, we present AHCODA-DB, a public data repository with standardized quality control and exclusion criteria aimed to enhance robustness of data, enabled with web-based mining tools for the analysis of individually and group-wise collected mouse phenotypic data. AHCODA-DB allows monitoring in vivo effects of compounds collected from conventional behavioural tests and from automated home-cage experiments assessing spontaneous behaviour, anxiety and cognition without human interference. AHCODA-DB includes such data from mutant mice (transgenics, knock-out, knock-in), (recombinant) inbred strains, and compound effects in wildtype mice and disease models. AHCODA-DB provides real time statistical analyses with single mouse resolution and versatile suite of data presentation tools. On March 9th, 2017 AHCODA-DB contained 650 k data points on 2419 parameters from 1563 mice. AHCODA-DB provides users with tools to systematically explore mouse behavioural data, both with positive and negative outcome, published and unpublished, across time and experiments with single mouse resolution. The standardized (automated) experimental settings and the large current dataset (1563 mice) in AHCODA-DB provide a unique framework for the interpretation of behavioural data and drug effects. The use of common ontologies allows data export to other databases such as the Mouse Phenome Database. Unbiased presentation of positive and negative data obtained under the highly standardized screening conditions increase cost efficiency of publicly funded mouse screening projects and help to reach consensus conclusions on drug responses and mouse behavioural phenotypes. The website is publicly accessible through https://public.sylics.com and can be viewed in every recent version of all commonly used browsers.

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

PubMed

Afgan, Enis; Sloggett, Clare; Goonasekera, Nuwan; Makunin, Igor; Benson, Derek; Crowe, Mark; Gladman, Simon; Kowsar, Yousef; Pheasant, Michael; Horst, Ron; Lonie, Andrew

2015-01-01

Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s) enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise. We designed and implemented the Genomics Virtual Laboratory (GVL) as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook) or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au) and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic. This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints, and explore the value added to the research community through the suite of services and resources provided by our implementation.

Recent advances on the encoding and selection methods of DNA-encoded chemical library.

PubMed

Shi, Bingbing; Zhou, Yu; Huang, Yiran; Zhang, Jianfu; Li, Xiaoyu

2017-02-01

DNA-encoded chemical library (DEL) has emerged as a powerful and versatile tool for ligand discovery in chemical biology research and in drug discovery. Encoding and selection methods are two of the most important technological aspects of DEL that can dictate the performance and utilities of DELs. In this digest, we have summarized recent advances on the encoding and selection strategies of DEL and also discussed the latest developments on DNA-encoded dynamic library, a new frontier in DEL research. Copyright © 2016 Elsevier Ltd. All rights reserved.

MEGARA: the new multi-object and integral field spectrograph for GTC

NASA Astrophysics Data System (ADS)

Carrasco, E.; Páez, G.; Izazaga-Pére, R.; Gil de Paz, A.; Gallego, J.; Iglesias-Páramo, J.

2017-07-01

MEGARA is an optical integral-field unit and multi-object spectrograph for the 10.4m Gran Telescopio Canarias. Both observational modes will provide identical spectral resolutions Rfwhm ˜ 6,000, 12,000 and 18,700. The spectrograph is a collimator-camera system. The unique characteristics of MEGARA in terms of throughput and versatility make this instrument the most efficient tool to date to analyze astrophysical objects at intermediate spectral resolutions. The instrument is currently at the telescope for on-sky commissioning. Here we describe the as-built main characteristics the instrument.

Current–Voltage Characterization of Individual As-Grown Nanowires Using a Scanning Tunneling Microscope

PubMed Central

2013-01-01

Utilizing semiconductor nanowires for (opto)electronics requires exact knowledge of their current–voltage properties. We report accurate on-top imaging and I–V characterization of individual as-grown nanowires, using a subnanometer resolution scanning tunneling microscope with no need for additional microscopy tools, thus allowing versatile application. We form Ohmic contacts to InP and InAs nanowires without any sample processing, followed by quantitative measurements of diameter dependent I–V properties with a very small spread in measured values compared to standard techniques. PMID:24059470

General-Purpose Electronic System Tests Aircraft

NASA Technical Reports Server (NTRS)

Glover, Richard D.

