Bridging the Gap: Linking Simulation and Testing

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

Krajewski, Paul E.; Carsley, John; Stoudt, Mark R.

2012-09-01

The Materials Genome Initiative (MGI) which is a key enabler for the Advanced Manufacturing Partnership, announced in 2011 by U.S. President Barack Obama, was established to accelerate the development and deployment of advanced materials. The MGI is driven by the need to "bridge the gap" between (I) experimental results and computational analysis to enable the rapid development and validation of new mateirals, and (II) the processes required to convert these materials into useable goods.

Recent advances in the application of transmission Raman spectroscopy to pharmaceutical analysis.

PubMed

Buckley, Kevin; Matousek, Pavel

2011-06-25

This article reviews recent advances in transmission Raman spectroscopy and its applications, from the perspective of pharmaceutical analysis. The emerging concepts enable rapid non-invasive volumetric analysis of pharmaceutical formulations and could lead to many important applications in pharmaceutical settings, including quantitative bulk analysis of intact pharmaceutical tablets and capsules in quality and process control. Crown Copyright © 2010. Published by Elsevier B.V. All rights reserved.

New Technologies for Rapid Bacterial Identification and Antibiotic Resistance Profiling.

PubMed

Kelley, Shana O

2017-04-01

Conventional approaches to bacterial identification and drug susceptibility testing typically rely on culture-based approaches that take 2 to 7 days to return results. The long turnaround times contribute to the spread of infectious disease, negative patient outcomes, and the misuse of antibiotics that can contribute to antibiotic resistance. To provide new solutions enabling faster bacterial analysis, a variety of approaches are under development that leverage single-cell analysis, microfluidic concentration and detection strategies, and ultrasensitive readout mechanisms. This review discusses recent advances in this area and the potential of new technologies to enable more effective management of infectious disease.

A Business Case Analysis of Pre-Positioned Expeditionary Assistance Kit Joint Capability Technology Demonstration

DTIC Science & Technology

2013-12-01

of power from sunlight or a wind turbine (same solar panel tarps used in NEST Raptor Solar Light Trailer) • Global Positioning System (GPS) devices...satellite-enabled rapid wireless communications to the most critical areas and functions, working with Joint Task Forces. The first priority after the...a rapid response wireless communications system from military, civilian government, and non-government organizations. The tasks performed by HFN

Applications of Mass Spectrometry for Cellular Lipid Analysis

PubMed Central

Wang, Chunyan; Wang, Miao; Han, Xianlin

2015-01-01

Mass spectrometric analysis of cellular lipids is an enabling technology for lipidomics, which is a rapidly-developing research field. In this review, we briefly discuss the principles, advantages, and possible limitations of electrospray ionization (ESI) and matrix assisted laser desorption/ionization (MALDI) mass spectrometry-based methodologies for the analysis of lipid species. The applications of these methodologies to lipidomic research are also summarized. PMID:25598407

Computational Analysis of the Caenorhabditis elegans Germline to Study the Distribution of Nuclei, Proteins, and the Cytoskeleton.

PubMed

Gopal, Sandeep; Pocock, Roger

2018-04-19

The Caenorhabditis elegans (C. elegans) germline is used to study several biologically important processes including stem cell development, apoptosis, and chromosome dynamics. While the germline is an excellent model, the analysis is often two dimensional due to the time and labor required for three-dimensional analysis. Major readouts in such studies are the number/position of nuclei and protein distribution within the germline. Here, we present a method to perform automated analysis of the germline using confocal microscopy and computational approaches to determine the number and position of nuclei in each region of the germline. Our method also analyzes germline protein distribution that enables the three-dimensional examination of protein expression in different genetic backgrounds. Further, our study shows variations in cytoskeletal architecture in distinct regions of the germline that may accommodate specific spatial developmental requirements. Finally, our method enables automated counting of the sperm in the spermatheca of each germline. Taken together, our method enables rapid and reproducible phenotypic analysis of the C. elegans germline.

Modelling and simulation of passive Lab-on-a-Chip (LoC) based micromixer for clinical application

NASA Astrophysics Data System (ADS)

Saikat, Chakraborty; Sharath, M.; Srujana, M.; Narayan, K.; Pattnaik, Prasant Kumar

2016-03-01

In biomedical application, micromixer is an important component because of many processes requires rapid and efficient mixing. At micro scale, the flow is Laminar due to small channel size which enables controlled rapid mixing. The reduction in analysis time along with high throughput can be achieved with the help of rapid mixing. In LoC application, micromixer is used for mixing of fluids especially for the devices which requires efficient mixing. Micromixer of this type of microfluidic devices with a rapid mixing is useful in application such as DNA/RNA synthesis, drug delivery system & biological agent detection. In this work, we design and simulate a microfluidic based passive rapid micromixer for lab-on-a-chip application.

Discerning Trends in Performance Across Multiple Events

NASA Technical Reports Server (NTRS)

Slater, Simon; Hiltz, Mike; Rice, Craig

2006-01-01

Mass Data is a computer program that enables rapid, easy discernment of trends in performance data across multiple flights and ground tests. The program can perform Fourier analysis and other functions for the purposes of frequency analysis and trending of all variables. These functions facilitate identification of past use of diagnosed systems and of anomalies in such systems, and enable rapid assessment of related current problems. Many variables, for computation of which it is usually necessary to perform extensive manual manipulation of raw downlist data, are automatically computed and made available to all users, regularly eliminating the need for what would otherwise be an extensive amount of engineering analysis. Data from flight, ground test, and simulation are preprocessed and stored in one central location for instantaneous access and comparison for diagnostic and trending purposes. Rules are created so that an event log is created for every flight, making it easy to locate information on similar maneuvers across many flights. The same rules can be created for test sets and simulations, and are searchable, so that information on like events is easily accessible.

SensorDB: a virtual laboratory for the integration, visualization and analysis of varied biological sensor data.

PubMed

Salehi, Ali; Jimenez-Berni, Jose; Deery, David M; Palmer, Doug; Holland, Edward; Rozas-Larraondo, Pablo; Chapman, Scott C; Georgakopoulos, Dimitrios; Furbank, Robert T

2015-01-01

To our knowledge, there is no software or database solution that supports large volumes of biological time series sensor data efficiently and enables data visualization and analysis in real time. Existing solutions for managing data typically use unstructured file systems or relational databases. These systems are not designed to provide instantaneous response to user queries. Furthermore, they do not support rapid data analysis and visualization to enable interactive experiments. In large scale experiments, this behaviour slows research discovery, discourages the widespread sharing and reuse of data that could otherwise inform critical decisions in a timely manner and encourage effective collaboration between groups. In this paper we present SensorDB, a web based virtual laboratory that can manage large volumes of biological time series sensor data while supporting rapid data queries and real-time user interaction. SensorDB is sensor agnostic and uses web-based, state-of-the-art cloud and storage technologies to efficiently gather, analyse and visualize data. Collaboration and data sharing between different agencies and groups is thereby facilitated. SensorDB is available online at http://sensordb.csiro.au.

Rapid Analysis and Manufacturing Propulsion Technology (RAMPT)

NASA Technical Reports Server (NTRS)

Fikes, John C.

2018-01-01

NASA's strategic plan calls for the development of enabling technologies, improved production methods, and advanced design and analysis tools related to the agency's objectives to expand human presence in the solar system. NASA seeks to advance exploration, science, innovation, benefits to humanity, and international collaboration, as well as facilitate and utilize U.S. commercial capabilities to deliver cargo and crew to space.

Enabling Real-time Water Decision Support Services Using Model as a Service

NASA Astrophysics Data System (ADS)

Zhao, T.; Minsker, B. S.; Lee, J. S.; Salas, F. R.; Maidment, D. R.; David, C. H.

2014-12-01

Through application of computational methods and an integrated information system, data and river modeling services can help researchers and decision makers more rapidly understand river conditions under alternative scenarios. To enable this capability, workflows (i.e., analysis and model steps) are created and published as Web services delivered through an internet browser, including model inputs, a published workflow service, and visualized outputs. The RAPID model, which is a river routing model developed at University of Texas Austin for parallel computation of river discharge, has been implemented as a workflow and published as a Web application. This allows non-technical users to remotely execute the model and visualize results as a service through a simple Web interface. The model service and Web application has been prototyped in the San Antonio and Guadalupe River Basin in Texas, with input from university and agency partners. In the future, optimization model workflows will be developed to link with the RAPID model workflow to provide real-time water allocation decision support services.

Research Instruments

NASA Technical Reports Server (NTRS)

1992-01-01

The GENETI-SCANNER, newest product of Perceptive Scientific Instruments, Inc. (PSI), rapidly scans slides, locates, digitizes, measures and classifies specific objects and events in research and diagnostic applications. Founded by former NASA employees, PSI's primary product line is based on NASA image processing technology. The instruments karyotype - a process employed in analysis and classification of chromosomes - using a video camera mounted on a microscope. Images are digitized, enabling chromosome image enhancement. The system enables karyotyping to be done significantly faster, increasing productivity and lowering costs. Product is no longer being manufactured.

Global Transcriptome Analysis Reveals Acclimation-Primed Processes Involved in the Acquisition of Desiccation Tolerance in Boea hygrometrica.

PubMed

Zhu, Yan; Wang, Bo; Phillips, Jonathan; Zhang, Zhen-Nan; Du, Hong; Xu, Tao; Huang, Lian-Cheng; Zhang, Xiao-Fei; Xu, Guang-Hui; Li, Wen-Long; Wang, Zhi; Wang, Ling; Liu, Yong-Xiu; Deng, Xin

2015-07-01

Boea hygrometrica resurrection plants require a period of acclimation by slow soil-drying in order to survive a subsequent period of rapid desiccation. The molecular basis of this observation was investigated by comparing gene expression profiles under different degrees of water deprivation. Transcripts were clustered according to the expression profiles in plants that were air-dried (rapid desiccation), soil-dried (gradual desiccation), rehydrated (acclimated) and air-dried after acclimation. Although phenotypically indistinguishable, it was shown by principal component analysis that the gene expression profiles in rehydrated, acclimated plants resemble those of desiccated plants more closely than those of hydrated acclimated plants. Enrichment analysis based on gene ontology was performed to deconvolute the processes that accompanied desiccation tolerance. Transcripts associated with autophagy and α-tocopherol accumulation were found to be activated in both air-dried, acclimated plants and soil-dried non-acclimated plants. Furthermore, transcripts associated with biosynthesis of ascorbic acid, cell wall catabolism, chaperone-assisted protein folding, respiration and macromolecule catabolism were activated and maintained during soil-drying and rehydration. Based on these findings, we hypothesize that activation of these processes leads to the establishment of an optimal physiological and cellular state that enables tolerance during rapid air-drying. Our study provides a novel insight into the transcriptional regulation of critical priming responses to enable survival following rapid dehydration in B. hygrometrica. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Using System Architecture, Review Entry Criteria, and Standard Work Package Data to Enable Rapid Development of Integrated Master Schedules

DTIC Science & Technology

2016-03-01

ENTRY CRITERIA, AND STANDARD WORK PACKAGE DATA TO ENABLE RAPID DEVELOPMENT OF INTEGRATED MASTER SCHEDULES by Burton W. Porter Jr. March 2016...2. REPORT DATE March 2016 3. REPORT TYPE AND DATES COVERED Master’s Thesis 4. TITLE AND SUBTITLE USING SYSTEM ARCHITECTURE, REVIEW ENTRY ... ENTRY CRITERIA, AND STANDARD WORK PACKAGE DATA TO ENABLE RAPID DEVELOPMENT OF INTEGRATED MASTER SCHEDULES Burton W. Porter Jr. Civilian

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

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

Hura, Greg L.; Menon, Angeli L.; Hammel, Michal

2009-07-20

We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes formore » 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.« less

Early warning systems and rapid response to the deteriorating patient in hospital: A realist evaluation.

PubMed

McGaughey, Jennifer; O'Halloran, Peter; Porter, Sam; Trinder, John; Blackwood, Bronagh

2017-12-01

To test the Rapid Response Systems programme theory against actual practice components of the Rapid Response Systems implemented to identify those contexts and mechanisms which have an impact on the successful achievement of desired outcomes in practice. Rapid Response Systems allow deteriorating patients to be recognized using Early Warning Systems, referred early via escalation protocols and managed at the bedside by competent staff. Realist evaluation. The research design was an embedded multiple case study approach of four wards in two hospitals in Northern Ireland which followed the principles of Realist Evaluation. We used various mixed methods including individual and focus group interviews, observation of nursing practice between June-November 2010 and document analysis of Early Warning Systems audit data between May-October 2010 and hospital acute care training records over 4.5 years from 2003-2008. Data were analysed using NiVivo8 and SPPS. A cross-case analysis highlighted similar patterns of factors which enabled or constrained successful recognition, referral and response to deteriorating patients in practice. Key enabling factors were the use of clinical judgement by experienced nurses and the empowerment of nurses as a result of organizational change associated with implementation of Early Warning System protocols. Key constraining factors were low staffing and inappropriate skill mix levels, rigid implementation of protocols and culturally embedded suboptimal communication processes. Successful implementation of Rapid Response Systems was dependent on adopting organizational and cultural changes that facilitated staff empowerment, flexible implementation of protocols and ongoing experiential learning. © 2017 John Wiley & Sons Ltd.

Rapid SAR and GPS Measurements and Models for Hazard Science and Situational Awareness

NASA Astrophysics Data System (ADS)

Owen, S. E.; Yun, S. H.; Hua, H.; Agram, P. S.; Liu, Z.; Moore, A. W.; Rosen, P. A.; Simons, M.; Webb, F.; Linick, J.; Fielding, E. J.; Lundgren, P.; Sacco, G. F.; Polet, J.; Manipon, G.

2016-12-01

The Advanced Rapid Imaging and Analysis (ARIA) project for Natural Hazards is focused on rapidly generating higher level geodetic imaging products and placing them in the hands of the solid earth science and local, national, and international natural hazard communities by providing science product generation, exploration, and delivery capabilities at an operational level. Space-based geodetic measurement techniques such as Interferometric Synthetic Aperture Radar (InSAR), Differential Global Positioning System (DGPS), SAR-based change detection, and image pixel tracking have recently become critical additions to our toolset for understanding and mapping the damage caused by earthquakes, volcanic eruptions, landslides, and floods. Analyses of these data sets are still largely handcrafted following each event and are not generated rapidly and reliably enough for response to natural disasters or for timely analysis of large data sets. The ARIA project, a joint venture co-sponsored by California Institute of Technology (Caltech) and by NASA through the Jet Propulsion Laboratory (JPL), has been capturing the knowledge applied to these responses and building it into an automated infrastructure to generate imaging products in near real-time that can improve situational awareness for disaster response. In addition, the ARIA project is developing the capabilities to provide automated imaging and analysis capabilities necessary to keep up with the imminent increase in raw data from geodetic imaging missions planned for launch by NASA, as well as international space agencies. We will present the progress we have made on automating the analysis of SAR data for hazard monitoring and response using data from Sentinel 1a/b as well as continuous GPS stations. Since the beginning of our project, our team has imaged events and generated response products for events around the world. These response products have enabled many conversations with those in the disaster response community about the potential usefulness of rapid SAR and GPS-based information. We will present progress on our data system technology that enables rapid and reliable production of imagery, as well as lessons learned from our engagement with FEMA and others in the hazard response community on the important actionable information that they need.

Multiscale nonlinear microscopy and widefield white light imaging enables rapid histological imaging of surgical specimen margins

PubMed Central

Giacomelli, Michael G.; Yoshitake, Tadayuki; Cahill, Lucas C.; Vardeh, Hilde; Quintana, Liza M.; Faulkner-Jones, Beverly E.; Brooker, Jeff; Connolly, James L.; Fujimoto, James G.

2018-01-01

The ability to histologically assess surgical specimens in real-time is a long-standing challenge in cancer surgery, including applications such as breast conserving therapy (BCT). Up to 40% of women treated with BCT for breast cancer require a repeat surgery due to postoperative histological findings of close or positive surgical margins using conventional formalin fixed paraffin embedded histology. Imaging technologies such as nonlinear microscopy (NLM), combined with exogenous fluorophores can rapidly provide virtual H&E imaging of surgical specimens without requiring microtome sectioning, facilitating intraoperative assessment of margin status. However, the large volume of typical surgical excisions combined with the need for rapid assessment, make comprehensive cellular resolution margin assessment during surgery challenging. To address this limitation, we developed a multiscale, real-time microscope with variable magnification NLM and real-time, co-registered position display using a widefield white light imaging system. Margin assessment can be performed rapidly under operator guidance to image specific regions of interest located using widefield imaging. Using simulated surgical margins dissected from human breast excisions, we demonstrate that multi-centimeter margins can be comprehensively imaged at cellular resolution, enabling intraoperative margin assessment. These methods are consistent with pathology assessment performed using frozen section analysis (FSA), however NLM enables faster and more comprehensive assessment of surgical specimens because imaging can be performed without freezing and cryo-sectioning. Therefore, NLM methods have the potential to be applied to a wide range of intra-operative applications. PMID:29761001

Principal component analysis of TOF-SIMS spectra, images and depth profiles: an industrial perspective

NASA Astrophysics Data System (ADS)

Pacholski, Michaeleen L.

2004-06-01

Principal component analysis (PCA) has been successfully applied to time-of-flight secondary ion mass spectrometry (TOF-SIMS) spectra, images and depth profiles. Although SIMS spectral data sets can be small (in comparison to datasets typically discussed in literature from other analytical techniques such as gas or liquid chromatography), each spectrum has thousands of ions resulting in what can be a difficult comparison of samples. Analysis of industrially-derived samples means the identity of most surface species are unknown a priori and samples must be analyzed rapidly to satisfy customer demands. PCA enables rapid assessment of spectral differences (or lack there of) between samples and identification of chemically different areas on sample surfaces for images. Depth profile analysis helps define interfaces and identify low-level components in the system.

Electronic Business Transaction Infrastructure Analysis Using Petri Nets and Simulation

ERIC Educational Resources Information Center

Feller, Andrew Lee

2010-01-01

Rapid growth in eBusiness has made industry and commerce increasingly dependent on the hardware and software infrastructure that enables high-volume transaction processing across the Internet. Large transaction volumes at major industrial-firm data centers rely on robust transaction protocols and adequately provisioned hardware capacity to ensure…

Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment

PubMed Central

Saeed, Isaam; Wong, Stephen Q.; Mar, Victoria; Goode, David L.; Caramia, Franco; Doig, Ken; Ryland, Georgina L.; Thompson, Ella R.; Hunter, Sally M.; Halgamuge, Saman K.; Ellul, Jason; Dobrovic, Alexander; Campbell, Ian G.; Papenfuss, Anthony T.; McArthur, Grant A.; Tothill, Richard W.

2014-01-01

Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation. Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging and laborious activity, and a major hurdle for many small research and clinical laboratories. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. Based on virtual machine technologies, TREVA is a solution for rapid and efficient deployment of complex bioinformatics pipelines to laboratories of all sizes, enabling reproducible results. The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is available at http://bioinformatics.petermac.org/treva/. PMID:24752294

Reclaiming Rapid Cognition: Improving Decision-making in Command and Control Agencies by Understanding and Enabling Rapid Cognition

DTIC Science & Technology

2007-06-01

Cognition Topics : Intro What is Rapid Cognition? Training Rapid Cognition Decision-Makers Getting Back to Basics—Enabling the Executors Why It...for public release; distribution unlimited 13. SUPPLEMENTARY NOTES Twelfth International Command and Control Research and Technology Symposium (12th...making process . . . when you have the time to do it. Scientists have found that high -stress, quick reaction jobs like firefighting, police officers, ER

Nano-enabled drug delivery: a research profile.

PubMed

Zhou, Xiao; Porter, Alan L; Robinson, Douglas K R; Shim, Min Suk; Guo, Ying

2014-07-01

Nano-enabled drug delivery (NEDD) systems are rapidly emerging as a key area for nanotechnology application. Understanding the status and developmental prospects of this area around the world is important to determine research priorities, and to evaluate and direct progress. Global research publication and patent databases provide a reservoir of information that can be tapped to provide intelligence for such needs. Here, we present a process to allow for extraction of NEDD-related information from these databases by involving topical experts. This process incorporates in-depth analysis of NEDD literature review papers to identify key subsystems and major topics. We then use these to structure global analysis of NEDD research topical trends and collaborative patterns, inform future innovation directions. This paper describes the process of how to derive nano-enabled drug delivery-related information from global research and patent databases in an effort to perform comprehensive global analysis of research trends and directions, along with collaborative patterns. Copyright © 2014 Elsevier Inc. All rights reserved.

Real-time development of data acquisition and analysis software for hands-on physiology education in neuroscience: G-PRIME.

PubMed

Lott, Gus K; Johnson, Bruce R; Bonow, Robert H; Land, Bruce R; Hoy, Ronald R

2009-01-01

We report on the real-time creation of an application for hands-on neurophysiology in an advanced undergraduate teaching laboratory. Enabled by the rapid software development tools included in the Matlab technical computing environment (The Mathworks, Natick, MA), a team, consisting of a neurophysiology educator and a biophysicist trained as an electrical engineer, interfaced to a course of approximately 15 students from engineering and biology backgrounds. The result is the powerful freeware data acquisition and analysis environment, "g-PRIME." The software was developed from week to week in response to curriculum demands, and student feedback. The program evolved from a simple software oscilloscope, enabling RC circuit analysis, to a suite of tools supporting analysis of neuronal excitability and synaptic transmission analysis in invertebrate model systems. The program has subsequently expanded in application to university courses, research, and high school projects in the US and abroad as free courseware.

User Oriented Techniques to Support Interaction and Decision Making with Large Educational Databases

ERIC Educational Resources Information Center

Hartley, Roger; Almuhaidib, Saud M. Y.

2007-01-01

Information Technology is developing rapidly and providing policy/decision makers with large amounts of information that require processing and analysis. Decision support systems (DSS) aim to provide tools that not only help such analyses, but enable the decision maker to experiment and simulate the effects of different policies and selection…

Einstein Slew Survey: Data analysis innovations

NASA Technical Reports Server (NTRS)

Elvis, Martin S.; Plummer, David; Schachter, Jonathan F.; Fabbiano, G.

1992-01-01

Several new methods were needed in order to make the Einstein Slew X-ray Sky Survey. The innovations which enabled the Slew Survey to be done are summarized. These methods included experimental approach to large projects, parallel processing on a LAN, percolation source detection, minimum action identifications, and rapid dissemination of the whole data base.

Rapid screening of selective serotonin re-uptake inhibitors in urine samples using solid-phase microextraction gas chromatography-mass spectrometry.

PubMed

Salgado-Petinal, Carmen; Lamas, J Pablo; Garcia-Jares, Carmen; Llompart, Maria; Cela, Rafael

2005-07-01

In this paper a solid-phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS) method is proposed for a rapid analysis of some frequently prescribed selective serotonin re-uptake inhibitors (SSRI)-venlafaxine, fluvoxamine, mirtazapine, fluoxetine, citalopram, and sertraline-in urine samples. The SPME-based method enables simultaneous determination of the target SSRI after simple in-situ derivatization of some of the target compounds. Calibration curves in water and in urine were validated and statistically compared. This revealed the absence of matrix effect and, in consequence, the possibility of quantifying SSRI in urine samples by external water calibration. Intra-day and inter-day precision was satisfactory for all the target compounds (relative standard deviation, RSD, <14%) and the detection limits achieved were <0.4 ng mL(-1) urine. The time required for the SPME step and for GC analysis (30 min each) enables high throughput. The method was applied to real urine samples from different patients being treated with some of these pharmaceuticals. Some SSRI metabolites were also detected and tentatively identified.

Rapid differentiation among bacteria that cause gastroenteritis by use of low-resolution Raman spectroscopy and PLS discriminant analysis.

PubMed

Mello, Cesar; Ribeiro, Diórginis; Novaes, Fábio; Poppi, Ronei J

2005-10-01

Use of classical microbiological methods to differentiate bacteria that cause gastroenteritis is cumbersome but usually very efficient. The high cost of reagents and the time required for such identifications, approximately four days, could have serious consequences, however, mainly when the patients are children, the elderly, or adults with low resistance. The search for new methods enabling rapid and reagentless differentiation of these microorganisms is, therefore, extremely relevant. In this work the main microorganisms responsible for gastroenteritis, Escherichia coli, Salmonella choleraesuis, and Shigella flexneri, were studied. For each microorganism sixty different dispersions were prepared in physiological solution. The Raman spectra of these dispersions were recorded using a diode laser operating in the near infrared region. Partial least-squares (PLS) discriminant analysis was used to differentiate among the bacteria by use of their respective Raman spectra. This approach enabled correct classification of 100% of the bacteria evaluated and unknown samples from the clinical environment, in less time ( approximately 10 h), by use of a low-cost, portable Raman spectrometer, which can be easily used in intensive care units and clinical environments.

An Accelerated Analytical Process for the Development of STR Profiles for Casework Samples.

PubMed

Laurin, Nancy; Frégeau, Chantal J

2015-07-01

Significant efforts are being devoted to the development of methods enabling rapid generation of short tandem repeat (STR) profiles in order to reduce turnaround times for the delivery of human identification results from biological evidence. Some of the proposed solutions are still costly and low throughput. This study describes the optimization of an analytical process enabling the generation of complete STR profiles (single-source or mixed profiles) for human identification in approximately 5 h. This accelerated process uses currently available reagents and standard laboratory equipment. It includes a 30-min lysis step, a 27-min DNA extraction using the Promega Maxwell(®) 16 System, DNA quantification in <1 h using the Qiagen Investigator(®) Quantiplex HYres kit, fast amplification (<26 min) of the loci included in AmpFℓSTR(®) Identifiler(®), and analysis of the profiles on the 3500-series Genetic Analyzer. This combination of fast individual steps produces high-quality profiling results and offers a cost-effective alternative approach to rapid DNA analysis. © 2015 American Academy of Forensic Sciences.

Rapid Harmonic Analysis of Piezoelectric MEMS Resonators.

PubMed

Puder, Jonathan M; Pulskamp, Jeffrey S; Rudy, Ryan Q; Cassella, Cristian; Rinaldi, Matteo; Chen, Guofeng; Bhave, Sunil A; Polcawich, Ronald G

2018-06-01

This paper reports on a novel simulation method combining the speed of analytical evaluation with the accuracy of finite-element analysis (FEA). This method is known as the rapid analytical-FEA technique (RAFT). The ability of the RAFT to accurately predict frequency response orders of magnitude faster than conventional simulation methods while providing deeper insights into device design not possible with other types of analysis is detailed. Simulation results from the RAFT across wide bandwidths are compared to measured results of resonators fabricated with various materials, frequencies, and topologies with good agreement. These include resonators targeting beam extension, disk flexure, and Lamé beam modes. An example scaling analysis is presented and other applications enabled are discussed as well. The supplemental material includes example code for implementation in ANSYS, although any commonly employed FEA package may be used.

Rapid self-assembly of DNA on a microfluidic chip

PubMed Central

Zheng, Yao; Footz, Tim; Manage, Dammika P; Backhouse, Christopher James

2005-01-01

Background DNA self-assembly methods have played a major role in enabling methods for acquiring genetic information without having to resort to sequencing, a relatively slow and costly procedure. However, even self-assembly processes tend to be very slow when they rely upon diffusion on a large scale. Miniaturisation and integration therefore hold the promise of greatly increasing this speed of operation. Results We have developed a rapid method for implementing the self-assembly of DNA within a microfluidic system by electrically extracting the DNA from an environment containing an uncharged denaturant. By controlling the parameters of the electrophoretic extraction and subsequent analysis of the DNA we are able to control when the hybridisation occurs as well as the degree of hybridisation. By avoiding off-chip processing or long thermal treatments we are able to perform this hybridisation rapidly and can perform hybridisation, sizing, heteroduplex analysis and single-stranded conformation analysis within a matter of minutes. The rapidity of this analysis allows the sampling of transient effects that may improve the sensitivity of mutation detection. Conclusions We believe that this method will aid the integration of self-assembly methods upon microfluidic chips. The speed of this analysis also appears to provide information upon the dynamics of the self-assembly process. PMID:15717935

Rapid analysis of protein interactions: On-chip micropurification of recombinant protein expressed in Esherichia coli.

PubMed

Natsume, Tohru; Taoka, Masato; Manki, Hiroshi; Kume, Shouen; Isobe, Toshiaki; Mikoshiba, Katsuhiko

2002-09-01

We describe a rapid analysis of interactions between antibodies and a recombinant protein present in total cell lysates. Using a surface plasmon resonance biosensor, a low concentration of glutathione-S-transferase (GST) fused protein expressed in small scale Esherichia coli culture was purified on an anti-GST antibody immobilized sensor chip. The 'on-chip purification' was verified using matrix-assisted laser desorption/ionization-time of flight mass spectrometry by measuring the molecular masses of recombinant proteins purified on the sensor chip. The specific binding of monoclonal antibodies for the on-chip micropurified recombinant proteins can then be monitored, thus enabling kinetic analysis and epitope mapping of the bound antibodies. This approach reduced time, resources and sample consumption by avoiding conventional steps related to concentration and purification.

Application of advanced computing techniques to the analysis and display of space science measurements

NASA Technical Reports Server (NTRS)

Klumpar, D. M.; Lapolla, M. V.; Horblit, B.

1995-01-01

A prototype system has been developed to aid the experimental space scientist in the display and analysis of spaceborne data acquired from direct measurement sensors in orbit. We explored the implementation of a rule-based environment for semi-automatic generation of visualizations that assist the domain scientist in exploring one's data. The goal has been to enable rapid generation of visualizations which enhance the scientist's ability to thoroughly mine his data. Transferring the task of visualization generation from the human programmer to the computer produced a rapid prototyping environment for visualizations. The visualization and analysis environment has been tested against a set of data obtained from the Hot Plasma Composition Experiment on the AMPTE/CCE satellite creating new visualizations which provided new insight into the data.

Centrifuge: rapid and sensitive classification of metagenomic sequences

PubMed Central

Song, Li; Breitwieser, Florian P.

2016-01-01

Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together, these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI nonredundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer-based indexing schemes, which require far more extensive space. PMID:27852649

The IceCube realtime alert system

NASA Astrophysics Data System (ADS)

Aartsen, M. G.; Ackermann, M.; Adams, J.; Aguilar, J. A.; Ahlers, M.; Ahrens, M.; Altmann, D.; Andeen, K.; Anderson, T.; Ansseau, I.; Anton, G.; Archinger, M.; Argüelles, C.; Auffenberg, J.; Axani, S.; Bai, X.; Barwick, S. W.; Baum, V.; Bay, R.; Beatty, J. J.; Becker Tjus, J.; Becker, K.-H.; BenZvi, S.; Berley, D.; Bernardini, E.; Bernhard, A.; Besson, D. Z.; Binder, G.; Bindig, D.; Bissok, M.; Blaufuss, E.; Blot, S.; Bohm, C.; Börner, M.; Bos, F.; Bose, D.; Böser, S.; Botner, O.; Braun, J.; Brayeur, L.; Bretz, H.-P.; Bron, S.; Burgman, A.; Carver, T.; Casier, M.; Cheung, E.; Chirkin, D.; Christov, A.; Clark, K.; Classen, L.; Coenders, S.; Collin, G. H.; Conrad, J. M.; Cowen, D. F.; Cross, R.; Day, M.; de André, J. P. A. M.; De Clercq, C.; del Pino Rosendo, E.; Dembinski, H.; De Ridder, S.; Desiati, P.; de Vries, K. D.; de Wasseige, G.; de With, M.; DeYoung, T.; Díaz-Vélez, J. C.; di Lorenzo, V.; Dujmovic, H.; Dumm, J. P.; Dunkman, M.; Eberhardt, B.; Ehrhardt, T.; Eichmann, B.; Eller, P.; Euler, S.; Evenson, P. A.; Fahey, S.; Fazely, A. R.; Feintzeig, J.; Felde, J.; Filimonov, K.; Finley, C.; Flis, S.; Fösig, C.-C.; Franckowiak, A.; Friedman, E.; Fuchs, T.; Gaisser, T. K.; Gallagher, J.; Gerhardt, L.; Ghorbani, K.; Giang, W.; Gladstone, L.; Glauch, T.; Glüsenkamp, T.; Goldschmidt, A.; Gonzalez, J. G.; Grant, D.; Griffith, Z.; Haack, C.; Hallgren, A.; Halzen, F.; Hansen, E.; Hansmann, T.; Hanson, K.; Hebecker, D.; Heereman, D.; Helbing, K.; Hellauer, R.; Hickford, S.; Hignight, J.; Hill, G. C.; Hoffman, K. D.; Hoffmann, R.; Hoshina, K.; Huang, F.; Huber, M.; Hultqvist, K.; In, S.; Ishihara, A.; Jacobi, E.; Japaridze, G. S.; Jeong, M.; Jero, K.; Jones, B. J. P.; Kang, W.; Kappes, A.; Karg, T.; Karle, A.; Katz, U.; Kauer, M.; Keivani, A.; Kelley, J. L.; Kheirandish, A.; Kim, J.; Kim, M.; Kintscher, T.; Kiryluk, J.; Kittler, T.; Klein, S. R.; Kohnen, G.; Koirala, R.; Kolanoski, H.; Konietz, R.; Köpke, L.; Kopper, C.; Kopper, S.; Koskinen, D. J.; Kowalski, M.; Krings, K.; Kroll, M.; Krückl, G.; Krüger, C.; Kunnen, J.; Kunwar, S.; Kurahashi, N.; Kuwabara, T.; Labare, M.; Lanfranchi, J. L.; Larson, M. J.; Lauber, F.; Lennarz, D.; Lesiak-Bzdak, M.; Leuermann, M.; Lu, L.; Lünemann, J.; Madsen, J.; Maggi, G.; Mahn, K. B. M.; Mancina, S.; Mandelartz, M.; Maruyama, R.; Mase, K.; Maunu, R.; McNally, F.; Meagher, K.; Medici, M.; Meier, M.; Meli, A.; Menne, T.; Merino, G.; Meures, T.; Miarecki, S.; Montaruli, T.; Moulai, M.; Nahnhauer, R.; Naumann, U.; Neer, G.; Niederhausen, H.; Nowicki, S. C.; Nygren, D. R.; Obertacke Pollmann, A.; Olivas, A.; O'Murchadha, A.; Palczewski, T.; Pandya, H.; Pankova, D. V.; Peiffer, P.; Penek, Ö.; Pepper, J. A.; Pérez de los Heros, C.; Pieloth, D.; Pinat, E.; Price, P. B.; Przybylski, G. T.; Quinnan, M.; Raab, C.; Rädel, L.; Rameez, M.; Rawlins, K.; Reimann, R.; Relethford, B.; Relich, M.; Resconi, E.; Rhode, W.; Richman, M.; Riedel, B.; Robertson, S.; Rongen, M.; Rott, C.; Ruhe, T.; Ryckbosch, D.; Rysewyk, D.; Sabbatini, L.; Sanchez Herrera, S. E.; Sandrock, A.; Sandroos, J.; Sarkar, S.; Satalecka, K.; Schlunder, P.; Schmidt, T.; Schoenen, S.; Schöneberg, S.; Schumacher, L.; Seckel, D.; Seunarine, S.; Soldin, D.; Song, M.; Spiczak, G. M.; Spiering, C.; Stanev, T.; Stasik, A.; Stettner, J.; Steuer, A.; Stezelberger, T.; Stokstad, R. G.; Stößl, A.; Ström, R.; Strotjohann, N. L.; Sullivan, G. W.; Sutherland, M.; Taavola, H.; Taboada, I.; Tatar, J.; Tenholt, F.; Ter-Antonyan, S.; Terliuk, A.; Tešić, G.; Tilav, S.; Toale, P. A.; Tobin, M. N.; Toscano, S.; Tosi, D.; Tselengidou, M.; Turcati, A.; Unger, E.; Usner, M.; Vandenbroucke, J.; van Eijndhoven, N.; Vanheule, S.; van Rossem, M.; van Santen, J.; Vehring, M.; Voge, M.; Vogel, E.; Vraeghe, M.; Walck, C.; Wallace, A.; Wallraff, M.; Wandkowsky, N.; Weaver, Ch.; Weiss, M. J.; Wendt, C.; Westerhoff, S.; Whelan, B. J.; Wickmann, S.; Wiebe, K.; Wiebusch, C. H.; Wille, L.; Williams, D. R.; Wills, L.; Wolf, M.; Wood, T. R.; Woolsey, E.; Woschnagg, K.; Xu, D. L.; Xu, X. W.; Xu, Y.; Yanez, J. P.; Yodh, G.; Yoshida, S.; Zoll, M.

2017-06-01

Although high-energy astrophysical neutrinos were discovered in 2013, their origin is still unknown. Aiming for the identification of an electromagnetic counterpart of a rapidly fading source, we have implemented a realtime analysis framework for the IceCube neutrino observatory. Several analyses selecting neutrinos of astrophysical origin are now operating in realtime at the detector site in Antarctica and are producing alerts for the community to enable rapid follow-up observations. The goal of these observations is to locate the astrophysical objects responsible for these neutrino signals. This paper highlights the infrastructure in place both at the South Pole site and at IceCube facilities in the north that have enabled this fast follow-up program to be implemented. Additionally, this paper presents the first realtime analyses to be activated within this framework, highlights their sensitivities to astrophysical neutrinos and background event rates, and presents an outlook for future discoveries.

Statistical intensity variation analysis for rapid volumetric imaging of capillary network flux

PubMed Central

Lee, Jonghwan; Jiang, James Y.; Wu, Weicheng; Lesage, Frederic; Boas, David A.

2014-01-01

We present a novel optical coherence tomography (OCT)-based technique for rapid volumetric imaging of red blood cell (RBC) flux in capillary networks. Previously we reported that OCT can capture individual RBC passage within a capillary, where the OCT intensity signal at a voxel fluctuates when an RBC passes the voxel. Based on this finding, we defined a metric of statistical intensity variation (SIV) and validated that the mean SIV is proportional to the RBC flux [RBC/s] through simulations and measurements. From rapidly scanned volume data, we used Hessian matrix analysis to vectorize a segment path of each capillary and estimate its flux from the mean of the SIVs gathered along the path. Repeating this process led to a 3D flux map of the capillary network. The present technique enabled us to trace the RBC flux changes over hundreds of capillaries with a temporal resolution of ~1 s during functional activation. PMID:24761298

NGSANE: a lightweight production informatics framework for high-throughput data analysis.

PubMed

Buske, Fabian A; French, Hugh J; Smith, Martin A; Clark, Susan J; Bauer, Denis C

2014-05-15

The initial steps in the analysis of next-generation sequencing data can be automated by way of software 'pipelines'. However, individual components depreciate rapidly because of the evolving technology and analysis methods, often rendering entire versions of production informatics pipelines obsolete. Constructing pipelines from Linux bash commands enables the use of hot swappable modular components as opposed to the more rigid program call wrapping by higher level languages, as implemented in comparable published pipelining systems. Here we present Next Generation Sequencing ANalysis for Enterprises (NGSANE), a Linux-based, high-performance-computing-enabled framework that minimizes overhead for set up and processing of new projects, yet maintains full flexibility of custom scripting when processing raw sequence data. Ngsane is implemented in bash and publicly available under BSD (3-Clause) licence via GitHub at https://github.com/BauerLab/ngsane. Denis.Bauer@csiro.au Supplementary data are available at Bioinformatics online.

SECIMTools: a suite of metabolomics data analysis tools.

PubMed

Kirpich, Alexander S; Ibarra, Miguel; Moskalenko, Oleksandr; Fear, Justin M; Gerken, Joseph; Mi, Xinlei; Ashrafi, Ali; Morse, Alison M; McIntyre, Lauren M

2018-04-20

Metabolomics has the promise to transform the area of personalized medicine with the rapid development of high throughput technology for untargeted analysis of metabolites. Open access, easy to use, analytic tools that are broadly accessible to the biological community need to be developed. While technology used in metabolomics varies, most metabolomics studies have a set of features identified. Galaxy is an open access platform that enables scientists at all levels to interact with big data. Galaxy promotes reproducibility by saving histories and enabling the sharing workflows among scientists. SECIMTools (SouthEast Center for Integrated Metabolomics) is a set of Python applications that are available both as standalone tools and wrapped for use in Galaxy. The suite includes a comprehensive set of quality control metrics (retention time window evaluation and various peak evaluation tools), visualization techniques (hierarchical cluster heatmap, principal component analysis, modular modularity clustering), basic statistical analysis methods (partial least squares - discriminant analysis, analysis of variance, t-test, Kruskal-Wallis non-parametric test), advanced classification methods (random forest, support vector machines), and advanced variable selection tools (least absolute shrinkage and selection operator LASSO and Elastic Net). SECIMTools leverages the Galaxy platform and enables integrated workflows for metabolomics data analysis made from building blocks designed for easy use and interpretability. Standard data formats and a set of utilities allow arbitrary linkages between tools to encourage novel workflow designs. The Galaxy framework enables future data integration for metabolomics studies with other omics data.

Portable Infrared Laser Spectroscopy for On-site Mycotoxin Analysis.

PubMed

Sieger, Markus; Kos, Gregor; Sulyok, Michael; Godejohann, Matthias; Krska, Rudolf; Mizaikoff, Boris

2017-03-09

Mycotoxins are toxic secondary metabolites of fungi that spoil food, and severely impact human health (e.g., causing cancer). Therefore, the rapid determination of mycotoxin contamination including deoxynivalenol and aflatoxin B 1 in food and feed samples is of prime interest for commodity importers and processors. While chromatography-based techniques are well established in laboratory environments, only very few (i.e., mostly immunochemical) techniques exist enabling direct on-site analysis for traders and manufacturers. In this study, we present MYCOSPEC - an innovative approach for spectroscopic mycotoxin contamination analysis at EU regulatory limits for the first time utilizing mid-infrared tunable quantum cascade laser (QCL) spectroscopy. This analysis technique facilitates on-site mycotoxin analysis by combining QCL technology with GaAs/AlGaAs thin-film waveguides. Multivariate data mining strategies (i.e., principal component analysis) enabled the classification of deoxynivalenol-contaminated maize and wheat samples, and of aflatoxin B 1 affected peanuts at EU regulatory limits of 1250 μg kg -1 and 8 μg kg -1 , respectively.

Portable Infrared Laser Spectroscopy for On-site Mycotoxin Analysis

PubMed Central

Sieger, Markus; Kos, Gregor; Sulyok, Michael; Godejohann, Matthias; Krska, Rudolf; Mizaikoff, Boris

2017-01-01

Mycotoxins are toxic secondary metabolites of fungi that spoil food, and severely impact human health (e.g., causing cancer). Therefore, the rapid determination of mycotoxin contamination including deoxynivalenol and aflatoxin B1 in food and feed samples is of prime interest for commodity importers and processors. While chromatography-based techniques are well established in laboratory environments, only very few (i.e., mostly immunochemical) techniques exist enabling direct on-site analysis for traders and manufacturers. In this study, we present MYCOSPEC - an innovative approach for spectroscopic mycotoxin contamination analysis at EU regulatory limits for the first time utilizing mid-infrared tunable quantum cascade laser (QCL) spectroscopy. This analysis technique facilitates on-site mycotoxin analysis by combining QCL technology with GaAs/AlGaAs thin-film waveguides. Multivariate data mining strategies (i.e., principal component analysis) enabled the classification of deoxynivalenol-contaminated maize and wheat samples, and of aflatoxin B1 affected peanuts at EU regulatory limits of 1250 μg kg−1 and 8 μg kg−1, respectively. PMID:28276454

Portable Infrared Laser Spectroscopy for On-site Mycotoxin Analysis

NASA Astrophysics Data System (ADS)

Sieger, Markus; Kos, Gregor; Sulyok, Michael; Godejohann, Matthias; Krska, Rudolf; Mizaikoff, Boris

2017-03-01

Mycotoxins are toxic secondary metabolites of fungi that spoil food, and severely impact human health (e.g., causing cancer). Therefore, the rapid determination of mycotoxin contamination including deoxynivalenol and aflatoxin B1 in food and feed samples is of prime interest for commodity importers and processors. While chromatography-based techniques are well established in laboratory environments, only very few (i.e., mostly immunochemical) techniques exist enabling direct on-site analysis for traders and manufacturers. In this study, we present MYCOSPEC - an innovative approach for spectroscopic mycotoxin contamination analysis at EU regulatory limits for the first time utilizing mid-infrared tunable quantum cascade laser (QCL) spectroscopy. This analysis technique facilitates on-site mycotoxin analysis by combining QCL technology with GaAs/AlGaAs thin-film waveguides. Multivariate data mining strategies (i.e., principal component analysis) enabled the classification of deoxynivalenol-contaminated maize and wheat samples, and of aflatoxin B1 affected peanuts at EU regulatory limits of 1250 μg kg-1 and 8 μg kg-1, respectively.

Optofluidic refractive-index sensors employing bent waveguide structures for low-cost, rapid chemical and biomedical sensing.

PubMed

Liu, I-Chen; Chen, Pin-Chuan; Chau, Lai-Kwan; Chang, Guo-En

2018-01-08

We propose and develop an intensity-detection-based refractive-index (RI) sensor for low-cost, rapid RI sensing. The sensor is composed of a polymer bent ridge waveguide (BRWG) structure on a low-cost glass substrate and is integrated with a microfluidic channel. Different-RI solutions flowing through the BRWG sensing region induce output optical power variations caused by optical bend losses, enabling simple and real-time RI detection. Additionally, the sensors are fabricated using rapid and cost-effective vacuum-less processes, attaining the low cost and high throughput required for mass production. A good RI solution of 5.31 10 -4 × RIU -1 is achieved from the RI experiments. This study demonstrates mass-producible and compact RI sensors for rapid and sensitive chemical analysis and biomedical sensing.

Structural Configuration Analysis of Crew Exploration Vehicle Concepts

NASA Technical Reports Server (NTRS)

Mukhopadhyay, V.

2006-01-01

Structural configuration modeling and finite element analysis of crew exploration vehicle (CEV) concepts are presented. In the structural configuration design approach, parametric solid models of the pressurized shell and tanks are developed. The CEV internal cabin pressure is same as in the International Space Station (ISS) to enable docking with the ISS without an intermediate airlock. Effects of this internal pressure load on the stress distribution, factor of safety, mass and deflections are investigated. Uniform 7 mm thick skin shell, 5 mm thick shell with ribs and frames, and isogrid skin construction options are investigated. From this limited study, the isogrid construction appears to provide most strength/mass ratio. Initial finite element analysis results on the service module tanks are also presented. These rapid finite element analyses, stress and factor of safety distribution results are presented as a part of lessons learned and to build up a structural mass estimation and sizing database for future technology support. This rapid structural analysis process may also facilitate better definition of the vehicles and components for rapid prototyping. However, these structural analysis results are highly conceptual and exploratory in nature and do not reflect current configuration designs being conducted at the program level by NASA and industry.

Integrated Modeling, Mapping, and Simulation (IMMS) framework for planning exercises.

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

Friedman-Hill, Ernest J.; Plantenga, Todd D.

2010-06-01

The Integrated Modeling, Mapping, and Simulation (IMMS) program is designing and prototyping a simulation and collaboration environment for linking together existing and future modeling and simulation tools to enable analysts, emergency planners, and incident managers to more effectively, economically, and rapidly prepare, analyze, train, and respond to real or potential incidents. When complete, the IMMS program will demonstrate an integrated modeling and simulation capability that supports emergency managers and responders with (1) conducting 'what-if' analyses and exercises to address preparedness, analysis, training, operations, and lessons learned, and (2) effectively, economically, and rapidly verifying response tactics, plans and procedures.

Next-generation phenomics for the Tree of Life.

PubMed

Burleigh, J Gordon; Alphonse, Kenzley; Alverson, Andrew J; Bik, Holly M; Blank, Carrine; Cirranello, Andrea L; Cui, Hong; Daly, Marymegan; Dietterich, Thomas G; Gasparich, Gail; Irvine, Jed; Julius, Matthew; Kaufman, Seth; Law, Edith; Liu, Jing; Moore, Lisa; O'Leary, Maureen A; Passarotti, Maria; Ranade, Sonali; Simmons, Nancy B; Stevenson, Dennis W; Thacker, Robert W; Theriot, Edward C; Todorovic, Sinisa; Velazco, Paúl M; Walls, Ramona L; Wolfe, Joanna M; Yu, Mengjie

2013-06-26

The phenotype represents a critical interface between the genome and the environment in which organisms live and evolve. Phenotypic characters also are a rich source of biodiversity data for tree building, and they enable scientists to reconstruct the evolutionary history of organisms, including most fossil taxa, for which genetic data are unavailable. Therefore, phenotypic data are necessary for building a comprehensive Tree of Life. In contrast to recent advances in molecular sequencing, which has become faster and cheaper through recent technological advances, phenotypic data collection remains often prohibitively slow and expensive. The next-generation phenomics project is a collaborative, multidisciplinary effort to leverage advances in image analysis, crowdsourcing, and natural language processing to develop and implement novel approaches for discovering and scoring the phenome, the collection of phentotypic characters for a species. This research represents a new approach to data collection that has the potential to transform phylogenetics research and to enable rapid advances in constructing the Tree of Life. Our goal is to assemble large phenomic datasets built using new methods and to provide the public and scientific community with tools for phenomic data assembly that will enable rapid and automated study of phenotypes across the Tree of Life.

A Federal Vision for Future Computing: A Nanotechnology-Inspired Grand Challenge

DTIC Science & Technology

2016-07-29

Science Foundation (NSF), Department of Defense (DOD), National Institute of Standards and Technology (NIST), Intelligence Community (IC) Introduction...multiple Federal agencies: • Intelligent big data sensors that act autonomously and are programmable via the network for increased flexibility, and... intelligence for scientific discovery enabled by rapid extreme-scale data analysis, capable of understanding and making sense of results and thereby

Enabling Near Real-Time Remote Search for Fast Transient Events with Lossy Data Compression

NASA Astrophysics Data System (ADS)

Vohl, Dany; Pritchard, Tyler; Andreoni, Igor; Cooke, Jeffrey; Meade, Bernard

2017-09-01

We present a systematic evaluation of JPEG2000 (ISO/IEC 15444) as a transport data format to enable rapid remote searches for fast transient events as part of the Deeper Wider Faster programme. Deeper Wider Faster programme uses 20 telescopes from radio to gamma rays to perform simultaneous and rapid-response follow-up searches for fast transient events on millisecond-to-hours timescales. Deeper Wider Faster programme search demands have a set of constraints that is becoming common amongst large collaborations. Here, we focus on the rapid optical data component of Deeper Wider Faster programme led by the Dark Energy Camera at Cerro Tololo Inter-American Observatory. Each Dark Energy Camera image has 70 total coupled-charged devices saved as a 1.2 gigabyte FITS file. Near real-time data processing and fast transient candidate identifications-in minutes for rapid follow-up triggers on other telescopes-requires computational power exceeding what is currently available on-site at Cerro Tololo Inter-American Observatory. In this context, data files need to be transmitted rapidly to a foreign location for supercomputing post-processing, source finding, visualisation and analysis. This step in the search process poses a major bottleneck, and reducing the data size helps accommodate faster data transmission. To maximise our gain in transfer time and still achieve our science goals, we opt for lossy data compression-keeping in mind that raw data is archived and can be evaluated at a later time. We evaluate how lossy JPEG2000 compression affects the process of finding transients, and find only a negligible effect for compression ratios up to 25:1. We also find a linear relation between compression ratio and the mean estimated data transmission speed-up factor. Adding highly customised compression and decompression steps to the science pipeline considerably reduces the transmission time-validating its introduction to the Deeper Wider Faster programme science pipeline and enabling science that was otherwise too difficult with current technology.

Potential use of combining the diffusion equation with the free Shrödinger equation to improve the Optical Coherence Tomography image analysis

NASA Astrophysics Data System (ADS)

Cabrera Fernandez, Delia; Salinas, Harry M.; Somfai, Gabor; Puliafito, Carmen A.

2006-03-01

Optical coherence tomography (OCT) is a rapidly emerging medical imaging technology. In ophthalmology, OCT is a powerful tool because it enables visualization of the cross sectional structure of the retina and anterior eye with higher resolutions than any other non-invasive imaging modality. Furthermore, OCT image information can be quantitatively analyzed, enabling objective assessment of features such as macular edema and diabetes retinopathy. We present specific improvements in the quantitative analysis of the OCT system, by combining the diffusion equation with the free Shrödinger equation. In such formulation, important features of the image can be extracted by extending the analysis from the real axis to the complex domain. Experimental results indicate that our proposed novel approach has good performance in speckle noise removal, enhancement and segmentation of the various cellular layers of the retina using the OCT system.

The use of big data in transfusion medicine.

PubMed

Pendry, K

2015-06-01

'Big data' refers to the huge quantities of digital information now available that describe much of human activity. The science of data management and analysis is rapidly developing to enable organisations to convert data into useful information and knowledge. Electronic health records and new developments in Pathology Informatics now support the collection of 'big laboratory and clinical data', and these digital innovations are now being applied to transfusion medicine. To use big data effectively, we must address concerns about confidentiality and the need for a change in culture and practice, remove barriers to adopting common operating systems and data standards and ensure the safe and secure storage of sensitive personal information. In the UK, the aim is to formulate a single set of data and standards for communicating test results and so enable pathology data to contribute to national datasets. In transfusion, big data has been used for benchmarking, detection of transfusion-related complications, determining patterns of blood use and definition of blood order schedules for surgery. More generally, rapidly available information can monitor compliance with key performance indicators for patient blood management and inventory management leading to better patient care and reduced use of blood. The challenges of enabling reliable systems and analysis of big data and securing funding in the restrictive financial climate are formidable, but not insurmountable. The promise is that digital information will soon improve the implementation of best practice in transfusion medicine and patient blood management globally. © 2015 British Blood Transfusion Society.

Cloud Based Metalearning System for Predictive Modeling of Biomedical Data

PubMed Central

Vukićević, Milan

2014-01-01

Rapid growth and storage of biomedical data enabled many opportunities for predictive modeling and improvement of healthcare processes. On the other side analysis of such large amounts of data is a difficult and computationally intensive task for most existing data mining algorithms. This problem is addressed by proposing a cloud based system that integrates metalearning framework for ranking and selection of best predictive algorithms for data at hand and open source big data technologies for analysis of biomedical data. PMID:24892101

Fiji: an open-source platform for biological-image analysis.

PubMed

Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinevez, Jean-Yves; White, Daniel James; Hartenstein, Volker; Eliceiri, Kevin; Tomancak, Pavel; Cardona, Albert

2012-06-28

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots.

PubMed

Hirata, Yoshito; Oda, Arisa; Ohta, Kunihiro; Aihara, Kazuyuki

2016-10-11

Single-cell analysis of the three-dimensional (3D) chromosome structure can reveal cell-to-cell variability in genome activities. Here, we propose to apply recurrence plots, a mathematical method of nonlinear time series analysis, to reconstruct the 3D chromosome structure of a single cell based on information of chromosomal contacts from genome-wide chromosome conformation capture (Hi-C) data. This recurrence plot-based reconstruction (RPR) method enables rapid reconstruction of a unique structure in single cells, even from incomplete Hi-C information.

Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots

NASA Astrophysics Data System (ADS)

Hirata, Yoshito; Oda, Arisa; Ohta, Kunihiro; Aihara, Kazuyuki

2016-10-01

Single-cell analysis of the three-dimensional (3D) chromosome structure can reveal cell-to-cell variability in genome activities. Here, we propose to apply recurrence plots, a mathematical method of nonlinear time series analysis, to reconstruct the 3D chromosome structure of a single cell based on information of chromosomal contacts from genome-wide chromosome conformation capture (Hi-C) data. This recurrence plot-based reconstruction (RPR) method enables rapid reconstruction of a unique structure in single cells, even from incomplete Hi-C information.

Computer graphics and cultural heritage, part 2: continuing inspiration for future tools.

PubMed

Arnold, David

2014-01-01

The availability of large quantities of cultural-heritage data will enable new, previously inconceivable, types of analysis and new applications. Currently, most emerging analysis methods are experimental research. It's likely to take many years before the research matures and provides cultural-heritage professionals with novel research methods that they use routinely. Indeed, we can expect further disruptive technologies to emerge in the foreseeable future and a "steady state" of continuing rapid change. Part 1 can be found at 10.1109/MCG.2014.47.

Orchestrating high-throughput genomic analysis with Bioconductor

PubMed Central

Huber, Wolfgang; Carey, Vincent J.; Gentleman, Robert; Anders, Simon; Carlson, Marc; Carvalho, Benilton S.; Bravo, Hector Corrada; Davis, Sean; Gatto, Laurent; Girke, Thomas; Gottardo, Raphael; Hahne, Florian; Hansen, Kasper D.; Irizarry, Rafael A.; Lawrence, Michael; Love, Michael I.; MacDonald, James; Obenchain, Valerie; Oleś, Andrzej K.; Pagès, Hervé; Reyes, Alejandro; Shannon, Paul; Smyth, Gordon K.; Tenenbaum, Dan; Waldron, Levi; Morgan, Martin

2015-01-01

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors. PMID:25633503

Adaptive Modeling, Engineering Analysis and Design of Advanced Aerospace Vehicles

NASA Technical Reports Server (NTRS)

Mukhopadhyay, Vivek; Hsu, Su-Yuen; Mason, Brian H.; Hicks, Mike D.; Jones, William T.; Sleight, David W.; Chun, Julio; Spangler, Jan L.; Kamhawi, Hilmi; Dahl, Jorgen L.

2006-01-01

This paper describes initial progress towards the development and enhancement of a set of software tools for rapid adaptive modeling, and conceptual design of advanced aerospace vehicle concepts. With demanding structural and aerodynamic performance requirements, these high fidelity geometry based modeling tools are essential for rapid and accurate engineering analysis at the early concept development stage. This adaptive modeling tool was used for generating vehicle parametric geometry, outer mold line and detailed internal structural layout of wing, fuselage, skin, spars, ribs, control surfaces, frames, bulkheads, floors, etc., that facilitated rapid finite element analysis, sizing study and weight optimization. The high quality outer mold line enabled rapid aerodynamic analysis in order to provide reliable design data at critical flight conditions. Example application for structural design of a conventional aircraft and a high altitude long endurance vehicle configuration are presented. This work was performed under the Conceptual Design Shop sub-project within the Efficient Aerodynamic Shape and Integration project, under the former Vehicle Systems Program. The project objective was to design and assess unconventional atmospheric vehicle concepts efficiently and confidently. The implementation may also dramatically facilitate physics-based systems analysis for the NASA Fundamental Aeronautics Mission. In addition to providing technology for design and development of unconventional aircraft, the techniques for generation of accurate geometry and internal sub-structure and the automated interface with the high fidelity analysis codes could also be applied towards the design of vehicles for the NASA Exploration and Space Science Mission projects.

Towards adaptive, streaming analysis of x-ray tomography data

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

Thomas, Mathew; Kleese van Dam, Kerstin; Marshall, Matthew J.

2015-03-04

Temporal and spatial resolution of chemical imaging methodologies such as x-ray tomography are rapidly increasing, leading to more complex experimental procedures and fast growing data volumes. Automated analysis pipelines and big data analytics are becoming essential to effectively evaluate the results of such experiments. Offering those data techniques in an adaptive, streaming environment can further substantially improve the scientific discovery process, by enabling experimental control and steering based on the evaluation of emerging phenomena as they are observed by the experiment. Pacific Northwest National Laboratory (PNNL)’ Chemical Imaging Initiative (CII - http://imaging.pnnl.gov/ ) has worked since 2011 towards developing amore » framework that allows users to rapidly compose and customize high throughput experimental analysis pipelines for multiple instrument types. The framework, named ‘Rapid Experimental Analysis’ (REXAN) Framework [1], is based on the idea of reusable component libraries and utilizes the PNNL developed collaborative data management and analysis environment ‘Velo’, to provide a user friendly analysis and data management environment for experimental facilities. This article will, discuss the capabilities established for X-Ray tomography, discuss lessons learned, and provide an overview of our more recent work in the Analysis in Motion Initiative (AIM - http://aim.pnnl.gov/ ) at PNNL to provide REXAN capabilities in a streaming environment.« less

Integrated microfluidic chip for rapid DNA digestion and time-resolved capillary electrophoresis analysis

PubMed Central

Lin, Che-Hsin; Wang, Yao-Nan; Fu, Lung-Ming

2012-01-01

An integrated microfluidic chip is proposed for rapid DNA digestion and time-resolved capillary electrophoresis (CE) analysis. The chip comprises two gel-filled chambers for DNA enrichment and purification, respectively, a T-form micromixer for DNA/restriction enzyme mixing, a serpentine channel for DNA digestion reaction, and a CE channel for on-line capillary electrophoresis analysis. The DNA and restriction enzyme are mixed electroomostically using a pinched-switching DC field. The experimental and numerical results show that a mixing performance of 97% is achieved within a distance of 1 mm from the T-junction when a driving voltage of 90 V/cm and a switching frequency of 4 Hz are applied. Successive mixing digestion and capillary electrophoresis operation clearly present the changes on digesting φx-174 DNA in different CE runs. The time-resolved electropherograms show that the proposed device enables a φx-174 DNA sample comprising 11 fragments to be concentrated and analyzed within 24 min. Overall, the results presented in this study show that the proposed microfluidic chip provides a rapid and effective tool for DNA digestion and CE analysis applications. PMID:22662085

Centrifuge: rapid and sensitive classification of metagenomic sequences.

PubMed

Kim, Daehwan; Song, Li; Breitwieser, Florian P; Salzberg, Steven L

2016-12-01

Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together, these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI nonredundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer-based indexing schemes, which require far more extensive space. © 2016 Kim et al.; Published by Cold Spring Harbor Laboratory Press.

Whispering gallery mode resonators for rapid label-free biosensing in small volume droplets.

PubMed

Wildgen, Sarah M; Dunn, Robert C

2015-03-23

Rapid biosensing requires fast mass transport of the analyte to the surface of the sensing element. To optimize analysis times, both mass transport in solution and the geometry and size of the sensing element need to be considered. Small dielectric spheres, tens of microns in diameter, can act as label-free biosensors using whispering gallery mode (WGM) resonances. WGM resonances are sensitive to the effective refractive index, which changes upon analyte binding to recognition sites on functionalized resonators. The spherical geometry and tens of microns diameter of these resonators provides an efficient target for sensing while their compact size enables detection in limited volumes. Here, we explore conditions leading to rapid analyte detection using WGM resonators as label-free sensors in 10 μL sample droplets. Droplet evaporation leads to potentially useful convective mixing, but also limits the time over which analysis can be completed. We show that active droplet mixing combined with initial binding rate measurements is required for accurate nanomolar protein quantification within the first minute following injection.

A DNA 'barcode blitz': rapid digitization and sequencing of a natural history collection.

PubMed

Hebert, Paul D N; Dewaard, Jeremy R; Zakharov, Evgeny V; Prosser, Sean W J; Sones, Jayme E; McKeown, Jaclyn T A; Mantle, Beth; La Salle, John

2013-01-01

DNA barcoding protocols require the linkage of each sequence record to a voucher specimen that has, whenever possible, been authoritatively identified. Natural history collections would seem an ideal resource for barcode library construction, but they have never seen large-scale analysis because of concerns linked to DNA degradation. The present study examines the strength of this barrier, carrying out a comprehensive analysis of moth and butterfly (Lepidoptera) species in the Australian National Insect Collection. Protocols were developed that enabled tissue samples, specimen data, and images to be assembled rapidly. Using these methods, a five-person team processed 41,650 specimens representing 12,699 species in 14 weeks. Subsequent molecular analysis took about six months, reflecting the need for multiple rounds of PCR as sequence recovery was impacted by age, body size, and collection protocols. Despite these variables and the fact that specimens averaged 30.4 years old, barcode records were obtained from 86% of the species. In fact, one or more barcode compliant sequences (>487 bp) were recovered from virtually all species represented by five or more individuals, even when the youngest was 50 years old. By assembling specimen images, distributional data, and DNA barcode sequences on a web-accessible informatics platform, this study has greatly advanced accessibility to information on thousands of species. Moreover, much of the specimen data became publically accessible within days of its acquisition, while most sequence results saw release within three months. As such, this study reveals the speed with which DNA barcode workflows can mobilize biodiversity data, often providing the first web-accessible information for a species. These results further suggest that existing collections can enable the rapid development of a comprehensive DNA barcode library for the most diverse compartment of terrestrial biodiversity - insects.

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.

PubMed

Scheurer, Maximilian; Rodenkirch, Peter; Siggel, Marc; Bernardi, Rafael C; Schulten, Klaus; Tajkhorshid, Emad; Rudack, Till

2018-02-06

Molecular dynamics (MD) simulations have become ubiquitous in all areas of life sciences. The size and model complexity of MD simulations are rapidly growing along with increasing computing power and improved algorithms. This growth has led to the production of a large amount of simulation data that need to be filtered for relevant information to address specific biomedical and biochemical questions. One of the most relevant molecular properties that can be investigated by all-atom MD simulations is the time-dependent evolution of the complex noncovalent interaction networks governing such fundamental aspects as molecular recognition, binding strength, and mechanical and structural stability. Extracting, evaluating, and visualizing noncovalent interactions is a key task in the daily work of structural biologists. We have developed PyContact, an easy-to-use, highly flexible, and intuitive graphical user interface-based application, designed to provide a toolkit to investigate biomolecular interactions in MD trajectories. PyContact is designed to facilitate this task by enabling identification of relevant noncovalent interactions in a comprehensible manner. The implementation of PyContact as a standalone application enables rapid analysis and data visualization without any additional programming requirements, and also preserves full in-program customization and extension capabilities for advanced users. The statistical analysis representation is interactively combined with full mapping of the results on the molecular system through the synergistic connection between PyContact and VMD. We showcase the capabilities and scientific significance of PyContact by analyzing and visualizing in great detail the noncovalent interactions underlying the ion permeation pathway of the human P2X 3 receptor. As a second application, we examine the protein-protein interaction network of the mechanically ultrastable cohesin-dockering complex. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Direct Analysis in Real Time-Mass Spectrometry & Kohonen Artificial Neural Networks for the Rapid Species Identification of Larvae, Pupae and Adult Life Stages of Carrion Insects.

PubMed

Beyramysoltan, Samira; Giffen, Justine E; Rosati, Jennifer Y; Musah, Rabi Ann

2018-06-20

Species determination of the various life stages of flies (order: Diptera) is challenging, particularly for the immature forms, because analogous life stages of different species are difficult to differentiate morphologically. It is demonstrated here that DART high-resolution mass spectrometry (DART-HRMS) combined with supervised Kohonen Self-Organizing Maps (SOM) enables accomplishment of species-level identification of larvae, pupae and adult life stages of carrion flies. DART-HRMS data for each life stage were acquired from analysis of ethanol suspensions representing Calliphoridae, Phoridae and Sarcophagidae families, without additional sample preparation. After preprocessing, the data were subjected to a combination of minimum Redundancy Maximal Relevance (mRMR) and Sparse Discriminant Analysis (SDA) methods to select the most significant variables for creating accurate SOM models. The resulting data were divided into training and validation sets, and then analyzed by the SOM method to define the proper discrimination models. The 5-fold venetian blind cross-validation misclassification error was below 7% for all life stages, and the validation samples were correctly identified in all cases. The multiclass SOM model also revealed which chemical components were the most significant markers for each species, with several of these being amino acids. The results show that processing of DART-HRMS data using artificial neural networks (ANNs) based on the Kohonen SOM approach enables rapid discrimination and identification of fly species even for the immature life stages. The ANNs can be continuously expanded to include a larger number of species, and can be used to screen DART-HRMS data from unknowns to rapidly determine species identity.

Open Innovation and Technology Maturity Analysis

DTIC Science & Technology

2007-09-11

Management Process Develop a framework which incorporates DoD Acquisition Management framework (e.g: TRLs), DoD Business Transformation strategies...Public Organizations (DoD): DoD Force Transformation : • Support the Joint Warfighting Capability of the DoD • Enable Rapid Access to Information for...Survey - 2007  Defense Transformation : Clear Leadership, Accountability, and Management Tools Are Needed to Enhance DOD’s Efforts to Transform Military

Effect of 5E Learning Model on Academic Achievement, Attitude and Science Process Skills: Meta-Analysis Study

ERIC Educational Resources Information Center

Cakir, Nevin Kozcu

2017-01-01

Today, with the development of science and technology and its rapid progress, the importance attached to science education has increased. This increase in interest has led to the development of the methods, techniques, and approaches that enable the students to be active, question and construct knowledge. The 5E learning model is one of them, and…

Rapid wide-field Mueller matrix polarimetry imaging based on four photoelastic modulators with no moving parts.

PubMed

Alali, Sanaz; Gribble, Adam; Vitkin, I Alex

2016-03-01

A new polarimetry method is demonstrated to image the entire Mueller matrix of a turbid sample using four photoelastic modulators (PEMs) and a charge coupled device (CCD) camera, with no moving parts. Accurate wide-field imaging is enabled with a field-programmable gate array (FPGA) optical gating technique and an evolutionary algorithm (EA) that optimizes imaging times. This technique accurately and rapidly measured the Mueller matrices of air, polarization elements, and turbid phantoms. The system should prove advantageous for Mueller matrix analysis of turbid samples (e.g., biological tissues) over large fields of view, in less than a second.

The A-Like Faker Assay for Measuring Yeast Chromosome III Stability.

PubMed

Novoa, Carolina A; Ang, J Sidney; Stirling, Peter C

2018-01-01

The ability to rapidly assess chromosome instability (CIN) has enabled profiling of most yeast genes for potential effects on genome stability. The A-like faker (ALF) assay is one of several qualitative and quantitative marker loss assays that indirectly measure loss or conversion of genetic material using a counterselection step. The ALF assay relies on the ability to count spurious mating events that occur upon loss of the MATα locus of haploid Saccharomyces cerevisiae strains. Here, we describe the deployment of the ALF assay for both rapid and simple qualitative, and more in-depth quantitative analysis allowing determination of absolute ALF frequencies.

Fabricated nanogap-rich plasmonic nanostructures through an optothermal surface bubble in a droplet.

PubMed

Karim, Farzia; Vasquez, Erick S; Zhao, Chenglong

2018-01-15

A rapid and cost-effective method for the fabrication of nanogap-rich structures is demonstrated in this Letter. The method utilizes the Marangoni convection around an optothermal surface bubble inside a liquid droplet with a nanoliter volume. The liquid droplet containing metallic nanoparticles reduces the sample consumption and confines the liquid flow. The optothermal surface bubble creates a strong convective flow that allows for the rapid deposition of the metallic nanoparticles to form nanogap-rich structures on any substrate under ambient conditions. This method will enable a broad range of applications such as biosensing, environmental analysis, and nonlinear optics.

Pixel-based approach for building heights determination by SAR radargrammetry

NASA Astrophysics Data System (ADS)

Dubois, C.; Thiele, A.; Hinz, S.

2013-10-01

Numerous advances have been made recently in photogrammetry, laser scanning, and remote sensing for the creation of 3D city models. More and more cities are interested in getting 3D city models, be it for urban planning purposes or for supporting public utility companies. In areas often affected by natural disaster, rapid updating of the 3D information may also be useful for helping rescue forces. The high resolutions that can be achieved by the new spaceborne SAR sensor generation enables the analysis of city areas at building level and make those sensors attractive for the extraction of 3D information. Moreover, they present the advantage of weather and sunlight independency, which make them more practicable than optical data, in particular for tasks where rapid response is required. Furthermore, their short revisit time and the possibility of multi-sensor constellation enable providing several acquisitions within a few hours. This opens up the floor for new applications, especially radargrammetric applications, which consider acquisitions taken under different incidence angles. In this paper, we present a new approach for determining building heights, relying only on the radargrammetric analysis of building layover. By taking into account same-side acquisitions, we present the workflow of building height determination. Focus is set on some geometric considerations, pixel-based approach for disparity map calculation, and analysis of the building layover signature for different configurations in order to determine building height.

Paper-based analytical devices for environmental analysis.

PubMed

Meredith, Nathan A; Quinn, Casey; Cate, David M; Reilly, Thomas H; Volckens, John; Henry, Charles S

2016-03-21

The field of paper-based microfluidics has experienced rapid growth over the past decade. Microfluidic paper-based analytical devices (μPADs), originally developed for point-of-care medical diagnostics in resource-limited settings, are now being applied in new areas, such as environmental analyses. Low-cost paper sensors show great promise for on-site environmental analysis; the theme of ongoing research complements existing instrumental techniques by providing high spatial and temporal resolution for environmental monitoring. This review highlights recent applications of μPADs for environmental analysis along with technical advances that may enable μPADs to be more widely implemented in field testing.

A nanosecond pulsed laser heating system for studying liquid and supercooled liquid films in ultrahigh vacuum

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

Xu, Yuntao; Dibble, Collin J.; Petrik, Nikolay G.

2016-04-26

A pulsed laser heating system has been developed that enables investigations of the dynamics and kinetics of nanoscale liquid films and liquid/solid interfaces on the nanosecond timescale in ultrahigh vacuum (UHV). Details of the design, implementation and characterization of a nanosecond pulsed laser system for transiently heating nanoscale films are described. Nanosecond pulses from a Nd:YAG laser are used to rapidly heat thin films of adsorbed water or other volatile materials on a clean, well-characterized Pt(111) crystal in UHV. Heating rates of ~1010 K/s for temperature increases of ~100 – 200 K are obtained. Subsequent rapid cooling (~5 × 109more » K/s) quenches the film, permitting in-situ, post-mortem analysis using a variety of surface science techniques. Lateral variations in the laser pulse energy are ~ ± 3% leading to a temperature uncertainty of ~ ± 5 K for a temperature jump of 200 K. Initial experiments with the apparatus demonstrate that crystalline ice films initially held at 90 K can be rapidly transformed into liquid water films with T > 273 K. No discernable recrystallization occurs during the rapid cooling back to cryogenic temperatures. In contrast, amorphous solid water films heated below the melting point rapidly crystallize. The nanosecond pulsed laser heating system can prepare nanoscale liquid and supercooled liquid films that persist for nanoseconds per heat pulse in an UHV environment, enabling experimental studies of a wide range of phenomena in liquids and at liquid/solid interfaces.« less

A nanosecond pulsed laser heating system for studying liquid and supercooled liquid films in ultrahigh vacuum.

PubMed

Xu, Yuntao; Dibble, Collin J; Petrik, Nikolay G; Smith, R Scott; Joly, Alan G; Tonkyn, Russell G; Kay, Bruce D; Kimmel, Greg A

2016-04-28

A pulsed laser heating system has been developed that enables investigations of the dynamics and kinetics of nanoscale liquid films and liquid/solid interfaces on the nanosecond time scale in ultrahigh vacuum (UHV). Details of the design, implementation, and characterization of a nanosecond pulsed laser system for transiently heating nanoscale films are described. Nanosecond pulses from a Nd:YAG laser are used to rapidly heat thin films of adsorbed water or other volatile materials on a clean, well-characterized Pt(111) crystal in UHV. Heating rates of ∼10(10) K/s for temperature increases of ∼100-200 K are obtained. Subsequent rapid cooling (∼5 × 10(9) K/s) quenches the film, permitting in-situ, post-heating analysis using a variety of surface science techniques. Lateral variations in the laser pulse energy are ∼±2.7% leading to a temperature uncertainty of ∼±4.4 K for a temperature jump of 200 K. Initial experiments with the apparatus demonstrate that crystalline ice films initially held at 90 K can be rapidly transformed into liquid water films with T > 273 K. No discernable recrystallization occurs during the rapid cooling back to cryogenic temperatures. In contrast, amorphous solid water films heated below the melting point rapidly crystallize. The nanosecond pulsed laser heating system can prepare nanoscale liquid and supercooled liquid films that persist for nanoseconds per heat pulse in an UHV environment, enabling experimental studies of a wide range of phenomena in liquids and at liquid/solid interfaces.

Ultrafast High-Resolution Mass Spectrometric Finger Pore Imaging in Latent Finger Prints

NASA Astrophysics Data System (ADS)

Elsner, Christian; Abel, Bernd

2014-11-01

Latent finger prints (LFPs) are deposits of sweat components in ridge and groove patterns, left after human fingers contact with a surface. Being important targets in biometry and forensic investigations they contain more information than topological patterns. With laser desorption mass spectrometry imaging (LD-MSI) we record `three-dimensional' finger prints with additional chemical information as the third dimension. Here we show the potential of fast finger pore imaging (FPI) in latent finger prints employing LD-MSI without a classical matrix in a high- spatial resolution mode. Thin films of gold rapidly sputtered on top of the sample are used for desorption. FPI employing an optical image for rapid spatial orientation and guiding of the desorption laser enables the rapid analysis of individual finger pores, and the chemical composition of their excretions. With this approach we rapidly detect metabolites, drugs, and characteristic excretions from the inside of the human organism by a minimally-invasive strategy, and distinguish them from chemicals in contact with fingers without any labeling. The fast finger pore imaging, analysis, and screening approach opens the door for a vast number of novel applications in such different fields as forensics, doping and medication control, therapy, as well as rapid profiling of individuals.

Thiol trapping and metabolic redistribution of sulfur metabolites enable cells to overcome cysteine overload

PubMed Central

Deshpande, Anup Arunrao; Bhatia, Muskan; Laxman, Sunil; Bachhawat, Anand Kumar

2017-01-01

Cysteine is an essential requirement in living organisms. However, due to its reactive thiol side chain, elevated levels of intracellular cysteine can be toxic and therefore need to be rapidly eliminated from the cellular milieu. In mammals and many other organisms, excess cysteine is believed to be primarily eliminated by the cysteine dioxygenase dependent oxidative degradation of cysteine, followed by the removal of the oxidative products. However, other mechanisms of tackling excess cysteine are also likely to exist, but have not thus far been explored. In this study, we use Saccharomyces cerevisiae, which naturally lacks a cysteine dioxygenase, to investigate mechanisms for tackling cysteine overload. Overexpressing the high affinity cysteine transporter, YCT1, enabled yeast cells to rapidly accumulate high levels of intracellular cysteine. Using targeted metabolite analysis, we observe that cysteine is initially rapidly interconverted to non-reactive cystine in vivo. A time course revealed that cells systematically convert excess cysteine to inert thiol forms; initially to cystine, and subsequently to cystathionine, S-Adenosyl-L-homocysteine (SAH) and S-Adenosyl L-methionine (SAM), in addition to eventually accumulating glutathione (GSH) and polyamines. Microarray based gene expression studies revealed the upregulation of arginine/ornithine biosynthesis a few hours after the cysteine overload, and suggest that the non-toxic, non-reactive thiol based metabolic products are eventually utilized for amino acid and polyamine biogenesis, thereby enabling cell growth. Thus, cells can handle potentially toxic amounts of cysteine by a combination of thiol trapping, metabolic redistribution to non-reactive thiols and subsequent consumption for anabolism. PMID:28435838

Large-scale deep learning for robotically gathered imagery for science

NASA Astrophysics Data System (ADS)

Skinner, K.; Johnson-Roberson, M.; Li, J.; Iscar, E.

2016-12-01

With the explosion of computing power, the intelligence and capability of mobile robotics has dramatically increased over the last two decades. Today, we can deploy autonomous robots to achieve observations in a variety of environments ripe for scientific exploration. These platforms are capable of gathering a volume of data previously unimaginable. Additionally, optical cameras, driven by mobile phones and consumer photography, have rapidly improved in size, power consumption, and quality making their deployment cheaper and easier. Finally, in parallel we have seen the rise of large-scale machine learning approaches, particularly deep neural networks (DNNs), increasing the quality of the semantic understanding that can be automatically extracted from optical imagery. In concert this enables new science using a combination of machine learning and robotics. This work will discuss the application of new low-cost high-performance computing approaches and the associated software frameworks to enable scientists to rapidly extract useful science data from millions of robotically gathered images. The automated analysis of imagery on this scale opens up new avenues of inquiry unavailable using more traditional manual or semi-automated approaches. We will use a large archive of millions of benthic images gathered with an autonomous underwater vehicle to demonstrate how these tools enable new scientific questions to be posed.

Implementation of fluorescence confocal mosaicing microscopy by "early adopter" Mohs surgeons: a review of recent progress

NASA Astrophysics Data System (ADS)

Jain, Manu; Rajadhyaksha, Milind; Nehal, Kishwer

2016-03-01

Confocal mosaicing microscopy (CMM) enables rapid imaging of large areas of fresh tissue ex vivo without the processing that is necessary for conventional histology. When performed with fluorescence mode using acridine orange (nuclear specific dye) it enhances nuclei-to-dermis contrast that enables detection of all types of BCCs including thin strands of infiltrative basal cell carcinomas (BCCs). Thus far, this technique has been mostly validated in research setting for the analysis of BCC tumor margins. Recently, CMM has been adopted and implemented in real clinical settings by some surgeons as an alternative tool to frozen section (FS) during Mohs surgery. In this review article we summarize the development of CMM guided imaging of ex vivo tissues from bench to bedside. We also present its current state of application in routine clinical workflow not only for the assessment of BCC margin but also for other skin cancers such as melanoma, SCC, and some infectious diseases where FS is not routinely performed. Lastly, we also discuss the potential limitations of this technology as well as future developments. As this technology advances further, it may serve as an adjunct to standard histology and enable rapid surgical pathology of skin cancers at the bedside.

Rapid quantification and sex determination of forensic evidence materials.

PubMed

Andréasson, Hanna; Allen, Marie

2003-11-01

DNA quantification of forensic evidence is very valuable for an optimal use of the available biological material. Moreover, sex determination is of great importance as additional information in criminal investigations as well as in identification of missing persons, no suspect cases, and ancient DNA studies. While routine forensic DNA analysis based on short tandem repeat markers includes a marker for sex determination, analysis of samples containing scarce amounts of DNA is often based on mitochondrial DNA, and sex determination is not performed. In order to allow quantification and simultaneous sex determination on minute amounts of DNA, an assay based on real-time PCR analysis of a marker within the human amelogenin gene has been developed. The sex determination is based on melting curve analysis, while an externally standardized kinetic analysis allows quantification of the nuclear DNA copy number in the sample. This real-time DNA quantification assay has proven to be highly sensitive, enabling quantification of single DNA copies. Although certain limitations were apparent, the system is a rapid, cost-effective, and flexible assay for analysis of forensic casework samples.

Hyperspectral image analysis for rapid and accurate discrimination of bacterial infections: A benchmark study.

PubMed

Arrigoni, Simone; Turra, Giovanni; Signoroni, Alberto

2017-09-01

With the rapid diffusion of Full Laboratory Automation systems, Clinical Microbiology is currently experiencing a new digital revolution. The ability to capture and process large amounts of visual data from microbiological specimen processing enables the definition of completely new objectives. These include the direct identification of pathogens growing on culturing plates, with expected improvements in rapid definition of the right treatment for patients affected by bacterial infections. In this framework, the synergies between light spectroscopy and image analysis, offered by hyperspectral imaging, are of prominent interest. This leads us to assess the feasibility of a reliable and rapid discrimination of pathogens through the classification of their spectral signatures extracted from hyperspectral image acquisitions of bacteria colonies growing on blood agar plates. We designed and implemented the whole data acquisition and processing pipeline and performed a comprehensive comparison among 40 combinations of different data preprocessing and classification techniques. High discrimination performance has been achieved also thanks to improved colony segmentation and spectral signature extraction. Experimental results reveal the high accuracy and suitability of the proposed approach, driving the selection of most suitable and scalable classification pipelines and stimulating clinical validations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gold nanoparticle-sensitized quartz crystal microbalance sensor for rapid and highly selective determination of Cu(II) ions.

PubMed

Jin, Yulong; Huang, Yanyan; Liu, Guoquan; Zhao, Rui

2013-09-21

A novel quartz crystal microbalance (QCM) sensor for rapid, highly selective and sensitive detection of copper ions was developed. As a signal amplifier, gold nanoparticles (Au NPs) were self-assembled onto the surface of the sensor. A simple dip-and-dry method enabled the whole detection procedure to be accomplished within 20 min. High selectivity of the sensor towards copper ions is demonstrated by both individual and coexisting assays with interference ions. This gold nanoparticle mediated amplification allowed a detection limit down to 3.1 μM. Together with good repeatability and regeneration, the QCM sensor was also applied to the analysis of copper contamination in drinking water. This work provides a flexible method for fabricating QCM sensors for the analysis of important small molecules in environmental and biological samples.

Investigation of Capabilities and Technologies Supporting Rapid UAV Launch System Development

DTIC Science & Technology

2015-06-01

NUMBERS 6. AUTHOR(S) Patrick Alan Livesay 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Naval Postgraduate School Monterey, CA 93943 8. PERFORMING ...to operate. This enabled the launcher design team to more clearly determine and articulate system require- ments and performance parameters. Next, a...Process (AHP) was performed to xvii prioritize the capabilities and assist in the decision-making process [1]. The AHP decision-analysis technique is

Enabling Technologies for Unified Life-Cycle Engineering of Structural Components

DTIC Science & Technology

1991-03-22

representations for entities in the ULCE system for unambiguous, reliable, and efficient retrieval, manipulation, and transfer of data. Develop a rapid analysis...approaches to these functions. It is reasonable to assume that program budgets for future systems will be more restrictive and that fixed- price contracting...enemy threats, economics, and politics. The requirements are voluminous and may stipulate firm fixed- price proposals with detailed schedules. At this

Size-tunable copper nanocluster aggregates and their application in hydrogen sulfide sensing on paper-based devices

NASA Astrophysics Data System (ADS)

Chen, Po-Cheng; Li, Yu-Chi; Ma, Jia-Yin; Huang, Jia-Yu; Chen, Chien-Fu; Chang, Huan-Tsung

2016-04-01

Polystyrene sulfonate (PSS), a strong polyelectrolyte, was used to prepare red photoluminescent PSS-penicillamine (PA) copper (Cu) nanoclusters (NC) aggregates, which displayed high selectivity and sensitivity to the detection of hydrogen sulfide (H2S). The size of the PSS-PA-Cu NC aggregates could be readily controlled from 5.5 μm to 173 nm using different concentrations of PSS, which enabled better dispersity and higher sensitivity towards H2S. PSS-PA-Cu NC aggregates provided rapid H2S detection by using the strong Cu-S interaction to quench NC photoluminescence as a sensing mechanism. As a result, a detection limit of 650 nM, which is lower than the maximum level permitted in drinking water by the World Health Organization, was achieved for the analysis of H2S in spring-water samples. Moreover, highly dispersed PSS-PA-Cu NC aggregates could be incorporated into a plate-format paper-based analytical device which enables ultra-low sample volumes (5 μL) and feature shorter analysis times (30 min) compared to conventional solution-based methods. The advantages of low reagent consumption, rapid result readout, limited equipment, and long-term storage make this platform sensitive and simple enough to use without specialized training in resource constrained settings.

Systems-Level Analysis of Innate Immunity

PubMed Central

Zak, Daniel E.; Tam, Vincent C.; Aderem, Alan

2014-01-01

Systems-level analysis of biological processes strives to comprehensively and quantitatively evaluate the interactions between the relevant molecular components over time, thereby enabling development of models that can be employed to ultimately predict behavior. Rapid development in measurement technologies (omics), when combined with the accessible nature of the cellular constituents themselves, is allowing the field of innate immunity to take significant strides toward this lofty goal. In this review, we survey exciting results derived from systems biology analyses of the immune system, ranging from gene regulatory networks to influenza pathogenesis and systems vaccinology. PMID:24655298

Nanoporous Glass Integrated in Volumetric Bar-Chart Chip for Point-of-Care Diagnostics of Non-Small Cell Lung Cancer.

PubMed

Li, Ying; Xuan, Jie; Song, Yujun; Qi, Wenjin; He, Bangshun; Wang, Ping; Qin, Lidong

2016-01-26

Point-of-care (POC) testing has the potential to enable rapid, low-cost, and large-scale screening. POC detection of a multiplexed biomarker panel can facilitate the early diagnosis of non-small cell lung cancer (NSCLC) and, thus, may allow for more timely surgical intervention for life-saving treatment. Herein, we report the nanoporous glass (NPG) integrated volumetric bar-chart chip (V-Chip) for POC detection of the three NSCLC biomarkers CEA, CYFRA 21-1, and SCCA, by the naked eye. The 3D nanostructures in the NPG membrane efficiently increase the number of binding sites for antibodies and decrease the diffusion distance between antibody and antigen, enabling the low detection limit and rapid analysis time of the NPG-V-Chip. We utilized the NPG-V-Chip to test the NSCLC biomarker panel and found that the limit of detection can reach 50 pg/mL (10-fold improvement over the original V-Chip), and the total assay time can be decreased from 4 to 0.5 h. We then detected CEA in 21 serum samples from patients with common cancers, and the on-chip results showed good correlation with the clinical results. We further assayed 10 lung cancer samples using the device and confirmed the results obtained using conventional ELISA methods. In summary, the NPG-V-Chip platform has the ability of multiplex, low detection limit, low cost, lack of need for accessory equipment, and rapid analysis time, which may render the V-Chip a useful platform for quantitative POC detection in resource-limited settings and personalized diagnostics.

Supporting tactical intelligence using collaborative environments and social networking

NASA Astrophysics Data System (ADS)

Wollocko, Arthur B.; Farry, Michael P.; Stark, Robert F.

2013-05-01

Modern military environments place an increased emphasis on the collection and analysis of intelligence at the tactical level. The deployment of analytical tools at the tactical level helps support the Warfighter's need for rapid collection, analysis, and dissemination of intelligence. However, given the lack of experience and staffing at the tactical level, most of the available intelligence is not exploited. Tactical environments are staffed by a new generation of intelligence analysts who are well-versed in modern collaboration environments and social networking. An opportunity exists to enhance tactical intelligence analysis by exploiting these personnel strengths, but is dependent on appropriately designed information sharing technologies. Existing social information sharing technologies enable users to publish information quickly, but do not unite or organize information in a manner that effectively supports intelligence analysis. In this paper, we present an alternative approach to structuring and supporting tactical intelligence analysis that combines the benefits of existing concepts, and provide detail on a prototype system embodying that approach. Since this approach employs familiar collaboration support concepts from social media, it enables new-generation analysts to identify the decision-relevant data scattered among databases and the mental models of other personnel, increasing the timeliness of collaborative analysis. Also, the approach enables analysts to collaborate visually to associate heterogeneous and uncertain data within the intelligence analysis process, increasing the robustness of collaborative analyses. Utilizing this familiar dynamic collaboration environment, we hope to achieve a significant reduction of time and skill required to glean actionable intelligence in these challenging operational environments.

Harnessing Whole Genome Sequencing in Medical Mycology.

PubMed

Cuomo, Christina A

2017-01-01

Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens. Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species. The scale and scope of species sequenced is rapidly expanding, leveraging technological advances to assemble and annotate genomes with higher precision. By using iteratively improved reference assemblies or those generated de novo for new species, recent studies have compared the sequence of isolates representing populations or clinical cohorts. Whole genome approaches provide the resolution necessary for comparison of closely related isolates, for example, in the analysis of outbreaks or sampled across time within a single host. Genomic analysis of fungal pathogens has enabled both basic research and diagnostic studies. The increased scale of sequencing can be applied across populations, and new metagenomic methods allow direct analysis of complex samples.

Utilizing Fission Technology to Enable Rapid and Affordable Access to any Point in the Solar System

NASA Technical Reports Server (NTRS)

Houts, Mike; Bonometti, Joe; Morton, Jeff; Hrbud, Ivana; Bitteker, Leo; VanDyke, Melissa; Godfroy, T.; Pedersen, K.; Dobson, C.; Patton, B.;

Emerging microengineering tools for functional analysis and phenotyping of blood cells

PubMed Central

Li, Xiang; Chen, Weiqiang; Li, Zida; Li, Ling; Gu, Hongchen; Fu, Jianping

2014-01-01

The available techniques for assessing blood cell functions are limited considering the various types of blood cells and their diverse functions. In the past decade, rapid advancement in microengineering has enabled an array of blood cell functional measurements that are difficult or impossible to achieve using conventional bulk platforms. Such miniaturized blood cell assay platforms also provide attractive capabilities of reducing chemical consumption, cost, assay time, as well as exciting opportunities of device integration, automation, and assay standardization. This review summarizes these contemporary microengineering tools and discusses their promising potential for constructing accurate in vitro models and rapid clinical diagnosis using minimal amount of whole blood samples. PMID:25283971

Statistical Methods for Rapid Aerothermal Analysis and Design Technology: Validation

NASA Technical Reports Server (NTRS)

DePriest, Douglas; Morgan, Carolyn

2003-01-01

The cost and safety goals for NASA s next generation of reusable launch vehicle (RLV) will require that rapid high-fidelity aerothermodynamic design tools be used early in the design cycle. To meet these requirements, it is desirable to identify adequate statistical models that quantify and improve the accuracy, extend the applicability, and enable combined analyses using existing prediction tools. The initial research work focused on establishing suitable candidate models for these purposes. The second phase is focused on assessing the performance of these models to accurately predict the heat rate for a given candidate data set. This validation work compared models and methods that may be useful in predicting the heat rate.

Large-scale Parallel Unstructured Mesh Computations for 3D High-lift Analysis

NASA Technical Reports Server (NTRS)

Mavriplis, Dimitri J.; Pirzadeh, S.

1999-01-01

A complete "geometry to drag-polar" analysis capability for the three-dimensional high-lift configurations is described. The approach is based on the use of unstructured meshes in order to enable rapid turnaround for complicated geometries that arise in high-lift configurations. Special attention is devoted to creating a capability for enabling analyses on highly resolved grids. Unstructured meshes of several million vertices are initially generated on a work-station, and subsequently refined on a supercomputer. The flow is solved on these refined meshes on large parallel computers using an unstructured agglomeration multigrid algorithm. Good prediction of lift and drag throughout the range of incidences is demonstrated on a transport take-off configuration using up to 24.7 million grid points. The feasibility of using this approach in a production environment on existing parallel machines is demonstrated, as well as the scalability of the solver on machines using up to 1450 processors.

Drop-on-Demand Single Cell Isolation and Total RNA Analysis

PubMed Central

Moon, Sangjun; Kim, Yun-Gon; Dong, Lingsheng; Lombardi, Michael; Haeggstrom, Edward; Jensen, Roderick V.; Hsiao, Li-Li; Demirci, Utkan

2011-01-01

Technologies that rapidly isolate viable single cells from heterogeneous solutions have significantly contributed to the field of medical genomics. Challenges remain both to enable efficient extraction, isolation and patterning of single cells from heterogeneous solutions as well as to keep them alive during the process due to a limited degree of control over single cell manipulation. Here, we present a microdroplet based method to isolate and pattern single cells from heterogeneous cell suspensions (10% target cell mixture), preserve viability of the extracted cells (97.0±0.8%), and obtain genomic information from isolated cells compared to the non-patterned controls. The cell encapsulation process is both experimentally and theoretically analyzed. Using the isolated cells, we identified 11 stem cell markers among 1000 genes and compare to the controls. This automated platform enabling high-throughput cell manipulation for subsequent genomic analysis employs fewer handling steps compared to existing methods. PMID:21412416

Fast Metabolic Response to Drug Intervention through Analysis on a Miniaturized, Highly Integrated Molecular Imaging System

PubMed Central

Wang, Jun; Hwang, Kiwook; Braas, Daniel; Dooraghi, Alex; Nathanson, David; Campbell, Dean O.; Gu, Yuchao; Sandberg, Troy; Mischel, Paul; Radu, Caius; Chatziioannou, Arion F.; Phelps, Michael E.; Christofk, Heather; Heath, James R.

2014-01-01

We report on a radiopharmaceutical imaging platform designed to capture the kinetics of cellular responses to drugs. Methods A portable in vitro molecular imaging system, comprised of a microchip and a beta-particle imaging camera, permits routine cell-based radioassays on small number of either suspension or adherent cells. We investigate the response kinetics of model lymphoma and glioblastoma cancer cell lines to [18F]fluorodeoxyglucose ([18F]FDG) uptake following drug exposure. Those responses are correlated with kinetic changes in the cell cycle, or with changes in receptor-tyrosine kinase signaling. Results The platform enables radioassays directly on multiple cell types, and yields results comparable to conventional approaches, but uses smaller sample sizes, permits a higher level of quantitation, and doesn’t require cell lysis. Conclusion The kinetic analysis enabled by the platform provides a rapid (~1 hour) drug screening assay. PMID:23978446

Rapid LC-MS/MS quantification of the major benzodiazepines and their metabolites on dried blood spots using a simple and cost-effective sample pretreatment.

PubMed

Déglon, Julien; Versace, François; Lauer, Estelle; Widmer, Christèle; Mangin, Patrice; Thomas, Aurélien; Staub, Christian

2012-06-01

Dried blood spots (DBS) sampling has gained popularity in the bioanalytical community as an alternative to conventional plasma sampling, as it provides numerous benefits in terms of sample collection and logistics. The aim of this work was to show that these advantages can be coupled with a simple and cost-effective sample pretreatment, with subsequent rapid LC-MS/MS analysis for quantitation of 15 benzodiazepines, six metabolites and three Z-drugs. For this purpose, a simplified offline procedure was developed that consisted of letting a 5-µl DBS infuse directly into 100 µl of MeOH, in a conventional LC vial. The parameters related to the DBS pretreatment, such as extraction time or internal standard addition, were investigated and optimized, demonstrating that passive infusion in a regular LC vial was sufficient to quantitatively extract the analytes of interest. The method was validated according to international criteria in the therapeutic concentration ranges of the selected compounds. The presented strategy proved to be efficient for the rapid analysis of the selected drugs. Indeed, the offline sample preparation was reduced to a minimum, using a small amount of organic solvent and consumables, without affecting the accuracy of the method. Thus, this approach enables simple and rapid DBS analysis, even when using a non-DBS-dedicated autosampler, while lowering the costs and environmental impact.

Whispering Gallery Mode Resonators for Rapid Label-Free Biosensing in Small Volume Droplets

PubMed Central

Wildgen, Sarah M.; Dunn, Robert C.

2015-01-01

Rapid biosensing requires fast mass transport of the analyte to the surface of the sensing element. To optimize analysis times, both mass transport in solution and the geometry and size of the sensing element need to be considered. Small dielectric spheres, tens of microns in diameter, can act as label-free biosensors using whispering gallery mode (WGM) resonances. WGM resonances are sensitive to the effective refractive index, which changes upon analyte binding to recognition sites on functionalized resonators. The spherical geometry and tens of microns diameter of these resonators provides an efficient target for sensing while their compact size enables detection in limited volumes. Here, we explore conditions leading to rapid analyte detection using WGM resonators as label-free sensors in 10 μL sample droplets. Droplet evaporation leads to potentially useful convective mixing, but also limits the time over which analysis can be completed. We show that active droplet mixing combined with initial binding rate measurements is required for accurate nanomolar protein quantification within the first minute following injection. PMID:25806835

Towards a tolerance toolkit: Gene expression signatures enabling the emergence of resistant bacterial strains

NASA Astrophysics Data System (ADS)

Erickson, Keesha; Chatterjee, Anushree

2014-03-01

Microbial pathogens are able to rapidly acquire tolerance to chemical toxins. Developing next-generation antibiotics that impede the emergence of resistance will help avoid a world-wide health crisis. Conversely, the ability to induce rapid tolerance gains could lead to high-yielding strains for sustainable production of biofuels and commodity chemicals. Achieving these goals requires an understanding of the general mechanisms allowing microbes to become resistant to diverse toxins. We apply top-down and bottom-up methodologies to identify biological network changes leading to adaptation and tolerance. Using a top-down approach, we perform evolution experiments to isolate resistant strains, collect samples for transcriptomic and proteomic analysis, and use the omics data to inform mathematical gene regulatory models. Using a bottom-up approach, we build and test synthetic genetic devices that enable increased or decreased expression of selected genes. Unique patterns in gene expression are identified in cultures actively gaining resistance, especially in pathways known to be involved with stress response, efflux, and mutagenesis. Genes correlated with tolerance could potentially allow the design of resistance-free antibiotics or robust chemical production strains.

Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle

PubMed Central

Mosadeghi, Ruzbeh; Reichermeier, Kurt M; Winkler, Martin; Schreiber, Anne; Reitsma, Justin M; Zhang, Yaru; Stengel, Florian; Cao, Junyue; Kim, Minsoo; Sweredoski, Michael J; Hess, Sonja; Leitner, Alexander; Aebersold, Ruedi; Peter, Matthias; Deshaies, Raymond J; Enchev, Radoslav I

2016-01-01

The COP9-Signalosome (CSN) regulates cullin–RING ubiquitin ligase (CRL) activity and assembly by cleaving Nedd8 from cullins. Free CSN is autoinhibited, and it remains unclear how it becomes activated. We combine structural and kinetic analyses to identify mechanisms that contribute to CSN activation and Nedd8 deconjugation. Both CSN and neddylated substrate undergo large conformational changes upon binding, with important roles played by the N-terminal domains of Csn2 and Csn4 and the RING domain of Rbx1 in enabling formation of a high affinity, fully active complex. The RING domain is crucial for deneddylation, and works in part through conformational changes involving insert-2 of Csn6. Nedd8 deconjugation and re-engagement of the active site zinc by the autoinhibitory Csn5 glutamate-104 diminish affinity for Cul1/Rbx1 by ~100-fold, resulting in its rapid ejection from the active site. Together, these mechanisms enable a dynamic deneddylation-disassembly cycle that promotes rapid remodeling of the cellular CRL network. DOI: http://dx.doi.org/10.7554/eLife.12102.001 PMID:27031283

High-Throughput Image Analysis of Fibrillar Materials: A Case Study on Polymer Nanofiber Packing, Alignment, and Defects in Organic Field Effect Transistors.

PubMed

Persson, Nils E; Rafshoon, Joshua; Naghshpour, Kaylie; Fast, Tony; Chu, Ping-Hsun; McBride, Michael; Risteen, Bailey; Grover, Martha; Reichmanis, Elsa

2017-10-18

High-throughput discovery of process-structure-property relationships in materials through an informatics-enabled empirical approach is an increasingly utilized technique in materials research due to the rapidly expanding availability of data. Here, process-structure-property relationships are extracted for the nucleation, growth, and deposition of semiconducting poly(3-hexylthiophene) (P3HT) nanofibers used in organic field effect transistors, via high-throughput image analysis. This study is performed using an automated image analysis pipeline combining existing open-source software and new algorithms, enabling the rapid evaluation of structural metrics for images of fibrillar materials, including local orientational order, fiber length density, and fiber length distributions. We observe that microfluidic processing leads to fibers that pack with unusually high density, while sonication yields fibers that pack sparsely with low alignment. This is attributed to differences in their crystallization mechanisms. P3HT nanofiber packing during thin film deposition exhibits behavior suggesting that fibers are confined to packing in two-dimensional layers. We find that fiber alignment, a feature correlated with charge carrier mobility, is driven by increasing fiber length, and that shorter fibers tend to segregate to the buried dielectric interface during deposition, creating potentially performance-limiting defects in alignment. Another barrier to perfect alignment is the curvature of P3HT fibers; we propose a mechanistic simulation of fiber growth that reconciles both this curvature and the log-normal distribution of fiber lengths inherent to the fiber populations under consideration.

Metabolomic fingerprinting employing DART-TOFMS for authentication of tomatoes and peppers from organic and conventional farming.

PubMed

Novotná, H; Kmiecik, O; Gałązka, M; Krtková, V; Hurajová, A; Schulzová, V; Hallmann, E; Rembiałkowska, E; Hajšlová, J

2012-01-01

The rapidly growing demand for organic food requires the availability of analytical tools enabling their authentication. Recently, metabolomic fingerprinting/profiling has been demonstrated as a challenging option for a comprehensive characterisation of small molecules occurring in plants, since their pattern may reflect the impact of various external factors. In a two-year pilot study, concerned with the classification of organic versus conventional crops, ambient mass spectrometry consisting of a direct analysis in real time (DART) ion source and a time-of-flight mass spectrometer (TOFMS) was employed. This novel methodology was tested on 40 tomato and 24 pepper samples grown under specified conditions. To calculate statistical models, the obtained data (mass spectra) were processed by the principal component analysis (PCA) followed by linear discriminant analysis (LDA). The results from the positive ionisation mode enabled better differentiation between organic and conventional samples than the results from the negative mode. In this case, the recognition ability obtained by LDA was 97.5% for tomato and 100% for pepper samples and the prediction abilities were above 80% for both sample sets. The results suggest that the year of production had stronger influence on the metabolomic fingerprints compared with the type of farming (organic versus conventional). In any case, DART-TOFMS is a promising tool for rapid screening of samples. Establishing comprehensive (multi-sample) long-term databases may further help to improve the quality of statistical classification models.

Terrestrial Planet Finder Coronagraph and Enabling Technologies

NASA Technical Reports Server (NTRS)

Ford, Virginia G.

2005-01-01

Starlight suppression research is Stowed in Delta IV-H advancing rapidly to approach the required contrast ratio. The current analysis of the TPF Coronagraph system indicates that it is feasible to achieve the stability required by using developing technologies: a) Wave Front Sensing and Control (DMs, control algorithms, and sensing); b) Laser metrology. Yet needed: a) Property data measured with great precision in the required environments; b) Modeling tools that are verified with testbeds.

Wide-field Imaging System and Rapid Direction of Optical Zoom (WOZ)

DTIC Science & Technology

2010-09-25

commercial software packages: SolidWorks, COMSOL Multiphysics, and ZEMAX optical design. SolidWorks is a computer aided design package, which as a live...interface to COMSOL. COMSOL is a finite element analysis/partial differential equation solver. ZEMAX is an optical design package. Both COMSOL and... ZEMAX have live interfaces to MatLab. Our initial investigations have enabled a model in SolidWorks to be updated in COMSOL, an FEA calculation

LOOS: an extensible platform for the structural analysis of simulations.

PubMed

Romo, Tod D; Grossfield, Alan

2009-01-01

We have developed LOOS (Lightweight Object-Oriented Structure-analysis library) as an object-oriented library designed to facilitate the rapid development of tools for the structural analysis of simulations. LOOS supports the native file formats of most common simulation packages including AMBER, CHARMM, CNS, Gromacs, NAMD, Tinker, and X-PLOR. Encapsulation and polymorphism are used to simultaneously provide a stable interface to the programmer and make LOOS easily extensible. A rich atom selection language based on the C expression syntax is included as part of the library. LOOS enables students and casual programmer-scientists to rapidly write their own analytical tools in a compact and expressive manner resembling scripting. LOOS is written in C++ and makes extensive use of the Standard Template Library and Boost, and is freely available under the GNU General Public License (version 3) LOOS has been tested on Linux and MacOS X, but is written to be portable and should work on most Unix-based platforms.

Validation of a rapid DNA process with the RapidHIT® ID system using GlobalFiler® Express chemistry, a platform optimized for decentralized testing environments.

PubMed

Salceda, Susana; Barican, Arnaldo; Buscaino, Jacklyn; Goldman, Bruce; Klevenberg, Jim; Kuhn, Melissa; Lehto, Dennis; Lin, Frank; Nguyen, Phong; Park, Charles; Pearson, Francesca; Pittaro, Rick; Salodkar, Sayali; Schueren, Robert; Smith, Corey; Troup, Charles; Tsou, Dean; Vangbo, Mattias; Wunderle, Justus; King, David

2017-05-01

The RapidHIT ® ID is a fully automated sample-to-answer system for short tandem repeat (STR)-based human identification. The RapidHIT ID has been optimized for use in decentralized environments and processes presumed single source DNA samples, generating Combined DNA Index System (CODIS)-compatible DNA profiles in less than 90min. The system is easy to use, requiring less than one minute of hands-on time. Profiles are reviewed using centralized linking software, RapidLINK™ (IntegenX, Pleasanton, CA), a software tool designed to collate DNA profiles from single or multiple RapidHIT ID systems at different geographic locations. The RapidHIT ID has been designed to employ GlobalFiler ® Express and AmpFLSTR ® NGMSElect™, Thermo Fisher Scientific (Waltham, MA) STR chemistries. The Developmental Validation studies were performed using GlobalFiler ® Express with single source reference samples according to Scientific Working Group for DNA Analysis Methods guidelines. These results show that multiple RapidHIT ID systems networked with RapidLINK software form a highly reliable system for wide-scale deployment in locations such as police booking stations and border crossings enabling real-time testing of arrestees, potential human trafficking victims, and other instances where rapid turnaround is essential. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

The promise and challenge of high-throughput sequencing of the antibody repertoire

PubMed Central

Georgiou, George; Ippolito, Gregory C; Beausang, John; Busse, Christian E; Wardemann, Hedda; Quake, Stephen R

2014-01-01

Efforts to determine the antibody repertoire encoded by B cells in the blood or lymphoid organs using high-throughput DNA sequencing technologies have been advancing at an extremely rapid pace and are transforming our understanding of humoral immune responses. Information gained from high-throughput DNA sequencing of immunoglobulin genes (Ig-seq) can be applied to detect B-cell malignancies with high sensitivity, to discover antibodies specific for antigens of interest, to guide vaccine development and to understand autoimmunity. Rapid progress in the development of experimental protocols and informatics analysis tools is helping to reduce sequencing artifacts, to achieve more precise quantification of clonal diversity and to extract the most pertinent biological information. That said, broader application of Ig-seq, especially in clinical settings, will require the development of a standardized experimental design framework that will enable the sharing and meta-analysis of sequencing data generated by different laboratories. PMID:24441474

Metal speciation of environmental samples using SPE and SFC-AED analysis

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

Mitchell, S.C.; Burford, M.D.; Robson, M.

1995-12-31

Due to growing public concern over heavy metals in the environment, soil, water and air particulate samples azre now routinely screened for their metal content. Conventional metal analysis typically involves acid digestion extraction and results in the generation of large aqueous and organic solvent waste. This harsh extraction process is usually used to obtain the total metal content of the sample, the extract being analysed by atomic emission or absorption spectroscoply techniques. A more selective method of metal extraction has been investigated which uses a supercritical fluid modified with a complexing agent. The relatively mild extraction method enables both organometallicmore » and inorganic metal species to be recovered intact. The various components from the supercritical fluid extract can be chromatographically separated using supercritical fluid chromatography (SFC) and positive identification of the metals achieved using atomic emission detection (AED). The aim of the study is to develop an analytical extraction procedure which enables a rapid, sensitive and quantitative analysis of metals in environmental samples, using just one extraction (eg SFE) and one analysis (eg SFC-AED) procedure.« less

Work flow analysis of around-the-clock processing of blood culture samples and integrated MALDI-TOF mass spectrometry analysis for the diagnosis of bloodstream infections.

PubMed

Schneiderhan, Wilhelm; Grundt, Alexander; Wörner, Stefan; Findeisen, Peter; Neumaier, Michael

2013-11-01

Because sepsis has a high mortality rate, rapid microbiological diagnosis is required to enable efficient therapy. The effectiveness of MALDI-TOF mass spectrometry (MALDI-TOF MS) analysis in reducing turnaround times (TATs) for blood culture (BC) pathogen identification when available in a 24-h hospital setting has not been determined. On the basis of data from a total number of 912 positive BCs collected within 140 consecutive days and work flow analyses of laboratory diagnostics, we evaluated different models to assess the TATs for batch-wise and for immediate response (real-time) MALDI-TOF MS pathogen identification of positive BC results during the night shifts. The results were compared to TATs from routine BC processing and biochemical identification performed during regular working hours. Continuous BC incubation together with batch-wise MALDI-TOF MS analysis enabled significant reductions of up to 58.7 h in the mean TATs for the reporting of the bacterial species. The TAT of batch-wise MALDI-TOF MS analysis was inferior by a mean of 4.9 h when compared to the model of the immediate work flow under ideal conditions with no constraints in staff availability. Together with continuous cultivation of BC, the 24-h availability of MALDI-TOF MS can reduce the TAT for microbial pathogen identification within a routine clinical laboratory setting. Batch-wise testing of positive BC loses a few hours compared to real-time identification but is still far superior to classical BC processing. Larger prospective studies are required to evaluate the contribution of rapid around-the-clock pathogen identification to medical decision-making for septicemic patients.

Developments in label-free microfluidic methods for single-cell analysis and sorting.

PubMed

Carey, Thomas R; Cotner, Kristen L; Li, Brian; Sohn, Lydia L

2018-04-24

Advancements in microfluidic technologies have led to the development of many new tools for both the characterization and sorting of single cells without the need for exogenous labels. Label-free microfluidics reduce the preparation time, reagents needed, and cost of conventional methods based on fluorescent or magnetic labels. Furthermore, these devices enable analysis of cell properties such as mechanical phenotype and dielectric parameters that cannot be characterized with traditional labels. Some of the most promising technologies for current and future development toward label-free, single-cell analysis and sorting include electronic sensors such as Coulter counters and electrical impedance cytometry; deformation analysis using optical traps and deformation cytometry; hydrodynamic sorting such as deterministic lateral displacement, inertial focusing, and microvortex trapping; and acoustic sorting using traveling or standing surface acoustic waves. These label-free microfluidic methods have been used to screen, sort, and analyze cells for a wide range of biomedical and clinical applications, including cell cycle monitoring, rapid complete blood counts, cancer diagnosis, metastatic progression monitoring, HIV and parasite detection, circulating tumor cell isolation, and point-of-care diagnostics. Because of the versatility of label-free methods for characterization and sorting, the low-cost nature of microfluidics, and the rapid prototyping capabilities of modern microfabrication, we expect this class of technology to continue to be an area of high research interest going forward. New developments in this field will contribute to the ongoing paradigm shift in cell analysis and sorting technologies toward label-free microfluidic devices, enabling new capabilities in biomedical research tools as well as clinical diagnostics. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices. © 2018 Wiley Periodicals, Inc.

Application development environment for advanced digital workstations

NASA Astrophysics Data System (ADS)

Valentino, Daniel J.; Harreld, Michael R.; Liu, Brent J.; Brown, Matthew S.; Huang, Lu J.

1998-06-01

One remaining barrier to the clinical acceptance of electronic imaging and information systems is the difficulty in providing intuitive access to the information needed for a specific clinical task (such as reaching a diagnosis or tracking clinical progress). The purpose of this research was to create a development environment that enables the design and implementation of advanced digital imaging workstations. We used formal data and process modeling to identify the diagnostic and quantitative data that radiologists use and the tasks that they typically perform to make clinical decisions. We studied a diverse range of radiology applications, including diagnostic neuroradiology in an academic medical center, pediatric radiology in a children's hospital, screening mammography in a breast cancer center, and thoracic radiology consultation for an oncology clinic. We used object- oriented analysis to develop software toolkits that enable a programmer to rapidly implement applications that closely match clinical tasks. The toolkits support browsing patient information, integrating patient images and reports, manipulating images, and making quantitative measurements on images. Collectively, we refer to these toolkits as the UCLA Digital ViewBox toolkit (ViewBox/Tk). We used the ViewBox/Tk to rapidly prototype and develop a number of diverse medical imaging applications. Our task-based toolkit approach enabled rapid and iterative prototyping of workstations that matched clinical tasks. The toolkit functionality and performance provided a 'hands-on' feeling for manipulating images, and for accessing textual information and reports. The toolkits directly support a new concept for protocol based-reading of diagnostic studies. The design supports the implementation of network-based application services (e.g., prefetching, workflow management, and post-processing) that will facilitate the development of future clinical applications.

Alignment-free design of highly discriminatory diagnostic primer sets for Escherichia coli O104:H4 outbreak strains.

PubMed

Pritchard, Leighton; Holden, Nicola J; Bielaszewska, Martina; Karch, Helge; Toth, Ian K

2012-01-01

An Escherichia coli O104:H4 outbreak in Germany in summer 2011 caused 53 deaths, over 4000 individual infections across Europe, and considerable economic, social and political impact. This outbreak was the first in a position to exploit rapid, benchtop high-throughput sequencing (HTS) technologies and crowdsourced data analysis early in its investigation, establishing a new paradigm for rapid response to disease threats. We describe a novel strategy for design of diagnostic PCR primers that exploited this rapid draft bacterial genome sequencing to distinguish between E. coli O104:H4 outbreak isolates and other pathogenic E. coli isolates, including the historical hæmolytic uræmic syndrome (HUSEC) E. coli HUSEC041 O104:H4 strain, which possesses the same serotype as the outbreak isolates. Primers were designed using a novel alignment-free strategy against eleven draft whole genome assemblies of E. coli O104:H4 German outbreak isolates from the E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium website, and a negative sequence set containing 69 E. coli chromosome and plasmid sequences from public databases. Validation in vitro against 21 'positive' E. coli O104:H4 outbreak and 32 'negative' non-outbreak EHEC isolates indicated that individual primer sets exhibited 100% sensitivity for outbreak isolates, with false positive rates of between 9% and 22%. A minimal combination of two primers discriminated between outbreak and non-outbreak E. coli isolates with 100% sensitivity and 100% specificity. Draft genomes of isolates of disease outbreak bacteria enable high throughput primer design and enhanced diagnostic performance in comparison to traditional molecular assays. Future outbreak investigations will be able to harness HTS rapidly to generate draft genome sequences and diagnostic primer sets, greatly facilitating epidemiology and clinical diagnostics. We expect that high throughput primer design strategies will enable faster, more precise responses to future disease outbreaks of bacterial origin, and help to mitigate their societal impact.

Enabling Microfluidics: From Clean Rooms to Makerspaces

DTIC Science & Technology

2016-09-30

anyone can make 133 and rapidly scale to bulk manufacturing . To enable others to take part in this type of product 134 design and development, we...cost molds for a fee; however, the 77 design process is slowed down waiting for molds to be manufactured and shipped. While 78 PDMS devices may be...finished prototype into a commercial product . An example of a rapid 101 prototyping method amenable to scaled-up manufacturing is laser cutting. Figure

Rapid Technology Assessment via Unified Deployment of Global Optical and Virtual Diagnostics

NASA Technical Reports Server (NTRS)

Jordan, Jeffrey D.; Watkins, A. Neal; Fleming, Gary A.; Leighty, Bradley D.; Schwartz, Richard J.; Ingram, JoAnne L.; Grinstead, Keith D., Jr.; Oglesby, Donald M.; Tyler, Charles

2003-01-01

This paper discusses recent developments in rapid technology assessment resulting from an active collaboration between researchers at the Air Force Research Laboratory (AFRL) at Wright Patterson Air Force Base (WPAFB) and the NASA Langley Research Center (LaRC). This program targets the unified development and deployment of global measurement technologies coupled with a virtual diagnostic interface to enable the comparative evaluation of experimental and computational results. Continuing efforts focus on the development of seamless data translation methods to enable integration of data sets of disparate file format in a common platform. Results from a successful low-speed wind tunnel test at WPAFB in which global surface pressure distributions were acquired simultaneously with model deformation and geometry measurements are discussed and comparatively evaluated with numerical simulations. Intensity- and lifetime-based pressure-sensitive paint (PSP) and projection moire interferometry (PMI) results are presented within the context of rapid technology assessment to enable simulation-based R&D.

A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis

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

Larimer, Curtis J.; Winder, Eric M.; Jeters, Robert T.

Here, the accumulation of bacteria in surface attached biofilms, or biofouling, can be detrimental to human health, dental hygiene, and many industrial processes. A critical need in identifying and preventing the deleterious effects of biofilms is the ability to observe and quantify their development. Analytical methods capable of assessing early stage fouling are cumbersome or lab-confined, subjective, and qualitative. Herein, a novel photographic method is described that uses biomolecular staining and image analysis to enhance contrast of early stage biofouling. A robust algorithm was developed to objectively and quantitatively measure surface accumulation of Pseudomonas putida from photographs and results weremore » compared to independent measurements of cell density. Results from image analysis quantified biofilm growth intensity accurately and with approximately the same precision of the more laborious cell counting method. This simple method for early stage biofilm detection enables quantifiable measurement of surface fouling and is flexible enough to be applied from the laboratory to the field. Broad spectrum staining highlights fouling biomass, photography quickly captures a large area of interest, and image analysis rapidly quantifies fouling in the image.« less

A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis

DOE PAGES

Larimer, Curtis J.; Winder, Eric M.; Jeters, Robert T.; ...

2015-12-07

Here, the accumulation of bacteria in surface attached biofilms, or biofouling, can be detrimental to human health, dental hygiene, and many industrial processes. A critical need in identifying and preventing the deleterious effects of biofilms is the ability to observe and quantify their development. Analytical methods capable of assessing early stage fouling are cumbersome or lab-confined, subjective, and qualitative. Herein, a novel photographic method is described that uses biomolecular staining and image analysis to enhance contrast of early stage biofouling. A robust algorithm was developed to objectively and quantitatively measure surface accumulation of Pseudomonas putida from photographs and results weremore » compared to independent measurements of cell density. Results from image analysis quantified biofilm growth intensity accurately and with approximately the same precision of the more laborious cell counting method. This simple method for early stage biofilm detection enables quantifiable measurement of surface fouling and is flexible enough to be applied from the laboratory to the field. Broad spectrum staining highlights fouling biomass, photography quickly captures a large area of interest, and image analysis rapidly quantifies fouling in the image.« less

Basal forebrain neuronal inhibition enables rapid behavioral stopping

PubMed Central

Mayse, Jeffrey D.; Nelson, Geoffrey M.; Avila, Irene; Gallagher, Michela; Lin, Shih-Chieh

2015-01-01

Cognitive inhibitory control, the ability to rapidly suppress responses inappropriate for the context, is essential for flexible and adaptive behavior. While most studies on inhibitory control have focused on the fronto-basal-ganglia circuit, here we explore a novel hypothesis and show that rapid behavioral stopping is enabled by neuronal inhibition in the basal forebrain (BF). In rats performing the stop signal task, putative noncholinergic BF neurons with phasic bursting responses to the go signal were inhibited nearly completely by the stop signal. The onset of BF neuronal inhibition was tightly coupled with and temporally preceded the latency to stop, the stop signal reaction time. Artificial inhibition of BF activity in the absence of the stop signal was sufficient to reproduce rapid behavioral stopping. These results reveal a novel subcortical mechanism of rapid inhibitory control by the BF, which provides bidirectional control over the speed of response generation and inhibition. PMID:26368943

Connection Analysis of Different Modes in Multimodal Transport

NASA Astrophysics Data System (ADS)

Zhao, Zhi; Lu, Ya Ya; Liu, Xing Hua; Jiang, Ying; Zhang, Yan Zhou

2018-06-01

As the most advanced way of transport organization, container multimodal transport provides high quality and efficient systematic logistics transportation services in a wide range of freight transport activities. So it has been widely promoted worldwide. China is in a period of sustained and rapid economic development, which needs greater support from logistics, while the rationalization of multimodal transport enables the best transport area of each transportation mode to be reflected. This paper makes an analysis of the connection between united transportation of railway and highway, rail and water transport and untied transportation of highway and water.

Analysis of fatty acids by graphite plate laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Park, K H; Kim, H J

2001-01-01

Fatty acids obtained from triglycerides (trioelin, tripalmitin), foods (milk, corn oil), and phospholipids (phosphotidylcholine, phosphotidylserine, phosphatidic acid) upon alkaline hydrolysis were observed directly without derivatization by graphite plate laser desorption/ionization time-of-flight mass spectrometry (GPLDI-TOFMS). Mass-to-charge ratios predicted for sodium adducts of expected fatty acids (e.g. palmitic, oleic, linoleic and arachidonic acids) were observed without interference. Although at present no quantitation is possible, the graphite plate method enables a simple and rapid qualitative analysis of fatty acids. Copyright 2001 John Wiley & Sons, Ltd.

[Pleural effusion: diagnosis and management].

PubMed

Pastré, J; Roussel, S; Israël Biet, D; Sanchez, O

2015-04-01

Pleural effusion management is a common clinical situation associated with numerous pulmonary, pleural or extra-pulmonary diseases. A systematic approach is needed to enable a rapid diagnosis and an appropriate treatment. Pleural fluid analysis is the first step to perform which allows a presumptive diagnosis in most cases. Otherwise, further analysis of the pleural fluid or thoracic imaging or pleural biopsy may be necessary. This review aims at highlighting the important elements of the work-up required by a pleural effusion. Copyright © 2014 Société nationale française de médecine interne (SNFMI). Published by Elsevier SAS. All rights reserved.

Smart phones: platform enabling modular, chemical, biological, and explosives sensing

NASA Astrophysics Data System (ADS)

Finch, Amethist S.; Coppock, Matthew; Bickford, Justin R.; Conn, Marvin A.; Proctor, Thomas J.; Stratis-Cullum, Dimitra N.

2013-05-01

Reliable, robust, and portable technologies are needed for the rapid identification and detection of chemical, biological, and explosive (CBE) materials. A key to addressing the persistent threat to U.S. troops in the current war on terror is the rapid detection and identification of the precursor materials used in development of improvised explosive devices, homemade explosives, and bio-warfare agents. However, a universal methodology for detection and prevention of CBE materials in the use of these devices has proven difficult. Herein, we discuss our efforts towards the development of a modular, robust, inexpensive, pervasive, archival, and compact platform (android based smart phone) enabling the rapid detection of these materials.

Rapid and label-free microfluidic neutrophil purification and phenotyping in diabetes mellitus

NASA Astrophysics Data System (ADS)

Hou, Han Wei; Petchakup, Chayakorn; Tay, Hui Min; Tam, Zhi Yang; Dalan, Rinkoo; Chew, Daniel Ek Kwang; Li, King Ho Holden; Boehm, Bernhard O.