1989-01-01

Versatile digital equipment supports research, development, and maintenance. Extended aircraft interrogation and display system is general-purpose assembly of digital electronic equipment on ground for testing of digital electronic systems on advanced aircraft. Many advanced features, including multiple 16-bit microprocessors, pipeline data-flow architecture, advanced operating system, and resident software-development tools. Basic collection of software includes program for handling many types of data and for displays in various formats. User easily extends basic software library. Hardware and software interfaces to subsystems provided by user designed for flexibility in configuration to meet user's requirements.

Current-voltage characterization of individual as-grown nanowires using a scanning tunneling microscope.

PubMed

Timm, Rainer; Persson, Olof; Engberg, David L J; Fian, Alexander; Webb, James L; Wallentin, Jesper; Jönsson, Andreas; Borgström, Magnus T; Samuelson, Lars; Mikkelsen, Anders

2013-11-13

Utilizing semiconductor nanowires for (opto)electronics requires exact knowledge of their current-voltage properties. We report accurate on-top imaging and I-V characterization of individual as-grown nanowires, using a subnanometer resolution scanning tunneling microscope with no need for additional microscopy tools, thus allowing versatile application. We form Ohmic contacts to InP and InAs nanowires without any sample processing, followed by quantitative measurements of diameter dependent I-V properties with a very small spread in measured values compared to standard techniques.

Flow-assisted single-beam optothermal manipulation of microparticles.

PubMed

Liu, Yangyang; Poon, Andrew W

2010-08-16

An optothermal tweezer was developed with a single-beam laser at 1550 nm for manipulation of colloidal microparticles. Strong absorption in water can thermally induce a localized flow, which exerts a Stokes' drag on the particles that complements the gradient force. Long-range capturing of 6 microm polystyrene particles over approximately 176 microm was observed with a tweezing power of approximately 7 mW. Transportation and levitation, targeted deposition and selective levitation of particles were explored to experimentally demonstrate the versatility of the optothermal tweezer as a multipurpose particle manipulation tool.

Versatility of erbium YAG laser: from fractional skin rejuvenation to full-field skin resurfacing.

PubMed

Holcomb, J David

2011-05-01

For the laser surgeon, the Er-YAG laser is an invaluable tool that delivers unsurpassed ablation efficiency, and with appropriate functionality (quasi long-pulse feature) provides sufficient tissue coagulation to remodel deep rhytids. As such, the 2940-nm wavelength is well suited for routine laser skin rejuvenation in full-field, fractional, and point-beam modes with additional benefits, including applicability to diverse skin types, short healing times, and a low likelihood of energy-related complications. Copyright © 2011 Elsevier Inc. All rights reserved.

An Inexpensive and Easy Ultrasound Phantom: A Novel Use for SPAM.

PubMed

Nolting, Laura; Hunt, Patrick; Cook, Thomas; Douglas, Barton

2016-04-01

Ultrasound models, commonly referred to as "phantoms," are simulation tools for ultrasound education. Commercially produced phantoms are available, but there are "homemade" alternatives such as raw poultry and gelatin molds. Precooked, processed meat, better known as SPAM (Hormel Foods Corporation, Austin, MN), can be used as an ultrasound phantom to teach several ultrasound applications. It is a versatile, hygienic, and easily manipulated medium that does not require refrigeration or preparatory work and can be easily discarded at the end of use. © 2016 by the American Institute of Ultrasound in Medicine.

CRISPR genetic screens to discover host-virus interactions.

PubMed

McDougall, William M; Perreira, Jill M; Reynolds, Erin C; Brass, Abraham L

2018-04-01

Viruses impose an immense burden on human health. With the goal of treating and preventing viral infections, researchers have carried out genetic screens to improve our understanding of viral dependencies and identify potential anti-viral strategies. The emergence of CRISPR genetic screening tools has facilitated this effort by enabling host-virus screens to be undertaken in a more versatile and fidelitous manner than previously possible. Here we review the growing number of CRISPR screens which continue to increase our understanding of host-virus interactions. Copyright © 2018 Elsevier B.V. All rights reserved.

In situ nanomechanical testing of twinned metals in a transmission electron microscope

DOE PAGES

Li, Nan; Wang, Jiangwei; Mao, Scott; ...

2016-04-01

This paper focuses on in situ transmission electron microscope (TEM) characterization to explore twins in face-centered-cubic and body-centered-cubic monolithic metals, and their impact on the overall mechanical performance. Taking advantage of simultaneous nanomechanical deformation and nanoscale imaging using versatile in situ TEM tools, direct correlation of these unique microscopic defects with macroscopic mechanical performance becomes possible. This article summarizes recent evidence to support the mechanisms related to strengthening and plasticity in metals, including nanotwinned Cu, Ni, Al, Au, and others in bulk, thin film, and nanowire forms.