2016-07-01

Advanced management of dysmetabolic syndromes such as diabetes will benefit from a timely mechanistic insight enabling personalized medicine approaches. Herein, we present a rapid microfluidic neutrophil sorting and functional phenotyping strategy for type 2 diabetes mellitus (T2DM) patients using small blood volumes (fingerprick ~100 μL). The developed inertial microfluidics technology enables single-step neutrophil isolation (>90% purity) without immuno-labeling and sorted neutrophils are used to characterize their rolling behavior on E-selectin, a critical step in leukocyte recruitment during inflammation. The integrated microfluidics testing methodology facilitates high throughput single-cell quantification of neutrophil rolling to detect subtle differences in speed distribution. Higher rolling speed was observed in T2DM patients (P < 0.01) which strongly correlated with neutrophil activation, rolling ligand P-selectin glycoprotein ligand 1 (PSGL-1) expression, as well as established cardiovascular risk factors (cholesterol, high-sensitive C-reactive protein (CRP) and HbA1c). Rolling phenotype can be modulated by common disease risk modifiers (metformin and pravastatin). Receiver operating characteristics (ROC) and principal component analysis (PCA) revealed neutrophil rolling as an important functional phenotype in T2DM diagnostics. These results suggest a new point-of-care testing methodology, and neutrophil rolling speed as a functional biomarker for rapid profiling of dysmetabolic subjects in clinical and patient-oriented settings.

Microbiological Quality and Food Safety of Plants Grown on ISS Project

NASA Technical Reports Server (NTRS)

Wheeler, Raymond M. (Compiler)

2014-01-01

The goal of this project is to select and advance methods to enable real-time sampling, microbiological analysis, and sanitation of crops grown on the International Space Station (ISS). These methods would validate the microbiological quality of crops grown for consumption to ensure safe and palatable fresh foods. This would be achieved through the development / advancement of microbiological sample collection, rapid pathogen detection and effective sanitation methods that are compatible with a microgravity environment.

Spatial tuning of acoustofluidic pressure nodes by altering net sonic velocity enables high-throughput, efficient cell sorting

DOE PAGES

Jung, Seung-Yong; Notton, Timothy; Fong, Erika; ...

2015-01-07

Particle sorting using acoustofluidics has enormous potential but widespread adoption has been limited by complex device designs and low throughput. Here, we report high-throughput separation of particles and T lymphocytes (600 μL min -1) by altering the net sonic velocity to reposition acoustic pressure nodes in a simple two-channel device. Finally, the approach is generalizable to other microfluidic platforms for rapid, high-throughput analysis.

Quantitative Image Informatics for Cancer Research (QIICR) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Imaging has enormous untapped potential to improve cancer research through software to extract and process morphometric and functional biomarkers. In the era of non-cytotoxic treatment agents, multi- modality image-guided ablative therapies and rapidly evolving computational resources, quantitative imaging software can be transformative in enabling minimally invasive, objective and reproducible evaluation of cancer treatment response. Post-processing algorithms are integral to high-throughput analysis and fine- grained differentiation of multiple molecular targets.

Size-tunable copper nanocluster aggregates and their application in hydrogen sulfide sensing on paper-based devices

PubMed Central

Chen, Po-Cheng; Li, Yu-Chi; Ma, Jia-Yin; Huang, Jia-Yu; Chen, Chien-Fu; Chang, Huan-Tsung

2016-01-01

Polystyrene sulfonate (PSS), a strong polyelectrolyte, was used to prepare red photoluminescent PSS-penicillamine (PA) copper (Cu) nanoclusters (NC) aggregates, which displayed high selectivity and sensitivity to the detection of hydrogen sulfide (H2S). The size of the PSS-PA-Cu NC aggregates could be readily controlled from 5.5 μm to 173 nm using different concentrations of PSS, which enabled better dispersity and higher sensitivity towards H2S. PSS-PA-Cu NC aggregates provided rapid H2S detection by using the strong Cu-S interaction to quench NC photoluminescence as a sensing mechanism. As a result, a detection limit of 650 nM, which is lower than the maximum level permitted in drinking water by the World Health Organization, was achieved for the analysis of H2S in spring-water samples. Moreover, highly dispersed PSS-PA-Cu NC aggregates could be incorporated into a plate-format paper-based analytical device which enables ultra-low sample volumes (5 μL) and feature shorter analysis times (30 min) compared to conventional solution-based methods. The advantages of low reagent consumption, rapid result readout, limited equipment, and long-term storage make this platform sensitive and simple enough to use without specialized training in resource constrained settings. PMID:27113330

Growth dynamics of Australia's polar dinosaurs.

PubMed

Woodward, Holly N; Rich, Thomas H; Chinsamy, Anusuya; Vickers-Rich, Patricia

2011-01-01

Analysis of bone microstructure in ornithopod and theropod dinosaurs from Victoria, Australia, documents ontogenetic changes, providing insight into the dinosaurs' successful habitation of Cretaceous Antarctic environments. Woven-fibered bone tissue in the smallest specimens indicates rapid growth rates during early ontogeny. Later ontogeny is marked by parallel-fibered tissue, suggesting reduced growth rates approaching skeletal maturity. Bone microstructure similarities between the ornithopods and theropods, including the presence of LAGs in each group, suggest there is no osteohistologic evidence supporting the hypothesis that polar theropods hibernated seasonally. Results instead suggest high-latitude dinosaurs had growth trajectories similar to their lower-latitude relatives and thus, rapid early ontogenetic growth and the cyclical suspensions of growth inherent in the theropod and ornithopod lineages enabled them to successfully exploit polar regions.

Emerging microengineered tools for functional analysis and phenotyping of blood cells.

PubMed

Li, Xiang; Chen, Weiqiang; Li, Zida; Li, Ling; Gu, Hongchen; Fu, Jianping

2014-11-01

The available techniques for assessing blood cell functions are limited considering the various types of blood cell and their diverse functions. In the past decade, rapid advances in microengineering have enabled an array of blood cell functional measurements that are difficult or impossible to achieve using conventional bulk platforms. Such miniaturized blood cell assay platforms also provide the attractive capabilities of reducing chemical consumption, cost, and assay time, as well as exciting opportunities for device integration, automation, and assay standardization. This review summarizes these contemporary microengineered tools and discusses their promising potential for constructing accurate in vitro models and rapid clinical diagnosis using minimal amounts of whole-blood samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microfluidic study of fast gas-liquid reactions.

PubMed

Li, Wei; Liu, Kun; Simms, Ryan; Greener, Jesse; Jagadeesan, Dinesh; Pinto, Sascha; Günther, Axel; Kumacheva, Eugenia

2012-02-15

We present a new concept for studies of the kinetics of fast gas-liquid reactions. The strategy relies on the microfluidic generation of highly monodisperse gas bubbles in the liquid reaction medium and subsequent analysis of time-dependent changes in bubble dimensions. Using reactions of CO(2) with secondary amines as an exemplary system, we demonstrate that the method enables rapid determination of reaction rate constant and conversion, and comparison of various binding agents. The proposed approach addresses two challenges in studies of gas-liquid reactions: a mass-transfer limitation and a poorly defined gas-liquid interface. The proposed strategy offers new possibilities in studies of the fundamental aspects of rapid multiphase reactions, and can be combined with throughput optimization of reaction conditions.

Mechanical System Analysis/Design Tool (MSAT) Quick Guide

NASA Technical Reports Server (NTRS)

Lee, HauHua; Kolb, Mark; Madelone, Jack

1998-01-01

MSAT is a unique multi-component multi-disciplinary tool that organizes design analysis tasks around object-oriented representations of configuration components, analysis programs and modules, and data transfer links between them. This creative modular architecture enables rapid generation of input stream for trade-off studies of various engine configurations. The data transfer links automatically transport output from one application as relevant input to the next application once the sequence is set up by the user. The computations are managed via constraint propagation - the constraints supplied by the user as part of any optimization module. The software can be used in the preliminary design stage as well as during the detail design of product development process.

Genotyping of Chromobacterium violaceum isolates by recA PCR-RFLP analysis.

PubMed

Scholz, Holger Christian; Witte, Angela; Tomaso, Herbert; Al Dahouk, Sascha; Neubauer, Heinrich

2005-03-15

Intraspecies variation of Chromobacterium violaceum was examined by comparative sequence - and by restriction fragment length polymorphism analysis of the recombinase A gene (recA-PCR-RFLP). Primers deduced from the known recA gene sequence of the type strain C. violaceum ATCC 12472(T) allowed the specific amplification of a 1040bp recA fragment from each of the 13 C. violaceum strains investigated, whereas other closely related organisms tested negative. HindII-PstI-recA RFLP analysis generated from 13 representative C. violaceum strains enabled us to identify at least three different genospecies. In conclusion, analysis of the recA gene provides a rapid and robust nucleotide sequence-based approach to specifically identify and classify C. violaceum on genospecies level.

A novel data-mining approach leveraging social media to monitor consumer opinion of sitagliptin.

PubMed

Akay, Altug; Dragomir, Andrei; Erlandsson, Björn-Erik

2015-01-01

A novel data mining method was developed to gauge the experience of the drug Sitagliptin (trade name Januvia) by patients with diabetes mellitus type 2. To this goal, we devised a two-step analysis framework. Initial exploratory analysis using self-organizing maps was performed to determine structures based on user opinions among the forum posts. The results were a compilation of user's clusters and their correlated (positive or negative) opinion of the drug. Subsequent modeling using network analysis methods was used to determine influential users among the forum members. These findings can open new avenues of research into rapid data collection, feedback, and analysis that can enable improved outcomes and solutions for public health and important feedback for the manufacturer.

BactoGeNIE: A large-scale comparative genome visualization for big displays

DOE PAGES

Aurisano, Jillian; Reda, Khairi; Johnson, Andrew; ...

2015-08-13

The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE throughmore » a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. In conclusion, BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics.« less

BactoGeNIE: a large-scale comparative genome visualization for big displays

PubMed Central

2015-01-01

Background The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. Results In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE through a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. Conclusions BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics. PMID:26329021

BactoGeNIE: A large-scale comparative genome visualization for big displays

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

Aurisano, Jillian; Reda, Khairi; Johnson, Andrew

The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE throughmore » a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. In conclusion, BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics.« less

A Service Oriented Architecture to Enable Sensor Webs

NASA Technical Reports Server (NTRS)

Sohlberg, Rob; Frye, Stu; Cappelaere, Pat; Ungar, Steve; Ames, Troy; Chien, Steve

2006-01-01

This viewgraph presentation reviews the development of a Service Oriented Architecture to assist in lowering the cost of new Earth Science products. This architecture will enable rapid and cost effective reconfiguration of new sensors.

Sensing and Active Flow Control for Advanced BWB Propulsion-Airframe Integration Concepts

NASA Technical Reports Server (NTRS)

Fleming, John; Anderson, Jason; Ng, Wing; Harrison, Neal

2005-01-01

In order to realize the substantial performance benefits of serpentine boundary layer ingesting diffusers, this study investigated the use of enabling flow control methods to reduce engine-face flow distortion. Computational methods and novel flow control modeling techniques were utilized that allowed for rapid, accurate analysis of flow control geometries. Results were validated experimentally using the Techsburg Ejector-based wind tunnel facility; this facility is capable of simulating the high-altitude, high subsonic Mach number conditions representative of BWB cruise conditions.

Sensor Webs to Constellations

NASA Astrophysics Data System (ADS)

Cole, M.

2017-12-01

Advanced technology plays a key role in enabling future Earth-observing missions needed for global monitoring and climate research. Rapid progress over the past decade and anticipated for the coming decades have diminished the size of some satellites while increasing the amount of data and required pace of integration and analysis. Sensor web developments provide correlations to constellations of smallsats. Reviewing current advances in sensor webs and requirements for constellations will improve planning, operations, and data management for future architectures of multiple satellites with a common mission goal.

Nanosurveyor: a framework for real-time data processing

DOE PAGES

Daurer, Benedikt J.; Krishnan, Hari; Perciano, Talita; ...

2017-01-31

Background: The ever improving brightness of accelerator based sources is enabling novel observations and discoveries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality. Results: Here we present an integrated software/algorithmic framework designed to capitalize on high-throughput experiments through efficient kernels, load-balanced workflows, which are scalable in design. We describe the streamlined processing pipeline of ptychography data analysis. Conclusions: The pipeline provides throughput, compression, and resolution as well as rapid feedback to the microscope operators.

A Study of Enabling Factors for Rapid Fielding: Combined Practices to Balance Speed and Stability

DTIC Science & Technology

2013-05-01

as contributors to the success of Agile projects, such as Scrum status meetings, continuous integration, test-driven development, etc. A second...Management Approach Type Product Size Team Size Sprint length / Prod Release Cycle A-P1 Pre- release Scrum Case management system ᝺M...SLOC 10-20 2 weeks/ TBD B-P1 12 years Scrum Analysis support system ᝺M SLOC 10-20 2 weeks/ 6 months – 1 year C-P1 3 years Scrum Training

Analysis of Processed Foods Containing Oils and Fats by Time of Flight Mass Spectrometry with an APCI Direct Probe.

PubMed

Ito, Shihomi; Chikasou, Masato; Inohana, Shuichi; Fujita, Kazuhiro

2016-01-01

Discriminating vegetable oils and animal and milk fats by infrared absorption spectroscopy is difficult due to similarities in their spectral patterns. Therefore, a rapid and simple method for analyzing vegetable oils, animal fats, and milk fats using TOF/MS with an APCI direct probe ion source was developed. This method enabled discrimination of these oils and fats based on mass spectra and detailed analyses of the ions derived from sterols, even in samples consisting of only a few milligrams. Analyses of the mass spectra of processed foods containing oils and milk fats, such as butter, cheese, and chocolate, enabled confirmation of the raw material origin based on specific ions derived from the oils and fats used to produce the final product.

Optimization of a yeast RNA interference system for controlling gene expression and enabling rapid metabolic engineering.

PubMed

Crook, Nathan C; Schmitz, Alexander C; Alper, Hal S

2014-05-16

Reduction of endogenous gene expression is a fundamental operation of metabolic engineering, yet current methods for gene knockdown (i.e., genome editing) remain laborious and slow, especially in yeast. In contrast, RNA interference allows facile and tunable gene knockdown via a simple plasmid transformation step, enabling metabolic engineers to rapidly prototype knockdown strategies in multiple strains before expending significant cost to undertake genome editing. Although RNAi is naturally present in a myriad of eukaryotes, it has only been recently implemented in Saccharomyces cerevisiae as a heterologous pathway and so has not yet been optimized as a metabolic engineering tool. In this study, we elucidate a set of design principles for the construction of hairpin RNA expression cassettes in yeast and implement RNA interference to quickly identify routes for improvement of itaconic acid production in this organism. The approach developed here enables rapid prototyping of knockdown strategies and thus accelerates and reduces the cost of the design-build-test cycle in yeast.

Near Real Time Review of Instrument Performance using the Airborne Data Processing and Analysis Software Package

NASA Astrophysics Data System (ADS)

Delene, D. J.

2014-12-01

Research aircraft that conduct atmospheric measurements carry an increasing array of instrumentation. While on-board personnel constantly review instrument parameters and time series plots, there are an overwhelming number of items. Furthermore, directing the aircraft flight takes up much of the flight scientist time. Typically, a flight engineer is given the responsibility of reviewing the status of on-board instruments. While major issues like not receiving data are quickly identified during a flight, subtle issues like low but believable concentration measurements may go unnoticed. Therefore, it is critical to review data after a flight in near real time. The Airborne Data Processing and Analysis (ADPAA) software package used by the University of North Dakota automates the post-processing of aircraft flight data. Utilizing scripts to process the measurements recorded by data acquisition systems enables the generation of data files within an hour of flight completion. The ADPAA Cplot visualization program enables plots to be quickly generated that enable timely review of all recorded and processed parameters. Near real time review of aircraft flight data enables instrument problems to be identified, investigated and fixed before conducting another flight. On one flight, near real time data review resulted in the identification of unusually low measurements of cloud condensation nuclei, and rapid data visualization enabled the timely investigation of the cause. As a result, a leak was found and fixed before the next flight. Hence, with the high cost of aircraft flights, it is critical to find and fix instrument problems in a timely matter. The use of a automated processing scripts and quick visualization software enables scientists to review aircraft flight data in near real time to identify potential problems.

Automated Test Case Generation for an Autopilot Requirement Prototype

NASA Technical Reports Server (NTRS)

Giannakopoulou, Dimitra; Rungta, Neha; Feary, Michael

2011-01-01

Designing safety-critical automation with robust human interaction is a difficult task that is susceptible to a number of known Human-Automation Interaction (HAI) vulnerabilities. It is therefore essential to develop automated tools that provide support both in the design and rapid evaluation of such automation. The Automation Design and Evaluation Prototyping Toolset (ADEPT) enables the rapid development of an executable specification for automation behavior and user interaction. ADEPT supports a number of analysis capabilities, thus enabling the detection of HAI vulnerabilities early in the design process, when modifications are less costly. In this paper, we advocate the introduction of a new capability to model-based prototyping tools such as ADEPT. The new capability is based on symbolic execution that allows us to automatically generate quality test suites based on the system design. Symbolic execution is used to generate both user input and test oracles user input drives the testing of the system implementation, and test oracles ensure that the system behaves as designed. We present early results in the context of a component in the Autopilot system modeled in ADEPT, and discuss the challenges of test case generation in the HAI domain.

Rapid on-site TLC-SERS detection of four antidiabetes drugs used as adulterants in botanical dietary supplements.

PubMed

Zhu, Qingxia; Cao, Yongbing; Cao, Yingying; Chai, Yifeng; Lu, Feng

2014-03-01

A novel facile method has been established for rapid on-site detection of antidiabetes chemicals used to adulterate botanical dietary supplements (BDS) for diabetes. Analytes and components of pharmaceutical matrices were separated by thin-layer chromatography (TLC) then surface-enhanced Raman spectroscopy (SERS) was used for qualitative identification of trace substances on the HPTLC plate. Optimization and standardization of the experimental conditions, for example the method used for preparation of silver colloids, the mobile phase, and the concentration of colloidal silver, resulted in a very robust and highly sensitive method which enabled successful detection when the amount of adulteration was as low as 0.001 % (w/w). The method was also highly selective, enabling successful identification of some chemicals in extremely complex herbal matrices. The established TLC-SERS method was used for analysis of real BDS used to treat diabetes, and the results obtained were verified by liquid chromatography-triple quadrupole mass spectrometry (LC-MS-MS). The study showed that TLC-SERS could be used for effective separation and detection of four chemicals used to adulterate BDS, and would have good prospects for on-site qualitative screening of BDS for adulterants.

Forest Landscape Assessment Tool (FLAT): rapid assessment for land management

Treesearch

Lisa Ciecko; David Kimmett; Jesse Saunders; Rachael Katz; Kathleen L. Wolf; Oliver Bazinet; Jeffrey Richardson; Weston Brinkley; Dale J. Blahna

2016-01-01

The Forest Landscape Assessment Tool (FLAT) is a set of procedures and tools used to rapidly determine forest ecological conditions and potential threats. FLAT enables planners and managers to understand baseline conditions, determine and prioritize restoration needs across a landscape system, and conduct ongoing monitoring to achieve land management goals. The rapid...

The rapid manufacture of uniform composite multicellular-biomaterial micropellets, their assembly into macroscopic organized tissues, and potential applications in cartilage tissue engineering.

PubMed

Babur, Betul Kul; Kabiri, Mahboubeh; Klein, Travis Jacob; Lott, William B; Doran, Michael Robert

2015-01-01

We and others have published on the rapid manufacture of micropellet tissues, typically formed from 100-500 cells each. The micropellet geometry enhances cellular biological properties, and in many cases the micropellets can subsequently be utilized as building blocks to assemble complex macrotissues. Generally, micropellets are formed from cells alone, however when replicating matrix-rich tissues such as cartilage it would be ideal if matrix or biomaterials supplements could be incorporated directly into the micropellet during the manufacturing process. Herein we describe a method to efficiently incorporate donor cartilage matrix into tissue engineered cartilage micropellets. We lyophilized bovine cartilage matrix, and then shattered it into microscopic pieces having average dimensions < 10 μm diameter; we termed this microscopic donor matrix "cartilage dust (CD)". Using a microwell platform, we show that ~0.83 μg CD can be rapidly and efficiently incorporated into single multicellular aggregates formed from 180 bone marrow mesenchymal stem/stromal cells (MSC) each. The microwell platform enabled the rapid manufacture of thousands of replica composite micropellets, with each micropellet having a material/CD core and a cellular surface. This micropellet organization enabled the rapid bulking up of the micropellet core matrix content, and left an adhesive cellular outer surface. This morphological organization enabled the ready assembly of the composite micropellets into macroscopic tissues. Generically, this is a versatile method that enables the rapid and uniform integration of biomaterials into multicellular micropellets that can then be used as tissue building blocks. In this study, the addition of CD resulted in an approximate 8-fold volume increase in the micropellets, with the donor matrix functioning to contribute to an increase in total cartilage matrix content. Composite micropellets were readily assembled into macroscopic cartilage tissues; the incorporation of CD enhanced tissue size and matrix content, but did not enhance chondrogenic gene expression.

The Rapid Manufacture of Uniform Composite Multicellular-Biomaterial Micropellets, Their Assembly into Macroscopic Organized Tissues, and Potential Applications in Cartilage Tissue Engineering

PubMed Central

Kul Babur, Betul; Kabiri, Mahboubeh; Klein, Travis Jacob; Lott, William B.; Doran, Michael Robert

2015-01-01

We and others have published on the rapid manufacture of micropellet tissues, typically formed from 100–500 cells each. The micropellet geometry enhances cellular biological properties, and in many cases the micropellets can subsequently be utilized as building blocks to assemble complex macrotissues. Generally, micropellets are formed from cells alone, however when replicating matrix-rich tissues such as cartilage it would be ideal if matrix or biomaterials supplements could be incorporated directly into the micropellet during the manufacturing process. Herein we describe a method to efficiently incorporate donor cartilage matrix into tissue engineered cartilage micropellets. We lyophilized bovine cartilage matrix, and then shattered it into microscopic pieces having average dimensions < 10 μm diameter; we termed this microscopic donor matrix “cartilage dust (CD)”. Using a microwell platform, we show that ~0.83 μg CD can be rapidly and efficiently incorporated into single multicellular aggregates formed from 180 bone marrow mesenchymal stem/stromal cells (MSC) each. The microwell platform enabled the rapid manufacture of thousands of replica composite micropellets, with each micropellet having a material/CD core and a cellular surface. This micropellet organization enabled the rapid bulking up of the micropellet core matrix content, and left an adhesive cellular outer surface. This morphological organization enabled the ready assembly of the composite micropellets into macroscopic tissues. Generically, this is a versatile method that enables the rapid and uniform integration of biomaterials into multicellular micropellets that can then be used as tissue building blocks. In this study, the addition of CD resulted in an approximate 8-fold volume increase in the micropellets, with the donor matrix functioning to contribute to an increase in total cartilage matrix content. Composite micropellets were readily assembled into macroscopic cartilage tissues; the incorporation of CD enhanced tissue size and matrix content, but did not enhance chondrogenic gene expression. PMID:26020956

Computing Shapes Of Cascade Diffuser Blades

NASA Technical Reports Server (NTRS)

Tran, Ken; Prueger, George H.

1993-01-01

Computer program generates sizes and shapes of cascade-type blades for use in axial or radial turbomachine diffusers. Generates shapes of blades rapidly, incorporating extensive cascade data to determine optimum incidence and deviation angle for blade design based on 65-series data base of National Advisory Commission for Aeronautics and Astronautics (NACA). Allows great variability in blade profile through input variables. Also provides for design of three-dimensional blades by allowing variable blade stacking. Enables designer to obtain computed blade-geometry data in various forms: as input for blade-loading analysis; as input for quasi-three-dimensional analysis of flow; or as points for transfer to computer-aided design.

RAPID COMMUNICATION: Diffusion thermopower in graphene

NASA Astrophysics Data System (ADS)

Vaidya, R. G.; Kamatagi, M. D.; Sankeshwar, N. S.; Mulimani, B. G.

2010-09-01

The diffusion thermopower of graphene, Sd, is studied for 30 < T < 300 K, considering the electrons to be scattered by impurities, vacancies, surface roughness and acoustic and optical phonons via deformation potential couplings. Sd is found to increase almost linearly with temperature, determined mainly by vacancy and impurity scatterings. A departure from linear behaviour due to optical phonons is noticed. As a function of carrier concentration, a change in the sign of |Sd| is observed. Our analysis of recent thermopower data obtains a good fit. The limitations of Mott formula are discussed. Detailed analysis of data will enable a better understanding of the scattering mechanisms operative in graphene.

Photocleavable DNA barcode-antibody conjugates allow sensitive and multiplexed protein analysis in single cells.

PubMed

Agasti, Sarit S; Liong, Monty; Peterson, Vanessa M; Lee, Hakho; Weissleder, Ralph

2012-11-14

DNA barcoding is an attractive technology, as it allows sensitive and multiplexed target analysis. However, DNA barcoding of cellular proteins remains challenging, primarily because barcode amplification and readout techniques are often incompatible with the cellular microenvironment. Here we describe the development and validation of a photocleavable DNA barcode-antibody conjugate method for rapid, quantitative, and multiplexed detection of proteins in single live cells. Following target binding, this method allows DNA barcodes to be photoreleased in solution, enabling easy isolation, amplification, and readout. As a proof of principle, we demonstrate sensitive and multiplexed detection of protein biomarkers in a variety of cancer cells.

Expanding the horizons for single-cell applications on lab-on-a-chip devices.

PubMed

Kim, Soo Hyeon; Fourmy, Dominique; Fujii, Teruo

2012-01-01

Stochastic events in gene expression, protein synthesis, and metabolite synthesis or degradation lead to cellular heterogeneity essential to life. In a tissue as we see in organs, there is strong heterogeneity among the constituting cells critical to its function. Thus, there exists a strong demand to develop new micro/nanosystems that would enable us to conduct single-cell analysis. This field is rapidly growing, as exemplified below with recent emerging technologies that now reveal sensitive single-cell "omics" analysis. We describe in the review some of the most promising technologies that will certainly transform our view of biology in the near future.

Task 1.5 Genomic Shift and Drift Trends of Emerging Pathogens

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

Borucki, M

2010-01-05

The Lawrence Livermore National Laboratory (LLNL) Bioinformatics group has recently taken on a role in DTRA's Transformation Medical Technologies Initiative (TMTI). The high-level goal of TMTI is to accelerate the development of broad-spectrum countermeasures. To achieve those goals, TMTI has a near term need to conduct analyses of genomic shift and drift trends of emerging pathogens, with a focused eye on select agent pathogens, as well as antibiotic and virulence markers. Most emerging human pathogens are zoonotic viruses with a genome composed of RNA. The high mutation rate of the replication enzymes of RNA viruses contributes to sequence drift andmore » provides one mechanism for these viruses to adapt to diverse hosts (interspecies transmission events) and cause new human and zoonotic diseases. Additionally, new viral pathogens frequently emerge due to genetic shift (recombination and segment reassortment) which allows for dramatic genotypic and phenotypic changes to occur rapidly. Bacterial pathogens also evolve via genetic drift and shift, although sequence drift generally occurs at a much slower rate for bacteria as compared to RNA viruses. However, genetic shift such as lateral gene transfer and inter- and intragenomic recombination enables bacteria to rapidly acquire new mechanisms of survival and antibiotic resistance. New technologies such as rapid whole genome sequencing of bacterial genomes, ultra-deep sequencing of RNA virus populations, metagenomic studies of environments rich in antibiotic resistance genes, and the use of microarrays for the detection and characterization of emerging pathogens provide mechanisms to address the challenges posed by the rapid emergence of pathogens. Bioinformatic algorithms that enable efficient analysis of the massive amounts of data generated by these technologies as well computational modeling of protein structures and evolutionary processes need to be developed to allow the technology to fulfill its potential.« less

Rapid Data Delivery System (RDDS)

USGS Publications Warehouse

Cress, Jill J.; Goplen, Susan E.

2007-01-01

Since the start of the active 2000 summer fire season, the U. S. Geological Survey (USGS) Rocky Mountain Geographic Science Center (RMGSC) has been actively engaged in providing crucial and timely support to Federal, State, and local natural hazards monitoring, analysis, response, and recovery activities. As part of this support, RMGSC has developed the Rapid Data Delivery System (RDDS) to provide emergency and incident response teams with timely access to geospatial data. The RDDS meets these needs by combining a simple web-enabled data viewer for the selection and preview of vector and raster geospatial data with an easy to use data ordering form. The RDDS viewer also incorporates geospatial locations for current natural hazard incidents, including wildfires, earthquakes, hurricanes, and volcanoes, allowing incident responders to quickly focus on their area of interest for data selection.

Rapid analysis method for the determination of 14C specific activity in irradiated graphite

PubMed Central

Remeikis, Vidmantas; Lagzdina, Elena; Garbaras, Andrius; Gudelis, Arūnas; Garankin, Jevgenij; Juodis, Laurynas; Duškesas, Grigorijus; Lingis, Danielius; Abdulajev, Vladimir; Plukis, Artūras

2018-01-01

14C is one of the limiting radionuclides used in the categorization of radioactive graphite waste; this categorization is crucial in selecting the appropriate graphite treatment/disposal method. We propose a rapid analysis method for 14C specific activity determination in small graphite samples in the 1–100 μg range. The method applies an oxidation procedure to the sample, which extracts 14C from the different carbonaceous matrices in a controlled manner. Because this method enables fast online measurement and 14C specific activity evaluation, it can be especially useful for characterizing 14C in irradiated graphite when dismantling graphite moderator and reflector parts, or when sorting radioactive graphite waste from decommissioned nuclear power plants. The proposed rapid method is based on graphite combustion and the subsequent measurement of both CO2 and 14C, using a commercial elemental analyser and the semiconductor detector, respectively. The method was verified using the liquid scintillation counting (LSC) technique. The uncertainty of this rapid method is within the acceptable range for radioactive waste characterization purposes. The 14C specific activity determination procedure proposed in this study takes approximately ten minutes, comparing favorably to the more complicated and time consuming LSC method. This method can be potentially used to radiologically characterize radioactive waste or used in biomedical applications when dealing with the specific activity determination of 14C in the sample. PMID:29370233

Adaptable data management for systems biology investigations.

PubMed

Boyle, John; Rovira, Hector; Cavnor, Chris; Burdick, David; Killcoyne, Sarah; Shmulevich, Ilya

2009-03-06

Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ranges from in-house protocols through to high-throughput instrumentation. To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage. The adaptable data management system discussed is designed to support the seamless mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, flow cytometry). We use different content graphs to represent different views upon the data. These views are designed for different roles: equipment specific views are used to gather instrumentation information; data processing oriented views are provided to enable the rapid development of analysis applications; and research project specific views are used to organize information for individual research experiments. This management system allows for both the rapid introduction of new types of information and the evolution of the knowledge it represents. Data management is an important aspect of any research enterprise. It is the foundation on which most applications are built, and must be easily extended to serve new functionality for new scientific areas. We have found that adopting a three-tier architecture for data management, built around distributed standardized content repositories, allows us to rapidly develop new applications to support a diverse user community.

Rapid analysis method for the determination of 14C specific activity in irradiated graphite.

PubMed

Remeikis, Vidmantas; Lagzdina, Elena; Garbaras, Andrius; Gudelis, Arūnas; Garankin, Jevgenij; Plukienė, Rita; Juodis, Laurynas; Duškesas, Grigorijus; Lingis, Danielius; Abdulajev, Vladimir; Plukis, Artūras

2018-01-01

14C is one of the limiting radionuclides used in the categorization of radioactive graphite waste; this categorization is crucial in selecting the appropriate graphite treatment/disposal method. We propose a rapid analysis method for 14C specific activity determination in small graphite samples in the 1-100 μg range. The method applies an oxidation procedure to the sample, which extracts 14C from the different carbonaceous matrices in a controlled manner. Because this method enables fast online measurement and 14C specific activity evaluation, it can be especially useful for characterizing 14C in irradiated graphite when dismantling graphite moderator and reflector parts, or when sorting radioactive graphite waste from decommissioned nuclear power plants. The proposed rapid method is based on graphite combustion and the subsequent measurement of both CO2 and 14C, using a commercial elemental analyser and the semiconductor detector, respectively. The method was verified using the liquid scintillation counting (LSC) technique. The uncertainty of this rapid method is within the acceptable range for radioactive waste characterization purposes. The 14C specific activity determination procedure proposed in this study takes approximately ten minutes, comparing favorably to the more complicated and time consuming LSC method. This method can be potentially used to radiologically characterize radioactive waste or used in biomedical applications when dealing with the specific activity determination of 14C in the sample.

Rapid Propellant Loading Approach Exploration

DTIC Science & Technology

2010-11-01

the impact upon ground operations of three configuration options. Ground operations management was addressed through a series of studies performed...and operations management system can enable safe rapid propellant loading operations with limited operator knowledge and involvement. A single

Autonomous Metabolomics for Rapid Metabolite Identification in Global Profiling

DOE PAGES

Benton, H. Paul; Ivanisevic, Julijana; Mahieu, Nathaniel G.; ...

2014-12-12

An autonomous metabolomic workflow combining mass spectrometry analysis with tandem mass spectrometry data acquisition was designed to allow for simultaneous data processing and metabolite characterization. Although previously tandem mass spectrometry data have been generated on the fly, the experiments described herein combine this technology with the bioinformatic resources of XCMS and METLIN. We can analyze large profiling datasets and simultaneously obtain structural identifications, as a result of this unique integration. Furthermore, validation of the workflow on bacterial samples allowed the profiling on the order of a thousand metabolite features with simultaneous tandem mass spectra data acquisition. The tandem mass spectrometrymore » data acquisition enabled automatic search and matching against the METLIN tandem mass spectrometry database, shortening the current workflow from days to hours. Overall, the autonomous approach to untargeted metabolomics provides an efficient means of metabolomic profiling, and will ultimately allow the more rapid integration of comparative analyses, metabolite identification, and data analysis at a systems biology level.« less

Unsupervised Discovery of Demixed, Low-Dimensional Neural Dynamics across Multiple Timescales through Tensor Component Analysis.

PubMed

Williams, Alex H; Kim, Tony Hyun; Wang, Forea; Vyas, Saurabh; Ryu, Stephen I; Shenoy, Krishna V; Schnitzer, Mark; Kolda, Tamara G; Ganguli, Surya

2018-06-27

Perceptions, thoughts, and actions unfold over millisecond timescales, while learned behaviors can require many days to mature. While recent experimental advances enable large-scale and long-term neural recordings with high temporal fidelity, it remains a formidable challenge to extract unbiased and interpretable descriptions of how rapid single-trial circuit dynamics change slowly over many trials to mediate learning. We demonstrate a simple tensor component analysis (TCA) can meet this challenge by extracting three interconnected, low-dimensional descriptions of neural data: neuron factors, reflecting cell assemblies; temporal factors, reflecting rapid circuit dynamics mediating perceptions, thoughts, and actions within each trial; and trial factors, describing both long-term learning and trial-to-trial changes in cognitive state. We demonstrate the broad applicability of TCA by revealing insights into diverse datasets derived from artificial neural networks, large-scale calcium imaging of rodent prefrontal cortex during maze navigation, and multielectrode recordings of macaque motor cortex during brain machine interface learning. Copyright © 2018 Elsevier Inc. All rights reserved.

Mid-infrared absorption spectroscopy using quantum cascade lasers

NASA Astrophysics Data System (ADS)

Haibach, Fred; Erlich, Adam; Deutsch, Erik

2011-06-01

Block Engineering has developed an absorption spectroscopy system based on widely tunable Quantum Cascade Lasers (QCL). The QCL spectrometer rapidly cycles through a user-selected range in the mid-infrared spectrum, between 6 to 12 μm (1667 to 833 cm-1), to detect and identify substances on surfaces based on their absorption characteristics from a standoff distance of up to 2 feet with an eye-safe laser. It can also analyze vapors and liquids in a single device. For military applications, the QCL spectrometer has demonstrated trace explosive, chemical warfare agent (CWA), and toxic industrial chemical (TIC) detection and analysis. The QCL's higher power density enables measurements from diffuse and highly absorbing materials and substrates. Other advantages over Fourier Transform Infrared (FTIR) spectroscopy include portability, ruggedness, rapid analysis, and the ability to function from a distance through free space or a fiber optic probe. This paper will discuss the basic technology behind the system and the empirical data on various safety and security applications.

BEAP profiles as rapid test system for status analysis and early detection of process incidents in biogas plants.

PubMed

Refai, Sarah; Berger, Stefanie; Wassmann, Kati; Hecht, Melanie; Dickhaus, Thomas; Deppenmeier, Uwe

2017-03-01

A method was developed to quantify the performance of microorganisms involved in different digestion levels in biogas plants. The test system was based on the addition of butyrate (BCON), ethanol (ECON), acetate (ACON) or propionate (PCON) to biogas sludge samples and the subsequent analysis of CH 4 formation in comparison to control samples. The combination of the four values was referred to as BEAP profile. Determination of BEAP profiles enabled rapid testing of a biogas plant's metabolic state within 24 h and an accurate mapping of all degradation levels in a lab-scale experimental setup. Furthermore, it was possible to distinguish between specific BEAP profiles for standard biogas plants and for biogas reactors with process incidents (beginning of NH 4 + -N inhibition, start of acidification, insufficient hydrolysis and potential mycotoxin effects). Finally, BEAP profiles also functioned as a warning system for the early prediction of critical NH 4 + -N concentrations leading to a drop of CH 4 formation.

Whole-Genome Sequencing in Outbreak Analysis

PubMed Central

Turner, Stephen D.; Riley, Margaret F.; Petri, William A.; Hewlett, Erik L.

2015-01-01

SUMMARY In addition to the ever-present concern of medical professionals about epidemics of infectious diseases, the relative ease of access and low cost of obtaining, producing, and disseminating pathogenic organisms or biological toxins mean that bioterrorism activity should also be considered when facing a disease outbreak. Utilization of whole-genome sequencing (WGS) in outbreak analysis facilitates the rapid and accurate identification of virulence factors of the pathogen and can be used to identify the path of disease transmission within a population and provide information on the probable source. Molecular tools such as WGS are being refined and advanced at a rapid pace to provide robust and higher-resolution methods for identifying, comparing, and classifying pathogenic organisms. If these methods of pathogen characterization are properly applied, they will enable an improved public health response whether a disease outbreak was initiated by natural events or by accidental or deliberate human activity. The current application of next-generation sequencing (NGS) technology to microbial WGS and microbial forensics is reviewed. PMID:25876885

Standing of nucleic acid testing strategies in veterinary diagnosis laboratories to uncover Mycobacterium tuberculosis complex members

PubMed Central

Costa, Pedro; Botelho, Ana; Couto, Isabel; Viveiros, Miguel; Inácio, João

2014-01-01

Nucleic acid testing (NAT) designate any molecular approach used for the detection, identification, and characterization of pathogenic microorganisms, enabling the rapid, specific, and sensitive diagnostic of infectious diseases, such as tuberculosis. These assays have been widely used since the 90s of the last century in human clinical laboratories and, subsequently, also in veterinary diagnostics. Most NAT strategies are based in the polymerase chain reaction (PCR) and its several enhancements and variations. From the conventional PCR, real-time PCR and its combinations, isothermal DNA amplification, to the nanotechnologies, here we review how the NAT assays have been applied to decipher if and which member of the Mycobacterium tuberculosis complex is present in a clinical sample. Recent advances in DNA sequencing also brought new challenges and have made possible to generate rapidly and at a low cost, large amounts of sequence data. This revolution with the high-throughput sequencing (HTS) technologies makes whole genome sequencing (WGS) and metagenomics the trendiest NAT strategies, today. The ranking of NAT techniques in the field of clinical diagnostics is rising, and we provide a SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis with our view of the use of molecular diagnostics for detecting tuberculosis in veterinary laboratories, notwithstanding the gold standard being still the classical culture of the agent. The complementary use of both classical and molecular diagnostics approaches is recommended to speed the diagnostic, enabling a fast decision by competent authorities and rapid tackling of the disease. PMID:25988157

Standing of nucleic acid testing strategies in veterinary diagnosis laboratories to uncover Mycobacterium tuberculosis complex members.

PubMed

Costa, Pedro; Botelho, Ana; Couto, Isabel; Viveiros, Miguel; Inácio, João

2014-01-01

Nucleic acid testing (NAT) designate any molecular approach used for the detection, identification, and characterization of pathogenic microorganisms, enabling the rapid, specific, and sensitive diagnostic of infectious diseases, such as tuberculosis. These assays have been widely used since the 90s of the last century in human clinical laboratories and, subsequently, also in veterinary diagnostics. Most NAT strategies are based in the polymerase chain reaction (PCR) and its several enhancements and variations. From the conventional PCR, real-time PCR and its combinations, isothermal DNA amplification, to the nanotechnologies, here we review how the NAT assays have been applied to decipher if and which member of the Mycobacterium tuberculosis complex is present in a clinical sample. Recent advances in DNA sequencing also brought new challenges and have made possible to generate rapidly and at a low cost, large amounts of sequence data. This revolution with the high-throughput sequencing (HTS) technologies makes whole genome sequencing (WGS) and metagenomics the trendiest NAT strategies, today. The ranking of NAT techniques in the field of clinical diagnostics is rising, and we provide a SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis with our view of the use of molecular diagnostics for detecting tuberculosis in veterinary laboratories, notwithstanding the gold standard being still the classical culture of the agent. The complementary use of both classical and molecular diagnostics approaches is recommended to speed the diagnostic, enabling a fast decision by competent authorities and rapid tackling of the disease.

Rapid, Sensitive Detection of Botulinum Toxin on a Flexible Microfluidics Platform

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

Warner, Marvin G.; Dockendorff, Brian P.; Feldhaus, Michael J.

2004-10-30

In this paper we will describe how high affinity reagents and a sensor configuration enabling rapid mass transport can be combined for rapid, sensitive biodetection. The system that we have developed includes a renewable surface immunoassay, which involves on-column detection of a fluorescently labeled secondary antibody in a sandwich immunoassay. Yeast display and directed molecular evolution were used to create high affinity antibodies to the botulinum toxin heavy chain receptor binding domain, AR1 and 3D12. A rotating rod renewable surface microcolumn was used to form a microliter-sized column containing beads functionalized with the capture antibody (AR1). The column was perfusedmore » with sample, wash solutions, and a fluorescently labeled secondary antibody (3D12) while the on-column fluorescence was monitored. Detection was accomplished in less than 5 minutes, with a total processing time of about 10 minutes. On-column detection of botulinum toxin was more sensitive and much faster than flow cytometry analysis on microbeads using the same reagents.« less

A Fluorescent Tile DNA Diagnocode System for In Situ Rapid and Selective Diagnosis of Cytosolic RNA Cancer Markers

PubMed Central

Park, Kyung Soo; Shin, Seung Won; Jang, Min Su; Shin, Woojung; Yang, Kisuk; Min, Junhong; Cho, Seung-Woo; Oh, Byung-Keun; Bae, Jong Wook; Jung, Sunghwan; Choi, Jeong-Woo; Um, Soong Ho

2015-01-01

Accurate cancer diagnosis often requires extraction and purification of genetic materials from cells, and sophisticated instrumentations that follow. Otherwise in order to directly treat the diagnostic materials to cells, multiple steps to optimize dose concentration and treatment time are necessary due to diversity in cellular behaviors. These processes may offer high precision but hinder fast analysis of cancer, especially in clinical situations that need rapid detection and characterization of cancer. Here we present a novel fluorescent tile DNA nanostructure delivered to cancer cytosol by employing nanoparticle technology. Its structural anisotropicity offers easy manipulation for multifunctionalities, enabling the novel DNA nanostructure to detect intracellular cancer RNA markers with high specificity within 30 minutes post treatment, while the nanoparticle property bypasses the requirement of treatment optimization, effectively reducing the complexity of applying the system for cancer diagnosis. Altogether, the system offers a precise and rapid detection of cancer, suggesting the future use in the clinical fields. PMID:26678430

Data-Driven Boundary Correction and Optimization of a Nearshore Wave and Hydrodynamic Model to Enable Rapid Environmental Assessment

DTIC Science & Technology

2011-09-30

Number : N00014 N00014-09-1-0503 http://ceprofs.civil.tamu.edu/jkaihatu/research/proj.html LONG-TERM GOALS The present project is part of a... number . 1. REPORT DATE 30 SEP 2011 2. REPORT TYPE 3. DATES COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE Data-Driven Boundary...Correction and Optimization of a Nearshore Wave and Hydrodynamic Model to Enable Rapid Environmental Assessment 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c

Hybrid Wing Body Planform Design with Vehicle Sketch Pad

NASA Technical Reports Server (NTRS)

Wells, Douglas P.; Olson, Erik D.

2011-01-01

The objective of this paper was to provide an update on NASA s current tools for design and analysis of hybrid wing body (HWB) aircraft with an emphasis on Vehicle Sketch Pad (VSP). NASA started HWB analysis using the Flight Optimization System (FLOPS). That capability is enhanced using Phoenix Integration's ModelCenter(Registered TradeMark). Model Center enables multifidelity analysis tools to be linked as an integrated structure. Two major components are linked to FLOPS as an example; a planform discretization tool and VSP. The planform discretization tool ensures the planform is smooth and continuous. VSP is used to display the output geometry. This example shows that a smooth & continuous HWB planform can be displayed as a three-dimensional model and rapidly sized and analyzed.

Kadenza: Kepler/K2 Raw Cadence Data Reader

NASA Astrophysics Data System (ADS)

Barentsen, Geert; Cardoso, José Vinícius de Miranda

2018-03-01

Kadenza enables time-critical data analyses to be carried out using NASA's Kepler Space Telescope. It enables users to convert Kepler's raw data files into user-friendly Target Pixel Files upon downlink from the spacecraft. The primary motivation for this tool is to enable the microlensing, supernova, and exoplanet communities to create quicklook lightcurves for transient events which require rapid follow-up.

On-line characterization of monoclonal antibody variants by liquid chromatography-mass spectrometry operating in a two-dimensional format.

PubMed

Alvarez, Melissa; Tremintin, Guillaume; Wang, Jennifer; Eng, Marian; Kao, Yung-Hsiang; Jeong, Justin; Ling, Victor T; Borisov, Oleg V

2011-12-01

Recombinant monoclonal antibodies (MAbs) have become one of the most rapidly growing classes of biotherapeutics in the treatment of human disease. MAbs are highly heterogeneous proteins, thereby requiring a battery of analytical technologies for their characterization. However, incompatibility between separation and subsequent detection is often encountered. Here we demonstrate the utility of a generic on-line liquid chromatography-mass spectrometry (LC-MS) method operated in a two-dimensional format toward the rapid characterization of MAb charge and size variants. Using a single chromatographic system capable of running two independent gradients, up to six fractions of interest from an ion exchange (IEC) or size exclusion (SEC) separation can be identified by trapping and desalting the fractions onto a series of reversed phase trap cartridges with subsequent on-line analysis by mass spectrometry. Analysis of poorly resolved and low-level peaks in the IEC or SEC profile was facilitated by preconcentrating fractions on the traps using multiple injections. An on-line disulfide reduction step was successfully incorporated into the workflow, allowing more detailed characterization of modified MAbs by providing chain-specific information. The system is fully automated, thereby enabling high-throughput analysis with minimal sample handling. This technology provides rapid data turnaround time, a much needed feature during product characterization and development of multiple biotherapeutic proteins. Copyright © 2011 Elsevier Inc. All rights reserved.

The Java Image Science Toolkit (JIST) for rapid prototyping and publishing of neuroimaging software.

PubMed

Lucas, Blake C; Bogovic, John A; Carass, Aaron; Bazin, Pierre-Louis; Prince, Jerry L; Pham, Dzung L; Landman, Bennett A

2010-03-01

Non-invasive neuroimaging techniques enable extraordinarily sensitive and specific in vivo study of the structure, functional response and connectivity of biological mechanisms. With these advanced methods comes a heavy reliance on computer-based processing, analysis and interpretation. While the neuroimaging community has produced many excellent academic and commercial tool packages, new tools are often required to interpret new modalities and paradigms. Developing custom tools and ensuring interoperability with existing tools is a significant hurdle. To address these limitations, we present a new framework for algorithm development that implicitly ensures tool interoperability, generates graphical user interfaces, provides advanced batch processing tools, and, most importantly, requires minimal additional programming or computational overhead. Java-based rapid prototyping with this system is an efficient and practical approach to evaluate new algorithms since the proposed system ensures that rapidly constructed prototypes are actually fully-functional processing modules with support for multiple GUI's, a broad range of file formats, and distributed computation. Herein, we demonstrate MRI image processing with the proposed system for cortical surface extraction in large cross-sectional cohorts, provide a system for fully automated diffusion tensor image analysis, and illustrate how the system can be used as a simulation framework for the development of a new image analysis method. The system is released as open source under the Lesser GNU Public License (LGPL) through the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC).

The Java Image Science Toolkit (JIST) for Rapid Prototyping and Publishing of Neuroimaging Software

PubMed Central

Lucas, Blake C.; Bogovic, John A.; Carass, Aaron; Bazin, Pierre-Louis; Prince, Jerry L.; Pham, Dzung

2010-01-01

Non-invasive neuroimaging techniques enable extraordinarily sensitive and specific in vivo study of the structure, functional response and connectivity of biological mechanisms. With these advanced methods comes a heavy reliance on computer-based processing, analysis and interpretation. While the neuroimaging community has produced many excellent academic and commercial tool packages, new tools are often required to interpret new modalities and paradigms. Developing custom tools and ensuring interoperability with existing tools is a significant hurdle. To address these limitations, we present a new framework for algorithm development that implicitly ensures tool interoperability, generates graphical user interfaces, provides advanced batch processing tools, and, most importantly, requires minimal additional programming or computational overhead. Java-based rapid prototyping with this system is an efficient and practical approach to evaluate new algorithms since the proposed system ensures that rapidly constructed prototypes are actually fully-functional processing modules with support for multiple GUI's, a broad range of file formats, and distributed computation. Herein, we demonstrate MRI image processing with the proposed system for cortical surface extraction in large cross-sectional cohorts, provide a system for fully automated diffusion tensor image analysis, and illustrate how the system can be used as a simulation framework for the development of a new image analysis method. The system is released as open source under the Lesser GNU Public License (LGPL) through the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC). PMID:20077162

Flexible opto-electronics enabled microfluidics systems with cloud connectivity for point-of-care micronutrient analysis.

PubMed

Lee, Stephen; Aranyosi, A J; Wong, Michelle D; Hong, Ji Hyung; Lowe, Jared; Chan, Carol; Garlock, David; Shaw, Scott; Beattie, Patrick D; Kratochvil, Zachary; Kubasti, Nick; Seagers, Kirsten; Ghaffari, Roozbeh; Swanson, Christina D

2016-04-15

In developing countries, the deployment of medical diagnostic technologies remains a challenge because of infrastructural limitations (e.g. refrigeration, electricity), and paucity of health professionals, distribution centers and transportation systems. Here we demonstrate the technical development and clinical testing of a novel electronics enabled microfluidic paper-based analytical device (EE-μPAD) for quantitative measurement of micronutrient concentrations in decentralized, resource-limited settings. The system performs immune-detection using paper-based microfluidics, instrumented with flexible electronics and optoelectronic sensors in a mechanically robust, ultrathin format comparable in size to a credit card. Autonomous self-calibration, plasma separation, flow monitoring, timing and data storage enable multiple devices to be run simultaneously. Measurements are wirelessly transferred to a mobile phone application that geo-tags the data and transmits it to a remote server for real time tracking of micronutrient deficiencies. Clinical tests of micronutrient levels from whole blood samples (n=95) show comparable sensitivity and specificity to ELISA-based tests. These results demonstrate instantaneous acquisition and global aggregation of diagnostics data using a fully integrated point of care system that will enable rapid and distributed surveillance of disease prevalence and geographical progression. Copyright © 2015 Elsevier B.V. All rights reserved.

A manual and an automatic TERS based virus discrimination

NASA Astrophysics Data System (ADS)

Olschewski, Konstanze; Kämmer, Evelyn; Stöckel, Stephan; Bocklitz, Thomas; Deckert-Gaudig, Tanja; Zell, Roland; Cialla-May, Dana; Weber, Karina; Deckert, Volker; Popp, Jürgen

2015-02-01

Rapid techniques for virus identification are more relevant today than ever. Conventional virus detection and identification strategies generally rest upon various microbiological methods and genomic approaches, which are not suited for the analysis of single virus particles. In contrast, the highly sensitive spectroscopic technique tip-enhanced Raman spectroscopy (TERS) allows the characterisation of biological nano-structures like virions on a single-particle level. In this study, the feasibility of TERS in combination with chemometrics to discriminate two pathogenic viruses, Varicella-zoster virus (VZV) and Porcine teschovirus (PTV), was investigated. In a first step, chemometric methods transformed the spectral data in such a way that a rapid visual discrimination of the two examined viruses was enabled. In a further step, these methods were utilised to perform an automatic quality rating of the measured spectra. Spectra that passed this test were eventually used to calculate a classification model, through which a successful discrimination of the two viral species based on TERS spectra of single virus particles was also realised with a classification accuracy of 91%.Rapid techniques for virus identification are more relevant today than ever. Conventional virus detection and identification strategies generally rest upon various microbiological methods and genomic approaches, which are not suited for the analysis of single virus particles. In contrast, the highly sensitive spectroscopic technique tip-enhanced Raman spectroscopy (TERS) allows the characterisation of biological nano-structures like virions on a single-particle level. In this study, the feasibility of TERS in combination with chemometrics to discriminate two pathogenic viruses, Varicella-zoster virus (VZV) and Porcine teschovirus (PTV), was investigated. In a first step, chemometric methods transformed the spectral data in such a way that a rapid visual discrimination of the two examined viruses was enabled. In a further step, these methods were utilised to perform an automatic quality rating of the measured spectra. Spectra that passed this test were eventually used to calculate a classification model, through which a successful discrimination of the two viral species based on TERS spectra of single virus particles was also realised with a classification accuracy of 91%. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07033j

Alignment-Free Design of Highly Discriminatory Diagnostic Primer Sets for Escherichia coli O104:H4 Outbreak Strains

PubMed Central

Bielaszewska, Martina; Karch, Helge; Toth, Ian K.

2012-01-01

Background An Escherichia coli O104:H4 outbreak in Germany in summer 2011 caused 53 deaths, over 4000 individual infections across Europe, and considerable economic, social and political impact. This outbreak was the first in a position to exploit rapid, benchtop high-throughput sequencing (HTS) technologies and crowdsourced data analysis early in its investigation, establishing a new paradigm for rapid response to disease threats. We describe a novel strategy for design of diagnostic PCR primers that exploited this rapid draft bacterial genome sequencing to distinguish between E. coli O104:H4 outbreak isolates and other pathogenic E. coli isolates, including the historical hæmolytic uræmic syndrome (HUSEC) E. coli HUSEC041 O104:H4 strain, which possesses the same serotype as the outbreak isolates. Methodology/Principal Findings Primers were designed using a novel alignment-free strategy against eleven draft whole genome assemblies of E. coli O104:H4 German outbreak isolates from the E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium website, and a negative sequence set containing 69 E. coli chromosome and plasmid sequences from public databases. Validation in vitro against 21 ‘positive’ E. coli O104:H4 outbreak and 32 ‘negative’ non-outbreak EHEC isolates indicated that individual primer sets exhibited 100% sensitivity for outbreak isolates, with false positive rates of between 9% and 22%. A minimal combination of two primers discriminated between outbreak and non-outbreak E. coli isolates with 100% sensitivity and 100% specificity. Conclusions/Significance Draft genomes of isolates of disease outbreak bacteria enable high throughput primer design and enhanced diagnostic performance in comparison to traditional molecular assays. Future outbreak investigations will be able to harness HTS rapidly to generate draft genome sequences and diagnostic primer sets, greatly facilitating epidemiology and clinical diagnostics. We expect that high throughput primer design strategies will enable faster, more precise responses to future disease outbreaks of bacterial origin, and help to mitigate their societal impact. PMID:22496820

High-performance 3D printing of hydrogels by water-dispersible photoinitiator nanoparticles

PubMed Central

Pawar, Amol A.; Saada, Gabriel; Cooperstein, Ido; Larush, Liraz; Jackman, Joshua A.; Tabaei, Seyed R.; Cho, Nam-Joon; Magdassi, Shlomo

2016-01-01

In the absence of water-soluble photoinitiators with high absorbance in the ultraviolet (UV)–visible range, rapid three-dimensional (3D) printing of hydrogels for tissue engineering is challenging. A new approach enabling rapid 3D printing of hydrogels in aqueous solutions is presented on the basis of UV-curable inks containing nanoparticles of highly efficient but water-insoluble photoinitiators. The extinction coefficient of the new water-dispersible nanoparticles of 2,4,6-trimethylbenzoyl-diphenylphosphine oxide (TPO) is more than 300 times larger than the best and most used commercially available water-soluble photoinitiator. The TPO nanoparticles absorb significantly in the range from 385 to 420 nm, making them suitable for use in commercially available, low-cost, light-emitting diode–based 3D printers using digital light processing. The polymerization rate at this range is very fast and enables 3D printing that otherwise is impossible to perform without adding solvents. The TPO nanoparticles were prepared by rapid conversion of volatile microemulsions into water-dispersible powder, a process that can be used for a variety of photoinitiators. Such water-dispersible photoinitiator nanoparticles open many opportunities to enable rapid 3D printing of structures prepared in aqueous solutions while bringing environmental advantages by using low-energy curing systems and avoiding the need for solvents. PMID:27051877

High-performance 3D printing of hydrogels by water-dispersible photoinitiator nanoparticles.

PubMed

Pawar, Amol A; Saada, Gabriel; Cooperstein, Ido; Larush, Liraz; Jackman, Joshua A; Tabaei, Seyed R; Cho, Nam-Joon; Magdassi, Shlomo

2016-04-01

In the absence of water-soluble photoinitiators with high absorbance in the ultraviolet (UV)-visible range, rapid three-dimensional (3D) printing of hydrogels for tissue engineering is challenging. A new approach enabling rapid 3D printing of hydrogels in aqueous solutions is presented on the basis of UV-curable inks containing nanoparticles of highly efficient but water-insoluble photoinitiators. The extinction coefficient of the new water-dispersible nanoparticles of 2,4,6-trimethylbenzoyl-diphenylphosphine oxide (TPO) is more than 300 times larger than the best and most used commercially available water-soluble photoinitiator. The TPO nanoparticles absorb significantly in the range from 385 to 420 nm, making them suitable for use in commercially available, low-cost, light-emitting diode-based 3D printers using digital light processing. The polymerization rate at this range is very fast and enables 3D printing that otherwise is impossible to perform without adding solvents. The TPO nanoparticles were prepared by rapid conversion of volatile microemulsions into water-dispersible powder, a process that can be used for a variety of photoinitiators. Such water-dispersible photoinitiator nanoparticles open many opportunities to enable rapid 3D printing of structures prepared in aqueous solutions while bringing environmental advantages by using low-energy curing systems and avoiding the need for solvents.

Radiomic analysis in prediction of Human Papilloma Virus status.

PubMed

Yu, Kaixian; Zhang, Youyi; Yu, Yang; Huang, Chao; Liu, Rongjie; Li, Tengfei; Yang, Liuqing; Morris, Jeffrey S; Baladandayuthapani, Veerabhadran; Zhu, Hongtu

2017-12-01

Human Papilloma Virus (HPV) has been associated with oropharyngeal cancer prognosis. Traditionally the HPV status is tested through invasive lab test. Recently, the rapid development of statistical image analysis techniques has enabled precise quantitative analysis of medical images. The quantitative analysis of Computed Tomography (CT) provides a non-invasive way to assess HPV status for oropharynx cancer patients. We designed a statistical radiomics approach analyzing CT images to predict HPV status. Various radiomics features were extracted from CT scans, and analyzed using statistical feature selection and prediction methods. Our approach ranked the highest in the 2016 Medical Image Computing and Computer Assisted Intervention (MICCAI) grand challenge: Oropharynx Cancer (OPC) Radiomics Challenge, Human Papilloma Virus (HPV) Status Prediction. Further analysis on the most relevant radiomic features distinguishing HPV positive and negative subjects suggested that HPV positive patients usually have smaller and simpler tumors.

Rapid Benefit Indicator (RBI) Checklist Tool - Quick Start ...

EPA Pesticide Factsheets

The Rapid Benefits Indicators (RBI) approach consists of five steps and is outlined in Assessing the Benefits of Wetland Restoration – A Rapid Benefits Indicators Approach for Decision Makers. This checklist tool is intended to be used to record information as you answer the questions in that guide. When performing a Rapid Benefits Indicator (RBI) assessment on wetlands restoration site(s) results can be recorded and reviewed using this VBA enabled MS Excel Checklist Tool.

Development of a dynamic headspace gas chromatography-mass spectrometry method for on-site analysis of sulfur mustard degradation products in sediments.

PubMed

Magnusson, R; Nordlander, T; Östin, A

2016-01-15

Sampling teams performing work at sea in areas where chemical munitions may have been dumped require rapid and reliable analytical methods for verifying sulfur mustard leakage from suspected objects. Here we present such an on-site analysis method based on dynamic headspace GC-MS for analysis of five cyclic sulfur mustard degradation products that have previously been detected in sediments from chemical weapon dumping sites: 1,4-oxathiane, 1,3-dithiolane, 1,4-dithiane, 1,4,5-oxadithiephane, and 1,2,5-trithiephane. An experimental design involving authentic Baltic Sea sediments spiked with the target analytes was used to develop an optimized protocol for sample preparation, headspace extraction and analysis that afforded recoveries of up to 60-90%. The optimized method needs no organic solvents, uses only two grams of sediment on a dry weight basis and involves a unique sample presentation whereby sediment is spread uniformly as a thin layer inside the walls of a glass headspace vial. The method showed good linearity for analyte concentrations of 5-200 ng/g dw, good repeatability, and acceptable carry-over. The method's limits of detection for spiked sediment samples ranged from 2.5 to 11 μg/kg dw, with matrix interference being the main limiting factor. The instrumental detection limits were one to two orders of magnitude lower. Full-scan GC-MS analysis enabled the use of automated mass spectral deconvolution for rapid identification of target analytes. Using this approach, analytes could be identified in spiked sediment samples at concentrations down to 13-65 μg/kg dw. On-site validation experiments conducted aboard the research vessel R/V Oceania demonstrated the method's practical applicability, enabling the successful identification of four cyclic sulfur mustard degradation products at concentrations of 15-308μg/kg in sediments immediately after being collected near a wreck at the Bornholm Deep dumpsite in the Baltic Sea. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparison of dissimilarity measures for cluster analysis of X-ray diffraction data from combinatorial libraries

NASA Astrophysics Data System (ADS)

Iwasaki, Yuma; Kusne, A. Gilad; Takeuchi, Ichiro

2017-12-01

Machine learning techniques have proven invaluable to manage the ever growing volume of materials research data produced as developments continue in high-throughput materials simulation, fabrication, and characterization. In particular, machine learning techniques have been demonstrated for their utility in rapidly and automatically identifying potential composition-phase maps from structural data characterization of composition spread libraries, enabling rapid materials fabrication-structure-property analysis and functional materials discovery. A key issue in development of an automated phase-diagram determination method is the choice of dissimilarity measure, or kernel function. The desired measure reduces the impact of confounding structural data issues on analysis performance. The issues include peak height changes and peak shifting due to lattice constant change as a function of composition. In this work, we investigate the choice of dissimilarity measure in X-ray diffraction-based structure analysis and the choice of measure's performance impact on automatic composition-phase map determination. Nine dissimilarity measures are investigated for their impact in analyzing X-ray diffraction patterns for a Fe-Co-Ni ternary alloy composition spread. The cosine, Pearson correlation coefficient, and Jensen-Shannon divergence measures are shown to provide the best performance in the presence of peak height change and peak shifting (due to lattice constant change) when the magnitude of peak shifting is unknown. With prior knowledge of the maximum peak shifting, dynamic time warping in a normalized constrained mode provides the best performance. This work also serves to demonstrate a strategy for rapid analysis of a large number of X-ray diffraction patterns in general beyond data from combinatorial libraries.

Local Debonding and Fiber Breakage in Composite Materials Modeled Accurately

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2001-01-01

A prerequisite for full utilization of composite materials in aerospace components is accurate design and life prediction tools that enable the assessment of component performance and reliability. Such tools assist both structural analysts, who design and optimize structures composed of composite materials, and materials scientists who design and optimize the composite materials themselves. NASA Glenn Research Center's Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) software package (http://www.grc.nasa.gov/WWW/LPB/mac) addresses this need for composite design and life prediction tools by providing a widely applicable and accurate approach to modeling composite materials. Furthermore, MAC/GMC serves as a platform for incorporating new local models and capabilities that are under development at NASA, thus enabling these new capabilities to progress rapidly to a stage in which they can be employed by the code's end users.

Tablet PC Enabled Body Sensor System for Rural Telehealth Applications

PubMed Central

Panicker, Nitha V.; Kumar, A. Sukesh

2016-01-01

Telehealth systems benefit from the rapid growth of mobile communication technology for measuring physiological signals. Development and validation of a tablet PC enabled noninvasive body sensor system for rural telehealth application are discussed in this paper. This system includes real time continuous collection of physiological parameters (blood pressure, pulse rate, and temperature) and fall detection of a patient with the help of a body sensor unit and wireless transmission of the acquired information to a tablet PC handled by the medical staff in a Primary Health Center (PHC). Abnormal conditions are automatically identified and alert messages are given to the medical officer in real time. Clinical validation is performed in a real environment and found to be successful. Bland-Altman analysis is carried out to validate the wrist blood pressure sensor used. The system works well for all measurements. PMID:26884757

Rapid Gorge Formation in an Artificially Created Waterfall

NASA Astrophysics Data System (ADS)

Anton, L.; Mather, A. E.; Stokes, M.; Munoz Martin, A.

2014-12-01

A number of studies have examined rates of gorge formation, nick point retreat, and the controls on those rates via bedrock erodibility, the effectiveness of bedrock erosion mechanisms and the role of hillslope processes. Most findings are based on conceptual / empirical models or long term landscape analysis; but studies of recent quantifiable events are scarce yet highly valuable. Here we present expert eye witness account and quantitative survey of large and rapid fluvial erosion events that occurred over an artificially created waterfall at a spillway mouth. In 6 years a ~270 m long, ~100 m deep and ~100 to 160 m wide canyon was carved, and ~1.58 x106 m3 of granite bedrock was removed from the spillway site. Available flow data indicates that the erosion took place under unremarkable flood discharge conditions. The analysis of historic topographic maps enables the reconstruction of the former topography and successive erosion events, enabling the quantification of bedrock erosion amounts, and rates. Analysis of bedrock erodibility and discontinuity patterns demonstrates that the bedrock is mechanically strong, and that similar rock strength and fracture patterns are found throughout the region. It is apparent that structural pre-conditioning through fracture density and orientation in relation to flow and slope direction is of paramount importance in the gorge development. The presented example provides an exceptional opportunity for studying the evolution process of a bedrock canyon and to precisely measure the rate of bedrock channel erosion over a six year period. Results illustrate the highly episodic nature of the erosion and highlight several key observations for the adjustability of bedrock rivers. The observations have implications for the efficiency of bedrock erosion and raise important questions about incision rates, driving mechanisms and timescale assumptions' in models of landscape change.

Short tandem repeat profiling: part of an overall strategy for reducing the frequency of cell misidentification.

PubMed

Nims, Raymond W; Sykes, Greg; Cottrill, Karin; Ikonomi, Pranvera; Elmore, Eugene

2010-12-01

The role of cell authentication in biomedical science has received considerable attention, especially within the past decade. This quality control attribute is now beginning to be given the emphasis it deserves by granting agencies and by scientific journals. Short tandem repeat (STR) profiling, one of a few DNA profiling technologies now available, is being proposed for routine identification (authentication) of human cell lines, stem cells, and tissues. The advantage of this technique over methods such as isoenzyme analysis, karyotyping, human leukocyte antigen typing, etc., is that STR profiling can establish identity to the individual level, provided that the appropriate number and types of loci are evaluated. To best employ this technology, a standardized protocol and a data-driven, quality-controlled, and publically searchable database will be necessary. This public STR database (currently under development) will enable investigators to rapidly authenticate human-based cultures to the individual from whom the cells were sourced. Use of similar approaches for non-human animal cells will require developing other suitable loci sets. While implementing STR analysis on a more routine basis should significantly reduce the frequency of cell misidentification, additional technologies may be needed as part of an overall authentication paradigm. For instance, isoenzyme analysis, PCR-based DNA amplification, and sequence-based barcoding methods enable rapid confirmation of a cell line's species of origin while screening against cross-contaminations, especially when the cells present are not recognized by the species-specific STR method. Karyotyping may also be needed as a supporting tool during establishment of an STR database. Finally, good cell culture practices must always remain a major component of any effort to reduce the frequency of cell misidentification.

Simultaneous dispersive liquid-liquid microextraction derivatisation and gas chromatography mass spectrometry analysis of subcritical water extracts of sweet and sour cherry stems.

PubMed

Švarc-Gajić, Jaroslava; Clavijo, Sabrina; Suárez, Ruth; Cvetanović, Aleksandra; Cerdà, Víctor

2018-03-01

Cherry stems have been used in traditional medicine mostly for the treatment of urinary tract infections. Extraction with subcritical water, according to its selectivity, efficiency and other aspects, differs substantially from conventional extraction techniques. The complexity of plant subcritical water extracts is due to the ability of subcritical water to extract different chemical classes of different physico-chemical properties and polarities in a single run. In this paper, dispersive liquid-liquid microextraction (DLLME) with simultaneous derivatisation was optimised for the analysis of complex subcritical water extracts of cherry stems to allow simple and rapid preparation prior to gas chromatography-mass spectrometry (GC-MS). After defining optimal extracting and dispersive solvents, the optimised method was used for the identification of compounds belonging to different chemical classes in a single analytical run. The developed sample preparation protocol enabled simultaneous extraction and derivatisation, as well as convenient coupling with GC-MS analysis, reducing the analysis time and number of steps. The applied analytical protocol allowed simple and rapid chemical screening of subcritical water extracts and was used for the comparison of subcritical water extracts of sweet and sour cherry stems. Graphical abstract DLLME GC MS analysis of cherry stem extracts obtained by subcritical water.

A method for the rapid detection of urinary tract infections.

PubMed

Olsson, Carl; Kapoor, Deepak; Howard, Glenn

2012-04-01

To determine the reliability of a rapid detection method compared with the reference standard streaked agar plate in diagnosing the presence of urinary tract infection (UTI). De-identified clean catch urine specimens from 980 office visit patients were processed during a 30-day period. Classic 1-μL and 10-μL streaked agar plates were used in parallel with the new CultureStat Rapid UTI Detection System (CSRUDS). Urine results were evaluated using the CSRUDS at 30 and 90 minutes after collection. A comparative analysis of the subsequent plate results versus the CSRUDS results was achieved for 973 of these samples. Positive UTI conditions were accurately identified by both CSRUDS and agar streak plate methods. CSRUDS accurately identified UTI negative conditions with 99.3% reliability at 90 minutes. The negative predictive value of CSRUDS was 99.2% at 30 minutes. Current agar plating for first-round UTI screening has substantial documented problems that can negatively affect an accurate and timely UTI diagnosis. A novel rapid detection system, the CSRUDS provides UTI negative/positive same-day results in ≤ 90 minutes from the start of test. Such rapidly available results will enable more accurate and timely clinical decisions to be made in the urology office, particularly regarding infection status before urologic instrumentation. Copyright © 2012 Elsevier Inc. All rights reserved.

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.

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

Mitochondria-Endoplasmic Reticulum Contact Sites Function as Immunometabolic Hubs that Orchestrate the Rapid Recall Response of Memory CD8+ T Cells.

PubMed

Bantug, Glenn R; Fischer, Marco; Grählert, Jasmin; Balmer, Maria L; Unterstab, Gunhild; Develioglu, Leyla; Steiner, Rebekah; Zhang, Lianjun; Costa, Ana S H; Gubser, Patrick M; Burgener, Anne-Valérie; Sauder, Ursula; Löliger, Jordan; Belle, Réka; Dimeloe, Sarah; Lötscher, Jonas; Jauch, Annaïse; Recher, Mike; Hönger, Gideon; Hall, Michael N; Romero, Pedro; Frezza, Christian; Hess, Christoph

2018-03-20

Glycolysis is linked to the rapid response of memory CD8 + T cells, but the molecular and subcellular structural elements enabling enhanced glucose metabolism in nascent activated memory CD8 + T cells are unknown. We found that rapid activation of protein kinase B (PKB or AKT) by mammalian target of rapamycin complex 2 (mTORC2) led to inhibition of glycogen synthase kinase 3β (GSK3β) at mitochondria-endoplasmic reticulum (ER) junctions. This enabled recruitment of hexokinase I (HK-I) to the voltage-dependent anion channel (VDAC) on mitochondria. Binding of HK-I to VDAC promoted respiration by facilitating metabolite flux into mitochondria. Glucose tracing pinpointed pyruvate oxidation in mitochondria, which was the metabolic requirement for rapid generation of interferon-γ (IFN-γ) in memory T cells. Subcellular organization of mTORC2-AKT-GSK3β at mitochondria-ER contact sites, promoting HK-I recruitment to VDAC, thus underpins the metabolic reprogramming needed for memory CD8 + T cells to rapidly acquire effector function. Copyright © 2018 Elsevier Inc. All rights reserved.

Mass spectrometry in the palm of your hand: future applications of in vivo tissue analysis.

PubMed

Fox, Simon A; Farah, Camile S

2018-05-21

Assessment and diagnosis of oral mucosal disorders continues to present clinical challenges with conventional methodologies being time consuming and hampered by subjectivity. These considerations also apply to surgical excision of malignant and potentially malignant lesions where accurate assessment of margins is critical to patient outcomes. These clinical needs are driving the development of new technologies which can enable rapid diagnosis based upon characteristic molecular profiles identified through clinical science. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Use of Variable Pressure Suits, Intermittent Recompression and Nitrox Breathing Mixtures during Lunar Extravehicular Activities

NASA Technical Reports Server (NTRS)

Gernhardt, Michael L.; Abercromby, Andrew F.

2009-01-01

This slide presentation reviews the use of variable pressure suits, intermittent recompression and Nitrox breathing mixtures to allow for multiple short extravehicular activities (EVAs) at different locations in a day. This new operational concept of multiple short EVAs requires short purge times and shorter prebreathes to assure rapid egress with a minimal loss of the vehicular air. Preliminary analysis has begun to evaluate the potential benefits of the intermittent recompression, and Nitrox breathing mixtures when used with variable pressure suits to enable reduce purges and prebreathe durations.

[Diagnosis of tropical malaria by express-methods].

PubMed

Popov, A F; Nikiforov, N D; Ivanis, V A; Barkun, S P; Sanin, B I; Fed'kina, L I

2004-01-01

An examination of a thick blood drop and of blood smear for the presence of plasmodia is a classic and indisputable diagnostic test for tropic malaria. However, express-methods, based on the immune-enzyme analysis, have been introduced into the health-care practice primarily in developing and underdeveloped countries. The diagnosis of tropic malaria by using the discussed methods enables, in the non-laboratory settings, a rapid and reliable detection of PI. falciparum in blood. This is important because an untimely diagnosis of tropic malaria increases the risk of the lethal outcome.

A low power, on demand electrothermal valve for wireless drug delivery applications

PubMed Central

Li, Po-Ying; Givrad, Tina K.; Sheybani, Roya; Holschneider, Daniel P.; Maarek, Jean-Michel I.

2014-01-01

We present a low power, on demand Parylene MEMS electrothermal valve. A novel Ω-shaped thermal resistive element requires low power (~mW) and enables rapid valve opening (~ms). Using both finite element analysis and valve opening experiments, a robust resistive element design for improved valve opening performance in water was obtained. In addition, a thermistor, as an inrush current limiter, was added into the valve circuit to provide variable current ramping. Wireless activation of the valve using RF inductive power transfer was demonstrated. PMID:20024057

Rapid thermal annealing of CH 3 NH 3 PbI 3 perovskite thin films by intense pulsed light with aid of diiodomethane additive

DOE PAGES

Ankireddy, Krishnamraju; Ghahremani, Amir H.; Martin, Blake; ...

2018-01-01

Perovskite thin films are thermally annealed using a rapid intense pulsed light technique enabled by an alkyl halide that collectively improves device performance when processed in ambient conditions.

High-resolution CT assessment of the pediatric airways: structure and function

NASA Astrophysics Data System (ADS)

Kramer, Sandra S.; Hoffman, Eric A.; Amirav, Israel

1994-05-01

The airway has always been a central focus for respiratory pathology in infants and children. Imaging of the larynx, trachea, and the central bronchi can be readily accomplished by radiographic or conventional CT techniques. Newer high resolution CT (HRCT) techniques have extended our view of the bronchi peripherally to the limits of scanner resolution, i.e., to bronchial generations 7 - 9, and rapid volumetric CT data acquisitions have made it possible to follow the same lung anatomic level through the rapidly occurring changes in a series of experimental protocols. These techniques together with a custom designed computer software program for image display and analysis have enabled us to objectively study changes in airway caliber and lung density that occurred in an animal mode of airway reactivity and thereby relate structure with function in the airways.

Sequential microfluidic droplet processing for rapid DNA extraction.

PubMed

Pan, Xiaoyan; Zeng, Shaojiang; Zhang, Qingquan; Lin, Bingcheng; Qin, Jianhua

2011-11-01

This work describes a novel droplet-based microfluidic device, which enables sequential droplet processing for rapid DNA extraction. The microdevice consists of a droplet generation unit, two reagent addition units and three droplet splitting units. The loading/washing/elution steps required for DNA extraction were carried out by sequential microfluidic droplet processing. The movement of superparamagnetic beads, which were used as extraction supports, was controlled with magnetic field. The microdevice could generate about 100 droplets per min, and it took about 1 min for each droplet to perform the whole extraction process. The extraction efficiency was measured to be 46% for λ-DNA, and the extracted DNA could be used in subsequent genetic analysis such as PCR, demonstrating the potential of the device for fast DNA extraction. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Web-Enabled Systems for Student Access.

ERIC Educational Resources Information Center

Harris, Chad S.; Herring, Tom

1999-01-01

California State University, Fullerton is developing a suite of server-based, Web-enabled applications that distribute the functionality of its student information system software to external customers without modifying the mainframe applications or databases. The cost-effective, secure, and rapidly deployable business solution involves using the…

Magnetite-doped polydimethylsiloxane (PDMS) for phosphopeptide enrichment.

PubMed

Sandison, Mairi E; Jensen, K Tveen; Gesellchen, F; Cooper, J M; Pitt, A R

2014-10-07

Reversible phosphorylation plays a key role in numerous biological processes. Mass spectrometry-based approaches are commonly used to analyze protein phosphorylation, but such analysis is challenging, largely due to the low phosphorylation stoichiometry. Hence, a number of phosphopeptide enrichment strategies have been developed, including metal oxide affinity chromatography (MOAC). Here, we describe a new material for performing MOAC that employs a magnetite-doped polydimethylsiloxane (PDMS), that is suitable for the creation of microwell array and microfluidic systems to enable low volume, high throughput analysis. Incubation time and sample loading were explored and optimized and demonstrate that the embedded magnetite is able to enrich phosphopeptides. This substrate-based approach is rapid, straightforward and suitable for simultaneously performing multiple, low volume enrichments.

Wide-Field Imaging of Single-Nanoparticle Extinction with Sub-nm2 Sensitivity

NASA Astrophysics Data System (ADS)

Payne, Lukas M.; Langbein, Wolfgang; Borri, Paola

2018-03-01

We report on a highly sensitive wide-field imaging technique for quantitative measurement of the optical extinction cross section σext of single nanoparticles. The technique is simple and high speed, and it enables the simultaneous acquisition of hundreds of nanoparticles for statistical analysis. Using rapid referencing, fast acquisition, and a deconvolution analysis, a shot-noise-limited sensitivity down to 0.4 nm2 is achieved. Measurements on a set of individual gold nanoparticles of 5 nm diameter using this method yield σext=(10.0 ±3.1 ) nm2, which is consistent with theoretical expectations and well above the background fluctuations of 0.9 nm2 .

A Fully Non-Metallic Gas Turbine Engine Enabled by Additive Manufacturing

NASA Technical Reports Server (NTRS)

Grady, Joseph E.

2015-01-01

The Non-Metallic Gas Turbine Engine project, funded by NASA Aeronautics Research Institute, represents the first comprehensive evaluation of emerging materials and manufacturing technologies that will enable fully nonmetallic gas turbine engines. This will be achieved by assessing the feasibility of using additive manufacturing technologies to fabricate polymer matrix composite and ceramic matrix composite turbine engine components. The benefits include: 50 weight reduction compared to metallic parts, reduced manufacturing costs, reduced part count and rapid design iterations. Two high payoff metallic components have been identified for replacement with PMCs and will be fabricated using fused deposition modeling (FDM) with high temperature polymer filaments. The CMC effort uses a binder jet process to fabricate silicon carbide test coupons and demonstration articles. Microstructural analysis and mechanical testing will be conducted on the PMC and CMC materials. System studies will assess the benefits of fully nonmetallic gas turbine engine in terms of fuel burn, emissions, reduction of part count, and cost. The research project includes a multidisciplinary, multiorganization NASA - industry team that includes experts in ceramic materials and CMCs, polymers and PMCs, structural engineering, additive manufacturing, engine design and analysis, and system analysis.

The NHERI RAPID Facility: Enabling the Next-Generation of Natural Hazards Reconnaissance

NASA Astrophysics Data System (ADS)

Wartman, J.; Berman, J.; Olsen, M. J.; Irish, J. L.; Miles, S.; Gurley, K.; Lowes, L.; Bostrom, A.

2017-12-01

The NHERI post-disaster, rapid response research (or "RAPID") facility, headquartered at the University of Washington (UW), is a collaboration between UW, Oregon State University, Virginia Tech, and the University of Florida. The RAPID facility will enable natural hazard researchers to conduct next-generation quick response research through reliable acquisition and community sharing of high-quality, post-disaster data sets that will enable characterization of civil infrastructure performance under natural hazard loads, evaluation of the effectiveness of current and previous design methodologies, understanding of socio-economic dynamics, calibration of computational models used to predict civil infrastructure component and system response, and development of solutions for resilient communities. The facility will provide investigators with the hardware, software and support services needed to collect, process and assess perishable interdisciplinary data following extreme natural hazard events. Support to the natural hazards research community will be provided through training and educational activities, field deployment services, and by promoting public engagement with science and engineering. Specifically, the RAPID facility is undertaking the following strategic activities: (1) acquiring, maintaining, and operating state-of-the-art data collection equipment; (2) developing and supporting mobile applications to support interdisciplinary field reconnaissance; (3) providing advisory services and basic logistics support for research missions; (4) facilitating the systematic archiving, processing and visualization of acquired data in DesignSafe-CI; (5) training a broad user base through workshops and other activities; and (6) engaging the public through citizen science, as well as through community outreach and education. The facility commenced operations in September 2016 and will begin field deployments beginning in September 2018. This poster will provide an overview of the vision for the RAPID facility, the equipment that will be available for use, the facility's operations, and opportunities for user training and facility use.

Gradient elution moving boundary electrophoresis enables rapid analysis of acids in complex biomass-derived streams

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

Munson, Matthew S.; Karp, Eric M.; Nimlos, Claire T.

Biomass conversion processes such as pretreatment, liquefaction, and pyrolysis often produce complex mixtures of intermediates that are a substantial challenge to analyze rapidly and reliably. To characterize these streams more comprehensively and efficiently, new techniques are needed to track species through biomass deconstruction and conversion processes. Here, we present the application of an emerging analytical method, gradient elution moving boundary electrophoresis (GEMBE), to quantify a suite of acids in a complex, biomass-derived streams from alkaline pretreatment of corn stover. GEMBE offers distinct advantages over common chromatography-spectrometry analytical approaches in terms of analysis time, sample preparation requirements, and cost of equipment.more » As demonstrated here, GEMBE is able to track 17 distinct compounds (oxalate, formate, succinate, malate, acetate, glycolate, protocatechuate, 3-hydroxypropanoate, lactate, glycerate, 2-hydroxybutanoate, 4-hydroxybenzoate, vanillate, p-coumarate, ferulate, sinapate, and acetovanillone). The lower limit of detection was compound dependent and ranged between 0.9 and 3.5 umol/L. Results from GEMBE were similar to recent results from an orthogonal method based on GCxGC-TOF/MS. Altogether, GEMBE offers a rapid, robust approach to analyze complex biomass-derived samples, and given the ease and convenience of deployment, may offer an analytical solution for online tracking of multiple types of biomass streams.« less

Rapid prototyping of an EEG-based brain-computer interface (BCI).

PubMed

Guger, C; Schlögl, A; Neuper, C; Walterspacher, D; Strein, T; Pfurtscheller, G

2001-03-01

The electroencephalogram (EEG) is modified by motor imagery and can be used by patients with severe motor impairments (e.g., late stage of amyotrophic lateral sclerosis) to communicate with their environment. Such a direct connection between the brain and the computer is known as an EEG-based brain-computer interface (BCI). This paper describes a new type of BCI system that uses rapid prototyping to enable a fast transition of various types of parameter estimation and classification algorithms to real-time implementation and testing. Rapid prototyping is possible by using Matlab, Simulink, and the Real-Time Workshop. It is shown how to automate real-time experiments and perform the interplay between on-line experiments and offline analysis. The system is able to process multiple EEG channels on-line and operates under Windows 95 in real-time on a standard PC without an additional digital signal processor (DSP) board. The BCI can be controlled over the Internet, LAN or modem. This BCI was tested on 3 subjects whose task it was to imagine either left or right hand movement. A classification accuracy between 70% and 95% could be achieved with two EEG channels after some sessions with feedback using an adaptive autoregressive (AAR) model and linear discriminant analysis (LDA).

An Efficient and Rapid Method to Monitor the Oxidative Degradation of Protein Pharmaceuticals: Probing Tyrosine Oxidation with Fluorogenic Derivatization.

PubMed

Bommana, Rupesh; Mozziconacci, Olivier; John Wang, Y; Schöneich, Christian

2017-07-01

The loss of potency of protein therapeutics can be linked to the oxidation of specific amino acid residues leading to a great variety of oxidative modifications. The comprehensive identification of these oxidative modifications requires high-resolution mass spectrometry analysis, which requires time and expensive resources. Here, we propose a fluorogenic derivatization method of oxidized Tyr and Phe yielding benzoxazole derivatives, as an orthogonal technique for the rapid screening of protein oxidation. Four model proteins, IgG1, human growth hormone (hGH), insulin and bovine serum albumin (BSA) were exposed to oxidation via peroxyl radicals and metal-catalyzed reactions and efficiently screened by fluorogenic derivatization of Tyr and Phe oxidation products. Complementary LC-MS analysis was done to identify the extent of methionine oxidation in oxidized proteins. The Fluorogenic derivatization technique can easily be adapted to a 96-well plate, in which several protein formulations can be screened in short time. Representatively for hGH, we show that the formation of benzoxazole parallels the oxidation of Met to methionine sulfoxide which enables estimation of Met oxidation by just recording the fluorescence. Our rapid fluorescence based screening allows for the fast comparison of the stability of multiple formulations.

Gradient elution moving boundary electrophoresis enables rapid analysis of acids in complex biomass-derived streams

DOE PAGES

Munson, Matthew S.; Karp, Eric M.; Nimlos, Claire T.; ...

2016-09-27

Biomass conversion processes such as pretreatment, liquefaction, and pyrolysis often produce complex mixtures of intermediates that are a substantial challenge to analyze rapidly and reliably. To characterize these streams more comprehensively and efficiently, new techniques are needed to track species through biomass deconstruction and conversion processes. Here, we present the application of an emerging analytical method, gradient elution moving boundary electrophoresis (GEMBE), to quantify a suite of acids in a complex, biomass-derived streams from alkaline pretreatment of corn stover. GEMBE offers distinct advantages over common chromatography-spectrometry analytical approaches in terms of analysis time, sample preparation requirements, and cost of equipment.more » As demonstrated here, GEMBE is able to track 17 distinct compounds (oxalate, formate, succinate, malate, acetate, glycolate, protocatechuate, 3-hydroxypropanoate, lactate, glycerate, 2-hydroxybutanoate, 4-hydroxybenzoate, vanillate, p-coumarate, ferulate, sinapate, and acetovanillone). The lower limit of detection was compound dependent and ranged between 0.9 and 3.5 umol/L. Results from GEMBE were similar to recent results from an orthogonal method based on GCxGC-TOF/MS. Altogether, GEMBE offers a rapid, robust approach to analyze complex biomass-derived samples, and given the ease and convenience of deployment, may offer an analytical solution for online tracking of multiple types of biomass streams.« less

K-Channel: A Multifunctional Architecture for Dynamically Reconfigurable Sample Processing in Droplet Microfluidics.

PubMed

Doonan, Steven R; Bailey, Ryan C

2017-04-04

By rapidly creating libraries of thousands of unique, miniaturized reactors, droplet microfluidics provides a powerful method for automating high-throughput chemical analysis. In order to engineer in-droplet assays, microfluidic devices must add reagents into droplets, remove fluid from droplets, and perform other necessary operations, each typically provided by a unique, specialized geometry. Unfortunately, modifying device performance or changing operations usually requires re-engineering the device among these specialized geometries, a time-consuming and costly process when optimizing in-droplet assays. To address this challenge in implementing droplet chemistry, we have developed the "K-channel," which couples a cross-channel flow to the segmented droplet flow to enable a range of operations on passing droplets. K-channels perform reagent injection (0-100% of droplet volume), fluid extraction (0-50% of droplet volume), and droplet splitting (1:1-1:5 daughter droplet ratio). Instead of modifying device dimensions or channel configuration, adjusting external conditions, such as applied pressure and electric field, selects the K-channel process and tunes its magnitude. Finally, interfacing a device-embedded magnet allows selective capture of 96% of droplet-encapsulated superparamagnetic beads during 1:1 droplet splitting events at ∼400 Hz. Addition of a second K-channel for injection (after the droplet splitting K-channel) enables integrated washing of magnetic beads within rapidly moving droplets. Ultimately, the K-channel provides an exciting opportunity to perform many useful droplet operations across a range of magnitudes without requiring architectural modifications. Therefore, we envision the K-channel as a versatile, easy to use microfluidic component enabling diverse, in-droplet (bio)chemical manipulations.

Rapid Covalent Fluorescence Labeling of Membrane Proteins on Live Cells via Coiled-Coil Templated Acyl Transfer.

PubMed

Reinhardt, Ulrike; Lotze, Jonathan; Mörl, Karin; Beck-Sickinger, Annette G; Seitz, Oliver

2015-10-21

Fluorescently labeled proteins enable the microscopic imaging of protein localization and function in live cells. In labeling reactions targeted against specific tag sequences, the size of the fluorophore-tag is of major concern. The tag should be small to prevent interference with protein function. Furthermore, rapid and covalent labeling methods are desired to enable the analysis of fast biological processes. Herein, we describe the development of a method in which the formation of a parallel coiled coil triggers the transfer of a fluorescence dye from a thioester-linked coil peptide conjugate onto a cysteine-modified coil peptide. This labeling method requires only small tag sequences (max 23 aa) and occurs with high tag specificity. We show that size matching of the coil peptides and a suitable thioester reactivity allow the acyl transfer reaction to proceed within minutes (rather than hours). We demonstrate the versatility of this method by applying it to the labeling of different G-protein coupled membrane receptors including the human neuropeptide Y receptors 1, 2, 4, 5, the neuropeptide FF receptors 1 and 2, and the dopamine receptor 1. The labeled receptors are fully functional and able to bind the respective ligand with high affinity. Activity is not impaired as demonstrated by activation, internalization, and recycling experiments.

Single-neuron identification of chemical constituents, physiological changes, and metabolism using mass spectrometry.

PubMed

Zhu, Hongying; Zou, Guichang; Wang, Ning; Zhuang, Meihui; Xiong, Wei; Huang, Guangming

2017-03-07

The use of single-cell assays has emerged as a cutting-edge technique during the past decade. Although single-cell mass spectrometry (MS) has recently achieved remarkable results, deep biological insights have not yet been obtained, probably because of various technical issues, including the unavoidable use of matrices, the inability to maintain cell viability, low throughput because of sample pretreatment, and the lack of recordings of cell physiological activities from the same cell. In this study, we describe a patch clamp/MS-based platform that enables the sensitive, rapid, and in situ chemical profiling of single living neurons. This approach integrates modified patch clamp technique and modified MS measurements to directly collect and detect nanoliter-scale samples from the cytoplasm of single neurons in mice brain slices. Abundant possible cytoplasmic constituents were detected in a single neuron at a relatively fast rate, and over 50 metabolites were identified in this study. The advantages of direct, rapid, and in situ sampling and analysis enabled us to measure the biological activities of the cytoplasmic constituents in a single neuron, including comparing neuron types by cytoplasmic chemical constituents; observing changes in constituent concentrations as the physiological conditions, such as age, vary; and identifying the metabolic pathways of small molecules.

Single-neuron identification of chemical constituents, physiological changes, and metabolism using mass spectrometry

PubMed Central

Zhu, Hongying; Zou, Guichang; Wang, Ning; Zhuang, Meihui; Xiong, Wei; Huang, Guangming

2017-01-01

The use of single-cell assays has emerged as a cutting-edge technique during the past decade. Although single-cell mass spectrometry (MS) has recently achieved remarkable results, deep biological insights have not yet been obtained, probably because of various technical issues, including the unavoidable use of matrices, the inability to maintain cell viability, low throughput because of sample pretreatment, and the lack of recordings of cell physiological activities from the same cell. In this study, we describe a patch clamp/MS-based platform that enables the sensitive, rapid, and in situ chemical profiling of single living neurons. This approach integrates modified patch clamp technique and modified MS measurements to directly collect and detect nanoliter-scale samples from the cytoplasm of single neurons in mice brain slices. Abundant possible cytoplasmic constituents were detected in a single neuron at a relatively fast rate, and over 50 metabolites were identified in this study. The advantages of direct, rapid, and in situ sampling and analysis enabled us to measure the biological activities of the cytoplasmic constituents in a single neuron, including comparing neuron types by cytoplasmic chemical constituents; observing changes in constituent concentrations as the physiological conditions, such as age, vary; and identifying the metabolic pathways of small molecules. PMID:28223513

Mojo Hand, a TALEN design tool for genome editing applications.

PubMed

Neff, Kevin L; Argue, David P; Ma, Alvin C; Lee, Han B; Clark, Karl J; Ekker, Stephen C

2013-01-16

Recent studies of transcription activator-like (TAL) effector domains fused to nucleases (TALENs) demonstrate enormous potential for genome editing. Effective design of TALENs requires a combination of selecting appropriate genetic features, finding pairs of binding sites based on a consensus sequence, and, in some cases, identifying endogenous restriction sites for downstream molecular genetic applications. We present the web-based program Mojo Hand for designing TAL and TALEN constructs for genome editing applications (http://www.talendesign.org). We describe the algorithm and its implementation. The features of Mojo Hand include (1) automatic download of genomic data from the National Center for Biotechnology Information, (2) analysis of any DNA sequence to reveal pairs of binding sites based on a user-defined template, (3) selection of restriction-enzyme recognition sites in the spacer between the TAL monomer binding sites including options for the selection of restriction enzyme suppliers, and (4) output files designed for subsequent TALEN construction using the Golden Gate assembly method. Mojo Hand enables the rapid identification of TAL binding sites for use in TALEN design. The assembly of TALEN constructs, is also simplified by using the TAL-site prediction program in conjunction with a spreadsheet management aid of reagent concentrations and TALEN formulation. Mojo Hand enables scientists to more rapidly deploy TALENs for genome editing applications.

Fast-responder: Rapid mobile-phone access to recent remote sensing imagery for first responders

NASA Astrophysics Data System (ADS)

Talbot, L. M.; Talbot, B. G.

We introduce Fast-Responder, a novel prototype data-dissemination application and architecture concept to rapidly deliver remote sensing imagery to smartphones to enable situational awareness. The architecture implements a Fast-Earth image caching system on the phone and interacts with a Fast-Earth server. Prototype evaluation successfully demonstrated that National Guard users could select a location, download multiple remote sensing images, and flicker between images, all in less than a minute on a 3G mobile commercial link. The Fast-Responder architecture is a significant advance that is designed to meet the needs of mobile users, such as National Guard response units, to rapidly access information during a crisis, such as a natural or man-made disaster. This paper focuses on the architecture design and advanced user interface concepts for small-screens for highly active mobile users. Novel Fast-Responder concepts can also enable rapid dissemination and evaluation of imagery on the desktop, opening new technology horizons for both desktop and mobile users.

Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics.

PubMed

Dutheil, Julien; Gaillard, Sylvain; Bazin, Eric; Glémin, Sylvain; Ranwez, Vincent; Galtier, Nicolas; Belkhir, Khalid

2006-04-04

A large number of bioinformatics applications in the fields of bio-sequence analysis, molecular evolution and population genetics typically share input/output methods, data storage requirements and data analysis algorithms. Such common features may be conveniently bundled into re-usable libraries, which enable the rapid development of new methods and robust applications. We present Bio++, a set of Object Oriented libraries written in C++. Available components include classes for data storage and handling (nucleotide/amino-acid/codon sequences, trees, distance matrices, population genetics datasets), various input/output formats, basic sequence manipulation (concatenation, transcription, translation, etc.), phylogenetic analysis (maximum parsimony, markov models, distance methods, likelihood computation and maximization), population genetics/genomics (diversity statistics, neutrality tests, various multi-locus analyses) and various algorithms for numerical calculus. Implementation of methods aims at being both efficient and user-friendly. A special concern was given to the library design to enable easy extension and new methods development. We defined a general hierarchy of classes that allow the developer to implement its own algorithms while remaining compatible with the rest of the libraries. Bio++ source code is distributed free of charge under the CeCILL general public licence from its website http://kimura.univ-montp2.fr/BioPP.

A Semi-Automatic Method for Image Analysis of Edge Dynamics in Living Cells

PubMed Central

Huang, Lawrence; Helmke, Brian P.

2011-01-01

Spatial asymmetry of actin edge ruffling contributes to the process of cell polarization and directional migration, but mechanisms by which external cues control actin polymerization near cell edges remain unclear. We designed a quantitative image analysis strategy to measure the spatiotemporal distribution of actin edge ruffling. Time-lapse images of endothelial cells (ECs) expressing mRFP-actin were segmented using an active contour method. In intensity line profiles oriented normal to the cell edge, peak detection identified the angular distribution of polymerized actin within 1 µm of the cell edge, which was localized to lamellipodia and edge ruffles. Edge features associated with filopodia and peripheral stress fibers were removed. Circular statistical analysis enabled detection of cell polarity, indicated by a unimodal distribution of edge ruffles. To demonstrate the approach, we detected a rapid, nondirectional increase in edge ruffling in serum-stimulated ECs and a change in constitutive ruffling orientation in quiescent, nonpolarized ECs. Error analysis using simulated test images demonstrate robustness of the method to variations in image noise levels, edge ruffle arc length, and edge intensity gradient. These quantitative measurements of edge ruffling dynamics enable investigation at the cellular length scale of the underlying molecular mechanisms regulating actin assembly and cell polarization. PMID:21643526

Adaptable data management for systems biology investigations

PubMed Central

Boyle, John; Rovira, Hector; Cavnor, Chris; Burdick, David; Killcoyne, Sarah; Shmulevich, Ilya

2009-01-01

Background Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ranges from in-house protocols through to high-throughput instrumentation. To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage. Results The adaptable data management system discussed is designed to support the seamless mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, flow cytometry). We use different content graphs to represent different views upon the data. These views are designed for different roles: equipment specific views are used to gather instrumentation information; data processing oriented views are provided to enable the rapid development of analysis applications; and research project specific views are used to organize information for individual research experiments. This management system allows for both the rapid introduction of new types of information and the evolution of the knowledge it represents. Conclusion Data management is an important aspect of any research enterprise. It is the foundation on which most applications are built, and must be easily extended to serve new functionality for new scientific areas. We have found that adopting a three-tier architecture for data management, built around distributed standardized content repositories, allows us to rapidly develop new applications to support a diverse user community. PMID:19265554

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.

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

PubMed Central

Deutsch, Eric W.; Mendoza, Luis; Shteynberg, David; Slagel, Joseph; Sun, Zhi; Moritz, Robert L.

2015-01-01

Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include mass spectrometry to define protein sequence, protein:protein interactions, and protein post-translational modifications. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative mass spectrometry proteomics. It supports all major operating systems and instrument vendors via open data formats. Here we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of tandem mass spectrometry datasets, as well as some major upcoming features. PMID:25631240

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.

PubMed

Deutsch, Eric W; Mendoza, Luis; Shteynberg, David; Slagel, Joseph; Sun, Zhi; Moritz, Robert L

2015-08-01

Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include MS to define protein sequence, protein:protein interactions, and protein PTMs. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative MS proteomics. It supports all major operating systems and instrument vendors via open data formats. Here, we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of MS/MS datasets, as well as some major upcoming features. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Best practices for germ-free derivation and gnotobiotic zebrafish husbandry

PubMed Central

Melancon, E.; De La Torre Canny, S. Gomez; Sichel, S.; Kelly, M.; Wiles, T.J.; Rawls, J.F.; Eisen, J.S.; Guillemin, K.

2017-01-01

All animals are ecosystems with resident microbial communities, referred to as microbiota, which play profound roles in host development, physiology, and evolution. Enabled by new DNA sequencing technologies, there is a burgeoning interest in animal–microbiota interactions, but dissecting the specific impacts of microbes on their hosts is experimentally challenging. Gnotobiology, the study of biological systems in which all members are known, enables precise experimental analysis of the necessity and sufficiency of microbes in animal biology by deriving animals germ-free (GF) and inoculating them with defined microbial lineages. Mammalian host models have long dominated gnotobiology, but we have recently adapted gnotobiotic approaches to the zebrafish (Danio rerio), an important aquatic model. Zebrafish offer several experimental attributes that enable rapid, large-scale gnotobiotic experimentation with high replication rates and exquisite optical resolution. Here we describe detailed protocols for three procedures that form the foundation of zebrafish gnotobiology: derivation of GF embryos, microbial association of GF animals, and long-term, GF husbandry. Our aim is to provide sufficient guidance in zebrafish gnotobiotic methodology to expand and enrich this exciting field of research. PMID:28129860

In-air microfluidics: Drop and jet coalescence enables rapid multi-phase 3D printing

NASA Astrophysics Data System (ADS)

Visser, Claas Willem; Kamperman, Tom; Lohse, Detlef; Karperien, Marcel; University of Twente Collaboration

2016-11-01

For the first time, we connect and integrate the fields of microfluidics and additive manufacturing, by presenting a unifying technology that we call In-air microfluidics (IAMF). We impact two liquid jets or a jet and a droplet train while flying in-air, and control their coalescence and solidification. This approach enables producing monodisperse emulsions, particles, and fibers with controlled shape and size (10 to 300 µm) and production rates 100x higher than droplet microfluidics. A single device is sufficient to process a variety of materials, and to produce different particle or fiber shapes, in marked contrast to current microfluidic devices or printers. In-air microfluidics also enables rapid deposition onto substrates, for example to form 3D printed (bio)materials which are partly-liquid but still shape-stable.

Rapid and accurate peripheral nerve detection using multipoint Raman imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kumamoto, Yasuaki; Minamikawa, Takeo; Kawamura, Akinori; Matsumura, Junichi; Tsuda, Yuichiro; Ukon, Juichiro; Harada, Yoshinori; Tanaka, Hideo; Takamatsu, Tetsuro

2017-02-01

Nerve-sparing surgery is essential to avoid functional deficits of the limbs and organs. Raman scattering, a label-free, minimally invasive, and accurate modality, is one of the best candidate technologies to detect nerves for nerve-sparing surgery. However, Raman scattering imaging is too time-consuming to be employed in surgery. Here we present a rapid and accurate nerve visualization method using a multipoint Raman imaging technique that has enabled simultaneous spectra measurement from different locations (n=32) of a sample. Five sec is sufficient for measuring n=32 spectra with good S/N from a given tissue. Principal component regression discriminant analysis discriminated spectra obtained from peripheral nerves (n=863 from n=161 myelinated nerves) and connective tissue (n=828 from n=121 tendons) with sensitivity and specificity of 88.3% and 94.8%, respectively. To compensate the spatial information of a multipoint-Raman-derived tissue discrimination image that is too sparse to visualize nerve arrangement, we used morphological information obtained from a bright-field image. When merged with the sparse tissue discrimination image, a morphological image of a sample shows what portion of Raman measurement points in arbitrary structure is determined as nerve. Setting a nerve detection criterion on the portion of "nerve" points in the structure as 40% or more, myelinated nerves (n=161) and tendons (n=121) were discriminated with sensitivity and specificity of 97.5%. The presented technique utilizing a sparse multipoint Raman image and a bright-field image has enabled rapid, safe, and accurate detection of peripheral nerves.

Analysis of air-, moisture- and solvent-sensitive chemical compounds by mass spectrometry using an inert atmospheric pressure solids analysis probe.

PubMed

Mosely, Jackie A; Stokes, Peter; Parker, David; Dyer, Philip W; Messinis, Antonis M

2018-02-01

A novel method has been developed that enables chemical compounds to be transferred from an inert atmosphere glove box and into the atmospheric pressure ion source of a mass spectrometer whilst retaining a controlled chemical environment. This innovative method is simple and cheap to implement on some commercially available mass spectrometers. We have termed this approach inert atmospheric pressure solids analysis probe ( iASAP) and demonstrate the benefit of this methodology for two air-/moisture-sensitive chemical compounds whose characterisation by mass spectrometry is now possible and easily achieved. The simplicity of the design means that moving between iASAP and standard ASAP is straightforward and quick, providing a highly flexible platform with rapid sample turnaround.

A single use electrochemical sensor based on biomimetic nanoceria for the detection of wine antioxidants.

PubMed

Andrei, Veronica; Sharpe, Erica; Vasilescu, Alina; Andreescu, Silvana

2016-08-15

We report the development and characterization of a disposable single use electrochemical sensor based on the oxidase-like activity of nanoceria particles for the detection of phenolic antioxidants. The use of nanoceria in the sensor design enables oxidation of phenolic compounds, particularly those with ortho-dihydroxybenzene functionality, to their corresponding quinones at the surface of a screen printed carbon electrode. Detection is carried out by electrochemical reduction of the resulting quinone at a low applied potential of -0.1V vs the Ag/AgCl electrode. The sensor was optimized and characterized with respect to particle loading, applied potential, response time, detection limit, linear concentration range and sensitivity. The method enabled rapid detection of common phenolic antioxidants including caffeic acid, gallic acid and quercetin in the µM concentration range, and demonstrated good functionality for the analysis of antioxidant content in several wine samples. The intrinsic oxidase-like activity of nanoceria shows promise as a robust tool for sensitive and cost effective analysis of antioxidants using electrochemical detection. Copyright © 2016 Elsevier B.V. All rights reserved.

Single-Cell Genomic Analysis in Plants

PubMed Central

Hu, Haifei; Scheben, Armin; Edwards, David

2018-01-01

Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis. PMID:29361790

Satellite image analysis using neural networks

NASA Technical Reports Server (NTRS)

Sheldon, Roger A.

1990-01-01

The tremendous backlog of unanalyzed satellite data necessitates the development of improved methods for data cataloging and analysis. Ford Aerospace has developed an image analysis system, SIANN (Satellite Image Analysis using Neural Networks) that integrates the technologies necessary to satisfy NASA's science data analysis requirements for the next generation of satellites. SIANN will enable scientists to train a neural network to recognize image data containing scenes of interest and then rapidly search data archives for all such images. The approach combines conventional image processing technology with recent advances in neural networks to provide improved classification capabilities. SIANN allows users to proceed through a four step process of image classification: filtering and enhancement, creation of neural network training data via application of feature extraction algorithms, configuring and training a neural network model, and classification of images by application of the trained neural network. A prototype experimentation testbed was completed and applied to climatological data.

Rapid In Situ Profiling of Lipid C═C Location Isomers in Tissue Using Ambient Mass Spectrometry with Photochemical Reactions.

PubMed

Tang, Fei; Guo, Chengan; Ma, Xiaoxiao; Zhang, Jian; Su, Yuan; Tian, Ran; Shi, Riyi; Xia, Yu; Wang, Xiaohao; Ouyang, Zheng

2018-05-01

Rapid and in situ profiling of lipids using ambient mass spectrometry (AMS) techniques has great potential for clinical diagnosis, biological studies, and biomarker discovery. In this study, the online photochemical reaction involving carbon-carbon double bonds was coupled with a surface sampling technique to develop a direct tissue-analysis method with specificity to lipid C═C isomers. This method enabled the in situ analysis of lipids from the surface of various tissues or tissue sections, which allowed the structural characterization of lipid isomers within 2 min. Under optimized reaction conditions, we have established a method for the relative quantitation of lipid C═C location isomers by comparing the abundances of the diagnostic ions arising from each isomer, which has been proven effective through the established linear relationship ( R 2 = 0.999) between molar ratio and diagnostic ion ratio of the FA 18:1 C═C location isomers. This method was then used for the rapid profiling of unsaturated lipid C═C isomers in the sections of rat brain, lung, liver, spleen, and kidney, as well as in normal and diseased rat tissues. Quantitative information on FA 18:1 and PC 16:0-18:1 C═C isomers was obtained, and significant differences were observed between different samples. To the best of our knowledge, this is the first study to report the direct analysis of lipid C═C isomers in tissues using AMS. Our results demonstrated that this method can serve as a rapid analytical approach for the profiling of unsaturated lipid C═C isomers in biological tissues and should contribute to functional lipidomics and clinical diagnosis.

A Cloud-based, Open-Source, Command-and-Control Software Paradigm for Space Situational Awareness (SSA)

NASA Astrophysics Data System (ADS)

Melton, R.; Thomas, J.

With the rapid growth in the number of space actors, there has been a marked increase in the complexity and diversity of software systems utilized to support SSA target tracking, indication, warning, and collision avoidance. Historically, most SSA software has been constructed with "closed" proprietary code, which limits interoperability, inhibits the code transparency that some SSA customers need to develop domain expertise, and prevents the rapid injection of innovative concepts into these systems. Open-source aerospace software, a rapidly emerging, alternative trend in code development, is based on open collaboration, which has the potential to bring greater transparency, interoperability, flexibility, and reduced development costs. Open-source software is easily adaptable, geared to rapidly changing mission needs, and can generally be delivered at lower costs to meet mission requirements. This paper outlines Ball's COSMOS C2 system, a fully open-source, web-enabled, command-and-control software architecture which provides several unique capabilities to move the current legacy SSA software paradigm to an open source model that effectively enables pre- and post-launch asset command and control. Among the unique characteristics of COSMOS is the ease with which it can integrate with diverse hardware. This characteristic enables COSMOS to serve as the command-and-control platform for the full life-cycle development of SSA assets, from board test, to box test, to system integration and test, to on-orbit operations. The use of a modern scripting language, Ruby, also permits automated procedures to provide highly complex decision making for the tasking of SSA assets based on both telemetry data and data received from outside sources. Detailed logging enables quick anomaly detection and resolution. Integrated real-time and offline data graphing renders the visualization of the both ground and on-orbit assets simple and straightforward.

Multifunctional Nanotechnology-Enabled Sensors for Rapid Capture and Detection of Pathogens.

PubMed

Mustafa, Fatima; Hassan, Rabeay Y A; Andreescu, Silvana

2017-09-15

Nanomaterial-based sensing approaches that incorporate different types of nanoparticles (NPs) and nanostructures in conjunction with natural or synthetic receptors as molecular recognition elements provide opportunities for the design of sensitive and selective assays for rapid detection of contaminants. This review summarizes recent advancements over the past ten years in the development of nanotechnology-enabled sensors and systems for capture and detection of pathogens. The most common types of nanostructures and NPs, their modification with receptor molecules and integration to produce viable sensing systems with biorecognition, amplification and signal readout are discussed. Examples of all-in-one systems that combine multifunctional properties for capture, separation, inactivation and detection are also provided. Current trends in the development of low-cost instrumentation for rapid assessment of food contamination are discussed as well as challenges for practical implementation and directions for future research.

Top-down production of drug nanocrystals: nanosuspension stabilization, miniaturization and transformation into solid products.

PubMed

Van Eerdenbrugh, Bernard; Van den Mooter, Guy; Augustijns, Patrick

2008-11-19

During the last 10-15 years, the formulation of drugs as nanocrystals has rapidly evolved into a mature drug delivery strategy, with currently five products on the market. The major characteristic of these systems is the rapid dissolution velocity, enabling bioavailability enhancement after oral administration. This mini-review focuses on recent advances with respect to three topics considering drug nanocrystals. The first topic is nanosuspension stabilization. A current literature status is provided and special attention is given to studies attempting to extend our physicochemical understanding of the underlying principles. The second part describes recent advances on miniaturization of nanosuspension production, to enable formulation screening during preclinical development. Finally, literature available on further nanosuspensions solidification is discussed, focussing on the maintenance of the preservation of the rapid dissolution properties of the nanocrystals after further downstream processing.

An immuno-wall microdevice exhibits rapid and sensitive detection of IDH1-R132H mutation specific to grade II and III gliomas

NASA Astrophysics Data System (ADS)

Yamamichi, Akane; Kasama, Toshihiro; Ohka, Fumiharu; Suzuki, Hiromichi; Kato, Akira; Motomura, Kazuya; Hirano, Masaki; Ranjit, Melissa; Chalise, Lushun; Kurimoto, Michihiro; Kondo, Goro; Aoki, Kosuke; Kaji, Noritada; Tokeshi, Manabu; Matsubara, Toshio; Senga, Takeshi; Kaneko, Mika K.; Suzuki, Hidenori; Hara, Masahito; Wakabayashi, Toshihiko; Baba, Yoshinobu; Kato, Yukinari; Natsume, Atsushi

2016-01-01

World Health Organization grade II and III gliomas most frequently occur in the central nervous system (CNS) in adults. Gliomas are not circumscribed; tumor edges are irregular and consist of tumor cells, normal brain tissue, and hyperplastic reactive glial cells. Therefore, the tumors are not fully resectable, resulting in recurrence, malignant progression, and eventual death. Approximately 69-80% of grade II and III gliomas harbor mutations in the isocitrate dehydrogenase 1 gene (IDH1), of which 83-90% are found to be the IDH1-R132H mutation. Detection of the IDH1-R132H mutation should help in the differential diagnosis of grade II and III gliomas from other types of CNS tumors and help determine the boundary between the tumor and normal brain tissue. In this study, we established a highly sensitive antibody-based device, referred to as the immuno-wall, to detect the IDH1-R132H mutation in gliomas. The immuno-wall causes an immunoreaction in microchannels fabricated using a photo-polymerizing polymer. This microdevice enables the analysis of the IDH1 status with a small sample within 15 min with substantially high sensitivity. Our results suggested that 10% content of the IDH1-R132H mutation in a sample of 0.33 μl volume, with 500 ng protein, or from 500 cells is theoretically sufficient for the analysis. The immuno-wall device will enable the rapid and highly sensitive detection of the IDH1-R132H mutation in routine clinical practice.

Integration of cell-free protein coexpression with an enzyme-linked immunosorbent assay enables rapid analysis of protein–protein interactions directly from DNA

PubMed Central

Layton, Curtis J; Hellinga, Homme W

2011-01-01

Assays that integrate detection of binding with cell-free protein expression directly from DNA can dramatically increase the pace at which protein–protein interactions (PPIs) can be analyzed by mutagenesis. In this study, we present a method that combines in vitro protein production with an enzyme-linked immunosorbent assay (ELISA) to measure PPIs. This method uses readily available commodity instrumentation and generic antibody–affinity tag interactions. It is straightforward and rapid to execute, enabling many interactions to be assessed in parallel. In traditional ELISAs, reporter complexes are assembled stepwise with one layer at a time. In the method presented here, all the members of the reporter complex are present and assembled together. The signal strength is dependent on all the intercomponent interaction affinities and concentrations. Although this assay is straightforward to execute, establishing proper conditions and analysis of the results require a thorough understanding of the processes that determine the signal strength. The formation of the fully assembled reporter sandwich can be modeled as a competition between Langmuir adsorption isotherms for the immobilized components and binding equilibria of the solution components. We have shown that modeling this process provides semiquantitative understanding of the effects of affinity and concentration and can guide strategies for the development of experimental protocols. We tested the method experimentally using the interaction between a synthetic ankyrin repeat protein (Off7) and maltose-binding protein. Measurements obtained for a collection of alanine mutations in the interface between these two proteins demonstrate that a range of affinities can be analyzed. PMID:21674663

An immuno-wall microdevice exhibits rapid and sensitive detection of IDH1-R132H mutation specific to grade II and III gliomas.

PubMed

Yamamichi, Akane; Kasama, Toshihiro; Ohka, Fumiharu; Suzuki, Hiromichi; Kato, Akira; Motomura, Kazuya; Hirano, Masaki; Ranjit, Melissa; Chalise, Lushun; Kurimoto, Michihiro; Kondo, Goro; Aoki, Kosuke; Kaji, Noritada; Tokeshi, Manabu; Matsubara, Toshio; Senga, Takeshi; Kaneko, Mika K; Suzuki, Hidenori; Hara, Masahito; Wakabayashi, Toshihiko; Baba, Yoshinobu; Kato, Yukinari; Natsume, Atsushi

2016-01-01

World Health Organization grade II and III gliomas most frequently occur in the central nervous system (CNS) in adults. Gliomas are not circumscribed; tumor edges are irregular and consist of tumor cells, normal brain tissue, and hyperplastic reactive glial cells. Therefore, the tumors are not fully resectable, resulting in recurrence, malignant progression, and eventual death. Approximately 69-80% of grade II and III gliomas harbor mutations in the isocitrate dehydrogenase 1 gene ( IDH1 ), of which 83-90% are found to be the IDH1-R132H mutation. Detection of the IDH1-R132H mutation should help in the differential diagnosis of grade II and III gliomas from other types of CNS tumors and help determine the boundary between the tumor and normal brain tissue. In this study, we established a highly sensitive antibody-based device, referred to as the immuno-wall, to detect the IDH1-R132H mutation in gliomas. The immuno-wall causes an immunoreaction in microchannels fabricated using a photo-polymerizing polymer. This microdevice enables the analysis of the IDH1 status with a small sample within 15 min with substantially high sensitivity. Our results suggested that 10% content of the IDH1-R132H mutation in a sample of 0.33 μl volume, with 500 ng protein, or from 500 cells is theoretically sufficient for the analysis. The immuno-wall device will enable the rapid and highly sensitive detection of the IDH1-R132H mutation in routine clinical practice.

RF-MEMS capacitive switches with high reliability

DOEpatents

Goldsmith, Charles L.; Auciello, Orlando H.; Carlisle, John A.; Sampath, Suresh; Sumant, Anirudha V.; Carpick, Robert W.; Hwang, James; Mancini, Derrick C.; Gudeman, Chris

2013-09-03

A reliable long life RF-MEMS capacitive switch is provided with a dielectric layer comprising a "fast discharge diamond dielectric layer" and enabling rapid switch recovery, dielectric layer charging and discharging that is efficient and effective to enable RF-MEMS switch operation to greater than or equal to 100 billion cycles.

The Comparison of Students' Satisfaction between Ubiquitous and Web-Based Learning Environments

ERIC Educational Resources Information Center

Virtanen, Mari Aulikki; Kääriäinen, Maria; Liikanen, Eeva; Haavisto, Elina

2017-01-01

Higher education is moving towards digitalized learning. The rapid development of technological resources, devices and wireless networks enables more flexible opportunities to study and learn in innovative learning environments. New technologies enable combining of authentic and virtual learning spaces and digital resources as multifunctional…

Robotics to enable older adults to remain living at home.

PubMed

Pearce, Alan J; Adair, Brooke; Miller, Kimberly; Ozanne, Elizabeth; Said, Catherine; Santamaria, Nick; Morris, Meg E

2012-01-01

Given the rapidly ageing population, interest is growing in robots to enable older people to remain living at home. We conducted a systematic review and critical evaluation of the scientific literature, from 1990 to the present, on the use of robots in aged care. The key research questions were as follows: (1) what is the range of robotic devices available to enable older people to remain mobile, independent, and safe? and, (2) what is the evidence demonstrating that robotic devices are effective in enabling independent living in community dwelling older people? Following database searches for relevant literature an initial yield of 161 articles was obtained. Titles and abstracts of articles were then reviewed by 2 independent people to determine suitability for inclusion. Forty-two articles met the criteria for question 1. Of these, 4 articles met the criteria for question 2. Results showed that robotics is currently available to assist older healthy people and people with disabilities to remain independent and to monitor their safety and social connectedness. Most studies were conducted in laboratories and hospital clinics. Currently limited evidence demonstrates that robots can be used to enable people to remain living at home, although this is an emerging smart technology that is rapidly evolving.

Rapid identification of regulated organic chemical compounds in toys using ambient ionization and a miniature mass spectrometry system.

PubMed

Guo, Xiangyu; Bai, Hua; Lv, Yueguang; Xi, Guangcheng; Li, Junfang; Ma, Xiaoxiao; Ren, Yue; Ouyang, Zheng; Ma, Qiang

2018-04-01

Rapid, on-site analysis was achieved through significantly simplified operation procedures for a wide variety of toy samples (crayon, temporary tattoo sticker, finger paint, modeling clay, and bubble solution) using a miniature mass spectrometry system with ambient ionization capability. The labor-intensive analytical protocols involving sample workup and chemical separation, traditionally required for MS-based analysis, were replaced by direct sampling analysis using ambient ionization methods. A Mini β ion trap miniature mass spectrometer was coupled with versatile ambient ionization methods, e.g. paper spray, extraction spray and slug-flow microextraction nanoESI for direct identification of prohibited colorants, carcinogenic primary aromatic amines, allergenic fragrances, preservatives and plasticizers from raw toy samples. The use of paper substrates coated with Co 3 O 4 nanoparticles allowed a great increase in sensitivity for paper spray. Limits of detection as low as 5μgkg -1 were obtained for target analytes. The methods being developed based on the integration of ambient ionization with miniature mass spectrometer represent alternatives to current in-lab MS analysis operation, and would enable fast, outside-the-lab screening of toy products to ensure children's safety and health. Copyright © 2017 Elsevier B.V. All rights reserved.

Spatiotemporal polarization modulation microscopy with a microretarder array

NASA Astrophysics Data System (ADS)

Ding, Changqin; Ulcickas, James R. W.; Simpson, Garth J.

2018-02-01

A patterned microretarder array positioned in the rear conjugate plane of a microscope enables rapid polarizationdependent nonlinear optical microscopy. The pattern introduced to the array results in periodic modulation of the polarization-state of the incident light as a function of position within the field of view with no moving parts or active control. Introduction of a single stationary optical element and a fixed polarizer into the beam of a nonlinear optical microscope enabled nonlinear optical tensor recovery, which informs on local structure and orientation. Excellent agreement was observed between the measured and predicted second harmonic generation (SHG) of z-cut quartz, selected as a test system with well-established nonlinear optical properties. Subsequent studies of spatially varying samples further support the general applicability of this relatively simple strategy for detailed polarization analysis in both conventional and nonlinear optical imaging of structurally diverse samples.

Direct visualization reveals kinetics of meiotic chromosome synapsis

DOE PAGES

Rog, Ofer; Dernburg, Abby  F.

2015-03-17

The synaptonemal complex (SC) is a conserved protein complex that stabilizes interactions along homologous chromosomes (homologs) during meiosis. The SC regulates genetic exchanges between homologs, thereby enabling reductional division and the production of haploid gametes. Here, we directly observe SC assembly (synapsis) by optimizing methods for long-term fluorescence recording in C. elegans. We report that synapsis initiates independently on each chromosome pair at or near pairing centers—specialized regions required for homolog associations. Once initiated, the SC extends rapidly and mostly irreversibly to chromosome ends. Quantitation of SC initiation frequencies and extension rates reveals that initiation is a rate-limiting step inmore » homolog interactions. Eliminating the dynein-driven chromosome movements that accompany synapsis severely retards SC extension, revealing a new role for these conserved motions. This work provides the first opportunity to directly observe and quantify key aspects of meiotic chromosome interactions and will enable future in vivo analysis of germline processes.« less

A framework for optimization and quantification of uncertainty and sensitivity for developing carbon capture systems

DOE PAGES

Eslick, John C.; Ng, Brenda; Gao, Qianwen; ...

2014-12-31

Under the auspices of the U.S. Department of Energy’s Carbon Capture Simulation Initiative (CCSI), a Framework for Optimization and Quantification of Uncertainty and Sensitivity (FOQUS) has been developed. This tool enables carbon capture systems to be rapidly synthesized and rigorously optimized, in an environment that accounts for and propagates uncertainties in parameters and models. FOQUS currently enables (1) the development of surrogate algebraic models utilizing the ALAMO algorithm, which can be used for superstructure optimization to identify optimal process configurations, (2) simulation-based optimization utilizing derivative free optimization (DFO) algorithms with detailed black-box process models, and (3) rigorous uncertainty quantification throughmore » PSUADE. FOQUS utilizes another CCSI technology, the Turbine Science Gateway, to manage the thousands of simulated runs necessary for optimization and UQ. Thus, this computational framework has been demonstrated for the design and analysis of a solid sorbent based carbon capture system.« less

Ambient Ionization Mass Spectrometry for Cancer Diagnosis and Surgical Margin Evaluation

PubMed Central

Ifa, Demian R.; Eberlin, Livia S.