The story of Clostridium botulinum: from food poisoning to Botox.

PubMed

Ting, Patricia T; Freiman, Anatoli

2004-01-01

In the last fifty years, Clostridium botulinum has become notorious for its ability to produce the deadly botulinum neurotoxins. While botulinum toxin A, better known as Botox, is universally recognised by the public as a cosmetic enhancement tool, the botulinum neurotoxins are commonly used off-label for many medical conditions in ophthalmology, neurology and dermatology. The versatility of these botulinum toxins has made Clostridium botulinum one of the most widely known bacterial pathogens in medical history. This article outlines the discovery of botulinum toxins through to their present day applications in medicine.

In situ nanomechanical testing of twinned metals in a transmission electron microscope

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

Li, Nan; Wang, Jiangwei; Mao, Scott

This paper focuses on in situ transmission electron microscope (TEM) characterization to explore twins in face-centered-cubic and body-centered-cubic monolithic metals, and their impact on the overall mechanical performance. Taking advantage of simultaneous nanomechanical deformation and nanoscale imaging using versatile in situ TEM tools, direct correlation of these unique microscopic defects with macroscopic mechanical performance becomes possible. This article summarizes recent evidence to support the mechanisms related to strengthening and plasticity in metals, including nanotwinned Cu, Ni, Al, Au, and others in bulk, thin film, and nanowire forms.

McStas 1.7 - a new version of the flexible Monte Carlo neutron scattering package

NASA Astrophysics Data System (ADS)

Willendrup, Peter; Farhi, Emmanuel; Lefmann, Kim

2004-07-01

Current neutron instrumentation is both complex and expensive, and accurate simulation has become essential both for building new instruments and for using them effectively. The McStas neutron ray-trace simulation package is a versatile tool for producing such simulations, developed in collaboration between Risø and ILL. The new version (1.7) has many improvements, among these added support for the popular Microsoft Windows platform. This presentation will demonstrate a selection of the new features through a simulation of the ILL IN6 beamline.

Application of Cell-Specific Isolation to the Study of Dopamine Signaling in Drosophila

PubMed Central

Iyer, Eswar Prasad R.; Iyer, Srividya Chandramouli; Cox, Daniel N.

2014-01-01

Dopamine neurotransmission accounts for a number of important brain functions across species including memory formation, the anticipation of reward, cognitive facilities, and drug addiction. Despite this functional significance, relatively little is known of the cellular pathways associated with drug-induced molecular adaptations within individual neurons. Due to its genetic tractability, simplicity, and economy of scale, Drosophila melanogaster has become an important tool in the study of neurological disease states, including drug addiction. To facilitate high-resolution functional analyses of dopamine signaling, it is highly advantageous to obtain genetic material, such as RNA or protein, from a homogeneous cell source. This process can be particularly challenging in most organisms including small model system organisms such as Drosophila melanogaster. Magnetic bead-based cell sorting has emerged as a powerful tool that can be used to isolate select populations of cells, from a whole organism or tissue such as the brain, for genomic as well as proteomic expression profiling. Coupled with the temporal and spatial specificity of the GAL4/UAS system, we demonstrate the application of magnetic bead-based cell sorting towards the isolation of dopaminergic neurons from the Drosophila adult nervous system. RNA derived from these neurons is of high quality and suitable for downstream applications such as microarray expression profiling or quantitative rtPCR. The versatility of this methodology stems from the fact that the cell-specific isolation method employed can be used under a variety of experimental conditions designed to survey molecular adaptations in dopamine signaling neurons including in response to drugs of abuse. PMID:23296786

A microfluidic device for automated, high-speed microinjection of Caenorhabditis elegans

PubMed Central

Song, Pengfei; Dong, Xianke; Liu, Xinyu

2016-01-01

The nematode worm Caenorhabditis elegans has been widely used as a model organism in biological studies because of its short and prolific life cycle, relatively simple body structure, significant genetic overlap with human, and facile/inexpensive cultivation. Microinjection, as an established and versatile tool for delivering liquid substances into cellular/organismal objects, plays an important role in C. elegans research. However, the conventional manual procedure of C. elegans microinjection is labor-intensive and time-consuming and thus hinders large-scale C. elegans studies involving microinjection of a large number of C. elegans on a daily basis. In this paper, we report a novel microfluidic device that enables, for the first time, fully automated, high-speed microinjection of C. elegans. The device is automatically regulated by on-chip pneumatic valves and allows rapid loading, immobilization, injection, and downstream sorting of single C. elegans. For demonstration, we performed microinjection experiments on 200 C. elegans worms and demonstrated an average injection speed of 6.6 worm/min (average worm handling time: 9.45 s/worm) and a success rate of 77.5% (post-sorting success rate: 100%), both much higher than the performance of manual operation (speed: 1 worm/4 min and success rate: 30%). We conducted typical viability tests on the injected C. elegans and confirmed that the automated injection system does not impose significant adverse effect on the physiological condition of the injected C. elegans. We believe that the developed microfluidic device holds great potential to become a useful tool for facilitating high-throughput, large-scale worm biology research. PMID:26958099

Mr-Moose: An advanced SED-fitting tool for heterogeneous multi-wavelength datasets

NASA Astrophysics Data System (ADS)

Drouart, G.; Falkendal, T.

2018-04-01

We present the public release of Mr-Moose, a fitting procedure that is able to perform multi-wavelength and multi-object spectral energy distribution (SED) fitting in a Bayesian framework. This procedure is able to handle a large variety of cases, from an isolated source to blended multi-component sources from an heterogeneous dataset (i.e. a range of observation sensitivities and spectral/spatial resolutions). Furthermore, Mr-Moose handles upper-limits during the fitting process in a continuous way allowing models to be gradually less probable as upper limits are approached. The aim is to propose a simple-to-use, yet highly-versatile fitting tool fro handling increasing source complexity when combining multi-wavelength datasets with fully customisable filter/model databases. The complete control of the user is one advantage, which avoids the traditional problems related to the "black box" effect, where parameter or model tunings are impossible and can lead to overfitting and/or over-interpretation of the results. Also, while a basic knowledge of Python and statistics is required, the code aims to be sufficiently user-friendly for non-experts. We demonstrate the procedure on three cases: two artificially-generated datasets and a previous result from the literature. In particular, the most complex case (inspired by a real source, combining Herschel, ALMA and VLA data) in the context of extragalactic SED fitting, makes Mr-Moose a particularly-attractive SED fitting tool when dealing with partially blended sources, without the need for data deconvolution.

MR-MOOSE: an advanced SED-fitting tool for heterogeneous multi-wavelength data sets

NASA Astrophysics Data System (ADS)

Drouart, G.; Falkendal, T.

2018-07-01

We present the public release of MR-MOOSE, a fitting procedure that is able to perform multi-wavelength and multi-object spectral energy distribution (SED) fitting in a Bayesian framework. This procedure is able to handle a large variety of cases, from an isolated source to blended multi-component sources from a heterogeneous data set (i.e. a range of observation sensitivities and spectral/spatial resolutions). Furthermore, MR-MOOSE handles upper limits during the fitting process in a continuous way allowing models to be gradually less probable as upper limits are approached. The aim is to propose a simple-to-use, yet highly versatile fitting tool for handling increasing source complexity when combining multi-wavelength data sets with fully customisable filter/model data bases. The complete control of the user is one advantage, which avoids the traditional problems related to the `black box' effect, where parameter or model tunings are impossible and can lead to overfitting and/or over-interpretation of the results. Also, while a basic knowledge of PYTHON and statistics is required, the code aims to be sufficiently user-friendly for non-experts. We demonstrate the procedure on three cases: two artificially generated data sets and a previous result from the literature. In particular, the most complex case (inspired by a real source, combining Herschel, ALMA, and VLA data) in the context of extragalactic SED fitting makes MR-MOOSE a particularly attractive SED fitting tool when dealing with partially blended sources, without the need for data deconvolution.

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

PubMed

Castro-Mondragon, Jaime Abraham; Jaeger, Sébastien; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

2017-07-27

Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Angular approach combined to mechanical model for tool breakage detection by eddy current sensors

NASA Astrophysics Data System (ADS)

Ritou, M.; Garnier, S.; Furet, B.; Hascoet, J. Y.