2017-01-01

Background There is a clinical need for new technologies that would enable rapid disease diagnosis based on diagnostic molecular signatures. Ambient ionization mass spectrometry has revolutionized the means by which molecular information can be obtained from tissue samples in real time and with minimal sample pretreatment. New developments in ambient ionization techniques applied to clinical research suggest that ambient ionization mass spectrometry will soon become a routine medical tool for tissue diagnosis. Content This review summarizes the main developments in ambient ionization techniques applied to tissue analysis, with focus on desorption electrospray ionization mass spectrometry, probe electrospray ionization, touch spray, and rapid evaporative ionization mass spectrometry. We describe their applications to human cancer research and surgical margin evaluation, highlighting integrated approaches tested for ex vivo and in vivo human cancer tissue analysis. We also discuss the challenges for clinical implementation of these tools and offer perspectives on the future of the field. Summary A variety of studies have showcased the value of ambient ionization mass spectrometry for rapid and accurate cancer diagnosis. Small molecules have been identified as potential diagnostic biomarkers, including metabolites, fatty acids, and glycerophospholipids. Statistical analysis allows tissue discrimination with high accuracy rates (>95%) being common. This young field has challenges to overcome before it is ready to be broadly accepted as a medical tool for cancer diagnosis. Growing research in new, integrated ambient ionization mass spectrometry technologies and the ongoing improvements in the existing tools make this field very promising for future translation into the clinic. PMID:26555455

Social Media Strategies for the United States Armed Forces: An Israeli Case Study

DTIC Science & Technology

2013-05-03

experiences a significant military failure. Discussion: The US military is facing pressure to adapt to a rapidly evolving information environment...Marine Corps, but as I explored the issue, it rapidly became apparent that the institutional structures that both enable and constrain social media use... rapidly changing nature of the information environment itself is causing drastic societal changes, with widespread effects on both individual and

HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.

PubMed

Bryan, Kenneth; Jarboui, Mohamed-Ali; Raso, Cinzia; Bernal-Llinares, Manuel; McCann, Brendan; Rauch, Jens; Boldt, Karsten; Lynn, David J

2016-06-03

Recent advances in mass-spectrometry-based proteomics are now facilitating ambitious large-scale investigations of the spatial and temporal dynamics of the proteome; however, the increasing size and complexity of these data sets is overwhelming current downstream computational methods, specifically those that support the postquantification analysis pipeline. Here we present HiQuant, a novel application that enables the design and execution of a postquantification workflow, including common data-processing steps, such as assay normalization and grouping, and experimental replicate quality control and statistical analysis. HiQuant also enables the interpretation of results generated from large-scale data sets by supporting interactive heatmap analysis and also the direct export to Cytoscape and Gephi, two leading network analysis platforms. HiQuant may be run via a user-friendly graphical interface and also supports complete one-touch automation via a command-line mode. We evaluate HiQuant's performance by analyzing a large-scale, complex interactome mapping data set and demonstrate a 200-fold improvement in the execution time over current methods. We also demonstrate HiQuant's general utility by analyzing proteome-wide quantification data generated from both a large-scale public tyrosine kinase siRNA knock-down study and an in-house investigation into the temporal dynamics of the KSR1 and KSR2 interactomes. Download HiQuant, sample data sets, and supporting documentation at http://hiquant.primesdb.eu .

Toward genome-enabled mycology.

PubMed

Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

2013-01-01

Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

airborne data analysis/monitor system

NASA Technical Reports Server (NTRS)

Stephison, D. B.

1981-01-01

An Airborne Data Analysis/Monitor System (ADAMS), a ROLM 1666 computer based system installed onboard test airplanes used during experimental testing is evaluated. In addition to the 1666 computer, the ADAMS hardware includes a DDC System 90 fixed head disk and a Miltape DD400 floppy disk. Boeing designed a DMA interface to the data acquisition system and an intelligent terminal to reduce system overhead and simplify operator commands. The ADAMS software includes RMX/RTOS and both ROLM FORTRAN and assembly language are used. The ADAMS provides real time displays that enable onboard test engineers to make rapid decisions about test conduct thus reducing the cost and time required to certify new model airplanes, and improved the quality of data derived from the test, leading to more rapid development of improvements resulting in quieter, safer, and more efficient airplanes. The availability of airborne data processing removes most of the weather and geographical restrictions imposed by telemetered flight test data systems. A data base is maintained to describe the airplane, the data acquisition system, the type of testing, and the conditions under which the test is performed.

GENOME ENABLED ECOLOGY OF PSEUDO-NITZSCHIA INFECTING VIRUSES AND THEIR IMPACT ON PSEUDO-NITZSCHIA COMMUNITIES

EPA Science Inventory

With short infection cycles and large burst sizes (viruses per cell), the infection dynamics of diatom viruses appear to be optimized for rapidly growing diatom populations. On the timescale of bloom events, total Pseudo-nitzschia virus abundance should increase rapidly ove...

Functional Specifications for the OCLC Interlibrary Loan Subsystem.

ERIC Educational Resources Information Center

Bova, Phyllis V.

This report covers functional specifications for the OCLC Interlibrary Loan (ILL) Subsystem, designed to permit participating libraries to increase the availability of library resources to patrons by enabling these libraries to form, transmit, and fulfill loan requests more rapidly and effectively. It will provide rapid access to a large on-line…

Construction and In Vivo Testing of Prokaryotic Riboregulators.

PubMed

Green, Alexander A

2017-01-01

RNAs that are transcribed and self-assemble within living cells are valuable tools for regulating and organizing cellular activities. Riboregulators, in particular, have been widely used for modulating translation and transcription in response to cognate transactivating or trigger RNAs, enabling cells to evaluate logic operations and to respond to environmental cues. Herein we detail a set of methods for the rapid construction and testing of prokaryotic riboregulators in Escherichia coli. These methods enable construction of dozens of riboregulator plasmids at the same time without the use of restriction enzymes. Furthermore, they facilitate rapid screening of devices and can be applied to a variety of other self-assembling in vivo RNA systems.

Phage-protease-peptide: a novel trifecta enabling multiplex detection of viable bacterial pathogens.

PubMed

Alcaine, S D; Tilton, L; Serrano, M A C; Wang, M; Vachet, R W; Nugen, S R

2015-10-01

Bacteriophages represent rapid, readily targeted, and easily produced molecular probes for the detection of bacterial pathogens. Molecular biology techniques have allowed researchers to make significant advances in the bioengineering of bacteriophage to further improve speed and sensitivity of detection. Despite their host specificity, bacteriophages have not been meaningfully leveraged in multiplex detection of bacterial pathogens. We propose a proof-of-principal phage-based scheme to enable multiplex detection. Our scheme involves bioengineering bacteriophage to carry a gene for a specific protease, which is expressed during infection of the target cell. Upon lysis, the protease is released to cleave a reporter peptide, and the signal detected. Here we demonstrate the successful (i) modification of T7 bacteriophage to carry tobacco etch virus (TEV) protease; (ii) expression of TEV protease by Escherichia coli following infection by our modified T7, an average of 2000 units of protease per phage are produced during infection; and (iii) proof-of-principle detection of E. coli in 3 h after a primary enrichment via TEV protease activity using a fluorescent peptide and using a designed target peptide for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (MALDI-TOF MS) analysis. This proof-of-principle can be translated to other phage-protease-peptide combinations to enable multiplex bacterial detection and readily adopted on multiple platforms, like MALDI-TOF MS or fluorescent readers, commonly found in labs.

Iron Oxide Films Prepared by Rapid Thermal Processing for Solar Energy Conversion

PubMed Central

Wickman, B.; Bastos Fanta, A.; Burrows, A.; Hellman, A.; Wagner, J. B.; Iandolo, B.

2017-01-01

Hematite is a promising and extensively investigated material for various photoelectrochemical (PEC) processes for energy conversion and storage, in particular for oxidation reactions. Thermal treatments during synthesis of hematite are found to affect the performance of hematite electrodes considerably. Herein, we present hematite thin films fabricated via one-step oxidation of Fe by rapid thermal processing (RTP). In particular, we investigate the effect of oxidation temperature on the PEC properties of hematite. Films prepared at 750 °C show the highest activity towards water oxidation. These films show the largest average grain size and the highest charge carrier density, as determined from electron microscopy and impedance spectroscopy analysis. We believe that the fast processing enabled by RTP makes this technique a preferred method for investigation of novel materials and architectures, potentially also on nanostructured electrodes, where retaining high surface area is crucial to maximize performance. PMID:28091573

Crowdsourced 'R&D' and medical research.

PubMed

Callaghan, Christian William

2015-09-01

Crowdsourced R&D, a research methodology increasingly applied to medical research, has properties well suited to large-scale medical data collection and analysis, as well as enabling rapid research responses to crises such as disease outbreaks. Multidisciplinary literature offers diverse perspectives of crowdsourced R&D as a useful large-scale medical data collection and research problem-solving methodology. Crowdsourced R&D has demonstrated 'proof of concept' in a host of different biomedical research applications. A wide range of quality and ethical issues relate to crowdsourced R&D. The rapid growth in applications of crowdsourced R&D in medical research is predicted by an increasing body of multidisciplinary theory. Further research in areas such as artificial intelligence may allow better coordination and management of the high volumes of medical data and problem-solving inputs generated by the crowdsourced R&D process. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

TMV-Gate vectors: Gateway compatible tobacco mosaic virus based expression vectors for functional analysis of proteins

PubMed Central

Kagale, Sateesh; Uzuhashi, Shihomi; Wigness, Merek; Bender, Tricia; Yang, Wen; Borhan, M. Hossein; Rozwadowski, Kevin

2012-01-01

Plant viral expression vectors are advantageous for high-throughput functional characterization studies of genes due to their capability for rapid, high-level transient expression of proteins. We have constructed a series of tobacco mosaic virus (TMV) based vectors that are compatible with Gateway technology to enable rapid assembly of expression constructs and exploitation of ORFeome collections. In addition to the potential of producing recombinant protein at grams per kilogram FW of leaf tissue, these vectors facilitate either N- or C-terminal fusions to a broad series of epitope tag(s) and fluorescent proteins. We demonstrate the utility of these vectors in affinity purification, immunodetection and subcellular localisation studies. We also apply the vectors to characterize protein-protein interactions and demonstrate their utility in screening plant pathogen effectors. Given its broad utility in defining protein properties, this vector series will serve as a useful resource to expedite gene characterization efforts. PMID:23166857

Predicting kinetics of polymorphic transformations from structure mapping and coordination analysis

NASA Astrophysics Data System (ADS)

Stevanović, Vladan; Trottier, Ryan; Musgrave, Charles; Therrien, Félix; Holder, Aaron; Graf, Peter

2018-03-01

To extend materials design and discovery into the space of metastable polymorphs, rapid and reliable assessment of transformation kinetics to lower energy structures is essential. Herein we focus on diffusionless polymorphic transformations and investigate routes to assess their kinetics using solely crystallographic arguments. As part of this investigation we developed a general algorithm to map crystal structures onto each other, and ascertain the low-energy (fast-kinetics) transformation pathways between them. Pathways with minimal dissociation of chemical bonds, along which the number of bonds (in ionic systems the first-shell coordination) does not decrease below that in the end structures, are shown to always be the fast-kinetics pathways. These findings enable the rapid assessment of the kinetics of polymorphic transformation and the identification of long-lived metastable structures. The utility is demonstrated on a number of transformations including those between high-pressure SnO2 phases, which lack a detailed atomic-level understanding.

Real-Time Continuous Identification of Greenhouse Plant Pathogens Based on Recyclable Microfluidic Bioassay System.

PubMed

Qu, Xiangmeng; Li, Min; Zhang, Hongbo; Lin, Chenglie; Wang, Fei; Xiao, Mingshu; Zhou, Yi; Shi, Jiye; Aldalbahi, Ali; Pei, Hao; Chen, Hong; Li, Li

2017-09-20

The development of a real-time continuous analytical platform for the pathogen detection is of great scientific importance for achieving better disease control and prevention. In this work, we report a rapid and recyclable microfluidic bioassay system constructed from oligonucleotide arrays for selective and sensitive continuous identification of DNA targets of fungal pathogens. We employ the thermal denaturation method to effectively regenerate the oligonucleotide arrays for multiple sample detection, which could considerably reduce the screening effort and costs. The combination of thermal denaturation and laser-induced fluorescence detection technique enables real-time continuous identification of multiple samples (<10 min per sample). As a proof of concept, we have demonstrated that two DNA targets of fungal pathogens (Botrytis cinerea and Didymella bryoniae) can be sequentially analyzed using our rapid microfluidic bioassay system, which provides a new paradigm in the design of microfluidic bioassay system and will be valuable for chemical and biomedical analysis.

Typhoon Neoguri Approaching Japan

NASA Image and Video Library

2014-07-09

NASA's Terra satellite captured this visible image on July 9 at 02:30 UTC (July 8 at 10:30 p.m. EDT) as Typhoon Neoguri was approaching Kyushu, Japan. The visible image revealed that Neoguri's eye had disappeared and the center has become somewhat elongated as the storm weakened into a tropical storm. The Joint Typhoon Warning Center or JTWC noted that an upper level analysis revealed that Neoguri is now in a more harsh environment as northerly vertical wind shear increased to as much as 30 knots. Credit: NASA/GSFC/Jeff Schmaltz/MODIS Land Rapid Response Credit: NASA/GSFC/Jeff Schmaltz/MODIS Land Rapid Response NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

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

Baker, Erin Shammel; Burnum-Johnson, Kristin E.; Jacobs, Jon M.

Rapid diagnosis of disease states using less invasive, safer, and more clinically acceptable approaches than presently employed is an imperative goal for the field of medicine. While mass spectrometry (MS)-based proteomics approaches have attempted to meet these objectives, challenges such as the enormous dynamic range of protein concentrations in clinically relevant biofluid samples coupled with the need to address human biodiversity have slowed their employment. Herein, we report on the use of a new platform that addresses these challenges by coupling technical advances in rapid gas phase multiplexed ion mobility spectrometry (IMS) separations [1, 2] with liquid chromatography (LC) andmore » MS to dramatically increase measurement sensitivity and throughput, further enabling future MS-based clinical applications. An initial application of the LC-IMS-MS platform for the analysis of blood serum samples from stratified post-liver transplant patients with recurrent fibrosis progression illustrates its potential utility for disease characterization and use in personalized medicine [3, 4].« less

The future of forensic DNA analysis

PubMed Central

Butler, John M.

2015-01-01

The author's thoughts and opinions on where the field of forensic DNA testing is headed for the next decade are provided in the context of where the field has come over the past 30 years. Similar to the Olympic motto of ‘faster, higher, stronger’, forensic DNA protocols can be expected to become more rapid and sensitive and provide stronger investigative potential. New short tandem repeat (STR) loci have expanded the core set of genetic markers used for human identification in Europe and the USA. Rapid DNA testing is on the verge of enabling new applications. Next-generation sequencing has the potential to provide greater depth of coverage for information on STR alleles. Familial DNA searching has expanded capabilities of DNA databases in parts of the world where it is allowed. Challenges and opportunities that will impact the future of forensic DNA are explored including the need for education and training to improve interpretation of complex DNA profiles. PMID:26101278

Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation

NASA Astrophysics Data System (ADS)

Tan, Tien-Chye; Kracher, Daniel; Gandini, Rosaria; Sygmund, Christoph; Kittl, Roman; Haltrich, Dietmar; Hällberg, B. Martin; Ludwig, Roland; Divne, Christina

2015-07-01

A new paradigm for cellulose depolymerization by fungi focuses on an oxidative mechanism involving cellobiose dehydrogenases (CDH) and copper-dependent lytic polysaccharide monooxygenases (LPMO); however, mechanistic studies have been hampered by the lack of structural information regarding CDH. CDH contains a haem-binding cytochrome (CYT) connected via a flexible linker to a flavin-dependent dehydrogenase (DH). Electrons are generated from cellobiose oxidation catalysed by DH and shuttled via CYT to LPMO. Here we present structural analyses that provide a comprehensive picture of CDH conformers, which govern the electron transfer between redox centres. Using structure-based site-directed mutagenesis, rapid kinetics analysis and molecular docking, we demonstrate that flavin-to-haem interdomain electron transfer (IET) is enabled by a haem propionate group and that rapid IET requires a closed CDH state in which the propionate is tightly enfolded by DH. Following haem reduction, CYT reduces LPMO to initiate oxygen activation at the copper centre and subsequent cellulose depolymerization.

Ionic solution and nanoparticle assisted MALDI-MS as bacterial biosensors for rapid analysis of yogurt.

PubMed

Lee, Chia-Hsun; Gopal, Judy; Wu, Hui-Fen

2012-01-15

Bacterial analysis from food samples is a highly challenging task because food samples contain intensive interferences from proteins and carbohydrates. Three different conditions of yogurt were analyzed: (1) the fresh yogurt immediately after purchasing, (2) the yogurt after expiry date stored in the refrigerator and (3) the yogurt left outside, without refrigeration. The shelf lives of both these yogurt was compared in terms of the decrease in bacterial signals. AB which initially contained 10(9) cells/mL drastically reduced to 10(7) cells/mL. However, Lin (Feng-Yin) yogurt which initially (fresh) had 10(8) cells/mL, even after two weeks beyond the expiry period showed no marked drop in bacterial count. Conventional MALDI-MS analysis showed limited sensitivity for analysis of yogurt bacteria amidst the complex milk proteins present in yogurt. A cost effective ionic solution, CrO(4)(2-) solution was used to enable the successful detection of bacterial signals (40-fold increased in sensitivity) selectively without the interference of the milk proteins. 0.035 mg of Ag nanoparticles (NPs) were also found to improve the detection of bacteria 2-6 times in yogurt samples. The current approach can be further applied as a rapid, sensitive and effective platform for bacterial analysis from food. Copyright © 2011 Elsevier B.V. All rights reserved.

Integrated microfluidic technology for sub-lethal and behavioral marine ecotoxicity biotests

NASA Astrophysics Data System (ADS)

Huang, Yushi; Reyes Aldasoro, Constantino Carlos; Persoone, Guido; Wlodkowic, Donald

2015-06-01

Changes in behavioral traits exhibited by small aquatic invertebrates are increasingly postulated as ethically acceptable and more sensitive endpoints for detection of water-born ecotoxicity than conventional mortality assays. Despite importance of such behavioral biotests, their implementation is profoundly limited by the lack of appropriate biocompatible automation, integrated optoelectronic sensors, and the associated electronics and analysis algorithms. This work outlines development of a proof-of-concept miniaturized Lab-on-a-Chip (LOC) platform for rapid water toxicity tests based on changes in swimming patterns exhibited by Artemia franciscana (Artoxkit M™) nauplii. In contrast to conventionally performed end-point analysis based on counting numbers of dead/immobile specimens we performed a time-resolved video data analysis to dynamically assess impact of a reference toxicant on swimming pattern of A. franciscana. Our system design combined: (i) innovative microfluidic device keeping free swimming Artemia sp. nauplii under continuous microperfusion as a mean of toxin delivery; (ii) mechatronic interface for user-friendly fluidic actuation of the chip; and (iii) miniaturized video acquisition for movement analysis of test specimens. The system was capable of performing fully programmable time-lapse and video-microscopy of multiple samples for rapid ecotoxicity analysis. It enabled development of a user-friendly and inexpensive test protocol to dynamically detect sub-lethal behavioral end-points such as changes in speed of movement or distance traveled by each animal.

Understanding Knowledge-Sharing Breakdowns: A Meeting of the Quantitative and Qualitative Minds

ERIC Educational Resources Information Center

Soller, Amy

2004-01-01

The rapid advance of distance learning and networking technology has enabled universities and corporations to reach out and educate students across time and space barriers. Although this technology enables structured collaborative learning activities, online groups often do not enjoy the same benefits as face-to-face learners, and their…

Developing Guidelines for Evaluating the Adaptation of Accessible Web-Based Learning Materials

ERIC Educational Resources Information Center

Radovan, Marko; Perdih, Mojca

2016-01-01

E-learning is a rapidly developing form of education. One of the key characteristics of e-learning is flexibility, which enables easier access to knowledge for everyone. Information and communications technology (ICT), which is e-learning's main component, enables alternative means of accessing the web-based learning materials that comprise the…

The research on medical image classification algorithm based on PLSA-BOW model.

PubMed

Cao, C H; Cao, H L

2016-04-29

With the rapid development of modern medical imaging technology, medical image classification has become more important for medical diagnosis and treatment. To solve the existence of polysemous words and synonyms problem, this study combines the word bag model with PLSA (Probabilistic Latent Semantic Analysis) and proposes the PLSA-BOW (Probabilistic Latent Semantic Analysis-Bag of Words) model. In this paper we introduce the bag of words model in text field to image field, and build the model of visual bag of words model. The method enables the word bag model-based classification method to be further improved in accuracy. The experimental results show that the PLSA-BOW model for medical image classification can lead to a more accurate classification.

Translating an AI application from Lisp to Ada: A case study

NASA Technical Reports Server (NTRS)

Davis, Gloria J.

1991-01-01

A set of benchmarks was developed to test the performance of a newly designed computer executing both Lisp and Ada. Among these was AutoClassII -- a large Artificial Intelligence (AI) application written in Common Lisp. The extraction of a representative subset of this complex application was aided by a Lisp Code Analyzer (LCA). The LCA enabled rapid analysis of the code, putting it in a concise and functionally readable form. An equivalent benchmark was created in Ada through manual translation of the Lisp version. A comparison of the execution results of both programs across a variety of compiler-machine combinations indicate that line-by-line translation coupled with analysis of the initial code can produce relatively efficient and reusable target code.

Flow cytogenetics and chromosome sorting.

PubMed

Cram, L S

1990-06-01

This review of flow cytogenetics and chromosome sorting provides an overview of general information in the field and describes recent developments in more detail. From the early developments of chromosome analysis involving single parameter or one color analysis to the latest developments in slit scanning of single chromosomes in a flow stream, the field has progressed rapidly and most importantly has served as an important enabling technology for the human genome project. Technological innovations that advanced flow cytogenetics are described and referenced. Applications in basic cell biology, molecular biology, and clinical investigations are presented. The necessary characteristics for large number chromosome sorting are highlighted. References to recent review articles are provided as a starting point for locating individual references that provide more detail. Specific references are provided for recent developments.

Multifunctional Nanotechnology-Enabled Sensors for Rapid Capture and Detection of Pathogens

PubMed Central

Mustafa, Fatima; Andreescu, Silvana

2017-01-01

Nanomaterial-based sensing approaches that incorporate different types of nanoparticles (NPs) and nanostructures in conjunction with natural or synthetic receptors as molecular recognition elements provide opportunities for the design of sensitive and selective assays for rapid detection of contaminants. This review summarizes recent advancements over the past ten years in the development of nanotechnology-enabled sensors and systems for capture and detection of pathogens. The most common types of nanostructures and NPs, their modification with receptor molecules and integration to produce viable sensing systems with biorecognition, amplification and signal readout are discussed. Examples of all-in-one systems that combine multifunctional properties for capture, separation, inactivation and detection are also provided. Current trends in the development of low-cost instrumentation for rapid assessment of food contamination are discussed as well as challenges for practical implementation and directions for future research. PMID:28914769

Science Partnerships Enabling Rapid Response: Designing a Strategy for Improving Scientific Collaboration during Crisis Response

NASA Astrophysics Data System (ADS)

Mease, L.; Gibbs, T.; Adiseshan, T.

2014-12-01

The 2010 Deepwater Horizon disaster required unprecedented engagement and collaboration with scientists from multiple disciplines across government, academia, and industry. Although this spurred the rapid advancement of valuable new scientific knowledge and tools, it also exposed weaknesses in the system of information dissemination and exchange among the scientists from those three sectors. Limited government communication with the broader scientific community complicated the rapid mobilization of the scientific community to assist with spill response, evaluation of impact, and public perceptions of the crisis. The lessons and new laws produced from prior spills such as Exxon Valdez were helpful, but ultimately did not lead to the actions necessary to prepare a suitable infrastructure that would support collaboration with non-governmental scientists. As oil demand pushes drilling into increasingly extreme environments, addressing the challenge of effective, science-based disaster response is an imperative. Our study employs a user-centered design process to 1) understand the obstacles to and opportunity spaces for effective scientific collaboration during environmental crises such as large oil spills, 2) identify possible tools and strategies to enable rapid information exchange between government responders and non-governmental scientists from multiple relevant disciplines, and 3) build a network of key influencers to secure sufficient buy-in for scaled implementation of appropriate tools and strategies. Our methods include user ethnography, complex system mapping, individual and system behavioral analysis, and large-scale system design to identify and prototype a solution to this crisis collaboration challenge. In this talk, we will present out insights gleaned from existing analogs of successful scientific collaboration during crises and our initial findings from the 60 targeted interviews we conducted that highlight key collaboration challenges that government agencies, academic research institutions, and industry scientists face during oil spill crises. We will also present a synthesis of leverage points in the system that may amplify the impact of an improved collaboration strategy among scientific stakeholders.

Modified Linear Theory Aircraft Design Tools and Sonic Boom Minimization Strategy Applied to Signature Freezing via F-function Lobe Balancing

NASA Astrophysics Data System (ADS)

Jung, Timothy Paul

Commercial supersonic travel has strong business potential; however, in order for the Federal Aviation Administration to lift its ban on supersonic flight overland, designers must reduce aircraft sonic boom strength to an acceptable level. An efficient methodology and associated tools for designing aircraft for minimized sonic booms are presented. The computer-based preliminary design tool, RapidF, based on modified linear theory, enables quick assessment of an aircraft's sonic boom with run times less than 30 seconds on a desktop computer. A unique feature of RapidF is that it tracks where on the aircraft each segment of the of the sonic boom came from, enabling precise modifications, speeding the design process. Sonic booms from RapidF are compared to flight test data, showing that it is capability of predicting a sonic boom duration, overpressure, and interior shock locations. After the preliminary design is complete, scaled flight tests should be conducted to validate the low boom design. When conducting such tests, it is insufficient to just scale the length; thus, equations to scale the weight and propagation distance are derived. Using RapidF, a conceptual supersonic business jet design is presented that uses F-function lobe balancing to create a frozen sonic boom using lifting surfaces. The leading shock is reduced from 1.4 to 0.83 psf, and the trailing shock from 1.2 to 0.87 psf, 41% and 28% reductions respectfully. By changing the incidence angle of the surfaces, different sonic boom shapes can be created, and allowing the lobes to be re-balanced for new flight conditions. Computational fluid dynamics is conducted to validate the sonic boom predictions. Off-design analysis is presented that varies weight, altitude, Mach number, and propagation angle, demonstrating that lobe-balance is robust. Finally, the Perceived Level of Loudness metric is analyzed, resulting in a modified design that incorporates other boom minimization techniques to further reduce the sonic boom.

Multimodal characterization of the semantic N400 response within a rapid evaluation brain vital sign framework.

PubMed

Ghosh Hajra, Sujoy; Liu, Careesa C; Song, Xiaowei; Fickling, Shaun D; Cheung, Teresa P L; D'Arcy, Ryan C N

2018-06-04

For nearly four decades, the N400 has been an important brainwave marker of semantic processing. It can be recorded non-invasively from the scalp using electrical and/or magnetic sensors, but largely within the restricted domain of research laboratories specialized to run specific N400 experiments. However, there is increasing evidence of significant clinical utility for the N400 in neurological evaluation, particularly at the individual level. To enable clinical applications, we recently reported a rapid evaluation framework known as "brain vital signs" that successfully incorporated the N400 response as one of the core components for cognitive function evaluation. The current study characterized the rapidly evoked N400 response to demonstrate that it shares consistent features with traditional N400 responses acquired in research laboratory settings-thereby enabling its translation into brain vital signs applications. Data were collected from 17 healthy individuals using magnetoencephalography (MEG) and electroencephalography (EEG), with analysis of sensor-level effects as well as evaluation of brain sources. Individual-level N400 responses were classified using machine learning to determine the percentage of participants in whom the response was successfully detected. The N400 response was observed in both M/EEG modalities showing significant differences to incongruent versus congruent condition in the expected time range (p < 0.05). Also as expected, N400-related brain activity was observed in the temporal and inferior frontal cortical regions, with typical left-hemispheric asymmetry. Classification robustly confirmed the N400 effect at the individual level with high accuracy (89%), sensitivity (0.88) and specificity (0.90). The brain vital sign N400 characteristics were highly consistent with features of the previously reported N400 responses acquired using traditional laboratory-based experiments. These results provide important evidence supporting clinical translation of the rapidly acquired N400 response as a potential tool for assessments of higher cognitive functions.

Rapid communication: Computational simulation and analysis of a candidate for the design of a novel silk-based biopolymer.

PubMed

Golas, Ewa I; Czaplewski, Cezary

2014-09-01

This work theoretically investigates the mechanical properties of a novel silk-derived biopolymer as polymerized in silico from sericin and elastin-like monomers. Molecular Dynamics simulations and Steered Molecular Dynamics were the principal computational methods used, the latter of which applies an external force onto the system and thereby enables an observation of its response to stress. The models explored herein are single-molecule approximations, and primarily serve as tools in a rational design process for the preliminary assessment of properties in a new material candidate. © 2014 Wiley Periodicals, Inc.

Arkansas Groundwater-Quality Network

USGS Publications Warehouse

Pugh, Aaron L.; Jackson, Barry T.; Miller, Roger

2014-01-01

Arkansas is the fourth largest user of groundwater in the United States, where groundwater accounts for two-thirds of the total water use. Groundwater use in the State increased by 510 percent between 1965 and 2005 (Holland, 2007). The Arkansas Groundwater-Quality Network is a Web map interface (http://ar.water.usgs.gov/wqx) that provides rapid access to the U.S. Geological Survey’s (USGS) National Water Information System (NWIS) and the U.S. Environmental Protection Agency’s (USEPA) STOrage and RETrieval (STORET) databases of ambient water information. The interface enables users to perform simple graphical analysis and download selected water-quality data.

Microfluidic device for acoustic cell lysis

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

Branch, Darren W.; Cooley, Erika Jane; Smith, Gennifer Tanabe

2015-08-04

A microfluidic acoustic-based cell lysing device that can be integrated with on-chip nucleic acid extraction. Using a bulk acoustic wave (BAW) transducer array, acoustic waves can be coupled into microfluidic cartridges resulting in the lysis of cells contained therein by localized acoustic pressure. Cellular materials can then be extracted from the lysed cells. For example, nucleic acids can be extracted from the lysate using silica-based sol-gel filled microchannels, nucleic acid binding magnetic beads, or Nafion-coated electrodes. Integration of cell lysis and nucleic acid extraction on-chip enables a small, portable system that allows for rapid analysis in the field.

Low-cost fluorimetric determination of radicals based on fluorogenic dimerization of the natural phenol sesamol.

PubMed

Makino, Yumi; Uchiyama, Seiichi; Ohno, Ken-ichi; Arakawa, Hidetoshi

2010-02-15

A novel fluorimetric method for determining radicals using the natural phenol sesamol as a fluorogenic reagent is reported. In this assay, sesamol was reacted with aqueous radicals to yield one isomer of a sesamol dimer exclusively. The dimer emitted purple fluorescence near 400 nm around neutral pH, where it assumed the monoanionic form. This method was applied to the straightforward detection of radical nitric oxide (NO). The ready availability of sesamol should enable rapid implementation of applications utilizing this new assay, particularly in high-throughput analysis or screening.

Precise and rapid isotopomic analysis by (1)H-(13)C 2D NMR: Application to triacylglycerol matrices.

PubMed

Merchak, Noelle; Silvestre, Virginie; Rouger, Laetitia; Giraudeau, Patrick; Rizk, Toufic; Bejjani, Joseph; Akoka, Serge

2016-08-15

An optimized HSQC sequence was tested and applied to triacylglycerol matrices to determine their isotopic and metabolomic profiles. Spectral aliasing and non-uniform sampling approaches were used to decrease the experimental time and to improve the resolution, respectively. An excellent long-term repeatability of signal integrals was achieved enabling to perform isotopic measurements. Thirty-two commercial vegetable oils were analyzed by this methodology. The results show that this method can be used to classify oil samples according to their geographical and botanical origins. Copyright © 2016 Elsevier B.V. All rights reserved.

Rapid immunohistochemical detection of tumor cells in gastric carcinoma.

PubMed

Mönig, Stefan P; Luebke, Thomas; Soheili, Afsoon; Landsberg, Stephanie; Dienes, H P; Hölscher, Arnulf H; Baldus, Stephan E

2006-11-01

The detection of single tumor cells or tumor cell clusters represents an important issue in intraoperative frozen section analysis. For example, surgical margins may be evaluated in order to minimize the number of additional operations. Furthermore, intraoperative diagnosis of lymph node micrometastasis (LNM) may help to define the area of appropriate lymph node dissection. In addition to haematoxylin and eosin (H&E)-stained sections, immunohistochemical detection of single tumor cells or cell clusters may be helpful in this context. The aim of this study was to evaluate the clinical significance, reliability and sensitivity of intraoperative rapid immunostaining of frozen sections. Therefore, we compared the results of rapid immunohistochemical staining of frozen sections and paraffin sections applying the EnVision and Histofine(R) detection systems. In a prospective immunohistochemical study, paraffin and frozen sections of 20 gastric cancer specimens were analyzed. Paraffin as well as frozen sections were stained immunohistochemically applying the EnVision and Histofine detection systems. As primary antibodies, AE1/AE3 (anti-cytokeratin), EMA (anti-MUC1) and B lymphocyte marker anti-CD20 were applied. The rapid immunostaining procedure was able to be completed within 10-13 min. Rapid immunohistochemical staining of frozen and paraffin sections of the same tumors resulted in comparable immunoreactivity. The rapid EnVision and Histofine procedures allowed immunostaining of frozen sections in less than 13 min. These methods can represent useful additional tools in routine surgical pathology and research, enabling a more accurate frozen section diagnosis compared to staining with H&E alone. Intraoperative rapid immunostaining can be a simple and useful technique to detect LNM.

In Situ California Bearing Ration Database

DTIC Science & Technology

2007-10-01

for use in this investigation ( Berney and Wahl 2007). The goal of the JRAC effort is to enable a rapid assessment of a soil with a miniaturized...variability - Benalla test section. Research Report ARR 220. Victoria, Australia: Australian Road Research Board. Berney , E.S., and R.E. Wahl. 2007. Rapid...number given to each unique soil that was identified in the Joint Rapid Airfield Construction program’s database ( Berney and Wahl 2007). Test or

Analysis, Mining and Visualization Service at NCSA

NASA Astrophysics Data System (ADS)

Wilhelmson, R.; Cox, D.; Welge, M.

2004-12-01

NCSA's goal is to create a balanced system that fully supports high-end computing as well as: 1) high-end data management and analysis; 2) visualization of massive, highly complex data collections; 3) large databases; 4) geographically distributed Grid computing; and 5) collaboratories, all based on a secure computational environment and driven with workflow-based services. To this end NCSA has defined a new technology path that includes the integration and provision of cyberservices in support of data analysis, mining, and visualization. NCSA has begun to develop and apply a data mining system-NCSA Data-to-Knowledge (D2K)-in conjunction with both the application and research communities. NCSA D2K will enable the formation of model-based application workflows and visual programming interfaces for rapid data analysis. The Java-based D2K framework, which integrates analytical data mining methods with data management, data transformation, and information visualization tools, will be configurable from the cyberservices (web and grid services, tools, ..) viewpoint to solve a wide range of important data mining problems. This effort will use modules, such as a new classification methods for the detection of high-risk geoscience events, and existing D2K data management, machine learning, and information visualization modules. A D2K cyberservices interface will be developed to seamlessly connect client applications with remote back-end D2K servers, providing computational resources for data mining and integration with local or remote data stores. This work is being coordinated with SDSC's data and services efforts. The new NCSA Visualization embedded workflow environment (NVIEW) will be integrated with D2K functionality to tightly couple informatics and scientific visualization with the data analysis and management services. Visualization services will access and filter disparate data sources, simplifying tasks such as fusing related data from distinct sources into a coherent visual representation. This approach enables collaboration among geographically dispersed researchers via portals and front-end clients, and the coupling with data management services enables recording associations among datasets and building annotation systems into visualization tools and portals, giving scientists a persistent, shareable, virtual lab notebook. To facilitate provision of these cyberservices to the national community, NCSA will be providing a computational environment for large-scale data assimilation, analysis, mining, and visualization. This will be initially implemented on the new 512 processor shared memory SGI's recently purchased by NCSA. In addition to standard batch capabilities, NCSA will provide on-demand capabilities for those projects requiring rapid response (e.g., development of severe weather, earthquake events) for decision makers. It will also be used for non-sequential interactive analysis of data sets where it is important have access to large data volumes over space and time.

An object-oriented approach to risk and reliability analysis : methodology and aviation safety applications.

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

Dandini, Vincent John; Duran, Felicia Angelica; Wyss, Gregory Dane

2003-09-01

This article describes how features of event tree analysis and Monte Carlo-based discrete event simulation can be combined with concepts from object-oriented analysis to develop a new risk assessment methodology, with some of the best features of each. The resultant object-based event scenario tree (OBEST) methodology enables an analyst to rapidly construct realistic models for scenarios for which an a priori discovery of event ordering is either cumbersome or impossible. Each scenario produced by OBEST is automatically associated with a likelihood estimate because probabilistic branching is integral to the object model definition. The OBEST methodology is then applied to anmore » aviation safety problem that considers mechanisms by which an aircraft might become involved in a runway incursion incident. The resulting OBEST model demonstrates how a close link between human reliability analysis and probabilistic risk assessment methods can provide important insights into aviation safety phenomenology.« less

Performance modeling and techno-economic analysis of a modular concentrated solar power tower with latent heat storage

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

Rea, Jonathan E.; Oshman, Christopher J.; Olsen, Michele L.

In this paper, we present performance simulations and techno-economic analysis of a modular dispatchable solar power tower. Using a heliostat field and power block three orders of magnitude smaller than conventional solar power towers, our unique configuration locates thermal storage and a power block directly on a tower receiver. To make the system dispatchable, a valved thermosyphon controls heat flow from a latent heat thermal storage tank to a Stirling engine. The modular design results in minimal balance of system costs and enables high deployment rates with a rapid realization of economies of scale. In this new analysis, we combinemore » performance simulations with techno-economic analysis to evaluate levelized cost of electricity, and find that the system has potential for cost-competitiveness with natural gas peaking plants and alternative dispatchable renewables.« less

Mid-L/D Lifting Body Entry Demise Analysis

NASA Technical Reports Server (NTRS)

Ling, Lisa

2017-01-01

The mid-lift-to-drag ratio (mid-L/D) lifting body is a fully autonomous spacecraft under design at NASA for enabling a rapid return of scientific payloads from the International Space Station (ISS). For contingency planning and risk assessment for the Earth-return trajectory, an entry demise analysis was performed to examine three potential failure scenarios: (1) nominal entry interface conditions with loss of control, (2) controlled entry at maximum flight path angle, and (3) controlled entry at minimum flight path angle. The objectives of the analysis were to predict the spacecraft breakup sequence and timeline, determine debris survival, and calculate the debris dispersion footprint. Sensitivity analysis was also performed to determine the effect of the initial pitch rate on the spacecraft stability and breakup during the entry. This report describes the mid-L/D lifting body and presents the results of the entry demise and sensitivity analyses.

GABBs: Cyberinfrastructure for Self-Service Geospatial Data Exploration, Computation, and Sharing

NASA Astrophysics Data System (ADS)

Song, C. X.; Zhao, L.; Biehl, L. L.; Merwade, V.; Villoria, N.

2016-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. In addressing these needs, the Geospatial data Analysis Building Blocks (GABBs) project aims at building geospatial modeling, data analysis and visualization capabilities in an open source web platform, HUBzero. Funded by NSF's Data Infrastructure Building Blocks initiative, GABBs is creating a geospatial data architecture that integrates spatial data management, mapping and visualization, and interfaces in the HUBzero platform for scientific collaborations. The geo-rendering enabled Rappture toolkit, a generic Python mapping library, geospatial data exploration and publication tools, and an integrated online geospatial data management solution are among the software building blocks from the project. The GABBS software will be available through Amazon's AWS Marketplace VM images and open source. Hosting services are also available to the user community. The outcome of the project will enable researchers and educators to self-manage their scientific data, rapidly create GIS-enable tools, share geospatial data and tools on the web, and build dynamic workflows connecting data and tools, all without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the GABBs architecture, toolkits and libraries, and showcase the scientific use cases that utilize GABBs capabilities, as well as the challenges and solutions for GABBs to interoperate with other cyberinfrastructure platforms.

Remote calorimetric detection of urea via flow injection analysis

PubMed Central

Gaddes, David E.; Demirel, Melik C.; Reeves, W. Brian; Tadigadapa, Srinivas

2017-01-01

The design and development of a calorimetric biosensing system enabling relatively high throughput sample analysis are reported. The calorimetric biosensor system consists of a thin (~20 μm) micromachined Y-cut quartz crystal resonator (QCR) as a temperature sensor placed in close proximity to a fluidic chamber packed with an immobilized enzyme. Layer by layer enzyme immobilization of urease is demonstrated and its activity as a function of the number of layers, pH, and time has been evaluated. This configuration enables a sensing system where a transducer element is physically separated from the analyte solution of interest and is thereby free from fouling effects typically associated with biochemical reactions occuring on the sensor surface. The performance of this biosensing system is demonstrated by detection of 1–200 mM urea in phosphate buffer via a flow injection analysis (FIA) technique. Miniaturized fluidic systems were used to provide continuous flow through a reaction column. Under this configuration the biosensor has an ultimate resolution of less than 1 mM urea and showed a linear response between 0–50 mM. This work demonstrates a sensing modality in which the sensor itself is not fouled or contaminated by the solution of interest and the enzyme immobilized Kapton® fluidic reaction column can be used as a disposable cartridge. Such a system enables reuse and reliability for long term sampling measurements. Based on this concept a biosensing system is envisioned which can perform rapid measurements to detect biomarkers such as glucose, creatinine, cholesterol, urea and lactate in urine and blood continuously over extended periods of time. PMID:26479269

Remote calorimetric detection of urea via flow injection analysis.

PubMed

Gaddes, David E; Demirel, Melik C; Reeves, W Brian; Tadigadapa, Srinivas

2015-12-07

The design and development of a calorimetric biosensing system enabling relatively high throughput sample analysis are reported. The calorimetric biosensor system consists of a thin (∼20 μm) micromachined Y-cut quartz crystal resonator (QCR) as a temperature sensor placed in close proximity to a fluidic chamber packed with an immobilized enzyme. Layer by layer enzyme immobilization of urease is demonstrated and its activity as a function of the number of layers, pH, and time has been evaluated. This configuration enables a sensing system where a transducer element is physically separated from the analyte solution of interest and is thereby free from fouling effects typically associated with biochemical reactions occuring on the sensor surface. The performance of this biosensing system is demonstrated by detection of 1-200 mM urea in phosphate buffer via a flow injection analysis (FIA) technique. Miniaturized fluidic systems were used to provide continuous flow through a reaction column. Under this configuration the biosensor has an ultimate resolution of less than 1 mM urea and showed a linear response between 0-50 mM. This work demonstrates a sensing modality in which the sensor itself is not fouled or contaminated by the solution of interest and the enzyme immobilized Kapton® fluidic reaction column can be used as a disposable cartridge. Such a system enables reuse and reliability for long term sampling measurements. Based on this concept a biosensing system is envisioned which can perform rapid measurements to detect biomarkers such as glucose, creatinine, cholesterol, urea and lactate in urine and blood continuously over extended periods of time.

Authentication of the botanical origin of honey by near-infrared spectroscopy.

PubMed

Ruoff, Kaspar; Luginbühl, Werner; Bogdanov, Stefan; Bosset, Jacques Olivier; Estermann, Barbara; Ziolko, Thomas; Amado, Renato

2006-09-06

Fourier transform near-infrared spectroscopy (FT-NIR) was evaluated for the authentication of eight unifloral and polyfloral honey types (n = 364 samples) previously classified using traditional methods such as chemical, pollen, and sensory analysis. Chemometric evaluation of the spectra was carried out by applying principal component analysis and linear discriminant analysis. The corresponding error rates were calculated according to Bayes' theorem. NIR spectroscopy enabled a reliable discrimination of acacia, chestnut, and fir honeydew honey from the other unifloral and polyfloral honey types studied. The error rates ranged from <0.1 to 6.3% depending on the honey type. NIR proved also to be useful for the classification of blossom and honeydew honeys. The results demonstrate that near-infrared spectrometry is a valuable, rapid, and nondestructive tool for the authentication of the above-mentioned honeys, but not for all varieties studied.

The National Nanotechnology Initiative: Research and Development Leading to a Revolution in Technology and Industry. Supplement to the President’s 2011 Budget

DTIC Science & Technology

2010-02-01

commercial “ pull ” to enable rapid establishment of domestic 21st century manufacturing and to rapidly reduce product cost. CNT electronics...Opportunities for Academic Liaison with Industry ( GOALI ), Partnerships for Innovation (PFI) , and Industry-University Cooperative Research Centers (IUCRC

Development of primer sets for loop-mediated isothermal amplification that enables rapid and specific detection of Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae

USDA-ARS?s Scientific Manuscript database

Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae are the three main pathogens causing bovine mastitis, with great losses to the dairy industry. Rapid and specific loop-mediated isothermal amplification methods (LAMP) for identification and differentiation of these three ...

A Targeted Q-PCR-Based Method for Point Mutation Testing by Analyzing Circulating DNA for Cancer Management Care.

PubMed

Thierry, Alain R

2016-01-01

Circulating cell-free DNA (cfDNA) is a valuable source of tumor material available with a simple blood sampling enabling a noninvasive quantitative and qualitative analysis of the tumor genome. cfDNA is released by tumor cells and exhibits the genetic and epigenetic alterations of the tumor of origin. Circulating cell-free DNA (cfDNA) analysis constitutes a hopeful approach to provide a noninvasive tumor molecular test for cancer patients. Based upon basic research on the origin and structure of cfDNA, new information on circulating cell-free DNA (cfDNA) structure, and specific determination of cfDNA fragmentation and size, we revisited Q-PCR-based method and recently developed a the allele-specific-Q-PCR-based method with blocker (termed as Intplex) which is the first multiplexed test for cfDNA. This technique, named Intplex(®) and based on a refined Q-PCR method, derived from critical observations made on the specific structure and size of cfDNA. It enables the simultaneous determination of five parameters: the cfDNA total concentration, the presence of a previously known point mutation, the mutant (tumor) cfDNA concentration (ctDNA), the proportion of mutant cfDNA, and the cfDNA fragmentation index. Intplex(®) has enabled the first clinical validation of ctDNA analysis in oncology by detecting KRAS and BRAF point mutations in mCRC patients and has demonstrated that a blood test could replace tumor section analysis for the detection of KRAS and BRAF mutations. The Intplex(®) test can be adapted to all mutations, genes, or cancers and enables rapid, highly sensitive, cost-effective, and repetitive analysis. As regards to the determination of mutations on cfDNA Intplex(®) is limited to the mutational status of known hotspot mutation; it is a "targeted approach." However, it offers the opportunity in detecting quantitatively and dynamically mutation and could constitute a noninvasive attractive tool potentially allowing diagnosis, prognosis, theranostics, therapeutic monitoring, and follow-up of cancer patients expanding the scope of personalized cancer medicine.

Integrated database for rapid mass movements in Norway

NASA Astrophysics Data System (ADS)

Jaedicke, C.; Lied, K.; Kronholm, K.

2009-03-01

Rapid gravitational slope mass movements include all kinds of short term relocation of geological material, snow or ice. Traditionally, information about such events is collected separately in different databases covering selected geographical regions and types of movement. In Norway the terrain is susceptible to all types of rapid gravitational slope mass movements ranging from single rocks hitting roads and houses to large snow avalanches and rock slides where entire mountainsides collapse into fjords creating flood waves and endangering large areas. In addition, quick clay slides occur in desalinated marine sediments in South Eastern and Mid Norway. For the authorities and inhabitants of endangered areas, the type of threat is of minor importance and mitigation measures have to consider several types of rapid mass movements simultaneously. An integrated national database for all types of rapid mass movements built around individual events has been established. Only three data entries are mandatory: time, location and type of movement. The remaining optional parameters enable recording of detailed information about the terrain, materials involved and damages caused. Pictures, movies and other documentation can be uploaded into the database. A web-based graphical user interface has been developed allowing new events to be entered, as well as editing and querying for all events. An integration of the database into a GIS system is currently under development. Datasets from various national sources like the road authorities and the Geological Survey of Norway were imported into the database. Today, the database contains 33 000 rapid mass movement events from the last five hundred years covering the entire country. A first analysis of the data shows that the most frequent type of recorded rapid mass movement is rock slides and snow avalanches followed by debris slides in third place. Most events are recorded in the steep fjord terrain of the Norwegian west coast, but major events are recorded all over the country. Snow avalanches account for most fatalities, while large rock slides causing flood waves and huge quick clay slides are the most damaging individual events in terms of damage to infrastructure and property and for causing multiple fatalities. The quality of the data is strongly influenced by the personal engagement of local observers and varying observation routines. This database is a unique source for statistical analysis including, risk analysis and the relation between rapid mass movements and climate. The database of rapid mass movement events will also facilitate validation of national hazard and risk maps.

High-Speed Tandem Mass Spectrometric in Situ Imaging by Nanospray Desorption Electrospray Ionization Mass Spectrometry

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

Lanekoff, Ingela T.; Burnum-Johnson, Kristin E.; Thomas, Mathew

Nanospray desorption electrospray ionization (nano-DESI) combined with tandem mass spectrometry (MS/MS), high-resolution mass analysis (m/m=17,500 at m/z 200), and rapid spectral acquisition enabled simultaneous imaging and identification of more than 300 molecules from 92 selected m/z windows (± 1 Da) with a spatial resolution of better than 150 um. Uterine sections of implantation sites on day 6 of pregnancy were analyzed in the ambient environment without any sample pre-treatment. MS/MS imaging was performed by scanning the sample under the nano-DESI probe at 10 um/s while acquiring higher-energy collision-induced dissociation (HCD) spectra for a targeted inclusion list of 92 m/z valuesmore » at a rate of ~6.3 spectra/s. Molecular ions and their corresponding fragments, separated using high-resolution mass analysis, were assigned based on accurate mass measurement. Using this approach, we were able to identify and image both abundant and low-abundance isobaric species within each m/z window. MS/MS analysis enabled efficient separation and identification of isobaric sodium and potassium adducts of phospholipids. Furthermore, we identified several metabolites associated with early pregnancy and obtained the first 2D images of these molecules.« less

SOURCE EXPLORER: Towards Web Browser Based Tools for Astronomical Source Visualization and Analysis

NASA Astrophysics Data System (ADS)

Young, M. D.; Hayashi, S.; Gopu, A.

2014-05-01

As a new generation of large format, high-resolution imagers come online (ODI, DECAM, LSST, etc.) we are faced with the daunting prospect of astronomical images containing upwards of hundreds of thousands of identifiable sources. Visualizing and interacting with such large datasets using traditional astronomical tools appears to be unfeasible, and a new approach is required. We present here a method for the display and analysis of arbitrarily large source datasets using dynamically scaling levels of detail, enabling scientists to rapidly move from large-scale spatial overviews down to the level of individual sources and everything in-between. Based on the recognized standards of HTML5+JavaScript, we enable observers and archival users to interact with their images and sources from any modern computer without having to install specialized software. We demonstrate the ability to produce large-scale source lists from the images themselves, as well as overlaying data from publicly available source ( 2MASS, GALEX, SDSS, etc.) or user provided source lists. A high-availability cluster of computational nodes allows us to produce these source maps on demand and customized based on user input. User-generated source lists and maps are persistent across sessions and are available for further plotting, analysis, refinement, and culling.

Hyperspectral and differential CARS microscopy for quantitative chemical imaging in human adipocytes

PubMed Central

Di Napoli, Claudia; Pope, Iestyn; Masia, Francesco; Watson, Peter; Langbein, Wolfgang; Borri, Paola

2014-01-01

In this work, we demonstrate the applicability of coherent anti-Stokes Raman scattering (CARS) micro-spectroscopy for quantitative chemical imaging of saturated and unsaturated lipids in human stem-cell derived adipocytes. We compare dual-frequency/differential CARS (D-CARS), which enables rapid imaging and simple data analysis, with broadband hyperspectral CARS microscopy analyzed using an unsupervised phase-retrieval and factorization method recently developed by us for quantitative chemical image analysis. Measurements were taken in the vibrational fingerprint region (1200–2000/cm) and in the CH stretch region (2600–3300/cm) using a home-built CARS set-up which enables hyperspectral imaging with 10/cm resolution via spectral focussing from a single broadband 5 fs Ti:Sa laser source. Through a ratiometric analysis, both D-CARS and phase-retrieved hyperspectral CARS determine the concentration of unsaturated lipids with comparable accuracy in the fingerprint region, while in the CH stretch region D-CARS provides only a qualitative contrast owing to its non-linear behavior. When analyzing hyperspectral CARS images using the blind factorization into susceptibilities and concentrations of chemical components recently demonstrated by us, we are able to determine vol:vol concentrations of different lipid components and spatially resolve inhomogeneities in lipid composition with superior accuracy compared to state-of-the art ratiometric methods. PMID:24877002

Science Autonomy in Robotic Exploration

NASA Technical Reports Server (NTRS)

Roush, Ted L.; DeVincenzi, Donald (Technical Monitor)

2001-01-01

Historical mission operations have involved: (1) return of scientific data; (2) evaluation of these data by scientists; (3) recommendations for future mission activity by scientists; (4) commands for these transmitted to the craft; and (5) the activity being undertaken. This cycle is repeated throughout the mission with command opportunities once or twice per day. For a rover, this historical cycle is not amenable to rapid long range traverses or rapid response to any novel or unexpected situations. In addition to real-time response issues, imaging and/or spectroscopic devices can produce tremendous data volumes during a traverse. However, such data volumes can rapidly exceed on-board memory capabilities prior to the ability to transmit it to Earth. Additionally, the necessary communication band-widths are restrictive enough so that only a small portion of these data can actually be returned to Earth. Such scenarios suggest enabling some science decisions to be made on-board the robots. These decisions involve automating various aspects of scientific discovery instead of the electromechanical control, health, and navigation issues associated with robotic operations. The robot retains access to the full data fidelity obtained by its scientific sensors, and is in the best position to implement actions based upon these data. Such an approach would eventually enable the robot to alter observations and assure only the highest quality data is obtained for analysis. Additionally, the robot can begin to understand what is scientifically interesting and implement alternative observing sequences, because the observed data deviate from expectations based upon current theories/models of planetary processes. Such interesting data and/or conclusions can then be prioritized and selectively transmitted to Earth; reducing memory and communications demands. Results of Ames' current work in this area will be presented.

Robotic Exploration: The Role of Science Autonomy

NASA Technical Reports Server (NTRS)

Roush, Ted L.; DeVincenzi, Donald (Technical Monitor)

2001-01-01

Historical mission operations have involved: (1) return of scientific data; (2) evaluation of these data by scientists; (3) recommendations for future mission activity by scientists; (4) commands for these transmitted to the craft; and (5) the activity being, undertaken. This cycle is repeated throughout the mission with command opportunities once or twice per day. For a rover, this historical cycle is not amenable to rapid long range traverses or rapid response to any novel or unexpected situations. In addition to real-time response issues, imaging and/or spectroscopic devices can produce tremendous data volumes during a traverse. However, such data volumes can rapidly exceed on-board memory capabilities prior to the ability to transmit it to Earth. Additionally, the necessary communication band-widths are restrictive enough so that only a small portion of these data can actually be returned to Earth. Such scenarios suggest enabling some science decisions to be made on-board the robots. These decisions involve automating various aspects of scientific discovery instead of the electromechanical control, health, and navigation issues associated with robotic operations. The robot retains access to the full data fidelity obtained by its scientific sensors, and is in the best position to implement actions based upon these data. Such an approach would eventually enable the robot to alter observations and assure only the highest quality data is obtained for analysis. Additionally, the robot can begin to understand what is scientifically interesting and implement alternative observing sequences, because the observed data deviate from expectations based upon current theories/models of planetary processes. Such interesting data and/or conclusions can then be prioritized and selectively transmitted to Earth; reducing memory and communications demands. Results of Ames' current work in this area will be presented.

Robotics to Enable Older Adults to Remain Living at Home

PubMed Central

Pearce, Alan J.; Adair, Brooke; Ozanne, Elizabeth; Said, Catherine; Santamaria, Nick; Morris, Meg E.

2012-01-01

Given the rapidly ageing population, interest is growing in robots to enable older people to remain living at home. We conducted a systematic review and critical evaluation of the scientific literature, from 1990 to the present, on the use of robots in aged care. The key research questions were as follows: (1) what is the range of robotic devices available to enable older people to remain mobile, independent, and safe? and, (2) what is the evidence demonstrating that robotic devices are effective in enabling independent living in community dwelling older people? Following database searches for relevant literature an initial yield of 161 articles was obtained. Titles and abstracts of articles were then reviewed by 2 independent people to determine suitability for inclusion. Forty-two articles met the criteria for question 1. Of these, 4 articles met the criteria for question 2. Results showed that robotics is currently available to assist older healthy people and people with disabilities to remain independent and to monitor their safety and social connectedness. Most studies were conducted in laboratories and hospital clinics. Currently limited evidence demonstrates that robots can be used to enable people to remain living at home, although this is an emerging smart technology that is rapidly evolving. PMID:23304507

HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC.

PubMed

Wood, Natasha; Bhattacharya, Tanmoy; Keele, Brandon F; Giorgi, Elena; Liu, Michael; Gaschen, Brian; Daniels, Marcus; Ferrari, Guido; Haynes, Barton F; McMichael, Andrew; Shaw, George M; Hahn, Beatrice H; Korber, Bette; Seoighe, Cathal

2009-05-01

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide evidence that the length variation seen in hypervariable loop regions of the envelope glycoprotein is a consequence of selection and not of mutational hotspots. Our results provide a detailed view of the process of diversification of HIV-1 following transmission, highlighting the role of CTL escape and hypermutation in shaping viral evolution during the establishment of new infections.

HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC

PubMed Central

Wood, Natasha; Bhattacharya, Tanmoy; Keele, Brandon F.; Giorgi, Elena; Liu, Michael; Gaschen, Brian; Daniels, Marcus; Ferrari, Guido; Haynes, Barton F.; McMichael, Andrew; Shaw, George M.; Hahn, Beatrice H.; Korber, Bette; Seoighe, Cathal

2009-01-01

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide evidence that the length variation seen in hypervariable loop regions of the envelope glycoprotein is a consequence of selection and not of mutational hotspots. Our results provide a detailed view of the process of diversification of HIV-1 following transmission, highlighting the role of CTL escape and hypermutation in shaping viral evolution during the establishment of new infections. PMID:19424423

Development of Liquid Propulsion Systems Testbed at MSFC

NASA Technical Reports Server (NTRS)

Alexander, Reginald; Nelson, Graham

2016-01-01

As NASA, the Department of Defense and the aerospace industry in general strive to develop capabilities to explore near-Earth, Cis-lunar and deep space, the need to create more cost effective techniques of propulsion system design, manufacturing and test is imperative in the current budget constrained environment. The physics of space exploration have not changed, but the manner in which systems are developed and certified needs to change if there is going to be any hope of designing and building the high performance liquid propulsion systems necessary to deliver crew and cargo to the further reaches of space. To further the objective of developing these systems, the Marshall Space Flight Center is currently in the process of formulating a Liquid Propulsion Systems testbed, which will enable rapid integration of components to be tested and assessed for performance in integrated systems. The manifestation of this testbed is a breadboard engine configuration (BBE) with facility support for consumables and/or other components as needed. The goal of the facility is to test NASA developed elements, but can be used to test articles developed by other government agencies, industry or academia. Joint government/private partnership is likely the approach that will be required to enable efficient propulsion system development. MSFC has recently tested its own additively manufactured liquid hydrogen pump, injector, and valves in a BBE hot firing. It is rapidly building toward testing the pump and a new CH4 injector in the BBE configuration to demonstrate a 22,000 lbf, pump-fed LO2/LCH4 engine for the Mars lander or in-space transportation. The value of having this BBE testbed is that as components are developed they may be easily integrated in the testbed and tested. MSFC is striving to enhance its liquid propulsion system development capability. Rapid design, analysis, build and test will be critical to fielding the next high thrust rocket engine. With the maturity of the BBE testbed, MSFC propulsion engineering will bring forward a national capability that enables growth of both commercial and government interests.

Spermatogenic Cell-Specific Gene Mutation in Mice via CRISPR-Cas9.

PubMed

Bai, Meizhu; Liang, Dan; Wang, Yinghua; Li, Qing; Wu, Yuxuan; Li, Jinsong

2016-05-20

Tissue-specific knockout technology enables the analysis of the gene function in specific tissues in adult mammals. However, conventional strategy for producing tissue-specific knockout mice is a time- and labor-consuming process, restricting rapid study of the gene function in vivo. CRISPR-Cas9 system from bacteria is a simple and efficient gene-editing technique, which has enabled rapid generation of gene knockout lines in mouse by direct injection of CRISPR-Cas9 into zygotes. Here, we demonstrate CRISPR-Cas9-mediated spermatogenic cell-specific disruption of Scp3 gene in testes in one step. We first generated transgenic mice by pronuclear injection of a plasmid containing Hspa2 promoter driving Cas9 expression and showed Cas9 specific expression in spermatogenic cells. We then produced transgenic mice carrying Hspa2 promoter driven Cas9 and constitutive expressed sgRNA targeting Scp3 gene. Male founders were infertile due to developmental arrest of spermatogenic cells while female founders could produce progeny normally. Consistently, male progeny from female founders were infertile and females could transmit the transgenes to the next generation. Our study establishes a CRISPR-Cas9-based one-step strategy to analyze the gene function in adult tissues by a temporal-spatial pattern. Copyright © 2016 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Modelling Complexity: Making Sense of Leadership Issues in 14-19 Education

ERIC Educational Resources Information Center

Briggs, Ann R. J.

2008-01-01

Modelling of statistical data is a well established analytical strategy. Statistical data can be modelled to represent, and thereby predict, the forces acting upon a structure or system. For the rapidly changing systems in the world of education, modelling enables the researcher to understand, to predict and to enable decisions to be based upon…

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

Ankireddy, Krishnamraju; Ghahremani, Amir H.; Martin, Blake

Perovskite thin films are thermally annealed using a rapid intense pulsed light technique enabled by an alkyl halide that collectively improves device performance when processed in ambient conditions.

Mathematical Modeling Of Life-Support Systems

NASA Technical Reports Server (NTRS)

Seshan, Panchalam K.; Ganapathi, Balasubramanian; Jan, Darrell L.; Ferrall, Joseph F.; Rohatgi, Naresh K.

1994-01-01

Generic hierarchical model of life-support system developed to facilitate comparisons of options in design of system. Model represents combinations of interdependent subsystems supporting microbes, plants, fish, and land animals (including humans). Generic model enables rapid configuration of variety of specific life support component models for tradeoff studies culminating in single system design. Enables rapid evaluation of effects of substituting alternate technologies and even entire groups of technologies and subsystems. Used to synthesize and analyze life-support systems ranging from relatively simple, nonregenerative units like aquariums to complex closed-loop systems aboard submarines or spacecraft. Model, called Generic Modular Flow Schematic (GMFS), coded in such chemical-process-simulation languages as Aspen Plus and expressed as three-dimensional spreadsheet.

The Case of Nuclear Propulsion

NASA Technical Reports Server (NTRS)

Koroteev, Anatoly S.; Ponomarev-Stepnoi, Nicolai N.; Smetannikov, Vladimir P.; Gafarov, Albert A.; Houts, Mike; VanDyke, Melissa; Godfroy, Tom; Martin, James; Bragg-Sitton, Shannon; Dickens, Ricky

2003-01-01

Fission technology can enable rapid, affordable access to any point in the solar system. If fission propulsion systems are to be developed to their full potential; however, near-term customers must be identified and initial fission systems successfully developed, launched, and utilized. Successful utilization will simultaneously develop the infrastructure and experience necessary for developing even higher power and performance systems. To be successful, development programs must devise strategies for rapidly converting paper reactor concepts into actual flight hardware. One approach to accomplishing this is to design highly testable systems, and to structure the program to contain frequent, significant hardware milestones. This paper discusses ongoing efforts in Russia and the United States aimed at enabling near-term utilization of space fission systems.

Optimization of routine KRAS mutation PCR-based testing procedure for rational individualized first-line-targeted therapy selection in metastatic colorectal cancer.

PubMed

Chretien, Anne-Sophie; Harlé, Alexandre; Meyer-Lefebvre, Magali; Rouyer, Marie; Husson, Marie; Ramacci, Carole; Harter, Valentin; Genin, Pascal; Leroux, Agnès; Merlin, Jean-Louis

2013-02-01

KRAS mutation detection represents a crucial issue in metastatic colorectal cancer (mCRC). The optimization of KRAS mutation detection delay enabling rational prescription of first-line treatment in mCRC including anti-EGFR-targeted therapy requires robust and rapid molecular biology techniques. Routine analysis of mutations in codons 12 and 13 on 674 paraffin-embedded tissue specimens of mCRC has been performed for KRAS mutations detection using three molecular biology techniques, that is, high-resolution melting (HRM), polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP), and allelic discrimination PCR (TaqMan PCR). Discordant cases were assessed with COBAS 4800 KRAS CE-IVD assay. Among the 674 tumor specimens, 1.5% (10/674) had excessive DNA degradation and could not be analyzed. KRAS mutations were detected in 38.0% (256/674) of the analysable specimens (82.4% in codon 12 and 17.6% in codon 13). Among 613 specimens in whom all three techniques were used, 12 (2.0%) cases of discordance between the three techniques were observed. 83.3% (10/12) of the discordances were due to PCR-RFLP as confirmed by COBAS 4800 retrospective analysis. The three techniques were statistically comparable (κ > 0.9; P < 0.001). From these results, optimization of the routine procedure consisted of proceeding to systematic KRAS detection using HRM and TaqMan and PCR-RFLP in case of discordance and allowed significant decrease in delays. The results showed an excellent correlation between the three techniques. Using HRM and TaqMan warrants high-quality and rapid-routine KRAS mutation detection in paraffin-embedded tumor specimens. The new procedure allowed a significant decrease in delays for reporting results, enabling rational prescription of first-line-targeted therapy in mCRC.

An immuno-wall microdevice exhibits rapid and sensitive detection of IDH1-R132H mutation specific to grade II and III gliomas

PubMed Central

Yamamichi, Akane; Kasama, Toshihiro; Ohka, Fumiharu; Suzuki, Hiromichi; Kato, Akira; Motomura, Kazuya; Hirano, Masaki; Ranjit, Melissa; Chalise, Lushun; Kurimoto, Michihiro; Kondo, Goro; Aoki, Kosuke; Kaji, Noritada; Tokeshi, Manabu; Matsubara, Toshio; Senga, Takeshi; Kaneko, Mika K.; Suzuki, Hidenori; Hara, Masahito; Wakabayashi, Toshihiko; Baba, Yoshinobu; Kato, Yukinari; Natsume, Atsushi

2016-01-01

Abstract World Health Organization grade II and III gliomas most frequently occur in the central nervous system (CNS) in adults. Gliomas are not circumscribed; tumor edges are irregular and consist of tumor cells, normal brain tissue, and hyperplastic reactive glial cells. Therefore, the tumors are not fully resectable, resulting in recurrence, malignant progression, and eventual death. Approximately 69–80% of grade II and III gliomas harbor mutations in the isocitrate dehydrogenase 1 gene (IDH1), of which 83–90% are found to be the IDH1-R132H mutation. Detection of the IDH1-R132H mutation should help in the differential diagnosis of grade II and III gliomas from other types of CNS tumors and help determine the boundary between the tumor and normal brain tissue. In this study, we established a highly sensitive antibody-based device, referred to as the immuno-wall, to detect the IDH1-R132H mutation in gliomas. The immuno-wall causes an immunoreaction in microchannels fabricated using a photo-polymerizing polymer. This microdevice enables the analysis of the IDH1 status with a small sample within 15 min with substantially high sensitivity. Our results suggested that 10% content of the IDH1-R132H mutation in a sample of 0.33 μl volume, with 500 ng protein, or from 500 cells is theoretically sufficient for the analysis. The immuno-wall device will enable the rapid and highly sensitive detection of the IDH1-R132H mutation in routine clinical practice. PMID:27877908

A New Method for Rapid Screening of End-Point PCR Products: Application to Single Genome Amplified HIV and SIV Envelope Amplicons

PubMed Central

Houzet, Laurent; Deleage, Claire; Satie, Anne-Pascale; Merlande, Laetitia; Mahe, Dominique; Dejucq-Rainsford, Nathalie

2015-01-01

PCR is the most widely applied technique for large scale screening of bacterial clones, mouse genotypes, virus genomes etc. A drawback of large PCR screening is that amplicon analysis is usually performed using gel electrophoresis, a step that is very labor intensive, tedious and chemical waste generating. Single genome amplification (SGA) is used to characterize the diversity and evolutionary dynamics of virus populations within infected hosts. SGA is based on the isolation of single template molecule using limiting dilution followed by nested PCR amplification and requires the analysis of hundreds of reactions per sample, making large scale SGA studies very challenging. Here we present a novel approach entitled Long Amplicon Melt Profiling (LAMP) based on the analysis of the melting profile of the PCR reactions using SYBR Green and/or EvaGreen fluorescent dyes. The LAMP method represents an attractive alternative to gel electrophoresis and enables the quick discrimination of positive reactions. We validate LAMP for SIV and HIV env-SGA, in 96- and 384-well plate formats. Because the melt profiling allows the screening of several thousands of PCR reactions in a cost-effective, rapid and robust way, we believe it will greatly facilitate any large scale PCR screening. PMID:26053379

Rapid Analysis of Ingredients in Cream Using Ultrasonic Mist-Direct Analysis in Real-Time Time-of-Flight Mass Spectrometry

NASA Astrophysics Data System (ADS)

Shimada, Haruo; Maeno, Katsuyuki; Kinoshita, Kazumasa; Shida, Yasuo

2017-07-01

A novel method for the simultaneous detection of ingredients in pharmaceutical applications such as creams and lotions was developed. An ultrasonic atomizer has been used to produce a mist containing ingredients. The analyte molecules in the mist can be ionized by using direct analysis in real time (DART) at lower temperature than traditionally used, and we thus solved the problem of normal DART-MS measurement using a high-temperature gas. Thereby, molecular-related ions of heat-unstable components and nonvolatile components became detectable. The deprotonated molecular ion of glycyrrhizic acid (m/z 821), which is unstable at high temperatures, was detected without pyrolysis by ultrasonic mist-DART-MS using unheated helium gas, although it was not detected by normal DART-MS using heated helium gas. The cationized molecular ions of derivatives of polyethylene glycol fatty acid monoesters, which are nonvolatile compounds, were also detected as m/z peaks observed from 800 to 2300. Although the protonated molecular ion of tocopherol acetate was not detected in ionization by ultrasonic mist, it was detected by ultrasonic mist-DART-MS even in the emulsion. It was not necessary to dissolve a sample completely to detect its ions. This method enabled us to obtain the composition of pharmaceutical applications simply and rapidly.

Coordinating Multiple Spacecraft Assets for Joint Science Campaigns

NASA Technical Reports Server (NTRS)

Estlin, Tara; Chien, Steve; Castano, Rebecca; Gaines, Daniel; de Granville, Charles; Doubleday, Josh; Anderson, Robert C.; Knight, Russell; Bornstein, Benjamin; Rabideau, Gregg;

Geospatial-enabled Data Exploration and Computation through Data Infrastructure Building Blocks

NASA Astrophysics Data System (ADS)

Song, C. X.; Biehl, L. L.; Merwade, V.; Villoria, N.

2015-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices and sensors. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. The GABBs project aims at enabling broader access to geospatial data exploration and computation by developing spatial data infrastructure building blocks that leverage capabilities of end-to-end application service and virtualized computing framework in HUBzero. Funded by NSF Data Infrastructure Building Blocks (DIBBS) initiative, GABBs provides a geospatial data architecture that integrates spatial data management, mapping and visualization and will make it available as open source. The outcome of the project will enable users to rapidly create tools and share geospatial data and tools on the web for interactive exploration of data without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the development of geospatial data infrastructure building blocks and the scientific use cases that help drive the software development, as well as seek feedback from the user communities.

Integrating Remote Sensing Data, Hybrid-Cloud Computing, and Event Notifications for Advanced Rapid Imaging & Analysis (Invited)

NASA Astrophysics Data System (ADS)

Hua, H.; Owen, S. E.; Yun, S.; Lundgren, P.; Fielding, E. J.; Agram, P.; Manipon, G.; Stough, T. M.; Simons, M.; Rosen, P. A.; Wilson, B. D.; Poland, M. P.; Cervelli, P. F.; Cruz, J.

2013-12-01

Space-based geodetic measurement techniques such as Interferometric Synthetic Aperture Radar (InSAR) and Continuous Global Positioning System (CGPS) are now important elements in our toolset for monitoring earthquake-generating faults, volcanic eruptions, hurricane damage, landslides, reservoir subsidence, and other natural and man-made hazards. Geodetic imaging's unique ability to capture surface deformation with high spatial and temporal resolution has revolutionized both earthquake science and volcanology. Continuous monitoring of surface deformation and surface change before, during, and after natural hazards improves decision-making from better forecasts, increased situational awareness, and more informed recovery. However, analyses of InSAR and GPS data sets are currently handcrafted following events and are not generated rapidly and reliably enough for use in operational response to natural disasters. Additionally, the sheer data volumes needed to handle a continuous stream of InSAR data sets also presents a bottleneck. It has been estimated that continuous processing of InSAR coverage of California alone over 3-years would reach PB-scale data volumes. Our Advanced Rapid Imaging and Analysis for Monitoring Hazards (ARIA-MH) science data system enables both science and decision-making communities to monitor areas of interest with derived geodetic data products via seamless data preparation, processing, discovery, and access. We will present our findings on the use of hybrid-cloud computing to improve the timely processing and delivery of geodetic data products, integrating event notifications from USGS to improve the timely processing for response, as well as providing browse results for quick looks with other tools for integrative analysis.

On the Rapid Rise of Social Networking Sites: New Findings and Policy Implications

ERIC Educational Resources Information Center

Livingstone, Sonia; Brake, David R

2010-01-01

Social networking sites have been rapidly adopted by children and, especially, teenagers and young people worldwide, enabling new opportunities for the presentation of the self, learning, construction of a wide circle of relationships, and the management of privacy and intimacy. On the other hand, there are also concerns that social networking…

Microwell Array Method for Rapid Generation of Uniform Agarose Droplets and Beads for Single Molecule Analysis.

PubMed

Li, Xingrui; Zhang, Dongfeng; Zhang, Huimin; Guan, Zhichao; Song, Yanling; Liu, Ruochen; Zhu, Zhi; Yang, Chaoyong

2018-02-20

Compartmentalization of aqueous samples in uniform emulsion droplets has proven to be a useful tool for many chemical, biological, and biomedical applications. Herein, we introduce an array-based emulsification method for rapid and easy generation of monodisperse agarose-in-oil droplets in a PDMS microwell array. The microwells are filled with agarose solution, and subsequent addition of hot oil results in immediate formation of agarose droplets due to the surface-tension of the liquid solution. Because droplet size is determined solely by the array unit dimensions, uniform droplets with preselectable diameters ranging from 20 to 100 μm can be produced with relative standard deviations less than 3.5%. The array-based droplet generation method was used to perform digital PCR for absolute DNA quantitation. The array-based droplet isolation and sol-gel switching property of agarose enable formation of stable beads by chilling the droplet array at -20 °C, thus, maintaining the monoclonality of each droplet and facilitating the selective retrieval of desired droplets. The monoclonality of droplets was demonstrated by DNA sequencing and FACS analysis, suggesting the robustness and flexibility of the approach for single molecule amplification and analysis. We believe our approach will lead to new possibilities for a great variety of applications, such as single-cell gene expression studies, aptamer selection, and oligonucleotide analysis.

Engineering the Ideal Gigapixel Image Viewer

NASA Astrophysics Data System (ADS)

Perpeet, D. Wassenberg, J.

2011-09-01

Despite improvements in automatic processing, analysts are still faced with the task of evaluating gigapixel-scale mosaics or images acquired by telescopes such as Pan-STARRS. Displaying such images in ‘ideal’ form is a major challenge even today, and the amount of data will only increase as sensor resolutions improve. In our opinion, the ideal viewer has several key characteristics. Lossless display - down to individual pixels - ensures all information can be extracted from the image. Support for all relevant pixel formats (integer or floating point) allows displaying data from different sensors. Smooth zooming and panning in the high-resolution data enables rapid screening and navigation in the image. High responsiveness to input commands avoids frustrating delays. Instantaneous image enhancement, e.g. contrast adjustment and image channel selection, helps with analysis tasks. Modest system requirements allow viewing on regular workstation computers or even laptops. To the best of our knowledge, no such software product is currently available. Meeting these goals requires addressing certain realities of current computer architectures. GPU hardware accelerates rendering and allows smooth zooming without high CPU load. Programmable GPU shaders enable instant channel selection and contrast adjustment without any perceptible slowdown or changes to the input data. Relatively low disk transfer speeds suggest the use of compression to decrease the amount of data to transfer. Asynchronous I/O allows decompressing while waiting for previous I/O operations to complete. The slow seek times of magnetic disks motivate optimizing the order of the data on disk. Vectorization and parallelization allow significant increases in computational capacity. Limited memory requires streaming and caching of image regions. We develop a viewer that takes the above issues into account. Its awareness of the computer architecture enables previously unattainable features such as smooth zooming and image enhancement within high-resolution data. We describe our implementation, disclosing its novel file format and lossless image codec whose decompression is faster than copying the raw data in memory. Both provide crucial performance boosts compared to conventional approaches. Usability tests demonstrate the suitability of our viewer for rapid analysis of large SAR datasets, multispectral satellite imagery and mosaics.

Flow cytometric analysis of microbial contamination in food industry technological lines--initial study.

PubMed

Józwa, Wojciech; Czaczyk, Katarzyna

2012-04-02

Flow cytometry constitutes an alternative for traditional methods of microorganisms identification and analysis, including methods requiring cultivation step. It enables the detection of pathogens and other microorganisms contaminants without the need to culture microbial cells meaning that the sample (water, waste or food e.g. milk, wine, beer) may be analysed directly. This leads to a significant reduction of time required for analysis allowing monitoring of production processes and immediate reaction in case of contamination or any disruption occurs. Apart from the analysis of raw materials or products on different stages of manufacturing process, the flow cytometry seems to constitute an ideal tool for the assessment of microbial contamination on the surface of technological lines. In the present work samples comprising smears from 3 different surfaces of technological lines from fruit and vegetable processing company from Greater Poland were analysed directly with flow cytometer. The measured parameters were forward and side scatter of laser light signals allowing the estimation of microbial cell contents in each sample. Flow cytometric analysis of the surface of food industry production lines enable the preliminary evaluation of microbial contamination within few minutes from the moment of sample arrival without the need of sample pretreatment. The presented method of fl ow cytometric initial evaluation of microbial state of food industry technological lines demonstrated its potential for developing a robust, routine method for the rapid and labor-saving detection of microbial contamination in food industry.

High-Throughput Phenotyping of Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes and Neurons Using Electric Field Stimulation and High-Speed Fluorescence Imaging

PubMed Central

Daily, Neil J.; Du, Zhong-Wei

2017-01-01

Abstract Electrophysiology of excitable cells, including muscle cells and neurons, has been measured by making direct contact with a single cell using a micropipette electrode. To increase the assay throughput, optical devices such as microscopes and microplate readers have been used to analyze electrophysiology of multiple cells. We have established a high-throughput (HTP) analysis of action potentials (APs) in highly enriched motor neurons and cardiomyocytes (CMs) that are differentiated from human induced pluripotent stem cells (iPSCs). A multichannel electric field stimulation (EFS) device enabled the ability to electrically stimulate cells and measure dynamic changes in APs of excitable cells ultra-rapidly (>100 data points per second) by imaging entire 96-well plates. We found that the activities of both neurons and CMs and their response to EFS and chemicals are readily discerned by our fluorescence imaging-based HTP phenotyping assay. The latest generation of calcium (Ca2+) indicator dyes, FLIPR Calcium 6 and Cal-520, with the HTP device enables physiological analysis of human iPSC-derived samples highlighting its potential application for understanding disease mechanisms and discovering new therapeutic treatments. PMID:28525289

R4SA for Controlling Robots

NASA Technical Reports Server (NTRS)

Aghazarian, Hrand

2009-01-01

The R4SA GUI mentioned in the immediately preceding article is a userfriendly interface for controlling one or more robot(s). This GUI makes it possible to perform meaningful real-time field experiments and research in robotics at an unmatched level of fidelity, within minutes of setup. It provides such powerful graphing modes as that of a digitizing oscilloscope that displays up to 250 variables at rates between 1 and 200 Hz. This GUI can be configured as multiple intuitive interfaces for acquisition of data, command, and control to enable rapid testing of subsystems or an entire robot system while simultaneously performing analysis of data. The R4SA software establishes an intuitive component-based design environment that can be easily reconfigured for any robotic platform by creating or editing setup configuration files. The R4SA GUI enables event-driven and conditional sequencing similar to those of Mars Exploration Rover (MER) operations. It has been certified as part of the MER ground support equipment and, therefore, is allowed to be utilized in conjunction with MER flight hardware. The R4SA GUI could also be adapted to use in embedded computing systems, other than that of the MER, for commanding and real-time analysis of data.

Rapid microbiology - raising awareness.

PubMed

Bailie, Jonathan

2016-01-01

A 'high-level overview' of some of the emerging rapid microbiology technologies designed to help healthcare engineering and infection control teams working in hospitals and other healthcare facilities more rapidly identify potentially hazardous levels of waterborne microorganisms in their water systems, enabling them to take prompt remedial action, and a look at the some of the 'pros and cons' of such testing techniques, was given by Nalco technical director, Howard Barnes, the vice-chair of the Legionella Control Association (LCA), at a recent LCA open day. HEJ editor, Jonathan Bailie, reports.

Embedded spacecraft thermal control using ultrasonic consolidation

NASA Astrophysics Data System (ADS)

Clements, Jared W.

Research has been completed in order to rapidly manufacture spacecraft thermal control technologies embedded in spacecraft structural panels using ultrasonic consolidation. This rapid manufacturing process enables custom thermal control designs in the time frame necessary for responsive space. Successfully embedded components include temperature sensors, heaters, wire harnessing, pre-manufactured heat pipes, and custom integral heat pipes. High conductivity inserts and custom integral pulsating heat pipes were unsuccessfully attempted. This research shows the viability of rapid manufacturing of spacecraft structures with embedded thermal control using ultrasonic consolidation.

LC-MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine

PubMed Central

Clasquin, Michelle F.; Melamud, Eugene; Rabinowitz, Joshua D.

2014-01-01

MAVEN is an open-source software program for interactive processing of LC-MS-based metabolomics data. MAVEN enables rapid and reliable metabolite quantitation from multiple reaction monitoring data or high-resolution full-scan mass spectrometry data. It automatically detects and reports peak intensities for isotope-labeled metabolites. Menu-driven, click-based navigation allows visualization of raw and analyzed data. Here we provide a User Guide for MAVEN. Step-by-step instructions are provided for data import, peak alignment across samples, identification of metabolites that differ strongly between biological conditions, quantitation and visualization of isotope-labeling patterns, and export of tables of metabolite-specific peak intensities. Together, these instructions describe a workflow that allows efficient processing of raw LC-MS data into a form ready for biological analysis. PMID:22389014

Design and Construction of a Field Capable Snapshot Hyperspectral Imaging Spectrometer

NASA Technical Reports Server (NTRS)

Arik, Glenda H.

2005-01-01

The computed-tomography imaging spectrometer (CTIS) is a device which captures the spatial and spectral content of a rapidly evolving same in a single image frame. The most recent CTIS design is optically all reflective and uses as its dispersive device a stated the-art reflective computer generated hologram (CGH). This project focuses on the instrument's transition from laboratory to field. This design will enable the CTIS to withstand a harsh desert environment. The system is modeled in optical design software using a tolerance analysis. The tolerances guide the design of the athermal mount and component parts. The parts are assembled into a working mount shell where the performance of the mounts is tested for thermal integrity. An interferometric analysis of the reflective CGH is also performed.

Some Observations on the Current Status of Performing Finite Element Analyses

NASA Technical Reports Server (NTRS)

Raju, Ivatury S.; Knight, Norman F., Jr; Shivakumar, Kunigal N.

2015-01-01

Aerospace structures are complex high-performance structures. Advances in reliable and efficient computing and modeling tools are enabling analysts to consider complex configurations, build complex finite element models, and perform analysis rapidly. Many of the early career engineers of today are very proficient in the usage of modern computers, computing engines, complex software systems, and visualization tools. These young engineers are becoming increasingly efficient in building complex 3D models of complicated aerospace components. However, the current trends demonstrate blind acceptance of the results of the finite element analysis results. This paper is aimed at raising an awareness of this situation. Examples of the common encounters are presented. To overcome the current trends, some guidelines and suggestions for analysts, senior engineers, and educators are offered.

LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine.

PubMed

Clasquin, Michelle F; Melamud, Eugene; Rabinowitz, Joshua D

2012-03-01

MAVEN is an open-source software program for interactive processing of LC-MS-based metabolomics data. MAVEN enables rapid and reliable metabolite quantitation from multiple reaction monitoring data or high-resolution full-scan mass spectrometry data. It automatically detects and reports peak intensities for isotope-labeled metabolites. Menu-driven, click-based navigation allows visualization of raw and analyzed data. Here we provide a User Guide for MAVEN. Step-by-step instructions are provided for data import, peak alignment across samples, identification of metabolites that differ strongly between biological conditions, quantitation and visualization of isotope-labeling patterns, and export of tables of metabolite-specific peak intensities. Together, these instructions describe a workflow that allows efficient processing of raw LC-MS data into a form ready for biological analysis.

Network-assisted crop systems genetics: network inference and integrative analysis.

PubMed

Lee, Tak; Kim, Hyojin; Lee, Insuk

2015-04-01

Although next-generation sequencing (NGS) technology has enabled the decoding of many crop species genomes, most of the underlying genetic components for economically important crop traits remain to be determined. Network approaches have proven useful for the study of the reference plant, Arabidopsis thaliana, and the success of network-based crop genetics will also require the availability of a genome-scale functional networks for crop species. In this review, we discuss how to construct functional networks and elucidate the holistic view of a crop system. The crop gene network then can be used for gene prioritization and the analysis of resequencing-based genome-wide association study (GWAS) data, the amount of which will rapidly grow in the field of crop science in the coming years. Copyright © 2015 Elsevier Ltd. All rights reserved.

New Millenium Program Serving Earth and Space Sciences

NASA Technical Reports Server (NTRS)

Li, Fuk

1999-01-01

A cross-Enterprise program is to identify and validate flight breakthrough technologies that will significantly benefit future space science and earth science missions. The breakthrough technologies are: enable new capabilities to meet earth and space science needs and reducing costs of future missions. The flight validation are: mitigates risks to first users and enables rapid technology infusion into future missions.

Improving the analysis, storage and sharing of neuroimaging data using relational databases and distributed computing.

PubMed

Hasson, Uri; Skipper, Jeremy I; Wilde, Michael J; Nusbaum, Howard C; Small, Steven L

2008-01-15

The increasingly complex research questions addressed by neuroimaging research impose substantial demands on computational infrastructures. These infrastructures need to support management of massive amounts of data in a way that affords rapid and precise data analysis, to allow collaborative research, and to achieve these aims securely and with minimum management overhead. Here we present an approach that overcomes many current limitations in data analysis and data sharing. This approach is based on open source database management systems that support complex data queries as an integral part of data analysis, flexible data sharing, and parallel and distributed data processing using cluster computing and Grid computing resources. We assess the strengths of these approaches as compared to current frameworks based on storage of binary or text files. We then describe in detail the implementation of such a system and provide a concrete description of how it was used to enable a complex analysis of fMRI time series data.

Improving the Analysis, Storage and Sharing of Neuroimaging Data using Relational Databases and Distributed Computing

PubMed Central

Hasson, Uri; Skipper, Jeremy I.; Wilde, Michael J.; Nusbaum, Howard C.; Small, Steven L.

2007-01-01

The increasingly complex research questions addressed by neuroimaging research impose substantial demands on computational infrastructures. These infrastructures need to support management of massive amounts of data in a way that affords rapid and precise data analysis, to allow collaborative research, and to achieve these aims securely and with minimum management overhead. Here we present an approach that overcomes many current limitations in data analysis and data sharing. This approach is based on open source database management systems that support complex data queries as an integral part of data analysis, flexible data sharing, and parallel and distributed data processing using cluster computing and Grid computing resources. We assess the strengths of these approaches as compared to current frameworks based on storage of binary or text files. We then describe in detail the implementation of such a system and provide a concrete description of how it was used to enable a complex analysis of fMRI time series data. PMID:17964812

Valuing flexibilities in the design of urban water management systems.

PubMed

Deng, Yinghan; Cardin, Michel-Alexandre; Babovic, Vladan; Santhanakrishnan, Deepak; Schmitter, Petra; Meshgi, Ali

2013-12-15

Climate change and rapid urbanization requires decision-makers to develop a long-term forward assessment on sustainable urban water management projects. This is further complicated by the difficulties of assessing sustainable designs and various design scenarios from an economic standpoint. A conventional valuation approach for urban water management projects, like Discounted Cash Flow (DCF) analysis, fails to incorporate uncertainties, such as amount of rainfall, unit cost of water, and other uncertainties associated with future changes in technological domains. Such approach also fails to include the value of flexibility, which enables managers to adapt and reconfigure systems over time as uncertainty unfolds. This work describes an integrated framework to value investments in urban water management systems under uncertainty. It also extends the conventional DCF analysis through explicit considerations of flexibility in systems design and management. The approach incorporates flexibility as intelligent decision-making mechanisms that enable systems to avoid future downside risks and increase opportunities for upside gains over a range of possible futures. A water catchment area in Singapore was chosen to assess the value of a flexible extension of standard drainage canals and a flexible deployment of a novel water catchment technology based on green roofs and porous pavements. Results show that integrating uncertainty and flexibility explicitly into the decision-making process can reduce initial capital expenditure, improve value for investment, and enable decision-makers to learn more about system requirements during the lifetime of the project. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dioctyl sulfosuccinate analysis in near-shore Gulf of Mexico water by direct-injection liquid chromatography-tandem mass spectrometry.

PubMed

Mathew, Johnson; Schroeder, David L; Zintek, Lawrence B; Schupp, Caitlin R; Kosempa, Michael G; Zachary, Adam M; Schupp, George C; Wesolowski, Dennis J

2012-03-30

Dioctyl sulfosuccinate (DOSS) was a major component of the dispersants most used in the 2010 Deepwater Horizon Oil Spill incident response. This analytical method quantifies salt water DOSS concentrations to a reporting limit of 20 μg/L, which was below the United States Environmental Protection Agency's (U.S. EPA) 40 μg/L DOSS Aquatic Life Benchmark. DOSS in Gulf of Mexico water samples were analyzed by direct-injection reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS). Sample preparation with 50% acetonitrile (ACN) enabled quantitative transfer of DOSS and increased DOSS response 20-fold by reducing aggregation. This increased sensitivity enabled the detection of a confirmatory transition over the calibration range of 10-200 μg/L. U.S. EPA Region 5 and Region 6 laboratories analyzed hundreds of near-shore surface Gulf of Mexico water samples, none contained more than the 20 ppb reporting limit. The matrix spike DOSS/deuterated surrogate (DOSS-D34) correlation of determination varied with mobile phase modifier (ammonium formate R(2)=0.95 and formic acid R(2)=0.27). Using ammonium formate, DOSS-D34 accurately measured DOSS matrix effect. The near-shore sodium concentrations varied more than 10,000-fold, but were not strongly correlated with DOSS recovery. DOSS detection by LC-MS/MS enabled rapid analysis which was valuable in guiding incident response. Published by Elsevier B.V.

Label-Free Delineation of Brain Tumors by Coherent Anti-Stokes Raman Scattering Microscopy in an Orthotopic Mouse Model and Human Glioblastoma

PubMed Central

Tamosaityte, Sandra; Leipnitz, Elke; Geiger, Kathrin D.; Schackert, Gabriele; Koch, Edmund; Steiner, Gerald; Kirsch, Matthias

2014-01-01

Background Coherent anti-Stokes Raman scattering (CARS) microscopy provides fine resolution imaging and displays morphochemical properties of unstained tissue. Here, we evaluated this technique to delineate and identify brain tumors. Methods Different human tumors (glioblastoma, brain metastases of melanoma and breast cancer) were induced in an orthotopic mouse model. Cryosections were investigated by CARS imaging tuned to probe C-H molecular vibrations, thereby addressing the lipid content of the sample. Raman microspectroscopy was used as reference. Histopathology provided information about the tumor's localization, cell proliferation and vascularization. Results The morphochemical contrast of CARS images enabled identifying brain tumors irrespective of the tumor type and properties: All tumors were characterized by a lower CARS signal intensity than the normal parenchyma. On this basis, tumor borders and infiltrations could be identified with cellular resolution. Quantitative analysis revealed that the tumor-related reduction of CARS signal intensity was more pronounced in glioblastoma than in metastases. Raman spectroscopy enabled relating the CARS intensity variation to the decline of total lipid content in the tumors. The analysis of the immunohistochemical stainings revealed no correlation between tumor-induced cytological changes and the extent of CARS signal intensity reductions. The results were confirmed on samples of human glioblastoma. Conclusions CARS imaging enables label-free, rapid and objective identification of primary and secondary brain tumors. Therefore, it is a potential tool for diagnostic neuropathology as well as for intraoperative tumor delineation. PMID:25198698

Device and Container for Reheating and Sterilization

NASA Technical Reports Server (NTRS)

Sastry, Sudhir K.; Heskitt, Brian F.; Jun, Soojin; Marcy, Joseph E.; Mahna, Ritesh

2012-01-01

Long-duration space missions require the development of improved foods and novel packages that do not represent a significant disposal issue. In addition, it would also be desirable if rapid heating technologies could be used on Earth as well, to improve food quality during a sterilization process. For this purpose, a package equipped with electrodes was developed that will enable rapid reheating of contents via ohmic heating to serving temperature during space vehicle transit. Further, the package is designed with a resealing feature, which enables the package, once used, to contain and sterilize waste, including human waste for storage prior to jettison during a long-duration mission. Ohmic heating is a technology that has been investigated on and off for over a century. Literature indicates that foods processed by ohmic heating are of superior quality to their conventionally processed counterparts. This is due to the speed and uniformity of ohmic heating, which minimizes exposure of sensitive materials to high temperatures. In principle, the material may be heated rapidly to sterilization conditions, cooled rapidly, and stored. The ohmic heating device herein is incorporated within a package. While this by itself is not novel, a reusable feature also was developed with the intent that waste may be stored and re-sterilized within the packages. These would then serve a useful function after their use in food processing and storage. The enclosure should be designed to minimize mass (and for NASA's purposes, Equivalent System Mass, or ESM), while enabling the sterilization function. It should also be electrically insulating. For this reason, Ultem high-strength, machinable electrical insulator was used.

Comparative Genomics and Host Resistance against Infectious Diseases

PubMed Central

Qureshi, Salman T.; Skamene, Emil

1999-01-01

The large size and complexity of the human genome have limited the identification and functional characterization of components of the innate immune system that play a critical role in front-line defense against invading microorganisms. However, advances in genome analysis (including the development of comprehensive sets of informative genetic markers, improved physical mapping methods, and novel techniques for transcript identification) have reduced the obstacles to discovery of novel host resistance genes. Study of the genomic organization and content of widely divergent vertebrate species has shown a remarkable degree of evolutionary conservation and enables meaningful cross-species comparison and analysis of newly discovered genes. Application of comparative genomics to host resistance will rapidly expand our understanding of human immune defense by facilitating the translation of knowledge acquired through the study of model organisms. We review the rationale and resources for comparative genomic analysis and describe three examples of host resistance genes successfully identified by this approach. PMID:10081670

Analysis of context dependence in social interaction networks of a massively multiplayer online role-playing game.

PubMed

Son, Seokshin; Kang, Ah Reum; Kim, Hyun-chul; Kwon, Taekyoung; Park, Juyong; Kim, Huy Kang

2012-01-01

Rapid advances in modern computing and information technology have enabled millions of people to interact online via various social network and gaming services. The widespread adoption of such online services have made possible analysis of large-scale archival data containing detailed human interactions, presenting a very promising opportunity to understand the rich and complex human behavior. In collaboration with a leading global provider of Massively Multiplayer Online Role-Playing Games (MMORPGs), here we present a network science-based analysis of the interplay between distinct types of user interaction networks in the virtual world. We find that their properties depend critically on the nature of the context-interdependence of the interactions, highlighting the complex and multilayered nature of human interactions, a robust understanding of which we believe may prove instrumental in the designing of more realistic future virtual arenas as well as provide novel insights to the science of collective human behavior.

Automated extraction of direct, reactive, and vat dyes from cellulosic fibers for forensic analysis by capillary electrophoresis.

PubMed

Dockery, C R; Stefan, A R; Nieuwland, A A; Roberson, S N; Baguley, B M; Hendrix, J E; Morgan, S L

2009-08-01

Systematic designed experiments were employed to find the optimum conditions for extraction of direct, reactive, and vat dyes from cotton fibers prior to forensic characterization. Automated microextractions were coupled with measurements of extraction efficiencies on a microplate reader UV-visible spectrophotometer to enable rapid screening of extraction efficiency as a function of solvent composition. Solvent extraction conditions were also developed to be compatible with subsequent forensic characterization of extracted dyes by capillary electrophoresis with UV-visible diode array detection. The capillary electrophoresis electrolyte successfully used in this work consists of 5 mM ammonium acetate in 40:60 acetonitrile-water at pH 9.3, with the addition of sodium dithionite reducing agent to facilitate analysis of vat dyes. The ultimate goal of these research efforts is enhanced discrimination of trace fiber evidence by analysis of extracted dyes.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

PubMed

Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver

2016-08-30

High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.

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

Uchibori, Akihiro; Kurihara, Akikazu; Ohshima, Hiroyuki

A multiphysics analysis system for sodium-water reaction phenomena in a steam generator of sodium-cooled fast reactors was newly developed. The analysis system consists of the mechanistic numerical analysis codes, SERAPHIM, TACT, and RELAP5. The SERAPHIM code calculates the multicomponent multiphase flow and sodium-water chemical reaction caused by discharging of pressurized water vapor. Applicability of the SERAPHIM code was confirmed through the analyses of the experiment on water vapor discharging in liquid sodium. The TACT code was developed to calculate heat transfer from the reacting jet to the adjacent tube and to predict the tube failure occurrence. The numerical models integratedmore » into the TACT code were verified through some related experiments. The RELAP5 code evaluates thermal hydraulic behavior of water inside the tube. The original heat transfer correlations were corrected for the tube rapidly heated by the reacting jet. The developed system enables evaluation of the wastage environment and the possibility of the failure propagation.« less

Analytical Validation of a Portable Mass Spectrometer Featuring Interchangeable, Ambient Ionization Sources for High Throughput Forensic Evidence Screening

NASA Astrophysics Data System (ADS)

Lawton, Zachary E.; Traub, Angelica; Fatigante, William L.; Mancias, Jose; O'Leary, Adam E.; Hall, Seth E.; Wieland, Jamie R.; Oberacher, Herbert; Gizzi, Michael C.; Mulligan, Christopher C.

2017-06-01

Forensic evidentiary backlogs are indicative of the growing need for cost-effective, high-throughput instrumental methods. One such emerging technology that shows high promise in meeting this demand while also allowing on-site forensic investigation is portable mass spectrometric (MS) instrumentation, particularly that which enables the coupling to ambient ionization techniques. While the benefits of rapid, on-site screening of contraband can be anticipated, the inherent legal implications of field-collected data necessitates that the analytical performance of technology employed be commensurate with accepted techniques. To this end, comprehensive analytical validation studies are required before broad incorporation by forensic practitioners can be considered, and are the focus of this work. Pertinent performance characteristics such as throughput, selectivity, accuracy/precision, method robustness, and ruggedness have been investigated. Reliability in the form of false positive/negative response rates is also assessed, examining the effect of variables such as user training and experience level. To provide flexibility toward broad chemical evidence analysis, a suite of rapidly-interchangeable ion sources has been developed and characterized through the analysis of common illicit chemicals and emerging threats like substituted phenethylamines. [Figure not available: see fulltext.

An algorithm for automated detection, localization and measurement of local calcium signals from camera-based imaging.

PubMed

Ellefsen, Kyle L; Settle, Brett; Parker, Ian; Smith, Ian F

2014-09-01

Local Ca(2+) transients such as puffs and sparks form the building blocks of cellular Ca(2+) signaling in numerous cell types. They have traditionally been studied by linescan confocal microscopy, but advances in TIRF microscopy together with improved electron-multiplied CCD (EMCCD) cameras now enable rapid (>500 frames s(-1)) imaging of subcellular Ca(2+) signals with high spatial resolution in two dimensions. This approach yields vastly more information (ca. 1 Gb min(-1)) than linescan imaging, rendering visual identification and analysis of local events imaged both laborious and subject to user bias. Here we describe a routine to rapidly automate identification and analysis of local Ca(2+) events. This features an intuitive graphical user-interfaces and runs under Matlab and the open-source Python software. The underlying algorithm features spatial and temporal noise filtering to reliably detect even small events in the presence of noisy and fluctuating baselines; localizes sites of Ca(2+) release with sub-pixel resolution; facilitates user review and editing of data; and outputs time-sequences of fluorescence ratio signals for identified event sites along with Excel-compatible tables listing amplitudes and kinetics of events. Copyright © 2014 Elsevier Ltd. All rights reserved.

Confocal mosaicing microscopy of human skin ex vivo: spectral analysis for digital staining to simulate histology-like appearance

NASA Astrophysics Data System (ADS)

Bini, Jason; Spain, James; Nehal, Kishwer; Hazelwood, Vikki; Dimarzio, Charles; Rajadhyaksha, Milind

2011-07-01

Confocal mosaicing microscopy enables rapid imaging of large areas of fresh tissue, without the processing that is necessary for conventional histology. Mosaicing may offer a means to perform rapid histology at the bedside. A possible barrier toward clinical acceptance is that the mosaics are based on a single mode of grayscale contrast and appear black and white, whereas histology is based on two stains (hematoxylin for nuclei, eosin for cellular cytoplasm and dermis) and appears purple and pink. Toward addressing this barrier, we report advances in digital staining: fluorescence mosaics that show only nuclei, are digitally stained purple and overlaid on reflectance mosaics, which show only cellular cytoplasm and dermis, and are digitally stained pink. With digital staining, the appearance of confocal mosaics mimics the appearance of histology. Using multispectral analysis and color matching functions, red, green, and blue (RGB) components of hematoxylin and eosin stains in tissue were determined. The resulting RGB components were then applied in a linear algorithm to transform fluorescence and reflectance contrast in confocal mosaics to the absorbance contrast seen in pathology. Optimization of staining with acridine orange showed improved quality of digitally stained mosaics, with good correlation to the corresponding histology.

Blending protein separation and peptide analysis through real-time proteolytic digestion.

PubMed

Slysz, Gordon W; Schriemer, David C

2005-03-15

Typical liquid- or gel-based protein separations require enzymatic digestion as an important first step in generating protein identifications. Traditional protocols involve long-term proteolytic digestion of the separated protein, often leading to sample loss and reduced sensitivity. Previously, we presented a rapid method of proteolytic digestion that showed excellent digestion of resistant and low concentrations of protein without requiring reduction and alkylation. Here, we demonstrate on-line, real-time tryptic digestion in conjunction with reversed-phase protein separation. The studies were aimed at optimizing pH and ionic strength and the size of the digestion element, to produce maximal protein digestion with minimal effects on chromatographic integrity. Upon establishing optimal conditions, the digestion element was attached downstream from a capillary C4 reversed-phase column. A four-protein mixture was processed through the combined system, and the resulting peptides were analyzed on-line by electrospray mass spectrometry. Extracted ion chromatograms for protein chromatography based on peptide elution were generated. These were shown to emulate ion chromatograms produced in a subsequent run without the digestion element, based on protein elution. The methodology will enable rapid and sensitive analysis of liquid-based protein separations using the power of bottom-up proteomics methodologies.

Deactivation of Multilayered MFI Nanosheet Zeolite during Upgrading of Biomass Pyrolysis Vapors

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

Xu, Mengze; Mukarakate, Calvin; Iisa, Kristiina

Here, the catalytic fast pyrolysis (CFP) of biomass is a promising technology for producing renewable transportation fuels and chemicals. MFI-type catalysts have shown promise for CFP because they produce gasoline range hydrocarbons from oxygenated pyrolysis compounds; however, rapid catalyst deactivation due to coking is one of the major technical barriers inhibiting the commercialization of this technology. Coke deposited on the surface of the catalysts blocks access to active sites in the micropores leading to rapid catalyst deactivation. Our strategy is to minimize rapid catalyst deactivation by adding mesoporosity through forming MFI nanosheet materials. The synthesized MFI nanosheet catalysts were fullymore » characterized and evaluated for cellulose pyrolysis vapor upgrading to produce olefins and aromatic hydrocarbons. The data obtained from pyrolysis-GCMS (py-GCMS), showed that fresh MFI nanosheets produced similar aromatic hydrocarbon and olefin yields compared to conventional HZSM-5. However, MFI nanosheets demonstrated a longer lifetime than HZSM-5 even though coke contents were also higher than for HZSM-5 because the mesopores enabled better accessibility to active acid sites. This conclusion was supported by results from post-reaction analysis of various spent catalysts collected at different points during the deactivation experiments.« less

Rapid extraction and assay of uranium from environmental surface samples

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

Barrett, Christopher A.; Chouyyok, Wilaiwan; Speakman, Robert J.

Extraction methods enabling faster removal and concentration of uranium compounds for improved trace and low-level assay are demonstrated for standard surface sampling material in support of nuclear safeguards efforts, health monitoring, and other nuclear analysis applications. A key problem with the existing surface sampling swipes is the requirement for complete digestion of sample and sampling matrix. This is a time-consuming and labour-intensive process that limits laboratory throughput, elevates costs, and increases background levels. Various extraction methods are explored for their potential to quickly and efficiently remove different chemical forms of uranium from standard surface sampling material. A combination of carbonatemore » and peroxide solutions is shown to give the most rapid and complete form of uranyl compound extraction and dissolution. This rapid extraction process is demonstrated to be compatible with standard inductive coupled plasma mass spectrometry methods for uranium isotopic assay as well as screening techniques such as x-ray fluorescence. The general approach described has application beyond uranium to other analytes of nuclear forensic interest (e.g., rare earth elements and plutonium) as well as heavy metals for environmental and industrial hygiene monitoring.« less

Deactivation of Multilayered MFI Nanosheet Zeolite during Upgrading of Biomass Pyrolysis Vapors

DOE PAGES

Xu, Mengze; Mukarakate, Calvin; Iisa, Kristiina; ...

2017-05-02

Here, the catalytic fast pyrolysis (CFP) of biomass is a promising technology for producing renewable transportation fuels and chemicals. MFI-type catalysts have shown promise for CFP because they produce gasoline range hydrocarbons from oxygenated pyrolysis compounds; however, rapid catalyst deactivation due to coking is one of the major technical barriers inhibiting the commercialization of this technology. Coke deposited on the surface of the catalysts blocks access to active sites in the micropores leading to rapid catalyst deactivation. Our strategy is to minimize rapid catalyst deactivation by adding mesoporosity through forming MFI nanosheet materials. The synthesized MFI nanosheet catalysts were fullymore » characterized and evaluated for cellulose pyrolysis vapor upgrading to produce olefins and aromatic hydrocarbons. The data obtained from pyrolysis-GCMS (py-GCMS), showed that fresh MFI nanosheets produced similar aromatic hydrocarbon and olefin yields compared to conventional HZSM-5. However, MFI nanosheets demonstrated a longer lifetime than HZSM-5 even though coke contents were also higher than for HZSM-5 because the mesopores enabled better accessibility to active acid sites. This conclusion was supported by results from post-reaction analysis of various spent catalysts collected at different points during the deactivation experiments.« less

Rapid, all-optical crystal orientation imaging of two-dimensional transition metal dichalcogenide monolayers

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

David, Sabrina N.; Zhai, Yao; van der Zande, Arend M.

Two-dimensional (2D) atomic materials such as graphene and transition metal dichalcogenides (TMDCs) have attracted significant research and industrial interest for their electronic, optical, mechanical, and thermal properties. While large-area crystal growth techniques such as chemical vapor deposition have been demonstrated, the presence of grain boundaries and orientation of grains arising in such growths substantially affect the physical properties of the materials. There is currently no scalable characterization method for determining these boundaries and orientations over a large sample area. We here present a second-harmonic generation based microscopy technique for rapidly mapping grain orientations and boundaries of 2D TMDCs. We experimentallymore » demonstrate the capability to map large samples to an angular resolution of ±1° with minimal sample preparation and without involved analysis. A direct comparison of the all-optical grain orientation maps against results obtained by diffraction-filtered dark-field transmission electron microscopy plus selected-area electron diffraction on identical TMDC samples is provided. This rapid and accurate tool should enable large-area characterization of TMDC samples for expedited studies of grain boundary effects and the efficient characterization of industrial-scale production techniques.« less

Plio-Pleistocene time evolution of the 100-ky cycle in marine paleoclimate records

NASA Technical Reports Server (NTRS)

Park, Jeffrey; Maasch, Kirk A.

1992-01-01

To constrain theories for the dynamical evolution of global ice mass through the late Neogene, it is important to determine whether major changes in the record were gradual or rapid. Of particular interest is the evolution of the near 100-ky ice age cycle in the middle Pleistocene. We have applied a new technique based on multiple taper spectrum analysis which allows us to model the time evolution of quasi-periodic signals. This technique uses both phase and amplitude information, and enables us to address the question of abrupt versus gradual onset of the 100-ky periodicity in the middle Pleistocene.

Cell-free protein synthesis: applications in proteomics and biotechnology.

PubMed

He, Mingyue

2008-01-01

Protein production is one of the key steps in biotechnology and functional proteomics. Expression of proteins in heterologous hosts (such as in E. coli) is generally lengthy and costly. Cell-free protein synthesis is thus emerging as an attractive alternative. In addition to the simplicity and speed for protein production, cell-free expression allows generation of functional proteins that are difficult to produce by in vivo systems. Recent exploitation of cell-free systems enables novel development of technologies for rapid discovery of proteins with desirable properties from very large libraries. This article reviews the recent development in cell-free systems and their application in the large scale protein analysis.

Positron Scanner for Locating Brain Tumors

DOE R&D Accomplishments Database

Rankowitz, S.; Robertson, J. S.; Higinbotham, W. A.; Rosenblum, M. J.

1962-03-01

A system is described that makes use of positron emitting isotopes for locating brain tumors. This system inherently provides more information about the distribution of radioactivity in the head in less time than existing scanners which use one or two detectors. A stationary circular array of 32 scintillation detectors scans a horizontal layer of the head from many directions simultaneously. The data, consisting of the number of counts in all possible coincidence pairs, are coded and stored in the memory of a Two-Dimensional Pulse-Height Analyzer. A unique method of displaying and interpreting the data is described that enables rapid approximate analysis of complex source distribution patterns. (auth)

A simple and effective method for detecting precipitated proteins in MALDI-TOF MS.

PubMed

Oshikane, Hiroyuki; Watabe, Masahiko; Nakaki, Toshio

2018-04-01

MALDI-TOF MS has developed rapidly into an essential analytical tool for the life sciences. Cinnamic acid derivatives are generally employed in routine molecular weight determinations of intact proteins using MALDI-TOF MS. However, a protein of interest may precipitate when mixed with matrix solution, perhaps preventing MS detection. We herein provide a simple approach to enable the MS detection of such precipitated protein species by means of a "direct deposition method" -- loading the precipitant directly onto the sample plate. It is thus expected to improve routine MS analysis of intact proteins. Copyright © 2018. Published by Elsevier Inc.

Genome Editing of Structural Variations: Modeling and Gene Correction.

PubMed

Park, Chul-Yong; Sung, Jin Jea; Kim, Dong-Wook

2016-07-01

The analysis of chromosomal structural variations (SVs), such as inversions and translocations, was made possible by the completion of the human genome project and the development of genome-wide sequencing technologies. SVs contribute to genetic diversity and evolution, although some SVs can cause diseases such as hemophilia A in humans. Genome engineering technology using programmable nucleases (e.g., ZFNs, TALENs, and CRISPR/Cas9) has been rapidly developed, enabling precise and efficient genome editing for SV research. Here, we review advances in modeling and gene correction of SVs, focusing on inversion, translocation, and nucleotide repeat expansion. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thermo-elastic optical coherence tomography.

PubMed

Wang, Tianshi; Pfeiffer, Tom; Wu, Min; Wieser, Wolfgang; Amenta, Gaetano; Draxinger, Wolfgang; van der Steen, Antonius F W; Huber, Robert; Soest, Gijs van

2017-09-01

The absorption of nanosecond laser pulses induces rapid thermo-elastic deformation in tissue. A sub-micrometer scale displacement occurs within a few microseconds after the pulse arrival. In this Letter, we investigate the laser-induced thermo-elastic deformation using a 1.5 MHz phase-sensitive optical coherence tomography (OCT) system. A displacement image can be reconstructed, which enables a new modality of phase-sensitive OCT, called thermo-elastic OCT. An analysis of the results shows that the optical absorption is a dominating factor for the displacement. Thermo-elastic OCT is capable of visualizing inclusions that do not appear on the structural OCT image, providing additional tissue type information.

Laser Capture Microdissection in the Genomic and Proteomic Era: Targeting the Genetic Basis of Cancer

PubMed Central

Domazet, Barbara; MacLennan, Gregory T.; Lopez-Beltran, Antonio; Montironi, Rodolfo; Cheng, Liang

2008-01-01

The advent of new technologies has enabled deeper insight into processes atsubcellular levels, which will ultimately improve diagnostic procedures and patient outcome. Thanks to cell enrichment methods, it is now possible to study cells in their native environment. This has greatly contributed to a rapid growth in several areas, such as gene expression analysis, proteomics, and metabolonomics. Laser capture microdissection (LCM) as a method of procuring subpopulations of cells under direct visual inspection is playing an important role in these areas. This review provides an overview of existing LCM technology and its downstream applications in genomics, proteomics, diagnostics and therapy. PMID:18787684

Laser capture microdissection in the genomic and proteomic era: targeting the genetic basis of cancer.

PubMed

Domazet, Barbara; Maclennan, Gregory T; Lopez-Beltran, Antonio; Montironi, Rodolfo; Cheng, Liang

2008-03-15

The advent of new technologies has enabled deeper insight into processes at subcellular levels, which will ultimately improve diagnostic procedures and patient outcome. Thanks to cell enrichment methods, it is now possible to study cells in their native environment. This has greatly contributed to a rapid growth in several areas, such as gene expression analysis, proteomics, and metabolonomics. Laser capture microdissection (LCM) as a method of procuring subpopulations of cells under direct visual inspection is playing an important role in these areas. This review provides an overview of existing LCM technology and its downstream applications in genomics, proteomics, diagnostics and therapy.

Duplex DNA-Invading γ-Modified Peptide Nucleic Acids Enable Rapid Identification of Bloodstream Infections in Whole Blood

PubMed Central

Nölling, Jörk; Rapireddy, Srinivas; Amburg, Joel I.; Crawford, Elizabeth M.; Prakash, Ranjit A.; Rabson, Arthur R.

2016-01-01

ABSTRACT Bloodstream infections are a leading cause of morbidity and mortality. Early and targeted antimicrobial intervention is lifesaving, yet current diagnostic approaches fail to provide actionable information within a clinically viable time frame due to their reliance on blood culturing. Here, we present a novel pathogen identification (PID) platform that features the use of duplex DNA-invading γ-modified peptide nucleic acids (γPNAs) for the rapid identification of bacterial and fungal pathogens directly from blood, without culturing. The PID platform provides species-level information in under 2.5 hours while reaching single-CFU-per-milliliter sensitivity across the entire 21-pathogen panel. The clinical utility of the PID platform was demonstrated through assessment of 61 clinical specimens, which showed >95% sensitivity and >90% overall correlation to blood culture findings. This rapid γPNA-based platform promises to improve patient care by enabling the administration of a targeted first-line antimicrobial intervention. PMID:27094328

Holokinetic centromeres and efficient telomere healing enable rapid karyotype evolution.

PubMed

Jankowska, Maja; Fuchs, Jörg; Klocke, Evelyn; Fojtová, Miloslava; Polanská, Pavla; Fajkus, Jiří; Schubert, Veit; Houben, Andreas

2015-12-01

Species with holocentric chromosomes are often characterized by a rapid karyotype evolution. In contrast to species with monocentric chromosomes where acentric fragments are lost during cell division, breakage of holocentric chromosomes creates fragments with normal centromere activity. To decipher the mechanism that allows holocentric species an accelerated karyotype evolution via chromosome breakage, we analyzed the chromosome complements of irradiated Luzula elegans plants. The resulting chromosomal fragments and rearranged chromosomes revealed holocentromere-typical CENH3 and histone H2AThr120ph signals as well as the same mitotic mobility like unfragmented chromosomes. Newly synthesized telomeres at break points become detectable 3 weeks after irradiation. The presence of active telomerase suggests a telomerase-based mechanism of chromosome healing. A successful transmission of holocentric chromosome fragments across different generations was found for most offspring of irradiated plants. Hence, a combination of holokinetic centromere activity and the fast formation of new telomeres at break points enables holocentric species a rapid karyotype evolution involving chromosome fissions and rearrangements.

Fast targeted gene transfection and optogenetic modification of single neurons using femtosecond laser irradiation

PubMed Central

Antkowiak, Maciej; Torres-Mapa, Maria Leilani; Witts, Emily C.; Miles, Gareth B.; Dholakia, Kishan; Gunn-Moore, Frank J.

2013-01-01

A prevailing problem in neuroscience is the fast and targeted delivery of DNA into selected neurons. The development of an appropriate methodology would enable the transfection of multiple genes into the same cell or different genes into different neighboring cells as well as rapid cell selective functionalization of neurons. Here, we show that optimized femtosecond optical transfection fulfills these requirements. We also demonstrate successful optical transfection of channelrhodopsin-2 in single selected neurons. We extend the functionality of this technique for wider uptake by neuroscientists by using fast three-dimensional laser beam steering enabling an image-guided “point-and-transfect” user-friendly transfection of selected cells. A sub-second transfection timescale per cell makes this method more rapid by at least two orders of magnitude when compared to alternative single-cell transfection techniques. This novel technology provides the ability to carry out large-scale cell selective genetic studies on neuronal ensembles and perform rapid genetic programming of neural circuits. PMID:24257461

Fast targeted gene transfection and optogenetic modification of single neurons using femtosecond laser irradiation.

PubMed

Antkowiak, Maciej; Torres-Mapa, Maria Leilani; Witts, Emily C; Miles, Gareth B; Dholakia, Kishan; Gunn-Moore, Frank J

2013-11-21

A prevailing problem in neuroscience is the fast and targeted delivery of DNA into selected neurons. The development of an appropriate methodology would enable the transfection of multiple genes into the same cell or different genes into different neighboring cells as well as rapid cell selective functionalization of neurons. Here, we show that optimized femtosecond optical transfection fulfills these requirements. We also demonstrate successful optical transfection of channelrhodopsin-2 in single selected neurons. We extend the functionality of this technique for wider uptake by neuroscientists by using fast three-dimensional laser beam steering enabling an image-guided "point-and-transfect" user-friendly transfection of selected cells. A sub-second transfection timescale per cell makes this method more rapid by at least two orders of magnitude when compared to alternative single-cell transfection techniques. This novel technology provides the ability to carry out large-scale cell selective genetic studies on neuronal ensembles and perform rapid genetic programming of neural circuits.

Effect of Back Contact and Rapid Thermal Processing Conditions on Flexible CdTe Device Performance

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

Mahabaduge, Hasitha; Meysing, D. M.; Rance, Will L.

Flexible CdTe solar cells on ultra-thin glass substrates can enable new applications that require high specific power, unique form-factors, and low manufacturing costs. To be successful, these cells must be cost competitive, have high efficiency, and have high reliability. Here we present back contact processing conditions that enabled us to achieve over 16% efficiency on flexible Corning (R) Willow (R) Glass substrates. We used co-evaporated ZnTe:Cu and Au as our back contact and used rapid thermal processing (RTP) to activate the back contact. Both the ZnTe to Cu ratio and the RTP activation temperature provide independent control over the devicemore » performance. We have investigated the influence of various RTP conditions to Cu activation and distribution. Current density-voltage, capacitance-voltage measurements along with device simulations were used to examine the device performance in terms of ZnTe to Cu ratio and rapid thermal activation temperature.« less

Rapid Raman spectroscopy of musculoskeletal tissue using a visible laser and an electron-multiplying CCD (EMCCD) detector

NASA Astrophysics Data System (ADS)

Golcuk, Kurtulus; Mandair, Gurjit S.; Callender, Andrew F.; Finney, William F.; Sahar, Nadder; Kohn, David H.; Morris, Michael D.

2006-02-01

Background fluorescence can often complicate the use of Raman microspectroscopy in the study of musculoskeletal tissues. Such fluorescence interferences are undesirable as the Raman spectra of matrix and mineral phases can be used to differentiate between normal and pathological or microdamaged bone. Photobleaching with the excitation laser provides a non-invasive method for reducing background fluorescence, enabling 532 nm Raman hyperspectral imaging of bone tissue. The signal acquisition time for a 400 point Raman line image is reduced to 1-4 seconds using electronmultiplying CCD (EMCCD) detector, enabling acquisition of Raman images in less than 10 minutes. Rapid photobleaching depends upon multiple scattering effects in the tissue specimen and is applicable to some, but not all experimental situations.

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor.

PubMed

Crow, Megan; Paul, Anirban; Ballouz, Sara; Huang, Z Josh; Gillis, Jesse

2018-02-28

Single-cell RNA-sequencing (scRNA-seq) technology provides a new avenue to discover and characterize cell types; however, the experiment-specific technical biases and analytic variability inherent to current pipelines may undermine its replicability. Meta-analysis is further hampered by the use of ad hoc naming conventions. Here we demonstrate our replication framework, MetaNeighbor, that quantifies the degree to which cell types replicate across datasets, and enables rapid identification of clusters with high similarity. We first measure the replicability of neuronal identity, comparing results across eight technically and biologically diverse datasets to define best practices for more complex assessments. We then apply this to novel interneuron subtypes, finding that 24/45 subtypes have evidence of replication, which enables the identification of robust candidate marker genes. Across tasks we find that large sets of variably expressed genes can identify replicable cell types with high accuracy, suggesting a general route forward for large-scale evaluation of scRNA-seq data.

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

PubMed Central

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A.; Caron, Christophe

2015-01-01

Summary: The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. Availability and implementation: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). Contact: contact@workflow4metabolomics.org PMID:25527831

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.

PubMed

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A; Caron, Christophe

2015-05-01

The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). contact@workflow4metabolomics.org. © The Author 2014. Published by Oxford University Press.

Biosynthesis and genetic encoding of phosphothreonine through parallel selection and deep sequencing

PubMed Central

Huguenin-Dezot, Nicolas; Liang, Alexandria D.; Schmied, Wolfgang H.; Rogerson, Daniel T.; Chin, Jason W.

2017-01-01

The phosphorylation of threonine residues in proteins regulates diverse processes in eukaryotic cells, and thousands of threonine phosphorylations have been identified. An understanding of how threonine phosphorylation regulates biological function will be accelerated by general methods to bio-synthesize defined phospho-proteins. Here we address limitations in current methods for discovering aminoacyl-tRNA synthetase/tRNA pairs for incorporating non-natural amino acids into proteins, by combining parallel positive selections with deep sequencing and statistical analysis, to create a rapid approach for directly discovering aminoacyl-tRNA synthetase/tRNA pairs that selectively incorporate non-natural substrates. Our approach is scalable and enables the direct discovery of aminoacyl-tRNA synthetase/tRNA pairs with mutually orthogonal substrate specificity. We biosynthesize phosphothreonine in cells, and use our new selection approach to discover a phosphothreonyl-tRNA synthetase/tRNACUA pair. By combining these advances we create an entirely biosynthetic route to incorporating phosphothreonine in proteins and biosynthesize several phosphoproteins; enabling phosphoprotein structure determination and synthetic protein kinase activation. PMID:28553966

Generating community-built tools for data sharing and analysis in environmental networks

USGS Publications Warehouse

Read, Jordan S.; Gries, Corinna; Read, Emily K.; Klug, Jennifer; Hanson, Paul C.; Hipsey, Matthew R.; Jennings, Eleanor; O'Reilley, Catherine; Winslow, Luke A.; Pierson, Don; McBride, Christopher G.; Hamilton, David

2016-01-01

Rapid data growth in many environmental sectors has necessitated tools to manage and analyze these data. The development of tools often lags behind the proliferation of data, however, which may slow exploratory opportunities and scientific progress. The Global Lake Ecological Observatory Network (GLEON) collaborative model supports an efficient and comprehensive data–analysis–insight life cycle, including implementations of data quality control checks, statistical calculations/derivations, models, and data visualizations. These tools are community-built and openly shared. We discuss the network structure that enables tool development and a culture of sharing, leading to optimized output from limited resources. Specifically, data sharing and a flat collaborative structure encourage the development of tools that enable scientific insights from these data. Here we provide a cross-section of scientific advances derived from global-scale analyses in GLEON. We document enhancements to science capabilities made possible by the development of analytical tools and highlight opportunities to expand this framework to benefit other environmental networks.