2014-02-01

The paper presents a new complete approach for Tool Condition Monitoring (TCM) in milling. The aim is the early detection of small damages so that catastrophic tool failures are prevented. A versatile in-process monitoring system is introduced for reliability concerns. The tool condition is determined by estimates of the radial eccentricity of the teeth. An adequate criterion is proposed combining mechanical model of milling and angular approach.Then, a new solution is proposed for the estimate of cutting force using eddy current sensors implemented close to spindle nose. Signals are analysed in the angular domain, notably by synchronous averaging technique. Phase shifts induced by changes of machining direction are compensated. Results are compared with cutting forces measured with a dynamometer table.The proposed method is implemented in an industrial case of pocket machining operation. One of the cutting edges has been slightly damaged during the machining, as shown by a direct measurement of the tool. A control chart is established with the estimates of cutter eccentricity obtained during the machining from the eddy current sensors signals. Efficiency and reliability of the method is demonstrated by a successful detection of the damage.

76 FR 31362 - Notice Pursuant to the National Cooperative Research and Production Act of 1993-Versatile Onboard...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-31

... Production Act of 1993--Versatile Onboard Traffic Embedded Roaming Sensors (Formerly Joint Venture To Perform Project Entitled Versatile Onboard Traffic Embedded Roaming Sensors) Notice is hereby given that, on April..., 15 U.S.C. 4301 et seq. (``the Act''), Versatile Onboard Traffic Embedded Roaming Sensors (formerly...

Multiphoton microscopy as a diagnostic imaging modality for pancreatic neoplasms without hematoxylin and eosin stains

NASA Astrophysics Data System (ADS)

Chen, Youting; Chen, Jing; Chen, Hong; Hong, Zhipeng; Zhu, Xiaoqin; Zhuo, Shuangmu; Chen, Yanling; Chen, Jianxin

2014-09-01

Hematoxylin and eosin (H&E) staining of tissue samples is the standard approach in histopathology for imaging and diagnosing cancer. Recent reports have shown that multiphoton microscopy (MPM) provides better sample interface with single-cell resolution, which enhances traditional H&E staining and offers a powerful diagnostic tool with potential applications in oncology. The purpose of this study was to further expand the versatility of MPM by establishing the optical parameters required for imaging unstained histological sections of pancreatic neoplasms, thereby providing an efficient and environmentally sustainable alternative to H&E staining while improving the accuracy of pancreatic cancer diagnoses. We found that the high-resolution MPM images clearly distinguish between the structure of normal pancreatic tissues compared with pancreatic neoplasms in unstained histological sections, and discernable differences in tissue architecture and cell morphology between normal versus tumorigenic cells led to enhanced optical diagnosis of cancerous tissue. Moreover, quantitative assessment of the cytomorphological features visualized from MPM images showed significant differences in the nuclear-cytoplasmic ratios of pancreatic neoplasms compared with normal pancreas, as well as further distinguished pancreatic malignant tumors from benign tumors. These results indicate that the MPM could potentially serve as an optical tool for the diagnosis of pancreatic neoplasms in unstained histological sections.

Object-oriented design and implementation of CFDLab: a computer-assisted learning tool for fluid dynamics using dual reciprocity boundary element methodology

NASA Astrophysics Data System (ADS)

Friedrich, J.

1999-08-01

As lecturers, our main concern and goal is to develop more attractive and efficient ways of communicating up-to-date scientific knowledge to our students and facilitate an in-depth understanding of physical phenomena. Computer-based instruction is very promising to help both teachers and learners in their difficult task, which involves complex cognitive psychological processes. This complexity is reflected in high demands on the design and implementation methods used to create computer-assisted learning (CAL) programs. Due to their concepts, flexibility, maintainability and extended library resources, object-oriented modeling techniques are very suitable to produce this type of pedagogical tool. Computational fluid dynamics (CFD) enjoys not only a growing importance in today's research, but is also very powerful for teaching and learning fluid dynamics. For this purpose, an educational PC program for university level called 'CFDLab 1.1' for Windows™ was developed with an interactive graphical user interface (GUI) for multitasking and point-and-click operations. It uses the dual reciprocity boundary element method as a versatile numerical scheme, allowing to handle a variety of relevant governing equations in two dimensions on personal computers due to its simple pre- and postprocessing including 2D Laplace, Poisson, diffusion, transient convection-diffusion.

RNA splicing process analysis for identifying antisense oligonucleotide inhibitors with padlock probe-based isothermal amplification† †Electronic supplementary information (ESI) available: Additional experimental materials, methods, DNA sequences and supplementary figures and tables. See DOI: 10.1039/c7sc01336a Click here for additional data file.