Strains, functions, and dynamics in the expanded Human Microbiome Project

PubMed Central

Lloyd-Price, Jason; Mahurkar, Anup; Rahnavard, Gholamali; Crabtree, Jonathan; Orvis, Joshua; Hall, A. Brantley; Brady, Arthur; Creasy, Heather H.; McCracken, Carrie; Giglio, Michelle G.; McDonald, Daniel; Franzosa, Eric A.; Knight, Rob; White, Owen; Huttenhower, Curtis

2018-01-01

Summary The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, microbial population diversity, biogeography, and molecular function. The NIH Human Microbiome Project (HMP) has provided one of the broadest such characterizations to date. Here, we introduce an expanded second phase of the study, abbreviated HMP1-II, comprising 1,631 new metagenomic samples (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to these data to provide new characterizations of microbiome personalization. Strain identification revealed distinct subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity, thus enabling an understanding of personalized microbiome function and dynamics. PMID:28953883

The maximum entropy production and maximum Shannon information entropy in enzyme kinetics

NASA Astrophysics Data System (ADS)

Dobovišek, Andrej; Markovič, Rene; Brumen, Milan; Fajmut, Aleš

2018-04-01

We demonstrate that the maximum entropy production principle (MEPP) serves as a physical selection principle for the description of the most probable non-equilibrium steady states in simple enzymatic reactions. A theoretical approach is developed, which enables maximization of the density of entropy production with respect to the enzyme rate constants for the enzyme reaction in a steady state. Mass and Gibbs free energy conservations are considered as optimization constraints. In such a way computed optimal enzyme rate constants in a steady state yield also the most uniform probability distribution of the enzyme states. This accounts for the maximal Shannon information entropy. By means of the stability analysis it is also demonstrated that maximal density of entropy production in that enzyme reaction requires flexible enzyme structure, which enables rapid transitions between different enzyme states. These results are supported by an example, in which density of entropy production and Shannon information entropy are numerically maximized for the enzyme Glucose Isomerase.

Structure–property relationships in atomic-scale junctions: Histograms and beyond

DOE PAGES

Mark S. Hybertsen; Venkataraman, Latha

2016-03-03

Over the past 10 years, there has been tremendous progress in the measurement, modeling and understanding of structure–function relationships in single molecule junctions. Numerous research groups have addressed significant scientific questions, directed both to conductance phenomena at the single molecule level and to the fundamental chemistry that controls junction functionality. Many different functionalities have been demonstrated, including single-molecule diodes, optically and mechanically activated switches, and, significantly, physical phenomena with no classical analogues, such as those based on quantum interference effects. Experimental techniques for reliable and reproducible single molecule junction formation and characterization have led to this progress. In particular, themore » scanning tunneling microscope based break-junction (STM-BJ) technique has enabled rapid, sequential measurement of large numbers of nanoscale junctions allowing a statistical analysis to readily distinguish reproducible characteristics. Furthermore, harnessing fundamental link chemistry has provided the necessary chemical control over junction formation, enabling measurements that revealed clear relationships between molecular structure and conductance characteristics.« less

Structure–property relationships in atomic-scale junctions: Histograms and beyond

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

Mark S. Hybertsen; Venkataraman, Latha

Over the past 10 years, there has been tremendous progress in the measurement, modeling and understanding of structure–function relationships in single molecule junctions. Numerous research groups have addressed significant scientific questions, directed both to conductance phenomena at the single molecule level and to the fundamental chemistry that controls junction functionality. Many different functionalities have been demonstrated, including single-molecule diodes, optically and mechanically activated switches, and, significantly, physical phenomena with no classical analogues, such as those based on quantum interference effects. Experimental techniques for reliable and reproducible single molecule junction formation and characterization have led to this progress. In particular, themore » scanning tunneling microscope based break-junction (STM-BJ) technique has enabled rapid, sequential measurement of large numbers of nanoscale junctions allowing a statistical analysis to readily distinguish reproducible characteristics. Furthermore, harnessing fundamental link chemistry has provided the necessary chemical control over junction formation, enabling measurements that revealed clear relationships between molecular structure and conductance characteristics.« less

Genomic Definition of Hypervirulent and Multidrug-Resistant Klebsiella pneumoniae Clonal Groups

PubMed Central

Bialek-Davenet, Suzanne; Criscuolo, Alexis; Ailloud, Florent; Passet, Virginie; Jones, Louis; Delannoy-Vieillard, Anne-Sophie; Garin, Benoit; Le Hello, Simon; Arlet, Guillaume; Nicolas-Chanoine, Marie-Hélène; Decré, Dominique

2014-01-01

Multidrug-resistant and highly virulent Klebsiella pneumoniae isolates are emerging, but the clonal groups (CGs) corresponding to these high-risk strains have remained imprecisely defined. We aimed to identify K. pneumoniae CGs on the basis of genome-wide sequence variation and to provide a simple bioinformatics tool to extract virulence and resistance gene data from genomic data. We sequenced 48 K. pneumoniae isolates, mostly of serotypes K1 and K2, and compared the genomes with 119 publicly available genomes. A total of 694 highly conserved genes were included in a core-genome multilocus sequence typing scheme, and cluster analysis of the data enabled precise definition of globally distributed hypervirulent and multidrug-resistant CGs. In addition, we created a freely accessible database, BIGSdb-Kp, to enable rapid extraction of medically and epidemiologically relevant information from genomic sequences of K. pneumoniae. Although drug-resistant and virulent K. pneumoniae populations were largely nonoverlapping, isolates with combined virulence and resistance features were detected. PMID:25341126

Developments in the Implementation of Acoustic Droplet Ejection for Protein Crystallography.

PubMed

Wu, Ping; Noland, Cameron; Ultsch, Mark; Edwards, Bonnie; Harris, David; Mayer, Robert; Harris, Seth F

2016-02-01

Acoustic droplet ejection (ADE) enables crystallization experiments at the low-nanoliter scale, resulting in rapid vapor diffusion equilibration dynamics and efficient reagent usage in the empirical discovery of structure-enabling protein crystallization conditions. We extend our validation of this technology applied to the diverse physicochemical property space of aqueous crystallization reagents where dynamic fluid analysis coupled to ADE aids in accurate and precise dispensations. Addition of crystallization seed stocks, chemical additives, or small-molecule ligands effectively modulates crystallization, and we here provide examples in optimization of crystal morphology and diffraction quality by the acoustic delivery of ultra-small volumes of these cofactors. Additional applications are discussed, including set up of in situ proteolysis and alternate geometries of crystallization that leverage the small scale afforded by acoustic delivery. Finally, we describe parameters of a system of automation in which the acoustic liquid handler is integrated with a robotic arm, plate centrifuge, peeler, sealer, and stacks, which allows unattended high-throughput crystallization experimentation. © 2015 Society for Laboratory Automation and Screening.

Correlative Analysis of Behavioral and Physiological Concomitants of Labor in Pregnant Rats

NASA Technical Reports Server (NTRS)

Baer, L. A.; Wade, C. E.; Ronca, A. E.; Dalton, Bonnie (Technical Monitor)

2002-01-01

During parturition, rats exhibit characteristic behavioral expressions of labor. Lordosis contractions, consisting of an elongation of the dams body, are observed beginning several hours prior to neonate births, whereas vertical contractions, repeated rapid lifts of the abdomen, occur immediately preceding the birth of each neonate. We analyzed underlying changes in intrauterine pressure (IUP) using a telemetric sensor that we modified for use in freely-moving rats. This technique enabled us to correlate behavioral expressions of labor contractions with IUP. A small telemetric blood pressure sensor was fitted within a fluid-filled balloon, similar in size to a full term rat fetus. On Gestational day 19 of the rats' 22-day pregnancy, a unit was surgically implanted within the uterus. The dams were simultaneously videotaped, enabling us to directly correlate IUP signals with behavioral expressions of labor contractions. Earlier phases of labor, consisting predominantly of lordosis contractions were characterized by lower pressures relative to later phases during which higher pressures and vertical contractions were frequently observed.

QuakeSim 2.0

NASA Technical Reports Server (NTRS)

Donnellan, Andrea; Parker, Jay W.; Lyzenga, Gregory A.; Granat, Robert A.; Norton, Charles D.; Rundle, John B.; Pierce, Marlon E.; Fox, Geoffrey C.; McLeod, Dennis; Ludwig, Lisa Grant

2012-01-01

QuakeSim 2.0 improves understanding of earthquake processes by providing modeling tools and integrating model applications and various heterogeneous data sources within a Web services environment. QuakeSim is a multisource, synergistic, data-intensive environment for modeling the behavior of earthquake faults individually, and as part of complex interacting systems. Remotely sensed geodetic data products may be explored, compared with faults and landscape features, mined by pattern analysis applications, and integrated with models and pattern analysis applications in a rich Web-based and visualization environment. Integration of heterogeneous data products with pattern informatics tools enables efficient development of models. Federated database components and visualization tools allow rapid exploration of large datasets, while pattern informatics enables identification of subtle, but important, features in large data sets. QuakeSim is valuable for earthquake investigations and modeling in its current state, and also serves as a prototype and nucleus for broader systems under development. The framework provides access to physics-based simulation tools that model the earthquake cycle and related crustal deformation. Spaceborne GPS and Inter ferometric Synthetic Aperture (InSAR) data provide information on near-term crustal deformation, while paleoseismic geologic data provide longerterm information on earthquake fault processes. These data sources are integrated into QuakeSim's QuakeTables database system, and are accessible by users or various model applications. UAVSAR repeat pass interferometry data products are added to the QuakeTables database, and are available through a browseable map interface or Representational State Transfer (REST) interfaces. Model applications can retrieve data from Quake Tables, or from third-party GPS velocity data services; alternatively, users can manually input parameters into the models. Pattern analysis of GPS and seismicity data has proved useful for mid-term forecasting of earthquakes, and for detecting subtle changes in crustal deformation. The GPS time series analysis has also proved useful as a data-quality tool, enabling the discovery of station anomalies and data processing and distribution errors. Improved visualization tools enable more efficient data exploration and understanding. Tools provide flexibility to science users for exploring data in new ways through download links, but also facilitate standard, intuitive, and routine uses for science users and end users such as emergency responders.

Methods for a Rapid Systematic Review and Metaanalysis in Evaluating Selective Serotonin Reuptake Inhibitors for Premature Ejaculation

ERIC Educational Resources Information Center

Martyn-St. James, Marrissa; Cooper, Katy; Kaltenthaler, Eva

2017-01-01

The aim of this study was to evaluate a rapid systematic review method in which randomised controlled trial (RCT) data was extracted from existing reviews and subsequent RCTs. The method enabled: identification of RCTs not included by existing reviews; cross-checking RCT data for consistency where there was more than one review; double data…

Rapid Development and Distribution of Mobile Media-Rich Clinical Practice Guidelines Nationwide in Colombia.

PubMed

Flórez-Arango, José F; Sriram Iyengar, M; Caicedo, Indira T; Escobar, German

2017-01-01

Development and electronic distribution of Clinical Practice Guidelines production is costly and challenging. This poster presents a rapid method to represent existing guidelines in auditable, computer executable multimedia format. We used a technology that enables a small number of clinicians to, in a short period of time, develop a substantial amount of computer executable guidelines without programming.

PyPathway: Python Package for Biological Network Analysis and Visualization.

PubMed

Xu, Yang; Luo, Xiao-Chun

2018-05-01

Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.

Risks to health care workers from nano-enabled medical products.

PubMed

Murashov, Vladimir; Howard, John

2015-01-01

Nanotechnology is rapidly expanding into the health care industry. However, occupational safety and health risks of nano-enabled medical products have not been thoroughly assessed. This manuscript highlights occupational risk mitigation practices for nano-enabled medical products throughout their life cycle for all major workplace settings including (1) medical research laboratories, (2) pharmaceutical manufacturing facilities, (3) clinical dispensing pharmacies, (4) health care delivery facilities, (5) home health care, (6) health care support, and (7) medical waste management. It further identifies critical research needs for ensuring worker protection in the health care industry.

Pre-existing Epithelial Diversity in Normal Human Livers: A Tissue-tethered Cytometric Analysis in Portal/Periportal Epithelial Cells

PubMed Central

Isse, Kumiko; Lesniak, Andrew; Grama, Kedar; Maier, John; Specht, Susan; Castillo-Rama, Marcela; Lunz, John; Roysam, Badrinath; Michalopoulos, George; Demetris, Anthony J.

2012-01-01

Routine light microscopy identifies two distinct epithelial cell populations in normal human livers: hepatocytes and biliary epithelial cells (BEC). Considerable epithelial diversity, however, arises during disease states when a variety of hepatocyte-BEC hybrid cells appear. This has been attributed to activation and differentiation of putative hepatic progenitor cells (HPC) residing in the Canals of Hering and/or metaplasia of pre-existing mature epithelial cells. A novel analytic approach consisting of multiplex labeling, high resolution whole slide imaging (WSI), and automated image analysis was used to determine if more complex epithelial cell phenotypes pre-existed in normal adult human livers, which might provide an alternative explanation for disease-induced epithelial diversity. “Virtually digested” WSI enabled quantitative cytometric analyses of individual cells displayed in a variety of formats (e.g. scatter plots) while still tethered to the WSI and tissue structure. We employed biomarkers specifically-associated with mature epithelial forms (HNF4α for hepatocytes, CK19 and HNF1β for BEC) and explored for the presence of cells with hybrid biomarker phenotypes. Results showed abundant hybrid cells in portal bile duct BEC, canals of Hering, and immediate periportal hepatocytes. These bi-potential cells likely serve as a reservoir for the epithelial diversity of ductular reactions, appearance of hepatocytes in bile ducts, and the rapid and fluid transition of BEC to hepatocytes, and vice versa. Conclusion Novel imaging and computational tools enable increased information extraction from tissue samples and quantify the considerable pre-existent hybrid epithelial diversity in normal human liver. This computationally-enabled tissue analysis approach offers much broader potential beyond the results presented here. PMID:23150208

A photo-cross-linking approach to monitor folding and assembly of newly synthesized proteins in a living cell.

PubMed

Miyazaki, Ryoji; Myougo, Naomi; Mori, Hiroyuki; Akiyama, Yoshinori

2018-01-12

Many proteins form multimeric complexes that play crucial roles in various cellular processes. Studying how proteins are correctly folded and assembled into such complexes in a living cell is important for understanding the physiological roles and the qualitative and quantitative regulation of the complex. However, few methods are suitable for analyzing these rapidly occurring processes. Site-directed in vivo photo-cross-linking is an elegant technique that enables analysis of protein-protein interactions in living cells with high spatial resolution. However, the conventional site-directed in vivo photo-cross-linking method is unsuitable for analyzing dynamic processes. Here, by combining an improved site-directed in vivo photo-cross-linking technique with a pulse-chase approach, we developed a new method that can analyze the folding and assembly of a newly synthesized protein with high spatiotemporal resolution. We demonstrate that this method, named the pulse-chase and in vivo photo-cross-linking experiment (PiXie), enables the kinetic analysis of the formation of an Escherichia coli periplasmic (soluble) protein complex (PhoA). We also used our new technique to investigate assembly/folding processes of two membrane complexes (SecD-SecF in the inner membrane and LptD-LptE in the outer membrane), which provided new insights into the biogenesis of these complexes. Our PiXie method permits analysis of the dynamic behavior of various proteins and enables examination of protein-protein interactions at the level of individual amino acid residues. We anticipate that our new technique will have valuable utility for studies of protein dynamics in many organisms. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Model My Watershed and BiG CZ Data Portal: Interactive geospatial analysis and hydrological modeling web applications that leverage the Amazon cloud for scientists, resource managers and students

NASA Astrophysics Data System (ADS)

Aufdenkampe, A. K.; Mayorga, E.; Tarboton, D. G.; Sazib, N. S.; Horsburgh, J. S.; Cheetham, R.

2016-12-01

The Model My Watershed Web app (http://wikiwatershed.org/model/) was designed to enable citizens, conservation practitioners, municipal decision-makers, educators, and students to interactively select any area of interest anywhere in the continental USA to: (1) analyze real land use and soil data for that area; (2) model stormwater runoff and water-quality outcomes; and (3) compare how different conservation or development scenarios could modify runoff and water quality. The BiG CZ Data Portal is a web application for scientists for intuitive, high-performance map-based discovery, visualization, access and publication of diverse earth and environmental science data via a map-based interface that simultaneously performs geospatial analysis of selected GIS and satellite raster data for a selected area of interest. The two web applications share a common codebase (https://github.com/WikiWatershed and https://github.com/big-cz), high performance geospatial analysis engine (http://geotrellis.io/ and https://github.com/geotrellis) and deployment on the Amazon Web Services (AWS) cloud cyberinfrastructure. Users can use "on-the-fly" rapid watershed delineation over the national elevation model to select their watershed or catchment of interest. The two web applications also share the goal of enabling the scientists, resource managers and students alike to share data, analyses and model results. We will present these functioning web applications and their potential to substantially lower the bar for studying and understanding our water resources. We will also present work in progress, including a prototype system for enabling citizen-scientists to register open-source sensor stations (http://envirodiy.org/mayfly/) to stream data into these systems, so that they can be reshared using Water One Flow web services.

Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

PubMed Central

Forsberg, Erica M; Huan, Tao; Rinehart, Duane; Benton, H Paul; Warth, Benedikt; Hilmers, Brian; Siuzdak, Gary

2018-01-01

Systems biology is the study of complex living organisms, and as such, analysis on a systems-wide scale involves the collection of information-dense data sets that are representative of an entire phenotype. To uncover dynamic biological mechanisms, bioinformatics tools have become essential to facilitating data interpretation in large-scale analyses. Global metabolomics is one such method for performing systems biology, as metabolites represent the downstream functional products of ongoing biological processes. We have developed XCMS Online, a platform that enables online metabolomics data processing and interpretation. A systems biology workflow recently implemented within XCMS Online enables rapid metabolic pathway mapping using raw metabolomics data for investigating dysregulated metabolic processes. In addition, this platform supports integration of multi-omic (such as genomic and proteomic) data to garner further systems-wide mechanistic insight. Here, we provide an in-depth procedure showing how to effectively navigate and use the systems biology workflow within XCMS Online without a priori knowledge of the platform, including uploading liquid chromatography (LCLC)–mass spectrometry (MS) data from metabolite-extracted biological samples, defining the job parameters to identify features, correcting for retention time deviations, conducting statistical analysis of features between sample classes and performing predictive metabolic pathway analysis. Additional multi-omics data can be uploaded and overlaid with previously identified pathways to enhance systems-wide analysis of the observed dysregulations. We also describe unique visualization tools to assist in elucidation of statistically significant dysregulated metabolic pathways. Parameter input takes 5–10 min, depending on user experience; data processing typically takes 1–3 h, and data analysis takes ~30 min. PMID:29494574

Elements of effective palliative care models: a rapid review

PubMed Central

2014-01-01

Background Population ageing, changes to the profiles of life-limiting illnesses and evolving societal attitudes prompt a critical evaluation of models of palliative care. We set out to identify evidence-based models of palliative care to inform policy reform in Australia. Method A rapid review of electronic databases and the grey literature was undertaken over an eight week period in April-June 2012. We included policy documents and comparative studies from countries within the Organisation for Economic Co-operation and Development (OECD) published in English since 2001. Meta-analysis was planned where >1 study met criteria; otherwise, synthesis was narrative using methods described by Popay et al. (2006). Results Of 1,959 peer-reviewed articles, 23 reported systematic reviews, 9 additional RCTs and 34 non-randomised comparative studies. Variation in the content of models, contexts in which these were implemented and lack of detailed reporting meant that elements of models constituted a more meaningful unit of analysis than models themselves. Case management was the element most consistently reported in models for which comparative studies provided evidence for effectiveness. Essential attributes of population-based palliative care models identified by policy and addressed by more than one element were communication and coordination between providers (including primary care), skill enhancement, and capacity to respond rapidly to individuals’ changing needs and preferences over time. Conclusion Models of palliative care should integrate specialist expertise with primary and community care services and enable transitions across settings, including residential aged care. The increasing complexity of care needs, services, interventions and contextual drivers warrants future research aimed at elucidating the interactions between different components and the roles played by patient, provider and health system factors. The findings of this review are limited by its rapid methodology and focus on model elements relevant to Australia’s health system. PMID:24670065

Young Children's Everyday Concepts of the Internet: A Platform for Cyber-Safety Education in the Early Years

ERIC Educational Resources Information Center

Edwards, Susan; Nolan, Andrea; Henderson, Michael; Mantilla, Ana; Plowman, Lydia; Skouteris, Helen

2018-01-01

Young children from around the world are accessing the internet in ever increasing numbers. The rapid increase in internet activity by children aged 4-5 years in particular is due to the ease access enabled them by touchscreen internet-enabled tablet technologies. With young children now online, often independently of adult supervision, the need…

Fast interactive exploration of 4D MRI flow data

NASA Astrophysics Data System (ADS)

Hennemuth, A.; Friman, O.; Schumann, C.; Bock, J.; Drexl, J.; Huellebrand, M.; Markl, M.; Peitgen, H.-O.

2011-03-01

1- or 2-directional MRI blood flow mapping sequences are an integral part of standard MR protocols for diagnosis and therapy control in heart diseases. Recent progress in rapid MRI has made it possible to acquire volumetric, 3-directional cine images in reasonable scan time. In addition to flow and velocity measurements relative to arbitrarily oriented image planes, the analysis of 3-dimensional trajectories enables the visualization of flow patterns, local features of flow trajectories or possible paths into specific regions. The anatomical and functional information allows for advanced hemodynamic analysis in different application areas like stroke risk assessment, congenital and acquired heart disease, aneurysms or abdominal collaterals and cranial blood flow. The complexity of the 4D MRI flow datasets and the flow related image analysis tasks makes the development of fast comprehensive data exploration software for advanced flow analysis a challenging task. Most existing tools address only individual aspects of the analysis pipeline such as pre-processing, quantification or visualization, or are difficult to use for clinicians. The goal of the presented work is to provide a software solution that supports the whole image analysis pipeline and enables data exploration with fast intuitive interaction and visualization methods. The implemented methods facilitate the segmentation and inspection of different vascular systems. Arbitrary 2- or 3-dimensional regions for quantitative analysis and particle tracing can be defined interactively. Synchronized views of animated 3D path lines, 2D velocity or flow overlays and flow curves offer a detailed insight into local hemodynamics. The application of the analysis pipeline is shown for 6 cases from clinical practice, illustrating the usefulness for different clinical questions. Initial user tests show that the software is intuitive to learn and even inexperienced users achieve good results within reasonable processing times.

The future of forensic DNA analysis.

PubMed

Butler, John M

2015-08-05

The author's thoughts and opinions on where the field of forensic DNA testing is headed for the next decade are provided in the context of where the field has come over the past 30 years. Similar to the Olympic motto of 'faster, higher, stronger', forensic DNA protocols can be expected to become more rapid and sensitive and provide stronger investigative potential. New short tandem repeat (STR) loci have expanded the core set of genetic markers used for human identification in Europe and the USA. Rapid DNA testing is on the verge of enabling new applications. Next-generation sequencing has the potential to provide greater depth of coverage for information on STR alleles. Familial DNA searching has expanded capabilities of DNA databases in parts of the world where it is allowed. Challenges and opportunities that will impact the future of forensic DNA are explored including the need for education and training to improve interpretation of complex DNA profiles. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

A rapid, maskless 3D prototyping for fabrication of capillary circuits: Toward urinary protein detection.

PubMed

Yan, Sheng; Zhu, Yuanqing; Tang, Shi-Yang; Li, Yuxing; Zhao, Qianbin; Yuan, Dan; Yun, Guolin; Zhang, Jun; Zhang, Shiwu; Li, Weihua

2018-04-01

Proteinuria is an established risk marker for progressive renal function loss and patients would significantly benefit from a point-of-care testing. Although extensive work has been done to develop the microfluidic devices for the detection of urinary protein, they need the complicated operation and bulky peripherals. Here, we present a rapid, maskless 3D prototyping for fabrication of capillary fluidic circuits using laser engraving. The capillary circuits can be fabricated in a short amount of time (<10 min) without the requirements of clean-room facilities and photomasks. The advanced capillary components (e.g., trigger valves, retention valves and retention bursting valves) were fabricated, enabling the sequential liquid delivery and sample-reagent mixing. With the integration of smartphone-based detection platform, the microfluidic device can quantify the urinary protein via a colorimetric analysis. By eliminating the bulky and expensive equipment, this smartphone-based detection platform is portable for on-site quantitative detection. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells.

PubMed

Zhou, Yuexin; Zhu, Shiyou; Cai, Changzu; Yuan, Pengfei; Li, Chunmei; Huang, Yanyi; Wei, Wensheng

2014-05-22

Targeted genome editing technologies are powerful tools for studying biology and disease, and have a broad range of research applications. In contrast to the rapid development of toolkits to manipulate individual genes, large-scale screening methods based on the complete loss of gene expression are only now beginning to be developed. Here we report the development of a focused CRISPR/Cas-based (clustered regularly interspaced short palindromic repeats/CRISPR-associated) lentiviral library in human cells and a method of gene identification based on functional screening and high-throughput sequencing analysis. Using knockout library screens, we successfully identified the host genes essential for the intoxication of cells by anthrax and diphtheria toxins, which were confirmed by functional validation. The broad application of this powerful genetic screening strategy will not only facilitate the rapid identification of genes important for bacterial toxicity but will also enable the discovery of genes that participate in other biological processes.

USGS remote sensing coordination for the 2010 Haiti earthquake

USGS Publications Warehouse

Duda, Kenneth A.; Jones, Brenda

2011-01-01

In response to the devastating 12 January 2010, earthquake in Haiti, the US Geological Survey (USGS) provided essential coordinating services for remote sensing activities. Communication was rapidly established between the widely distributed response teams and data providers to define imaging requirements and sensor tasking opportunities. Data acquired from a variety of sources were received and archived by the USGS, and these products were subsequently distributed using the Hazards Data Distribution System (HDDS) and other mechanisms. Within six weeks after the earthquake, over 600,000 files representing 54 terabytes of data were provided to the response community. The USGS directly supported a wide variety of groups in their use of these data to characterize post-earthquake conditions and to make comparisons with pre-event imagery. The rapid and continuing response achieved was enabled by existing imaging and ground systems, and skilled personnel adept in all aspects of satellite data acquisition, processing, distribution and analysis. The information derived from image interpretation assisted senior planners and on-site teams to direct assistance where it was most needed.

Rapid estimation of glucosinolate thermal degradation rate constants in leaves of Chinese kale and broccoli (Brassica oleracea) in two seasons.

PubMed

Hennig, Kristin; Verkerk, Ruud; Bonnema, Guusje; Dekker, Matthijs

2012-08-15

Kinetic modeling was used as a tool to quantitatively estimate glucosinolate thermal degradation rate constants. Literature shows that thermal degradation rates differ in different vegetables. Well-characterized plant material, leaves of broccoli and Chinese kale plants grown in two seasons, was used in the study. It was shown that a first-order reaction is appropriate to model glucosinolate degradation independent from the season. No difference in degradation rate constants of structurally identical glucosinolates was found between broccoli and Chinese kale leaves when grown in the same season. However, glucosinolate degradation rate constants were highly affected by the season (20-80% increase in spring compared to autumn). These results suggest that differences in glucosinolate degradation rate constants can be due to variation in environmental as well as genetic factors. Furthermore, a methodology to estimate rate constants rapidly is provided to enable the analysis of high sample numbers for future studies.

Use of Computed Tomography for Characterizing Materials Grown Terrestrially and in Microgravity

NASA Technical Reports Server (NTRS)

Gillies, Donald C.; Engel, H. P.

2001-01-01

The purpose behind this work is to provide NASA Principal Investigators (PIs) rapid information, nondestructively, about their samples. This information will be in the form of density values throughout the samples, especially within slices 1 mm high. With correct interpretation and good calibration, these values will enable the PI to obtain macro chemical compositional analysis for his/her samples. Alternatively, the technique will provide information about the porosity level and its distribution within the sample. Experience gained with a NASA Microgravity Research Division-sponsored Advanced Technology Development (ATD) project on this topic has brought the technique to a level of maturity at which it has become a viable characterization tool for many of the Materials Science Pls, but with equipment that could never be supported within their own facilities. The existing computed tomography (CT) facility at NASA's Kennedy Space Center (KSC) is ideally situated to furnish information rapidly and conveniently to PIs, particularly immediately before and after flight missions.

Use of Computed Tomography for Characterizing Materials Grown Terrestrially and in Microgravity

NASA Technical Reports Server (NTRS)

Gillies, Donald C.; Engel, H. P.

2000-01-01

The purpose behind this work is to provide NASA Principal Investigators (PI) rapid information, non-destructively, about their samples. This information will be in the form of density values throughout the samples, especially within slices 1 mm high. With correct interpretation and good calibration, these values will enable the PI to obtain macro chemical compositional analysis for his/her samples. Alternatively, the technique will provide information about the porosity level and its distribution within the sample. Experience gained with a NASA MRD-sponsored Advanced Technology Development (ATD) project on this topic has brought the technique to a level of maturity at which it has become a viable characterization tool for many of the Materials Science PIs, but with equipment that could never be supported within their own facilities. The existing computed tomography (CT) facility at NASA's Kennedy Space Center (KSC) is ideally situated to furnish information rapidly and conveniently to PIs, particularly immediately before and after flight missions.

Rapid DNA Amplification Using a Battery-Powered Thin-Film Resistive Thermocycler

PubMed Central

Herold, Keith E.; Sergeev, Nikolay; Matviyenko, Andriy; Rasooly, Avraham

2010-01-01

Summary A prototype handheld, compact, rapid thermocycler was developed for multiplex analysis of nucleic acids in an inexpensive, portable configuration. Instead of the commonly used Peltier heating/cooling element, electric thin-film resistive heater and a miniature fan enable rapid heating and cooling of glass capillaries leading to a simple, low-cost Thin-Film Resistive Thermocycler (TFRT). Computer-based pulse width modulation control yields heating rates of 6–7 K/s and cooling rates of 5 K/s. The four capillaries are closely coupled to the heater, resulting in low power consumption. The energy required by a nominal PCR cycle (20 s at each temperature) was found to be 57 ± 2 J yielding an average power of approximately 1.0 W (not including the computer and the control system). Thus the device can be powered by a standard 9 V alkaline battery (or other 9 V power supply). The prototype TFRT was demonstrated (in a benchtop configuration) for detection of three important food pathogens (E. coli ETEC, Shigella dysenteriae, and Salmonella enterica). PCR amplicons were analyzed by gel electrophoresis. The 35 cycle PCR protocol using a single channel was completed in less then 18 min. Simple and efficient heating/cooling, low cost, rapid amplification, and low power consumption make the device suitable for portable DNA amplification applications including clinical point of care diagnostics and field use. PMID:19159110

Multifunctional Collaborative Modeling and Analysis Methods in Engineering Science

NASA Technical Reports Server (NTRS)

Ransom, Jonathan B.; Broduer, Steve (Technical Monitor)

2001-01-01

Engineers are challenged to produce better designs in less time and for less cost. Hence, to investigate novel and revolutionary design concepts, accurate, high-fidelity results must be assimilated rapidly into the design, analysis, and simulation process. This assimilation should consider diverse mathematical modeling and multi-discipline interactions necessitated by concepts exploiting advanced materials and structures. Integrated high-fidelity methods with diverse engineering applications provide the enabling technologies to assimilate these high-fidelity, multi-disciplinary results rapidly at an early stage in the design. These integrated methods must be multifunctional, collaborative, and applicable to the general field of engineering science and mechanics. Multifunctional methodologies and analysis procedures are formulated for interfacing diverse subdomain idealizations including multi-fidelity modeling methods and multi-discipline analysis methods. These methods, based on the method of weighted residuals, ensure accurate compatibility of primary and secondary variables across the subdomain interfaces. Methods are developed using diverse mathematical modeling (i.e., finite difference and finite element methods) and multi-fidelity modeling among the subdomains. Several benchmark scalar-field and vector-field problems in engineering science are presented with extensions to multidisciplinary problems. Results for all problems presented are in overall good agreement with the exact analytical solution or the reference numerical solution. Based on the results, the integrated modeling approach using the finite element method for multi-fidelity discretization among the subdomains is identified as most robust. The multiple-method approach is advantageous when interfacing diverse disciplines in which each of the method's strengths are utilized. The multifunctional methodology presented provides an effective mechanism by which domains with diverse idealizations are interfaced. This capability rapidly provides the high-fidelity results needed in the early design phase. Moreover, the capability is applicable to the general field of engineering science and mechanics. Hence, it provides a collaborative capability that accounts for interactions among engineering analysis methods.

Next generation tools for genomic data generation, distribution, and visualization

PubMed Central

2010-01-01

Background With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data. Results Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser. Conclusions These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq. PMID:20828407

Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies.

PubMed

O'Grady, John; Schwender, Jörg; Shachar-Hill, Yair; Morgan, John A

2012-03-01

For the past decade, flux maps have provided researchers with an in-depth perspective on plant metabolism. As a rapidly developing field, significant headway has been made recently in computation, experimentation, and overall understanding of metabolic flux analysis. These advances are particularly applicable to the study of plant metabolism. New dynamic computational methods such as non-stationary metabolic flux analysis are finding their place in the toolbox of metabolic engineering, allowing more organisms to be studied and decreasing the time necessary for experimentation, thereby opening new avenues by which to explore the vast diversity of plant metabolism. Also, improved methods of metabolite detection and measurement have been developed, enabling increasingly greater resolution of flux measurements and the analysis of a greater number of the multitude of plant metabolic pathways. Methods to deconvolute organelle-specific metabolism are employed with increasing effectiveness, elucidating the compartmental specificity inherent in plant metabolism. Advances in metabolite measurements have also enabled new types of experiments, such as the calculation of metabolic fluxes based on (13)CO(2) dynamic labelling data, and will continue to direct plant metabolic engineering. Newly calculated metabolic flux maps reveal surprising and useful information about plant metabolism, guiding future genetic engineering of crops to higher yields. Due to the significant level of complexity in plants, these methods in combination with other systems biology measurements are necessary to guide plant metabolic engineering in the future.

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.

PubMed

Scheltema, Richard A; Jankevics, Andris; Jansen, Ritsert C; Swertz, Morris A; Breitling, Rainer

2011-04-01

The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these methods into configurations best suited to the research question is hampered by heterogeneous file formats and monolithic software development. The mzXML, mzData, and mzML file formats have enabled uniform access to unprocessed raw data. In this paper we present our efforts to produce an equally simple and powerful format, PeakML, to uniformly exchange processed intermediary and result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, and annotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakML Viewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groups or companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch data processing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace information underlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.

Using Enabling Technologies to Facilitate the Comparison of Satellite Observations with the Model Forecasts for Hurricane Study

NASA Astrophysics Data System (ADS)

Li, P.; Knosp, B.; Hristova-Veleva, S. M.; Niamsuwan, N.; Johnson, M. P.; Shen, T. P. J.; Tanelli, S.; Turk, J.; Vu, Q. A.

2014-12-01

Due to their complexity and volume, the satellite data are underutilized in today's hurricane research and operations. To better utilize these data, we developed the JPL Tropical Cyclone Information System (TCIS) - an Interactive Data Portal providing fusion between Near-Real-Time satellite observations and model forecasts to facilitate model evaluation and improvement. We have collected satellite observations and model forecasts in the Atlantic Basin and the East Pacific for the hurricane seasons since 2010 and supported the NASA Airborne Campaigns for Hurricane Study such as the Genesis and Rapid Intensification Processes (GRIP) in 2010 and the Hurricane and Severe Storm Sentinel (HS3) from 2012 to 2014. To enable the direct inter-comparisons of the satellite observations and the model forecasts, the TCIS was integrated with the NASA Earth Observing System Simulator Suite (NEOS3) to produce synthetic observations (e.g. simulated passive microwave brightness temperatures) from a number of operational hurricane forecast models (HWRF and GFS). An automated process was developed to trigger NEOS3 simulations via web services given the location and time of satellite observations, monitor the progress of the NEOS3 simulations, display the synthetic observation and ingest them into the TCIS database when they are done. In addition, three analysis tools, the joint PDF analysis of the brightness temperatures, ARCHER for finding the storm-center and the storm organization and the Wave Number Analysis tool for storm asymmetry and morphology analysis were integrated into TCIS to provide statistical and structural analysis on both observed and synthetic data. Interactive tools were built in the TCIS visualization system to allow the spatial and temporal selections of the datasets, the invocation of the tools with user specified parameters, and the display and the delivery of the results. In this presentation, we will describe the key enabling technologies behind the design of the TCIS interactive data portal and analysis tools, including the spatial database technology for the representation and query of the level 2 satellite data, the automatic process flow using web services, the interactive user interface using the Google Earth API, and a common and expandable Python wrapper to invoke the analysis tools.

Nanomanipulation-Coupled Matrix-Assisted Laser Desorption/ Ionization-Direct Organelle Mass Spectrometry: A Technique for the Detailed Analysis of Single Organelles

NASA Astrophysics Data System (ADS)

Phelps, Mandy S.; Sturtevant, Drew; Chapman, Kent D.; Verbeck, Guido F.

2016-02-01

We describe a novel technique combining precise organelle microextraction with deposition and matrix-assisted laser desorption/ionization (MALDI) for a rapid, minimally invasive mass spectrometry (MS) analysis of single organelles from living cells. A dual-positioner nanomanipulator workstation was utilized for both extraction of organelle content and precise co-deposition of analyte and matrix solution for MALDI-direct organelle mass spectrometry (DOMS) analysis. Here, the triacylglycerol (TAG) profiles of single lipid droplets from 3T3-L1 adipocytes were acquired and results validated with nanoelectrospray ionization (NSI) MS. The results demonstrate the utility of the MALDI-DOMS technique as it enabled longer mass analysis time, higher ionization efficiency, MS imaging of the co-deposited spot, and subsequent MS/MS capabilities of localized lipid content in comparison to NSI-DOMS. This method provides selective organellar resolution, which complements current biochemical analyses and prompts for subsequent subcellular studies to be performed where limited samples and analyte volume are of concern.

GrigoraSNPs: Optimized Analysis of SNPs for DNA Forensics.

PubMed

Ricke, Darrell O; Shcherbina, Anna; Michaleas, Adam; Fremont-Smith, Philip

2018-04-16

High-throughput sequencing (HTS) of single nucleotide polymorphisms (SNPs) enables additional DNA forensic capabilities not attainable using traditional STR panels. However, the inclusion of sets of loci selected for mixture analysis, extended kinship, phenotype, biogeographic ancestry prediction, etc., can result in large panel sizes that are difficult to analyze in a rapid fashion. GrigoraSNP was developed to address the allele-calling bottleneck that was encountered when analyzing SNP panels with more than 5000 loci using HTS. GrigoraSNPs uses a MapReduce parallel data processing on multiple computational threads plus a novel locus-identification hashing strategy leveraging target sequence tags. This tool optimizes the SNP calling module of the DNA analysis pipeline with runtimes that scale linearly with the number of HTS reads. Results are compared with SNP analysis pipelines implemented with SAMtools and GATK. GrigoraSNPs removes a computational bottleneck for processing forensic samples with large HTS SNP panels. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

Dielectrophoresis-Based Sample Handling in General-Purpose Programmable Diagnostic Instruments

PubMed Central

Gascoyne, Peter R. C.; Vykoukal, Jody V.

2009-01-01

As the molecular origins of disease are better understood, the need for affordable, rapid, and automated technologies that enable microscale molecular diagnostics has become apparent. Widespread use of microsystems that perform sample preparation and molecular analysis could ensure that the benefits of new biomedical discoveries are realized by a maximum number of people, even those in environments lacking any infrastructure. While progress has been made in developing miniaturized diagnostic systems, samples are generally processed off-device using labor-intensive and time-consuming traditional sample preparation methods. We present the concept of an integrated programmable general-purpose sample analysis processor (GSAP) architecture where raw samples are routed to separation and analysis functional blocks contained within a single device. Several dielectrophoresis-based methods that could serve as the foundation for building GSAP functional blocks are reviewed including methods for cell and particle sorting, cell focusing, cell ac impedance analysis, cell lysis, and the manipulation of molecules and reagent droplets. PMID:19684877

Launch vehicle design and GNC sizing with ASTOS

NASA Astrophysics Data System (ADS)

Cremaschi, Francesco; Winter, Sebastian; Rossi, Valerio; Wiegand, Andreas

2018-03-01

The European Space Agency (ESA) is currently involved in several activities related to launch vehicle designs (Future Launcher Preparatory Program, Ariane 6, VEGA evolutions, etc.). Within these activities, ESA has identified the importance of developing a simulation infrastructure capable of supporting the multi-disciplinary design and preliminary guidance navigation and control (GNC) design of different launch vehicle configurations. Astos Solutions has developed the multi-disciplinary optimization and launcher GNC simulation and sizing tool (LGSST) under ESA contract. The functionality is integrated in the Analysis, Simulation and Trajectory Optimization Software for space applications (ASTOS) and is intended to be used from the early design phases up to phase B1 activities. ASTOS shall enable the user to perform detailed vehicle design tasks and assessment of GNC systems, covering all aspects of rapid configuration and scenario management, sizing of stages, trajectory-dependent estimation of structural masses, rigid and flexible body dynamics, navigation, guidance and control, worst case analysis, launch safety analysis, performance analysis, and reporting.

Microfluidic direct injection method for analysis of urinary 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) using molecularly imprinted polymers coupled on-line with LC-MS/MS.

PubMed

Shah, Kumar A; Peoples, Michael C; Halquist, Matthew S; Rutan, Sarah C; Karnes, H Thomas

2011-01-25

The work described in this paper involves development of a high-throughput on-line microfluidic sample extraction method using capillary micro-columns packed with MIP beads coupled with tandem mass spectrometry for the analysis of urinary NNAL. The method was optimized and matrix effects were evaluated and resolved. The method enabled low sample volume (200 μL) and rapid analysis of urinary NNAL by direct injection onto the microfluidic column packed with molecularly imprinted beads engineered to NNAL. The method was validated according to the FDA bioanalytical method validation guidance. The dynamic range extended from 20.0 to 2500.0 pg/mL with a percent relative error of ±5.9% and a run time of 7.00 min. The lower limit of quantitation was 20.0 pg/mL. The method was used for the analysis of NNAL and NNAL-Gluc concentrations in smokers' urine. Copyright © 2010 Elsevier B.V. All rights reserved.

Quantum cascade lasers (QCLs) in biomedical spectroscopy.

PubMed

Schwaighofer, Andreas; Brandstetter, Markus; Lendl, Bernhard

2017-10-02

Quantum cascade lasers (QCL) are the first room temperature semiconductor laser source for the mid-IR spectral region, triggering substantial development for the advancement of mid-IR spectroscopy. Mid-IR spectroscopy in general provides rapid, label-free and objective analysis, particularly important in the field of biomedical analysis. Due to their unique properties, QCLs offer new possibilities for development of analytical methods to enable quantification of clinically relevant concentration levels and to support medical diagnostics. Compared to FTIR spectroscopy, novel and elaborated measurement techniques can be implemented that allow miniaturized and portable instrumentation. This review illustrates the characteristics of QCLs with a particular focus on their benefits for biomedical analysis. Recent applications of QCL-based spectroscopy for analysis of a variety of clinically relevant samples including breath, urine, blood, interstitial fluid, and biopsy samples are summarized. Further potential for technical advancements is discussed in combination with future prospects for employment of QCL-based devices in routine and point-of-care diagnostics.

Rapid determination of floral aroma compounds of lilac blossom by fast gas chromatography combined with surface acoustic wave sensor.

PubMed

Oh, Se Yeon; Shin, Hyun Du; Kim, Sung Jean; Hong, Jongki

2008-03-07

A novel analytical method using fast gas chromatography combined with surface acoustic wave sensor (GC/SAW) has been developed for the detection of volatile aroma compounds emanated from lilac blossom (Syringa species: Syringa vulgaris variginata and Syringa dilatata). GC/SAW could detect and quantify various fragrance emitted from lilac blossom, enabling to provide fragrance pattern analysis results. The fragrance pattern analysis could easily characterize the delicate differences in aromas caused by the substantial difference of chemical composition according to different color and shape of petals. Moreover, the method validation of GC/SAW was performed for the purpose of volatile floral actual aroma analysis, achieving a high reproducibility and excellent sensitivity. From the validation results, GC/SAW could serve as an alternative analytical technique for the analysis of volatile floral actual aroma of lilac. In addition, headspace solid-phase microextraction (HS-SPME) GC-MS was employed to further confirm the identification of fragrances emitted from lilac blossom and compared to GC/SAW.

Label-free SPR detection of gluten peptides in urine for non-invasive celiac disease follow-up.

PubMed

Soler, Maria; Estevez, M-Carmen; Moreno, Maria de Lourdes; Cebolla, Angel; Lechuga, Laura M

2016-05-15

Motivated by the necessity of new and efficient methods for dietary gluten control of celiac patients, we have developed a simple and highly sensitive SPR biosensor for the detection of gluten peptides in urine. The sensing methodology enables rapid and label-free quantification of the gluten immunogenic peptides (GIP) by using G12 mAb. The overall performance of the biosensor has been in-depth optimized and evaluated in terms of sensitivity, selectivity and reproducibility, reaching a limit of detection of 0.33 ng mL(-1). Besides, the robustness and stability of the methodology permit the continuous use of the biosensor for more than 100 cycles with excellent repeatability. Special efforts have been focused on preventing and minimizing possible interferences coming from urine matrix enabling a direct analysis in this fluid without requiring extraction or purification procedures. Our SPR biosensor has proven to detect and identify gluten consumption by evaluating urine samples from healthy and celiac individuals with different dietary gluten conditions. This novel biosensor methodology represents a novel approach to quantify the digested gluten peptides in human urine with outstanding sensitivity in a rapid and non-invasive manner. Our technique should be considered as a promising opportunity to develop Point-of-Care (POC) devices for an efficient, simple and accurate gluten free diet (GFD) monitoring as well as therapy follow-up of celiac disease patients. Copyright © 2015 Elsevier B.V. All rights reserved.

Current use of high-resolution mass spectrometry in drug screening relevant to clinical and forensic toxicology and doping control.

PubMed

Ojanperä, Ilkka; Kolmonen, Marjo; Pelander, Anna

2012-05-01

Clinical and forensic toxicology and doping control deal with hundreds or thousands of drugs that may cause poisoning or are abused, are illicit, or are prohibited in sports. Rapid and reliable screening for all these compounds of different chemical and pharmaceutical nature, preferably in a single analytical method, is a substantial effort for analytical toxicologists. Combined chromatography-mass spectrometry techniques with standardised reference libraries have been most commonly used for the purpose. In the last ten years, the focus has shifted from gas chromatography-mass spectrometry to liquid chromatography-mass spectrometry, because of progress in instrument technology and partly because of the polarity and low volatility of many new relevant substances. High-resolution mass spectrometry (HRMS), which enables accurate mass measurement at high resolving power, has recently evolved to the stage that is rapidly causing a shift from unit-resolution, quadrupole-dominated instrumentation. The main HRMS techniques today are time-of-flight mass spectrometry and Orbitrap Fourier-transform mass spectrometry. Both techniques enable a range of different drug-screening strategies that essentially rely on measuring a compound's or a fragment's mass with sufficiently high accuracy that its elemental composition can be determined directly. Accurate mass and isotopic pattern acts as a filter for confirming the identity of a compound or even identification of an unknown. High mass resolution is essential for improving confidence in accurate mass results in the analysis of complex biological samples. This review discusses recent applications of HRMS in analytical toxicology.

Initial Determination of Low Earth Orbits Using Commercial Telescopes

DTIC Science & Technology

2008-03-01

many new technologies have significantly changed the face of private astronomy . Developments such as inexpensive but high-quality sensors, rapid... astronomy . Unpar- alleled access to quality equipment, rapid personal computing, and extensive community support enable nearly anyone to achieve feats in...other subdisciplines of astronomy , this field benefits greatly from recent advances. This project examines how modern equipment is used to track Low Earth

Microgrid Modeling and Simulation Study

DTIC Science & Technology

2016-09-01

will be used to guide DOD M&S strategy and planning, as well as develop a comprehensive microgrid M&S capability and prioritize future efforts...contingencies and sequencing (Short term investment) Peer-to-peer Rapid send- listen techniques M&S is needed to determine an approach for handling...tactical microgrid network with interconnected grids. ○ Rapid Send- Listen Techniques is a specific enabler necessary for communications in a

High-throughput differentiation of heparin from other glycosaminoglycans by pyrolysis mass spectrometry.

PubMed

Nemes, Peter; Hoover, William J; Keire, David A

2013-08-06

Sensors with high chemical specificity and enhanced sample throughput are vital to screening food products and medical devices for chemical or biochemical contaminants that may pose a threat to public health. For example, the rapid detection of oversulfated chondroitin sulfate (OSCS) in heparin could prevent reoccurrence of heparin adulteration that caused hundreds of severe adverse events including deaths worldwide in 2007-2008. Here, rapid pyrolysis is integrated with direct analysis in real time (DART) mass spectrometry to rapidly screen major glycosaminoglycans, including heparin, chondroitin sulfate A, dermatan sulfate, and OSCS. The results demonstrate that, compared to traditional liquid chromatography-based analyses, pyrolysis mass spectrometry achieved at least 250-fold higher sample throughput and was compatible with samples volume-limited to about 300 nL. Pyrolysis yielded an abundance of fragment ions (e.g., 150 different m/z species), many of which were specific to the parent compound. Using multivariate and statistical data analysis models, these data enabled facile differentiation of the glycosaminoglycans with high throughput. After method development was completed, authentically contaminated samples obtained during the heparin crisis by the FDA were analyzed in a blinded manner for OSCS contamination. The lower limit of differentiation and detection were 0.1% (w/w) OSCS in heparin and 100 ng/μL (20 ng) OSCS in water, respectively. For quantitative purposes the linear dynamic range spanned approximately 3 orders of magnitude. Moreover, this chemical readout was successfully employed to find clues in the manufacturing history of the heparin samples that can be used for surveillance purposes. The presented technology and data analysis protocols are anticipated to be readily adaptable to other chemical and biochemical agents and volume-limited samples.

Rapid determination of sugar level in snack products using infrared spectroscopy.

PubMed

Wang, Ting; Rodriguez-Saona, Luis E

2012-08-01

Real-time spectroscopic methods can provide a valuable window into food manufacturing to permit optimization of production rate, quality and safety. There is a need for cutting edge sensor technology directed at improving efficiency, throughput and reliability of critical processes. The aim of the research was to evaluate the feasibility of infrared systems combined with chemometric analysis to develop rapid methods for determination of sugars in cereal products. Samples were ground and spectra were collected using a mid-infrared (MIR) spectrometer equipped with a triple-bounce ZnSe MIRacle attenuated total reflectance accessory or Fourier transform near infrared (NIR) system equipped with a diffuse reflection-integrating sphere. Sugar contents were determined using a reference HPLC method. Partial least squares regression (PLSR) was used to create cross-validated calibration models. The predictability of the models was evaluated on an independent set of samples and compared with reference techniques. MIR and NIR spectra showed characteristic absorption bands for sugars, and generated excellent PLSR models (sucrose: SEP < 1.7% and r > 0.96). Multivariate models accurately and precisely predicted sugar level in snacks allowing for rapid analysis. This simple technique allows for reliable prediction of quality parameters, and automation enabling food manufacturers for early corrective actions that will ultimately save time and money while establishing a uniform quality. The U.S. snack food industry generates billions of dollars in revenue each year and vibrational spectroscopic methods combined with pattern recognition analysis could permit optimization of production rate, quality, and safety of many food products. This research showed that infrared spectroscopy is a powerful technique for near real-time (approximately 1 min) assessment of sugar content in various cereal products. © 2012 Institute of Food Technologists®

ADAPT, a Novel Scaffold Protein-Based Probe for Radionuclide Imaging of Molecular Targets That Are Expressed in Disseminated Cancers.

PubMed

Garousi, Javad; Lindbo, Sarah; Nilvebrant, Johan; Åstrand, Mikael; Buijs, Jos; Sandström, Mattias; Honarvar, Hadis; Orlova, Anna; Tolmachev, Vladimir; Hober, Sophia

2015-10-15

Small engineered scaffold proteins have attracted attention as probes for radionuclide-based molecular imaging. One class of these imaging probes, termed ABD-Derived Affinity Proteins (ADAPT), has been created using the albumin-binding domain (ABD) of streptococcal protein G as a stable protein scaffold. In this study, we report the development of a clinical lead probe termed ADAPT6 that binds HER2, an oncoprotein overexpressed in many breast cancers that serves as a theranostic biomarker for several approved targeting therapies. Surface-exposed amino acids of ABD were randomized to create a combinatorial library enabling selection of high-affinity binders to various proteins. Furthermore, ABD was engineered to enable rapid purification, to eradicate its binding to albumin, and to enable rapid blood clearance. Incorporation of a unique cysteine allowed site-specific conjugation to a maleimido derivative of a DOTA chelator, enabling radionuclide labeling, ¹¹¹In for SPECT imaging and ⁶⁸Ga for PET imaging. Pharmacologic studies in mice demonstrated that the fully engineered molecule (111)In/⁶⁸Ga-DOTA-(HE)3-ADAPT6 was specifically bound and taken up by HER2-expressing tumors, with a high tumor-to-normal tissue ratio in xenograft models of human cancer. Unbound tracer underwent rapid renal clearance followed by high renal reabsorption. HER2-expressing xenografts were visualized by gamma-camera or PET at 1 hour after infusion. PET experiments demonstrated feasibility for discrimination of xenografts with high or low HER2 expression. Our results offer a preclinical proof of concept for the use of ADAPT probes for noninvasive in vivo imaging. ©2015 American Association for Cancer Research.

The NASA ISS-RapidScat Mission (Invited)

NASA Astrophysics Data System (ADS)

Rodriguez, E.

2013-12-01

After NASA's QuikSCAT satellite stopped spinning on November 2009, an observational gap opened in the international ocean surface winds constellation of observing satellites that also includes EUMETSAT's ASCAT and ISRO's OSCAT. While QuikSCAT continues to provide calibration data to the ISRO OSCAT on OceanSat-2 scatterometer, these data are sorely limited due to the satellite's hampered capabilities. Recognizing this gap, NASA has put together in a matter of a few months the ISS-RapidScat mission, which is a partnership between JPL, the ISS, ESA, KSC, and SpaceX. This mission, expected to launch in spring of 2014, is a very low-cost mission, enabled by the creative use of spare parts and a very rapid development process that nevertheless has great benefit to the science and operational weather and marine support communities. Since it uses the QuikSCAT engineering model, the RapidScat data will be quite similar to QuikSAT's in terms of data quality and spatial resolution, although modest gains in the latter are foreseen. However, due to the lower orbit and inclination, the RapidScat swath will be approximately a factor of two smaller than QuikSCAT's, and its geographic coverage will be limited to latitudes smaller than about 55 deg. Nevertheless, the unique sampling capabilities of the ISS non-sun-synchronous orbit opens up new science applications not available for typical sun-synchronous scatterometers. Foremost among these, is the ability to provide many more data that are collocated in space and time with each of the satellites in the international scatterometer constellation. Sun-synchronous satellites typically see each other with a suitably small temporal separation at high latitudes, and therefore, cross-calibration is limited in terms of the conditions that occur. RapidScat's orbit enables coincident wind observations in nearly every orbit, with a global geographical distribution, which will enable the determination of the global patterns of wind biases between all satellites in the constellation. Of great interest as well will be the ability of RapidScat to observe both the diurnal and semi-diurnal wind cycles. Previously, the diurnal cycle had been partially observed by combining scatterometer pairs, but its seasonal and yearly changes had not been characterized. Due to relative biases, the semi-diurnal cycle has not been observed from space. RapidScat will also be able to observed the diurnal cycle over land, which will improve the knowledge of scatterometer calibration targets and complement soil moisture and vegetation missions. Finally, although it has a smaller swath than QuikSCAT's, RapidScat's data will serve as a useful complement to the winds acquired from other platforms. This may be of significant advantage when covering rapidly developing systems, such as tropical hurricanes.

An Overview of the Role of Systems Analysis in NASA's Hypersonics Project

NASA Technical Reports Server (NTRS)

Robinson, Jeffrey S.; Martin John G.; Bowles, Jeffrey V> ; Mehta, Unmeel B.; Snyder, CHristopher A.

2006-01-01

NASA's Aeronautics Research Mission Directorate recently restructured its Vehicle Systems Program, refocusing it towards understanding the fundamental physics that govern flight in all speed regimes. Now called the Fundamental Aeronautics Program, it is comprised of four new projects, Subsonic Fixed Wing, Subsonic Rotary Wing, Supersonics, and Hypersonics. The Aeronautics Research Mission Directorate has charged the Hypersonics Project with having a basic understanding of all systems that travel at hypersonic speeds within the Earth's and other planets atmospheres. This includes both powered and unpowered systems, such as re-entry vehicles and vehicles powered by rocket or airbreathing propulsion that cruise in and accelerate through the atmosphere. The primary objective of the Hypersonics Project is to develop physics-based predictive tools that enable the design, analysis and optimization of such systems. The Hypersonics Project charges the systems analysis discipline team with providing it the decision-making information it needs to properly guide research and technology development. Credible, rapid, and robust multi-disciplinary system analysis processes and design tools are required in order to generate this information. To this end, the principal challenges for the systems analysis team are the introduction of high fidelity physics into the analysis process and integration into a design environment, quantification of design uncertainty through the use of probabilistic methods, reduction in design cycle time, and the development and implementation of robust processes and tools enabling a wide design space and associated technology assessment capability. This paper will discuss the roles and responsibilities of the systems analysis discipline team within the Hypersonics Project as well as the tools, methods, processes, and approach that the team will undertake in order to perform its project designated functions.

Toward Accurate and Quantitative Comparative Metagenomics

PubMed Central

Nayfach, Stephen; Pollard, Katherine S.

2016-01-01

Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

A standardized kit for automated quantitative assessment of candidate protein biomarkers in human plasma.

PubMed

Percy, Andrew J; Mohammed, Yassene; Yang, Juncong; Borchers, Christoph H

2015-12-01

An increasingly popular mass spectrometry-based quantitative approach for health-related research in the biomedical field involves the use of stable isotope-labeled standards (SIS) and multiple/selected reaction monitoring (MRM/SRM). To improve inter-laboratory precision and enable more widespread use of this 'absolute' quantitative technique in disease-biomarker assessment studies, methods must be standardized. Results/methodology: Using this MRM-with-SIS-peptide approach, we developed an automated method (encompassing sample preparation, processing and analysis) for quantifying 76 candidate protein markers (spanning >4 orders of magnitude in concentration) in neat human plasma. The assembled biomarker assessment kit - the 'BAK-76' - contains the essential materials (SIS mixes), methods (for acquisition and analysis), and tools (Qualis-SIS software) for performing biomarker discovery or verification studies in a rapid and standardized manner.

A new detection method for the K variant of butyrylcholinesterase based on PCR primer introduced restriction analysis (PCR-PIRA).

PubMed Central

Shibuta, K; Abe, M; Suzuki, T

1994-01-01

The K variant of human butyrylcholinesterase is caused by a G/A transition in the butyrylcholinesterase gene, which neither creates nor destroys any restriction site. In an attempt to detect the K variant both simply and rapidly, we developed a two step method of "PCR primer introduced restriction analysis" (PCR-PIRA). The first step was used to introduce a new Fun4HI site into the normal allele for a screening test, while the second step was performed to create a new MaeIII site on the variant allele for a specific test. This method thus enabled us to distinguish clearly the K variant from the normal allele, and also showed that the frequency of the K variant allele is 0.164 in the Japanese population. Images PMID:7966197

High-throughput tetrad analysis.

PubMed

Ludlow, Catherine L; Scott, Adrian C; Cromie, Gareth A; Jeffery, Eric W; Sirr, Amy; May, Patrick; Lin, Jake; Gilbert, Teresa L; Hays, Michelle; Dudley, Aimée M

2013-07-01

Tetrad analysis has been a gold-standard genetic technique for several decades. Unfortunately, the need to manually isolate, disrupt and space tetrads has relegated its application to small-scale studies and limited its integration with high-throughput DNA sequencing technologies. We have developed a rapid, high-throughput method, called barcode-enabled sequencing of tetrads (BEST), that uses (i) a meiosis-specific GFP fusion protein to isolate tetrads by FACS and (ii) molecular barcodes that are read during genotyping to identify spores derived from the same tetrad. Maintaining tetrad information allows accurate inference of missing genetic markers and full genotypes of missing (and presumably nonviable) individuals. An individual researcher was able to isolate over 3,000 yeast tetrads in 3 h, an output equivalent to that of almost 1 month of manual dissection. BEST is transferable to other microorganisms for which meiotic mapping is significantly more laborious.

Toward Accurate and Quantitative Comparative Metagenomics.

PubMed

Nayfach, Stephen; Pollard, Katherine S

2016-08-25

Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. Copyright © 2016 Elsevier Inc. All rights reserved.

Collaborating and sharing data in epilepsy research.

PubMed

Wagenaar, Joost B; Worrell, Gregory A; Ives, Zachary; Dümpelmann, Matthias; Matthias, Dümpelmann; Litt, Brian; Schulze-Bonhage, Andreas

2015-06-01

Technological advances are dramatically advancing translational research in Epilepsy. Neurophysiology, imaging, and metadata are now recorded digitally in most centers, enabling quantitative analysis. Basic and translational research opportunities to use these data are exploding, but academic and funding cultures prevent this potential from being realized. Research on epileptogenic networks, antiepileptic devices, and biomarkers could progress rapidly if collaborative efforts to digest this "big neuro data" could be organized. Higher temporal and spatial resolution data are driving the need for novel multidimensional visualization and analysis tools. Crowd-sourced science, the same that drives innovation in computer science, could easily be mobilized for these tasks, were it not for competition for funding, attribution, and lack of standard data formats and platforms. As these efforts mature, there is a great opportunity to advance Epilepsy research through data sharing and increase collaboration between the international research community.

Planar micromixer

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

Fiechtner, Gregory J; Singh, Anup K; Wiedenman, Boyd J

2008-03-18

The present embodiment describes a laminar-mixing embodiment that utilizes simple, three-dimensional injection. Also described is the use of the embodiment in combination with wide and shallow sections of channel to affect rapid mixing in microanalytical systems. The shallow channel sections are constructed using all planar micromachining techniques, including those based on isotropic etching. The planar construction enables design using minimum dispersion concepts that, in turn, enable simultaneous mixing and injection into subsequent chromatography channels.

Pellet to Part Manufacturing System for CNCs

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

Roschli, Alex C.; Love, Lonnie J.; Post, Brian K.

Oak Ridge National Laboratory’s Manufacturing Demonstration Facility worked with Hybrid Manufacturing Technologies to develop a compact prototype composite additive manufacturing head that can effectively extrude injection molding pellets. The head interfaces with conventional CNC machine tools enabling rapid conversion of conventional machine tools to additive manufacturing tools. The intent was to enable wider adoption of Big Area Additive Manufacturing (BAAM) technology and combine BAAM technology with conventional machining systems.