PubMed Central

Ren, Xiaojun; Deng, Ruijie; Wang, Lida; Zhang, Kaixiang

2017-01-01

RNA splicing, which mainly involves two transesterification steps, is a fundamental process of gene expression and its abnormal regulation contributes to serious genetic diseases. Antisense oligonucleotides (ASOs) are genetic control tools that can be used to specifically control genes through alteration of the RNA splicing pathway. Despite intensive research, how ASOs or various other factors influence the multiple processes of RNA splicing still remains obscure. This is largely due to an inability to analyze the splicing efficiency of each step in the RNA splicing process with high sensitivity. We addressed this limitation by introducing a padlock probe-based isothermal amplification assay to achieve quantification of the specific products in different splicing steps. With this amplified assay, the roles that ASOs play in RNA splicing inhibition in the first and second steps could be distinguished. We identified that 5′-ASO could block RNA splicing by inhibiting the first step, while 3′-ASO could block RNA splicing by inhibiting the second step. This method provides a versatile tool for assisting efficient ASO design and discovering new splicing modulators and therapeutic drugs. PMID:28989608

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

Dai, Sheng; Liu, Rui; Mahurin, Shannon Mark

A facile and versatile synthesis using dopamine as a carbon source gives hollow carbon spheres and yolk-shell Au{at}Carbon nanocomposites. The uniform nature of dopamine coatings and their high carbon yield endow the products with high structural integrity. The Au{at}C nanocomposites are catalytically active.

A highly versatile automatized setup for quantitative measurements of PHIP enhancements

NASA Astrophysics Data System (ADS)

Kiryutin, Alexey S.; Sauer, Grit; Hadjiali, Sara; Yurkovskaya, Alexandra V.; Breitzke, Hergen; Buntkowsky, Gerd

2017-12-01

The design and application of a versatile and inexpensive experimental extension to NMR spectrometers is described that allows to carry out highly reproducible PHIP experiments directly in the NMR sample tube, i.e. under PASADENA condition, followed by the detection of the NMR spectra of hyperpolarized products with high spectral resolution. Employing this high resolution it is feasible to study kinetic processes in the solution with high accuracy. As a practical example the dissolution of hydrogen gas in the liquid and the PHIP kinetics during the hydrogenation reaction of Fmoc-O-propargyl-L-tyrosine in acetone-d6 are monitored. The timing of the setup is fully controlled by the pulse-programmer of the NMR spectrometer. By flushing with an inert gas it is possible to efficiently quench the hydrogenation reaction in a controlled fashion and to detect the relaxation of hyperpolarization without a background reaction. The proposed design makes it possible to carry out PHIP experiments in an automatic mode and reliably determine the enhancement of polarized signals.

Emerging applications of label-free optical biosensors

NASA Astrophysics Data System (ADS)

Zanchetta, Giuliano; Lanfranco, Roberta; Giavazzi, Fabio; Bellini, Tommaso; Buscaglia, Marco

2017-01-01

Innovative technical solutions to realize optical biosensors with improved performance are continuously proposed. Progress in material fabrication enables developing novel substrates with enhanced optical responses. At the same time, the increased spectrum of available biomolecular tools, ranging from highly specific receptors to engineered bioconjugated polymers, facilitates the preparation of sensing surfaces with controlled functionality. What remains often unclear is to which extent this continuous innovation provides effective breakthroughs for specific applications. In this review, we address this challenging question for the class of label-free optical biosensors, which can provide a direct signal upon molecular binding without using secondary probes. Label-free biosensors have become a consolidated approach for the characterization and screening of molecular interactions in research laboratories. However, in the last decade, several examples of other applications with high potential impact have been proposed. We review the recent advances in label-free optical biosensing technology by focusing on the potential competitive advantage provided in selected emerging applications, grouped on the basis of the target type. In particular, direct and real-time detection allows the development of simpler, compact, and rapid analytical methods for different kinds of targets, from proteins to DNA and viruses. The lack of secondary interactions facilitates the binding of small-molecule targets and minimizes the perturbation in single-molecule detection. Moreover, the intrinsic versatility of label-free sensing makes it an ideal platform to be integrated with biomolecular machinery with innovative functionality, as in case of the molecular tools provided by DNA nanotechnology.