Ames Coronagraph Experiment: Enabling Missions to Directly Image Exoplanets

NASA Technical Reports Server (NTRS)

Belikov, Ruslan

2014-01-01

Technology to find biomarkers and life on other worlds is rapidly maturing. If there is a habitable planet around the nearest star, we may be able to detect it this decade with a small satellite mission. In the 2030 decade, we will likely know if there is life in our Galactic neighborhood (1000 nearest stars). The Ames Coronagraph Experiment is developing coronagraphic technologies to enable such missions.

Thermal tolerance in the keystone species Daphnia magna-a candidate gene and an outlier analysis approach.

PubMed

Jansen, M; Geerts, A N; Rago, A; Spanier, K I; Denis, C; De Meester, L; Orsini, L

2017-04-01

Changes in temperature have occurred throughout Earth's history. However, current warming trends exacerbated by human activities impose severe and rapid loss of biodiversity. Although understanding the mechanisms orchestrating organismal response to climate change is important, remarkably few studies document their role in nature. This is because only few systems enable the combined analysis of genetic and plastic responses to environmental change over long time spans. Here, we characterize genetic and plastic responses to temperature increase in the aquatic keystone grazer Daphnia magna combining a candidate gene and an outlier analysis approach. We capitalize on the short generation time of our species, facilitating experimental evolution, and the production of dormant eggs enabling the analysis of long-term response to environmental change through a resurrection ecology approach. We quantify plasticity in the expression of 35 candidate genes in D. magna populations resurrected from a lake that experienced changes in average temperature over the past century and from experimental populations differing in thermal tolerance isolated from a selection experiment. By measuring expression in multiple genotypes from each of these populations in control and heat treatments, we assess plastic responses to extreme temperature events. By measuring evolutionary changes in gene expression between warm- and cold-adapted populations, we assess evolutionary response to temperature changes. Evolutionary response to temperature increase is also assessed via an outlier analysis using EST-linked microsatellite loci. This study provides the first insights into the role of plasticity and genetic adaptation in orchestrating adaptive responses to environmental change in D. magna. © 2017 John Wiley & Sons Ltd.

The MSFC Collaborative Engineering Process for Preliminary Design and Concept Definition Studies

NASA Technical Reports Server (NTRS)

Mulqueen, Jack; Jones, David; Hopkins, Randy

2011-01-01

This paper describes a collaborative engineering process developed by the Marshall Space Flight Center's Advanced Concepts Office for performing rapid preliminary design and mission concept definition studies for potential future NASA missions. The process has been developed and demonstrated for a broad range of mission studies including human space exploration missions, space transportation system studies and in-space science missions. The paper will describe the design team structure and specialized analytical tools that have been developed to enable a unique rapid design process. The collaborative engineering process consists of integrated analysis approach for mission definition, vehicle definition and system engineering. The relevance of the collaborative process elements to the standard NASA NPR 7120.1 system engineering process will be demonstrated. The study definition process flow for each study discipline will be will be outlined beginning with the study planning process, followed by definition of ground rules and assumptions, definition of study trades, mission analysis and subsystem analyses leading to a standardized set of mission concept study products. The flexibility of the collaborative engineering design process to accommodate a wide range of study objectives from technology definition and requirements definition to preliminary design studies will be addressed. The paper will also describe the applicability of the collaborative engineering process to include an integrated systems analysis approach for evaluating the functional requirements of evolving system technologies and capabilities needed to meet the needs of future NASA programs.

Analysis of free amino acids in Amur sturgeon by ultra-performance liquid chromatography using pre-column derivatization with 6-aminoquinolyl-carbamyl.

PubMed

Sun, Yanchun; Xu, Xianzhu; Mou, Zhenbo; Wang, Jing; Tan, Zhijun; Wu, Song

2012-12-01

A rapid, sensitive, and reliable ultra-performance liquid chromatography (UPLC) coupled with photodiode array detection method was developed for the amino acid analysis of Amur sturgeon (Acipenser schrenckii Brandt). The method uses minimal sample volume and automated online precolumn derivitization of amino acids with fluorescent 6-aminoquinolyl-carbamyl reagent. The chromatographic separation was achieved by UPLC, which used a column with 1.7 μm particle packing that enabled higher speed of analysis, peak capacity, greater resolution, and increased sensitivity. Amino acid derivatives obtained under optimal conditions were separated on a Waters UPLC BEH C(18) column with Acetonitrile-acetate buffer as mobile phase. Matrix effects were investigated and good linearities with correlation coefficients better than 0.9949 were obtained over a wide range of 5-1000 μmol/L for all amino acids. The simple sample preparation and minimal sample volume make the method useful for the quantitation of 17 amino acids in Amur sturgeon samples. It is concluded that a rapid and robust platform based on UPLC was established, and a total of 17 amino acids of Amur sturgeon were tentatively detected. This method showed good accuracy and repeatability that can be used for the quantification of amino acids in real samples. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An integrated passive micromixer-magnetic separation-capillary electrophoresis microdevice for rapid and multiplex pathogen detection at the single-cell level.

PubMed

Jung, Jae Hwan; Kim, Gha-Young; Seo, Tae Seok

2011-10-21

Here we report an integrated microdevice consisting of an efficient passive mixer, a magnetic separation chamber, and a capillary electrophoretic microchannel in which DNA barcode assay, target pathogen separation, and barcode DNA capillary electrophoretic analysis were performed sequentially within 30 min for multiplex pathogen detection at the single-cell level. The intestine-shaped serpentine 3D micromixer provides a high mixing rate to generate magnetic particle-pathogenic bacteria-DNA barcode labelled AuNP complexes quantitatively. After magnetic separation and purification of those complexes, the barcode DNA strands were released and analyzed by the microfluidic capillary electrophoresis within 5 min. The size of the barcode DNA strand was controlled depending on the target bacteria (Staphylococcus aureus, Escherichia coli O157:H7, and Salmonella typhimurium), and the different elution time of the barcode DNA peak in the electropherogram allows us to recognize the target pathogen with ease in the monoplex as well as in the multiplex analysis. In addition, the quantity of the DNA barcode strand (∼10(4)) per AuNP is enough to be observed in the laser-induced confocal fluorescence detector, thereby making single-cell analysis possible. This novel integrated microdevice enables us to perform rapid, sensitive, and multiplex pathogen detection with sample-in-answer-out capability to be applied for biosafety testing, environmental screening, and clinical trials.

High-throughput analysis using non-depletive SPME: challenges and applications to the determination of free and total concentrations in small sample volumes.

PubMed

Boyacı, Ezel; Bojko, Barbara; Reyes-Garcés, Nathaly; Poole, Justen J; Gómez-Ríos, Germán Augusto; Teixeira, Alexandre; Nicol, Beate; Pawliszyn, Janusz

2018-01-18

In vitro high-throughput non-depletive quantitation of chemicals in biofluids is of growing interest in many areas. Some of the challenges facing researchers include the limited volume of biofluids, rapid and high-throughput sampling requirements, and the lack of reliable methods. Coupled to the above, growing interest in the monitoring of kinetics and dynamics of miniaturized biosystems has spurred the demand for development of novel and revolutionary methodologies for analysis of biofluids. The applicability of solid-phase microextraction (SPME) is investigated as a potential technology to fulfill the aforementioned requirements. As analytes with sufficient diversity in their physicochemical features, nicotine, N,N-Diethyl-meta-toluamide, and diclofenac were selected as test compounds for the study. The objective was to develop methodologies that would allow repeated non-depletive sampling from 96-well plates, using 100 µL of sample. Initially, thin film-SPME was investigated. Results revealed substantial depletion and consequent disruption in the system. Therefore, new ultra-thin coated fibers were developed. The applicability of this device to the described sampling scenario was tested by determining the protein binding of the analytes. Results showed good agreement with rapid equilibrium dialysis. The presented method allows high-throughput analysis using small volumes, enabling fast reliable free and total concentration determinations without disruption of system equilibrium.

Abnormal sleep/wake dynamics in orexin knockout mice.

PubMed

Diniz Behn, Cecilia G; Klerman, Elizabeth B; Mochizuki, Takatoshi; Lin, Shih-Chieh; Scammell, Thomas E

2010-03-01

Narcolepsy with cataplexy is caused by a loss of orexin (hypocretin) signaling, but the physiologic mechanisms that result in poor maintenance of wakefulness and fragmented sleep remain unknown. Conventional scoring of sleep cannot reveal much about the process of transitioning between states or the variations within states. We developed an EEG spectral analysis technique to determine whether the state instability in a mouse model of narcolepsy reflects abnormal sleep or wake states, faster movements between states, or abnormal transitions between states. We analyzed sleep recordings in orexin knockout (OXKO) mice and wild type (WT) littermates using a state space analysis technique. This non-categorical approach allows quantitative and unbiased examination of sleep/wake states and state transitions. OXKO mice spent less time in deep, delta-rich NREM sleep and in active, theta-rich wake and instead spent more time near the transition zones between states. In addition, while in the midst of what should be stable wake, OXKO mice initiated rapid changes into NREM sleep with high velocities normally seen only in transition regions. Consequently, state transitions were much more frequent and rapid even though the EEG progressions during state transitions were normal. State space analysis enables visualization of the boundaries between sleep and wake and shows that narcoleptic mice have less distinct and more labile states of sleep and wakefulness. These observations provide new perspectives on the abnormal state dynamics resulting from disrupted orexin signaling and highlight the usefulness of state space analysis in understanding narcolepsy and other sleep disorders.

Bacterial community structure analysis of sediment in the Sagami River, Japan using a rapid approach based on two-dimensional DNA gel electrophoresis mapping with selective primer pairs.

PubMed

Liu, Guo-hua; Rajendran, Narasimmalu; Amemiya, Takashi; Itoh, Kiminori

2011-11-01

A rapid approach based on two-dimensional DNA gel electrophroesis (2-DGE) mapping with selective primer pairs was employed to analyze bacterial community structure in sediments from upstream, midstream and downstream of Sagami River in Japan. The 2-DGE maps indicated that Alpha- and Delta-proteobacteria were major bacterial populations in the upstream and midstream sediments. Further bacterial community structure analysis showed that richness proportion of Alpha- and Delta-proteobacterial groups reflected a trend toward decreasing from the upstream to downstream sediments. The biomass proportion of bacterial populations in the midstream sediment showed a significantly difference from that in the other sediments, suggesting that there may be an environmental pressure on the midstream bacterial community. Lorenz curves, together with Gini coefficients were successfully applied to the 2-DGE mapping data for resolving evenness of bacterial populations, and showed that the plotted curve from high-resolution 2-DGE mapping became less linear and more an exponential function than that of the 1-DGE methods such as chain length analysis and denaturing gradient gel electrophoresis, suggesting that the 2-DGE mapping may achieve a more detailed evaluation of bacterial community. In conclusion, the 2-DGE mapping combined with the selective primer pairs enables bacterial community structure analysis in river sediment and thus it can also monitor sediment pollution based on the change of bacterial community structure.

Rapid Detection Method for the Four Most Common CHEK2 Mutations Based on Melting Profile Analysis.

PubMed

Borun, Pawel; Salanowski, Kacper; Godlewski, Dariusz; Walkowiak, Jaroslaw; Plawski, Andrzej

2015-12-01

CHEK2 is a tumor suppressor gene, and the mutations affecting the functionality of the protein product increase cancer risk in various organs. The elevated risk, in a significant percentage of cases, is determined by the occurrence of one of the four most common mutations in the CHEK2 gene, including c.470T>C (p.I157T), c.444+1G>A (IVS2+1G>A), c.1100delC, and c.1037+1538_1224+328del5395 (del5395). We have developed and validated a rapid and effective method for their detection based on high-resolution melting analysis and comparative-high-resolution melting, a novel approach enabling simultaneous detection of copy number variations. The analysis is performed in two polymerase chain reactions followed by melting analysis, without any additional reagents or handling other than that used in standard high-resolution melting. Validation of the method was conducted in a group of 103 patients with diagnosed breast cancer, a group of 240 unrelated patients with familial history of cancer associated with the CHEK2 gene mutations, and a 100-person control group. The results of the analyses for all three groups were fully consistent with the results from other methods. The method we have developed improves the identification of the CHEK2 mutation carriers, reduces the cost of such analyses, as well as facilitates their implementation. Along with the increased efficiency, the method maintains accuracy and reliability comparable to other more labor-consuming techniques.

Oasis: online analysis of small RNA deep sequencing data.

PubMed

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

2015-07-01

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

Developing and sustaining specialist and advanced practice roles in nursing and midwifery: A discourse on enablers and barriers.

PubMed

Fealy, Gerard M; Casey, Mary; O'Leary, Denise F; Mcnamara, Martin S; O'Brien, Denise; O'Connor, Laserina; Smith, Rita; Stokes, Diarmuid

2018-06-12

The aim of this discursive paper is to collate, synthesise and discuss published evidence and expert professional opinion on enablers and barriers to the development and sustainability of specialist and advanced practice roles in nursing and midwifery. Expanded practice is a response to population health needs, healthcare costs and practitioners' willingness to expand their scope of practice through enhanced responsibility, accountability and professional autonomy. This discursive paper is based on a rapid review of literature on enablers and barriers to the development and sustainability of specialist and advanced practice roles and is part of a wider policy analysis. We analysed and synthesised of 36 research articles, reviews and discussion papers on enablers and barriers in the development and sustainability of expanded practice roles. Several factors enable role expansion, including: role clarity; credentialing and endorsement; availability of education for expanded roles; individual practitioners' dispositions towards role expansion; support from peers, other professionals and the work organisation; and costs. Where limited or absent, these same factors can constrain role expansion. Enabling nurses and midwives to practice to their full scope of education and expertise is a global challenge for disciplinary leadership, a national challenge for professional regulation, and a local challenge for employers and individual clinicians. These challenges need to be addressed through multi-stakeholder coordinated efforts at these four levels. This discursive paper synthesises empirical evidence and expert professional opinion on the factors that enable or hinder the development and sustainability of specialist and advanced practice roles. Providing a critical appraisal of current knowledge, it provides a reference source for disciplinary debate and policy development regarding the nursing and midwifery resource and informs clinicians of the myriad issues that can impact on their capacity to expand their scope of practice. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Interactive access to LP DAAC satellite data archives through a combination of open-source and custom middleware web services

USGS Publications Warehouse

Davis, Brian N.; Werpy, Jason; Friesz, Aaron M.; Impecoven, Kevin; Quenzer, Robert; Maiersperger, Tom; Meyer, David J.

2015-01-01

Current methods of searching for and retrieving data from satellite land remote sensing archives do not allow for interactive information extraction. Instead, Earth science data users are required to download files over low-bandwidth networks to local workstations and process data before science questions can be addressed. New methods of extracting information from data archives need to become more interactive to meet user demands for deriving increasingly complex information from rapidly expanding archives. Moving the tools required for processing data to computer systems of data providers, and away from systems of the data consumer, can improve turnaround times for data processing workflows. The implementation of middleware services was used to provide interactive access to archive data. The goal of this middleware services development is to enable Earth science data users to access remote sensing archives for immediate answers to science questions instead of links to large volumes of data to download and process. Exposing data and metadata to web-based services enables machine-driven queries and data interaction. Also, product quality information can be integrated to enable additional filtering and sub-setting. Only the reduced content required to complete an analysis is then transferred to the user.

Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels

PubMed Central

Kim, Eunkyoung; Liu, Yi; Ben-Yoav, Hadar; Winkler, Thomas E.; Yan, Kun; Shi, Xiaowen; Shen, Jana; Kelly, Deanna L.; Ghodssi, Reza; Bentley, William E.

2017-01-01

The Information Age transformed our lives but it has had surprisingly little impact on the way chemical information (e.g., from our biological world) is acquired, analyzed and communicated. Sensor systems are poised to change this situation by providing rapid access to chemical information. This access will be enabled by technological advances from various fields: biology enables the synthesis, design and discovery of molecular recognition elements as well as the generation of cell-based signal processors; physics and chemistry are providing nano-components that facilitate the transmission and transduction of signals rich with chemical information; microfabrication is yielding sensors capable of receiving these signals through various modalities; and signal processing analysis enhances the extraction of chemical information. The authors contend that integral to the development of functional sensor systems will be materials that (i) enable the integrative and hierarchical assembly of various sensing components (for chemical recognition and signal transduction) and (ii) facilitate meaningful communication across modalities. It is suggested that stimuli-responsive self-assembling biopolymers can perform such integrative functions, and redox provides modality-spanning communication capabilities. Recent progress toward the development of electrochemical sensors to manage schizophrenia is used to illustrate the opportunities and challenges for enlisting sensors for chemical information processing. PMID:27616350

Ion channel drug discovery and research: the automated Nano-Patch-Clamp technology.

PubMed

Brueggemann, A; George, M; Klau, M; Beckler, M; Steindl, J; Behrends, J C; Fertig, N

2004-01-01

Unlike the genomics revolution, which was largely enabled by a single technological advance (high throughput sequencing), rapid advancement in proteomics will require a broader effort to increase the throughput of a number of key tools for functional analysis of different types of proteins. In the case of ion channels -a class of (membrane) proteins of great physiological importance and potential as drug targets- the lack of adequate assay technologies is felt particularly strongly. The available, indirect, high throughput screening methods for ion channels clearly generate insufficient information. The best technology to study ion channel function and screen for compound interaction is the patch clamp technique, but patch clamping suffers from low throughput, which is not acceptable for drug screening. A first step towards a solution is presented here. The nano patch clamp technology, which is based on a planar, microstructured glass chip, enables automatic whole cell patch clamp measurements. The Port-a-Patch is an automated electrophysiology workstation, which uses planar patch clamp chips. This approach enables high quality and high content ion channel and compound evaluation on a one-cell-at-a-time basis. The presented automation of the patch process and its scalability to an array format are the prerequisites for any higher throughput electrophysiology instruments.

Genetic screens in human cells using the CRISPR-Cas9 system.

PubMed

Wang, Tim; Wei, Jenny J; Sabatini, David M; Lander, Eric S

2014-01-03

The bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system for genome editing has greatly expanded the toolbox for mammalian genetics, enabling the rapid generation of isogenic cell lines and mice with modified alleles. Here, we describe a pooled, loss-of-function genetic screening approach suitable for both positive and negative selection that uses a genome-scale lentiviral single-guide RNA (sgRNA) library. sgRNA expression cassettes were stably integrated into the genome, which enabled a complex mutant pool to be tracked by massively parallel sequencing. We used a library containing 73,000 sgRNAs to generate knockout collections and performed screens in two human cell lines. A screen for resistance to the nucleotide analog 6-thioguanine identified all expected members of the DNA mismatch repair pathway, whereas another for the DNA topoisomerase II (TOP2A) poison etoposide identified TOP2A, as expected, and also cyclin-dependent kinase 6, CDK6. A negative selection screen for essential genes identified numerous gene sets corresponding to fundamental processes. Last, we show that sgRNA efficiency is associated with specific sequence motifs, enabling the prediction of more effective sgRNAs. Collectively, these results establish Cas9/sgRNA screens as a powerful tool for systematic genetic analysis in mammalian cells.

Heterogeneous Compression of Large Collections of Evolutionary Trees.

PubMed

Matthews, Suzanne J

2015-01-01

Compressing heterogeneous collections of trees is an open problem in computational phylogenetics. In a heterogeneous tree collection, each tree can contain a unique set of taxa. An ideal compression method would allow for the efficient archival of large tree collections and enable scientists to identify common evolutionary relationships over disparate analyses. In this paper, we extend TreeZip to compress heterogeneous collections of trees. TreeZip is the most efficient algorithm for compressing homogeneous tree collections. To the best of our knowledge, no other domain-based compression algorithm exists for large heterogeneous tree collections or enable their rapid analysis. Our experimental results indicate that TreeZip averages 89.03 percent (72.69 percent) space savings on unweighted (weighted) collections of trees when the level of heterogeneity in a collection is moderate. The organization of the TRZ file allows for efficient computations over heterogeneous data. For example, consensus trees can be computed in mere seconds. Lastly, combining the TreeZip compressed (TRZ) file with general-purpose compression yields average space savings of 97.34 percent (81.43 percent) on unweighted (weighted) collections of trees. Our results lead us to believe that TreeZip will prove invaluable in the efficient archival of tree collections, and enables scientists to develop novel methods for relating heterogeneous collections of trees.

Options For Development of Space Fission Propulsion Systems

NASA Technical Reports Server (NTRS)

Houta, Mike; VanDyke, Melissa; Godfroy, Tom; Pedersen, Kevin; Martin, James; Dickens, Ricky; Salvail, Pat; Hrbud, Ivana; Rodgers, Stephen L. (Technical Monitor)

2001-01-01

Fission technology can enable rapid, affordable access to any point in the solar system. Potential fission-based transportation options include high specific power continuous impulse propulsion systems and bimodal nuclear thermal rockets. Despite their tremendous potential for enhancing or enabling deep space and planetary missions, to date space fission system have only been used in Earth orbit. The first step towards utilizing advanced fission propulsion systems is development of a safe, near-term, affordable fission system that can enhance or enable near-term missions of interest. An evolutionary approach for developing space fission propulsion systems is proposed.

Curb Mounting, Vertical Mobility, and Inverted Mobility on Rough Surfaces Using Microspine-Enabled Robots

NASA Technical Reports Server (NTRS)

Parness, Aaron

2012-01-01

Three robots that extend microspine technology to enable advanced mobility are presented. First, the Durable Reconnaissance and Observation Platform (DROP) and the ReconRobotics Scout platform use a new rotary configuration of microspines to provide improved soldier-portable reconnaissance by moving rapidly over curbs and obstacles, transitioning from horizontal to vertical surfaces, climbing rough walls and surviving impacts. Next, the four-legged LEMUR robot uses new configurations of opposed microspines to anchor to both manmade and natural rough surfaces. Using these anchors as feet enables mobility in unstructured environments, from urban disaster areas to deserts and caves.

Enabling the environmentally clean air transportation of the future: a vision of computational fluid dynamics in 2030

PubMed Central

Slotnick, Jeffrey P.; Khodadoust, Abdollah; Alonso, Juan J.; Darmofal, David L.; Gropp, William D.; Lurie, Elizabeth A.; Mavriplis, Dimitri J.; Venkatakrishnan, Venkat

2014-01-01

As global air travel expands rapidly to meet demand generated by economic growth, it is essential to continue to improve the efficiency of air transportation to reduce its carbon emissions and address concerns about climate change. Future transports must be ‘cleaner’ and designed to include technologies that will continue to lower engine emissions and reduce community noise. The use of computational fluid dynamics (CFD) will be critical to enable the design of these new concepts. In general, the ability to simulate aerodynamic and reactive flows using CFD has progressed rapidly during the past several decades and has fundamentally changed the aerospace design process. Advanced simulation capabilities not only enable reductions in ground-based and flight-testing requirements, but also provide added physical insight, and enable superior designs at reduced cost and risk. In spite of considerable success, reliable use of CFD has remained confined to a small region of the operating envelope due, in part, to the inability of current methods to reliably predict turbulent, separated flows. Fortunately, the advent of much more powerful computing platforms provides an opportunity to overcome a number of these challenges. This paper summarizes the findings and recommendations from a recent NASA-funded study that provides a vision for CFD in the year 2030, including an assessment of critical technology gaps and needed development, and identifies the key CFD technology advancements that will enable the design and development of much cleaner aircraft in the future. PMID:25024413

Petaminer: Using ROOT for efficient data storage in MySQL database

NASA Astrophysics Data System (ADS)

Cranshaw, J.; Malon, D.; Vaniachine, A.; Fine, V.; Lauret, J.; Hamill, P.

2010-04-01

High Energy and Nuclear Physics (HENP) experiments store Petabytes of event data and Terabytes of calibration data in ROOT files. The Petaminer project is developing a custom MySQL storage engine to enable the MySQL query processor to directly access experimental data stored in ROOT files. Our project is addressing the problem of efficient navigation to PetaBytes of HENP experimental data described with event-level TAG metadata, which is required by data intensive physics communities such as the LHC and RHIC experiments. Physicists need to be able to compose a metadata query and rapidly retrieve the set of matching events, where improved efficiency will facilitate the discovery process by permitting rapid iterations of data evaluation and retrieval. Our custom MySQL storage engine enables the MySQL query processor to directly access TAG data stored in ROOT TTrees. As ROOT TTrees are column-oriented, reading them directly provides improved performance over traditional row-oriented TAG databases. Leveraging the flexible and powerful SQL query language to access data stored in ROOT TTrees, the Petaminer approach enables rich MySQL index-building capabilities for further performance optimization.

Processing Shotgun Proteomics Data on the Amazon Cloud with the Trans-Proteomic Pipeline*

PubMed Central

Slagel, Joseph; Mendoza, Luis; Shteynberg, David; Deutsch, Eric W.; Moritz, Robert L.

2015-01-01

Cloud computing, where scalable, on-demand compute cycles and storage are available as a service, has the potential to accelerate mass spectrometry-based proteomics research by providing simple, expandable, and affordable large-scale computing to all laboratories regardless of location or information technology expertise. We present new cloud computing functionality for the Trans-Proteomic Pipeline, a free and open-source suite of tools for the processing and analysis of tandem mass spectrometry datasets. Enabled with Amazon Web Services cloud computing, the Trans-Proteomic Pipeline now accesses large scale computing resources, limited only by the available Amazon Web Services infrastructure, for all users. The Trans-Proteomic Pipeline runs in an environment fully hosted on Amazon Web Services, where all software and data reside on cloud resources to tackle large search studies. In addition, it can also be run on a local computer with computationally intensive tasks launched onto the Amazon Elastic Compute Cloud service to greatly decrease analysis times. We describe the new Trans-Proteomic Pipeline cloud service components, compare the relative performance and costs of various Elastic Compute Cloud service instance types, and present on-line tutorials that enable users to learn how to deploy cloud computing technology rapidly with the Trans-Proteomic Pipeline. We provide tools for estimating the necessary computing resources and costs given the scale of a job and demonstrate the use of cloud enabled Trans-Proteomic Pipeline by performing over 1100 tandem mass spectrometry files through four proteomic search engines in 9 h and at a very low cost. PMID:25418363

Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

PubMed

Slagel, Joseph; Mendoza, Luis; Shteynberg, David; Deutsch, Eric W; Moritz, Robert L

2015-02-01

Cloud computing, where scalable, on-demand compute cycles and storage are available as a service, has the potential to accelerate mass spectrometry-based proteomics research by providing simple, expandable, and affordable large-scale computing to all laboratories regardless of location or information technology expertise. We present new cloud computing functionality for the Trans-Proteomic Pipeline, a free and open-source suite of tools for the processing and analysis of tandem mass spectrometry datasets. Enabled with Amazon Web Services cloud computing, the Trans-Proteomic Pipeline now accesses large scale computing resources, limited only by the available Amazon Web Services infrastructure, for all users. The Trans-Proteomic Pipeline runs in an environment fully hosted on Amazon Web Services, where all software and data reside on cloud resources to tackle large search studies. In addition, it can also be run on a local computer with computationally intensive tasks launched onto the Amazon Elastic Compute Cloud service to greatly decrease analysis times. We describe the new Trans-Proteomic Pipeline cloud service components, compare the relative performance and costs of various Elastic Compute Cloud service instance types, and present on-line tutorials that enable users to learn how to deploy cloud computing technology rapidly with the Trans-Proteomic Pipeline. We provide tools for estimating the necessary computing resources and costs given the scale of a job and demonstrate the use of cloud enabled Trans-Proteomic Pipeline by performing over 1100 tandem mass spectrometry files through four proteomic search engines in 9 h and at a very low cost. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Interactive terrain visualization enables virtual field work during rapid scientific response to the 2010 Haiti earthquake

USGS Publications Warehouse

Cowgill, Eric; Bernardin, Tony S.; Oskin, Michael E.; Bowles, Christopher; Yikilmaz, M. Burak; Kreylos, Oliver; Elliott, Austin J.; Bishop, Scott; Gold, Ryan D.; Morelan, Alexander; Bawden, Gerald W.; Hamann, Bernd; Kellogg, Louise

2012-01-01

The moment magnitude (Mw) 7.0 12 January 2010 Haiti earthquake is the first major earthquake for which a large-footprint LiDAR (light detection and ranging) survey was acquired within several weeks of the event. Here, we describe the use of virtual reality data visualization to analyze massive amounts (67 GB on disk) of multiresolution terrain data during the rapid scientific response to a major natural disaster. In particular, we describe a method for conducting virtual field work using both desktop computers and a 4-sided, 22 m3 CAVE immersive virtual reality environment, along with KeckCAVES (Keck Center for Active Visualization in the Earth Sciences) software tools LiDAR Viewer, to analyze LiDAR point-cloud data, and Crusta, for 2.5 dimensional surficial geologic mapping on a bare-earth digital elevation model. This system enabled virtual field work that yielded remote observations of the topographic expression of active faulting within an ∼75-km-long section of the eastern Enriquillo–Plantain Garden fault spanning the 2010 epicenter. Virtual field observations indicated that the geomorphic evidence of active faulting and ancient surface rupture varies along strike. Landform offsets of 6–50 m along the Enriquillo–Plantain Garden fault east of the 2010 epicenter and closest to Port-au-Prince attest to repeated recent surface-rupturing earthquakes there. In the west, the fault trace is well defined by displaced landforms, but it is not as clear as in the east. The 2010 epicenter is within a transition zone between these sections that extends from Grand Goâve in the west to Fayette in the east. Within this transition, between L'Acul (lat 72°40′W) and the Rouillone River (lat 72°35′W), the Enriquillo–Plantain Garden fault is undefined along an embayed low-relief range front, with little evidence of recent surface rupture. Based on the geometry of the eastern and western faults that show evidence of recent surface rupture, we propose that the 2010 event occurred within a stepover that appears to have served as a long-lived boundary between rupture segments, explaining the lack of 2010 surface rupture. This study demonstrates how virtual reality–based data visualization has the potential to transform rapid scientific response by enabling virtual field studies and real-time interactive analysis of massive terrain data sets.

New method for the rapid extraction of natural products: efficient isolation of shikimic acid from star anise.

PubMed

Just, Jeremy; Deans, Bianca J; Olivier, Wesley J; Paull, Brett; Bissember, Alex C; Smith, Jason A

2015-05-15

A new, practical, rapid, and high-yielding process for the pressurized hot water extraction (PHWE) of multigram quantities of shikimic acid from star anise (Illicium verum) using an unmodified household espresso machine has been developed. This operationally simple and inexpensive method enables the efficient and straightforward isolation of shikimic acid and the facile preparation of a range of its synthetic derivatives.

Using magnetic levitation for non-destructive quality control of plastic parts.

PubMed

Hennek, Jonathan W; Nemiroski, Alex; Subramaniam, Anand Bala; Bwambok, David K; Yang, Dian; Harburg, Daniel V; Tricard, Simon; Ellerbee, Audrey K; Whitesides, George M

2015-03-04

Magnetic levitation (MagLev) enables rapid and non-destructive quality control of plastic parts. The feasibility of MagLev as a method to: i) rapidly assess injection-molded plastic parts for defects during process optimization, ii) monitor the degradation of plastics after exposure to harsh environmental conditions, and iii) detect counterfeit polymers by density is demonstrated. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Epidemiology of Cystic Fibrosis.

PubMed

Spoonhower, Kimberly A; Davis, Pamela B

2016-03-01

Improved quality of care and rapidly emerging therapeutic strategies to restore chloride transport profoundly impact the epidemiology and pathobiology of cystic fibrosis (CF) in the twenty-first century. CF now serves as a model for chronic illness management, continuous quality improvement via registry data, and a seamless link between basic science research, translational studies, clinical trials, and outcomes research to enable rapid expansion of treatment options. Copyright © 2016 Elsevier Inc. All rights reserved.

Towards Single-Step Biofabrication of Organs on a Chip via 3D Printing.

PubMed

Knowlton, Stephanie; Yenilmez, Bekir; Tasoglu, Savas

2016-09-01

Organ-on-a-chip engineering employs microfabrication of living tissues within microscale fluid channels to create constructs that closely mimic human organs. With the advent of 3D printing, we predict that single-step fabrication of these devices will enable rapid design and cost-effective iterations in the development stage, facilitating rapid innovation in this field. Copyright © 2016 Elsevier Ltd. All rights reserved.

The origins of music in auditory scene analysis and the roles of evolution and culture in musical creation

PubMed Central

Trainor, Laurel J.

2015-01-01

Whether music was an evolutionary adaptation that conferred survival advantages or a cultural creation has generated much debate. Consistent with an evolutionary hypothesis, music is unique to humans, emerges early in development and is universal across societies. However, the adaptive benefit of music is far from obvious. Music is highly flexible, generative and changes rapidly over time, consistent with a cultural creation hypothesis. In this paper, it is proposed that much of musical pitch and timing structure adapted to preexisting features of auditory processing that evolved for auditory scene analysis (ASA). Thus, music may have emerged initially as a cultural creation made possible by preexisting adaptations for ASA. However, some aspects of music, such as its emotional and social power, may have subsequently proved beneficial for survival and led to adaptations that enhanced musical behaviour. Ontogenetic and phylogenetic evidence is considered in this regard. In particular, enhanced auditory–motor pathways in humans that enable movement entrainment to music and consequent increases in social cohesion, and pathways enabling music to affect reward centres in the brain should be investigated as possible musical adaptations. It is concluded that the origins of music are complex and probably involved exaptation, cultural creation and evolutionary adaptation. PMID:25646512

Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics.

PubMed

Kelstrup, Christian D; Bekker-Jensen, Dorte B; Arrey, Tabiwang N; Hogrebe, Alexander; Harder, Alexander; Olsen, Jesper V

2018-01-05

Progress in proteomics is mainly driven by advances in mass spectrometric (MS) technologies. Here we benchmarked the performance of the latest MS instrument in the benchtop Orbitrap series, the Q Exactive HF-X, against its predecessor for proteomics applications. A new peak-picking algorithm, a brighter ion source, and optimized ion transfers enable productive MS/MS acquisition above 40 Hz at 7500 resolution. The hardware and software improvements collectively resulted in improved peptide and protein identifications across all comparable conditions, with an increase of up to 50 percent at short LC-MS gradients, yielding identification rates of more than 1000 unique peptides per minute. Alternatively, the Q Exactive HF-X is capable of achieving the same proteome coverage as its predecessor in approximately half the gradient time or at 10-fold lower sample loads. The Q Exactive HF-X also enables rapid phosphoproteomics with routine analysis of more than 5000 phosphopeptides with short single-shot 15 min LC-MS/MS measurements, or 16 700 phosphopeptides quantified across ten conditions in six gradient hours using TMT10-plex and offline peptide fractionation. Finally, exciting perspectives for data-independent acquisition are highlighted with reproducible identification of 55 000 unique peptides covering 5900 proteins in half an hour of MS analysis.

Propulsion Powertrain Real-Time Simulation Using Hardware-in-the-Loop (HIL) for Aircraft Electric Propulsion System

NASA Technical Reports Server (NTRS)

Choi, Benjamin B.; Brown, Gerald V.

2017-01-01

It is essential to design a propulsion powertrain real-time simulator using the hardware-in-the-loop (HIL) system that emulates an electrified aircraft propulsion (EAP) systems power grid. This simulator would enable us to facilitate in-depth understanding of the system principles, to validate system model analysis and performance prediction, and to demonstrate the proof-of-concept of the EAP electrical system. This paper describes how subscale electrical machines with their controllers can mimic the power components in an EAP powertrain. In particular, three powertrain emulations are presented to mimic 1) a gas turbo-=shaft engine driving a generator, consisting of two permanent magnet (PM) motors with brushless motor drives, coupled by a shaft, 2) a motor driving a propulsive fan, and 3) a turbo-shaft engine driven fan (turbofan engine) operation. As a first step towards the demonstration, experimental dynamic characterization of the two motor drive systems, coupled by a mechanical shaft, were performed. The previously developed analytical motor models1 were then replaced with the experimental motor models to perform the real-time demonstration in the predefined flight path profiles. This technique can convert the plain motor system into a unique EAP power grid emulator that enables rapid analysis and real-time simulation performance using hardware-in-the-loop (HIL).

The origins of music in auditory scene analysis and the roles of evolution and culture in musical creation.

PubMed

Trainor, Laurel J

2015-03-19

Whether music was an evolutionary adaptation that conferred survival advantages or a cultural creation has generated much debate. Consistent with an evolutionary hypothesis, music is unique to humans, emerges early in development and is universal across societies. However, the adaptive benefit of music is far from obvious. Music is highly flexible, generative and changes rapidly over time, consistent with a cultural creation hypothesis. In this paper, it is proposed that much of musical pitch and timing structure adapted to preexisting features of auditory processing that evolved for auditory scene analysis (ASA). Thus, music may have emerged initially as a cultural creation made possible by preexisting adaptations for ASA. However, some aspects of music, such as its emotional and social power, may have subsequently proved beneficial for survival and led to adaptations that enhanced musical behaviour. Ontogenetic and phylogenetic evidence is considered in this regard. In particular, enhanced auditory-motor pathways in humans that enable movement entrainment to music and consequent increases in social cohesion, and pathways enabling music to affect reward centres in the brain should be investigated as possible musical adaptations. It is concluded that the origins of music are complex and probably involved exaptation, cultural creation and evolutionary adaptation.

Fluorescent microparticles for sensing cell microenvironment oxygen levels within 3D scaffolds.

PubMed

Acosta, Miguel A; Ymele-Leki, Patrick; Kostov, Yordan V; Leach, Jennie B

2009-06-01

We present the development and characterization of fluorescent oxygen-sensing microparticles designed for measuring oxygen concentration in microenvironments existing within standard cell culture and transparent three-dimensional (3D) cell scaffolds. The microparticle synthesis employs poly(dimethylsiloxane) to encapsulate silica gel particles bound with an oxygen-sensitive luminophore as well as a reference or normalization fluorophore that is insensitive to oxygen. We developed a rapid, automated and non-invasive sensor analysis method based on fluorescence microscopy to measure oxygen concentration in a hydrogel scaffold. We demonstrate that the microparticles are non-cytotoxic and that their response is comparable to that of a traditional dissolved oxygen meter. Microparticle size (5-40 microm) was selected for microscale-mapping of oxygen concentration to allow measurements local to individual cells. Two methods of calibration were evaluated and revealed that the sensor system enables characterization of a range of hypoxic to hyperoxic conditions relevant to cell and tissue biology (i.e., pO(2) 10-160 mmHg). The calibration analysis also revealed that the microparticles have a high fraction of quenched luminophore (0.90+/-0.02), indicating that the reported approach provides significant advantages for sensor performance. This study thus reports a versatile oxygen-sensing technology that enables future correlations of local oxygen concentration with individual cell response in cultured engineered tissues.

Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation

PubMed Central

Bock, Lars V.; Blau, Christian; Vaiana, Andrea C.; Grubmüller, Helmut

2015-01-01

During ribosomal translation, the two ribosomal subunits remain associated through intersubunit bridges, despite rapid large-scale intersubunit rotation. The absence of large barriers hindering rotation is a prerequisite for rapid rotation. Here, we investigate how such a flat free-energy landscape is achieved, in particular considering the large shifts the bridges undergo at the periphery. The dynamics and energetics of the intersubunit contact network are studied using molecular dynamics simulations of the prokaryotic ribosome in intermediate states of spontaneous translocation. Based on observed occupancies of intersubunit contacts, residues were grouped into clusters. In addition to the central contact clusters, peripheral clusters were found to maintain strong steady interactions by changing contacts in the course of rotation. The peripheral B1 bridges are stabilized by a changing contact pattern of charged residues that adapts to the rotational state. In contrast, steady strong interactions of the B4 bridge are ensured by the flexible helix H34 following the movement of protein S15. The tRNAs which span the subunits contribute to the intersubunit binding enthalpy to an almost constant degree, despite their different positions in the ribosome. These mechanisms keep the intersubunit interaction strong and steady during rotation, thereby preventing dissociation and enabling rapid rotation. PMID:26109353

Rapid Focused Ion Beam Milling Based Fabrication of Plasmonic Nanoparticles and Assemblies via "Sketch and Peel" Strategy.

PubMed

Chen, Yiqin; Bi, Kaixi; Wang, Qianjin; Zheng, Mengjie; Liu, Qing; Han, Yunxin; Yang, Junbo; Chang, Shengli; Zhang, Guanhua; Duan, Huigao

2016-12-27

Focused ion beam (FIB) milling is a versatile maskless and resistless patterning technique and has been widely used for the fabrication of inverse plasmonic structures such as nanoholes and nanoslits for various applications. However, due to its subtractive milling nature, it is an impractical method to fabricate isolated plasmonic nanoparticles and assemblies which are more commonly adopted in applications. In this work, we propose and demonstrate an approach to reliably and rapidly define plasmonic nanoparticles and their assemblies using FIB milling via a simple "sketch and peel" strategy. Systematic experimental investigations and mechanism studies reveal that the high reliability of this fabrication approach is enabled by a conformally formed sidewall coating due to the ion-milling-induced redeposition. Particularly, we demonstrated that this strategy is also applicable to the state-of-the-art helium ion beam milling technology, with which high-fidelity plasmonic dimers with tiny gaps could be directly and rapidly prototyped. Because the proposed approach enables rapid and reliable patterning of arbitrary plasmonic nanostructures that are not feasible to fabricate via conventional FIB milling process, our work provides the FIB milling technology an additional nanopatterning capability and thus could greatly increase its popularity for utilization in fundamental research and device prototyping.

Eliminating Size-Associated Diffusion Constraints for Rapid On-Surface Bioassays with Nanoparticle Probes.

PubMed

Li, Junwei; Zrazhevskiy, Pavel; Gao, Xiaohu

2016-02-24

Nanoparticle probes enable implementation of advanced on-surface assay formats, but impose often underappreciated size-associated constraints, in particular on assay kinetics and sensitivity. The present study highlights substantially slower diffusion-limited assay kinetics due to the rapid development of a nanoprobe depletion layer next to the surface, which static incubation and mixing of bulk solution employed in conventional assay setups often fail to disrupt. In contrast, cyclic solution draining and replenishing yields reaction-limited assay kinetics irrespective of the probe size. Using common surface bioassays, enzyme-linked immunosorbent assays and immunofluorescence, this study shows that this conceptually distinct approach effectively "erases" size-dependent diffusion constraints, providing a straightforward route to rapid on-surface bioassays employing bulky probes and procedures involving multiple labeling cycles, such as multicycle single-cell molecular profiling. For proof-of-concept, the study demonstrates that the assay time can be shortened from hours to minutes with the same probe concentration and, at a typical incubation time, comparable target labeling can be achieved with up to eight times lower nanoprobe concentration. The findings are expected to enable realization of novel assay formats and stimulate development of rapid on-surface bioassays with nanoparticle probes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid ABO genotyping by high-speed droplet allele-specific PCR using crude samples.

PubMed

Taira, Chiaki; Matsuda, Kazuyuki; Takeichi, Naoya; Furukawa, Satomi; Sugano, Mitsutoshi; Uehara, Takeshi; Okumura, Nobuo; Honda, Takayuki

2018-01-01

ABO genotyping has common tools for personal identification of forensic and transplantation field. We developed a new method based on a droplet allele-specific PCR (droplet-AS-PCR) that enabled rapid PCR amplification. We attempted rapid ABO genotyping using crude DNA isolated from dried blood and buccal cells. We designed allele-specific primers for three SNPs (at nucleotides 261, 526, and 803) in exons 6 and 7 of the ABO gene. We pretreated dried blood and buccal cells with proteinase K, and obtained crude DNAs without DNA purification. Droplet-AS-PCR allowed specific amplification of the SNPs at the three loci using crude DNA, with results similar to those for DNA extracted from fresh peripheral blood. The sensitivity of the methods was 5%-10%. The genotyping of extracted DNA and crude DNA were completed within 8 and 9 minutes, respectively. The genotypes determined by the droplet-AS-PCR method were always consistent with those obtained by direct sequencing. The droplet-AS-PCR method enabled rapid and specific amplification of three SNPs of the ABO gene from crude DNA treated with proteinase K. ABO genotyping by the droplet-AS-PCR has the potential to be applied to various fields including a forensic medicine and transplantation medical care. © 2017 Wiley Periodicals, Inc.

Recombinational Cloning Using Gateway and In-Fusion Cloning Schemes

PubMed Central

Throop, Andrea L.; LaBaer, Joshua

2015-01-01

The comprehensive study of protein structure and function, or proteomics, depends on the obtainability of full-length cDNAs in species-specific expression vectors and subsequent functional analysis of the expressed protein. Recombinational cloning is a universal cloning technique based on site-specific recombination that is independent of the insert DNA sequence of interest, which differentiates this method from the classical restriction enzyme-based cloning methods. Recombinational cloning enables rapid and efficient parallel transfer of DNA inserts into multiple expression systems. This unit summarizes strategies for generating expression-ready clones using the most popular recombinational cloning technologies, including the commercially available Gateway® (Life Technologies) and In-Fusion® (Clontech) cloning technologies. PMID:25827088

Construction and engineering of large biochemical pathways via DNA assembler

PubMed Central

Shao, Zengyi; Zhao, Huimin

2015-01-01

Summary DNA assembler enables rapid construction and engineering of biochemical pathways in a one-step fashion by exploitation of the in vivo homologous recombination mechanism in Saccharomyces cerevisiae. It has many applications in pathway engineering, metabolic engineering, combinatorial biology, and synthetic biology. Here we use two examples including the zeaxanthin biosynthetic pathway and the aureothin biosynthetic gene cluster to describe the key steps in the construction of pathways containing multiple genes using the DNA assembler approach. Methods for construct design, pathway assembly, pathway confirmation, and functional analysis are shown. The protocol for fine genetic modifications such as site-directed mutagenesis for engineering the aureothin gene cluster is also illustrated. PMID:23996442

The technology and biology of single-cell RNA sequencing.

PubMed

Kolodziejczyk, Aleksandra A; Kim, Jong Kyoung; Svensson, Valentine; Marioni, John C; Teichmann, Sarah A

2015-05-21

The differences between individual cells can have profound functional consequences, in both unicellular and multicellular organisms. Recently developed single-cell mRNA-sequencing methods enable unbiased, high-throughput, and high-resolution transcriptomic analysis of individual cells. This provides an additional dimension to transcriptomic information relative to traditional methods that profile bulk populations of cells. Already, single-cell RNA-sequencing methods have revealed new biology in terms of the composition of tissues, the dynamics of transcription, and the regulatory relationships between genes. Rapid technological developments at the level of cell capture, phenotyping, molecular biology, and bioinformatics promise an exciting future with numerous biological and medical applications. Copyright © 2015 Elsevier Inc. All rights reserved.

Three-dimensional segmentation of luminal and adventitial borders in serial intravascular ultrasound images

NASA Technical Reports Server (NTRS)

Shekhar, R.; Cothren, R. M.; Vince, D. G.; Chandra, S.; Thomas, J. D.; Cornhill, J. F.

1999-01-01

Intravascular ultrasound (IVUS) provides exact anatomy of arteries, allowing accurate quantitative analysis. Automated segmentation of IVUS images is a prerequisite for routine quantitative analyses. We present a new three-dimensional (3D) segmentation technique, called active surface segmentation, which detects luminal and adventitial borders in IVUS pullback examinations of coronary arteries. The technique was validated against expert tracings by computing correlation coefficients (range 0.83-0.97) and William's index values (range 0.37-0.66). The technique was statistically accurate, robust to image artifacts, and capable of segmenting a large number of images rapidly. Active surface segmentation enabled geometrically accurate 3D reconstruction and visualization of coronary arteries and volumetric measurements.

Two schemes for rapid generation of digital video holograms using PC cluster

NASA Astrophysics Data System (ADS)

Park, Hanhoon; Song, Joongseok; Kim, Changseob; Park, Jong-Il

2017-12-01

Computer-generated holography (CGH), which is a process of generating digital holograms, is computationally expensive. Recently, several methods/systems of parallelizing the process using graphic processing units (GPUs) have been proposed. Indeed, use of multiple GPUs or a personal computer (PC) cluster (each PC with GPUs) enabled great improvements in the process speed. However, extant literature has less often explored systems involving rapid generation of multiple digital holograms and specialized systems for rapid generation of a digital video hologram. This study proposes a system that uses a PC cluster and is able to more efficiently generate a video hologram. The proposed system is designed to simultaneously generate multiple frames and accelerate the generation by parallelizing the CGH computations across a number of frames, as opposed to separately generating each individual frame while parallelizing the CGH computations within each frame. The proposed system also enables the subprocesses for generating each frame to execute in parallel through multithreading. With these two schemes, the proposed system significantly reduced the data communication time for generating a digital hologram when compared with that of the state-of-the-art system.

Exploratory Climate Data Visualization and Analysis Using DV3D and UVCDAT

NASA Technical Reports Server (NTRS)

Maxwell, Thomas

2012-01-01

Earth system scientists are being inundated by an explosion of data generated by ever-increasing resolution in both global models and remote sensors. Advanced tools for accessing, analyzing, and visualizing very large and complex climate data are required to maintain rapid progress in Earth system research. To meet this need, NASA, in collaboration with the Ultra-scale Visualization Climate Data Analysis Tools (UVCOAT) consortium, is developing exploratory climate data analysis and visualization tools which provide data analysis capabilities for the Earth System Grid (ESG). This paper describes DV3D, a UV-COAT package that enables exploratory analysis of climate simulation and observation datasets. OV3D provides user-friendly interfaces for visualization and analysis of climate data at a level appropriate for scientists. It features workflow inte rfaces, interactive 40 data exploration, hyperwall and stereo visualization, automated provenance generation, and parallel task execution. DV30's integration with CDAT's climate data management system (COMS) and other climate data analysis tools provides a wide range of high performance climate data analysis operations. DV3D expands the scientists' toolbox by incorporating a suite of rich new exploratory visualization and analysis methods for addressing the complexity of climate datasets.

Sponsors meet scientists to speed pediatric medicines development.

PubMed

Davis, Jonathan M; Smoyer, William E; Connor, Edward M; Huskins, W Charles; Pastern, Cindy; Purucker, Mary; Schrader, Elisabeth C; Jackson, Cynthia R; Kaskel, Frederick J; Hirschfeld, Steven

2015-03-18

The Point-Person Project, a child-health research initiative, enables rapid response to opportunities for participation in multicenter pediatric clinical trials. Copyright © 2015, American Association for the Advancement of Science.

Validation of the AVM Blast Computational Modeling and Simulation Tool Set

DTIC Science & Technology

2015-08-04

by-construction" methodology is powerful and would not be possible without high -level design languages to support validation and verification. [1,4...to enable the making of informed design decisions.  Enable rapid exploration of the design trade-space for high -fidelity requirements tradeoffs...live-fire tests, the jump height of the target structure is recorded by using either high speed cameras or a string pot. A simple projectile motion

Inner ear tissue preservation by rapid freezing: Improving fixation by high-pressure freezing and hybrid methods

PubMed Central

Bullen, A.; Taylor, R.R.; Kachar, B.; Moores, C.; Fleck, R.A.; Forge, A.

2014-01-01

In the preservation of tissues in as ‘close to life’ state as possible, rapid freeze fixation has many benefits over conventional chemical fixation. One technique by which rapid freeze-fixation can be achieved, high pressure freezing (HPF), has been shown to enable ice crystal artefact-free freezing and tissue preservation to greater depths (more than 40 μm) than other quick-freezing methods. Despite increasingly becoming routine in electron microscopy, the use of HPF for the fixation of inner ear tissue has been limited. Assessment of the quality of preservation showed routine HPF techniques were suitable for preparation of inner ear tissues in a variety of species. Good preservation throughout the depth of sensory epithelia was achievable. Comparison to chemically fixed tissue indicated that fresh frozen preparations exhibited overall superior structural preservation of cells. However, HPF fixation caused characteristic artefacts in stereocilia that suggested poor quality freezing of the actin bundles. The hybrid technique of pre-fixation and high pressure freezing was shown to produce cellular preservation throughout the tissue, similar to that seen in HPF alone. Pre-fixation HPF produced consistent high quality preservation of stereociliary actin bundles. Optimising the preparation of samples with minimal artefact formation allows analysis of the links between ultrastructure and function in inner ear tissues. PMID:25016142

Unambiguous identification and discovery of bacterial siderophores by direct injection 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Walker, Lawrence R; Tfaily, Malak M; Shaw, Jared B; Hess, Nancy J; Paša-Tolić, Ljiljana; Koppenaal, David W

2017-01-25

Under iron-limiting conditions, bacteria produce low molecular mass Fe(iii) binding molecules known as siderophores to sequester the Fe(iii), along with other elements, increasing their bioavailability. Siderophores are thought to influence iron cycling and biogeochemistry in both marine and terrestrial ecosystems and hence the need for rapid, confident characterization of these compounds has increased. In this study, the type of siderophores produced by two marine bacterial species, Synechococcus sp. PCC 7002 and Vibrio cyclitrophicus 1F53, were characterized by use of a newly developed 21 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR MS) with direct injection electrospray ionization. This technique allowed for the rapid detection of synechobactins from Synechococcus sp. PCC 7002 as well as amphibactins from Vibrio cyclitrophicus 1F53 based on high mass accuracy and resolution allowing for observation of specific Fe isotopes and isotopic fine structure enabling highly confident identification of these siderophores. When combined with molecular network analysis two new amphibactins were discovered and verified by tandem MS. These results show that high-field FTICR MS is a powerful technique that will greatly improve the ability to rapidly identify and discover metal binding species in the environment.

Unambiguous identification and discovery of bacterial siderophores by direct injection 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry

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

Walker, Lawrence R.; Tfaily, Malak M.; Shaw, Jared B.

Under iron-limiting conditions, bacteria produce low molecular mass Fe(III) binding molecules known as siderophores to sequester the Fe(III), along with other elements, increasing their bioavailibility. Siderophores are thought to influence iron cycling and biogeochemistry in both marine and terrestrial ecosystems and hence the need for rapid, confident characterization of these compounds has increased. In this study, the type of siderophores produced by two marine bacterial species, Synechococcus sp. PCC 7002 and Vibrio cyclitrophicus 1F53, were characterized using a newly developed 21T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR MS) with direct injection electrospray ionization. This technique allowed for themore » rapid detection of synechobactins from Synechococcus sp. PCC 7002 as well as amphibactins from Vibrio cyclitrophicus 1F53 based on high mass accuracy and resolution allowing for observation of specific Fe isotopic peaks and fine isotopic structure enables highly confident identification of these sideropohores. When combined with molecular network analysis two new amphibactins were discovered and verified by tandem MS. These results show that high-field FTICR MS is a powerful technique that will greatly improve the ability to rapidly identify and discover metal binding species in the environment.« less

DNA barcoding and morphological analysis for rapid identification of most economically important crop-infesting Sunn pests belonging to Eurygaster Laporte, 1833 (Hemiptera, Scutelleridae).

PubMed

Syromyatnikov, Mikhail Y; Golub, Victor B; Kokina, Anastasia V; Victoria A Soboleva; Popov, Vasily N

2017-01-01

The genus Eurygaster Laporte, 1833 includes ten species five of which inhabit the European part of Russia. The harmful species of the genus is E. integriceps . Eurygaster species identification based on the morphological traits is very difficult, while that of the species at the egg or larval stages is extremely difficult or impossible. Eurygaster integriceps , E. maura , and E. testudinaria differ only slightly between each other morphologically, E. maura and E. testudinaria being almost indiscernible. DNA barcoding based on COI sequences have shown that E. integriceps differs significantly from these closely related species, which enables its rapid and accurate identification. Based on COI nucleotide sequences, three species of Sunn pests, E. maura , E. testudinarius , E. dilaticollis , could not be differentiated from each other through DNA barcoding. The difference in the DNA sequences between the COI gene of E. integriceps and COI genes of E. maura and E. testudinarius was more than 4%. In the present study DNA barcoding of two Eurygaster species was performed for the first time on E. integriceps , the most dangerous pest in the genus, and E. dilaticollis that only inhabits natural ecosystems. The PCR-RFLP method was developed in this work for the rapid identification of E. integriceps .

DNA barcoding and morphological analysis for rapid identification of most economically important crop-infesting Sunn pests belonging to Eurygaster Laporte, 1833 (Hemiptera, Scutelleridae)

PubMed Central

Syromyatnikov, Mikhail Y.; Golub, Victor B.; Kokina, Anastasia V.; Victoria A. Soboleva; Popov, Vasily N.

2017-01-01

Abstract The genus Eurygaster Laporte, 1833 includes ten species five of which inhabit the European part of Russia. The harmful species of the genus is E. integriceps. Eurygaster species identification based on the morphological traits is very difficult, while that of the species at the egg or larval stages is extremely difficult or impossible. Eurygaster integriceps, E. maura, and E. testudinaria differ only slightly between each other morphologically, E. maura and E. testudinaria being almost indiscernible. DNA barcoding based on COI sequences have shown that E. integriceps differs significantly from these closely related species, which enables its rapid and accurate identification. Based on COI nucleotide sequences, three species of Sunn pests, E. maura, E. testudinarius, E. dilaticollis, could not be differentiated from each other through DNA barcoding. The difference in the DNA sequences between the COI gene of E. integriceps and COI genes of E. maura and E. testudinarius was more than 4%. In the present study DNA barcoding of two Eurygaster species was performed for the first time on E. integriceps, the most dangerous pest in the genus, and E. dilaticollis that only inhabits natural ecosystems. The PCR-RFLP method was developed in this work for the rapid identification of E. integriceps. PMID:29118620

disLocate: tools to rapidly quantify local intermolecular structure to assess two-dimensional order in self-assembled systems.

PubMed

Bumstead, Matt; Liang, Kunyu; Hanta, Gregory; Hui, Lok Shu; Turak, Ayse

2018-01-24

Order classification is particularly important in photonics, optoelectronics, nanotechnology, biology, and biomedicine, as self-assembled and living systems tend to be ordered well but not perfectly. Engineering sets of experimental protocols that can accurately reproduce specific desired patterns can be a challenge when (dis)ordered outcomes look visually similar. Robust comparisons between similar samples, especially with limited data sets, need a finely tuned ensemble of accurate analysis tools. Here we introduce our numerical Mathematica package disLocate, a suite of tools to rapidly quantify the spatial structure of a two-dimensional dispersion of objects. The full range of tools available in disLocate give different insights into the quality and type of order present in a given dispersion, accessing the translational, orientational and entropic order. The utility of this package allows for researchers to extract the variation and confidence range within finite sets of data (single images) using different structure metrics to quantify local variation in disorder. Containing all metrics within one package allows for researchers to easily and rapidly extract many different parameters simultaneously, allowing robust conclusions to be drawn on the order of a given system. Quantifying the experimental trends which produce desired morphologies enables engineering of novel methods to direct self-assembly.

Analyzing and strengthening the vaccine safety program in Manitoba.

PubMed

Montalban, J M; Ogbuneke, C; Hilderman, T

2014-12-04

The emergence of a novel influenza A virus in 2009 and the rapid introduction of new pandemic vaccines prompted an analysis of the current state of the adverse events following immunization (AEFI) surveillance response in several provinces. To highlight aspects of the situational analysis of the Manitoba Health, Healthy Living and Seniors (MHHLS's) AEFI surveillance system and to demonstrate how common business techniques could be usefully applied to a provincial vaccine safety monitoring program. Situational analysis of the AEFI surveillance system in Manitoba was developed through a strengths-weaknesses-opportunities-threats (SWOT) analysis and informed by the National Immunization Strategy vaccine safety priorities. Strategy formulation was developed by applying the threats-opportunities-weaknesses-strengths (TOWS) matrix. Thirteen strategies were formulated that use strengths to either take advantage of opportunities or avoid threats, that exploit opportunities to overcome weaknesses, or that rectify weaknesses to circumvent threats. These strategies entailed the development of various tools and resources, most of which are either actively underway or completed. The SWOT analysis and the TOWS matrix enabled MHHLS to enhance the capacity of its vaccine safety program.

Analyzing and strengthening the vaccine safety program in Manitoba

PubMed Central

Montalban, JM; Ogbuneke, C; Hilderman, T

2014-01-01

Background: The emergence of a novel influenza A virus in 2009 and the rapid introduction of new pandemic vaccines prompted an analysis of the current state of the adverse events following immunization (AEFI) surveillance response in several provinces. Objectives To highlight aspects of the situational analysis of the Manitoba Health, Healthy Living and Seniors (MHHLS’s) AEFI surveillance system and to demonstrate how common business techniques could be usefully applied to a provincial vaccine safety monitoring program. Method Situational analysis of the AEFI surveillance system in Manitoba was developed through a strengths-weaknesses-opportunities-threats (SWOT) analysis and informed by the National Immunization Strategy vaccine safety priorities. Strategy formulation was developed by applying the threats-opportunities-weaknesses-strengths (TOWS) matrix. Results Thirteen strategies were formulated that use strengths to either take advantage of opportunities or avoid threats, that exploit opportunities to overcome weaknesses, or that rectify weaknesses to circumvent threats. These strategies entailed the development of various tools and resources, most of which are either actively underway or completed. Conclusion The SWOT analysis and the TOWS matrix enabled MHHLS to enhance the capacity of its vaccine safety program. PMID:29769910

Rapid determination of nanowires electrical properties using a dielectrophoresis-well based system

NASA Astrophysics Data System (ADS)

Constantinou, Marios; Hoettges, Kai F.; Krylyuk, Sergiy; Katz, Michael B.; Davydov, Albert; Rigas, Grigorios-Panagiotis; Stolojan, Vlad; Hughes, Michael P.; Shkunov, Maxim

2017-03-01

The use of high quality semiconducting nanomaterials for advanced device applications has been hampered by the unavoidable growth variability of electrical properties of one-dimensional nanomaterials, such as nanowires and nanotubes, thus highlighting the need for the characterization of efficient semiconducting nanomaterials. In this study, we demonstrate a low-cost, industrially scalable dielectrophoretic (DEP) nanowire assembly method for the rapid analysis of the electrical properties of inorganic single crystalline nanowires, by identifying key features in the DEP frequency response spectrum from 1 kHz to 20 MHz in just 60 s. Nanowires dispersed in anisole were characterized using a three-dimensional DEP chip (3DEP), and the resultant spectrum demonstrated a sharp change in nanowire response to DEP signal in 1-20 MHz frequency range. The 3DEP analysis, directly confirmed by field-effect transistor data, indicates that nanowires of higher quality are collected at high DEP signal frequency range above 10 MHz, whereas lower quality nanowires, with two orders of magnitude lower current per nanowire, are collected at lower DEP signal frequencies. These results show that the 3DEP platform can be used as a very efficient characterization tool of the electrical properties of rod-shaped nanoparticles to enable dielectrophoretic selective deposition of nanomaterials with superior conductivity properties.

Confocal mosaicing microscopy of human skin ex vivo: spectral analysis for digital staining to simulate histology-like appearance

PubMed Central

Bini, Jason; Spain, James; Nehal, Kishwer; Hazelwood, Vikki; DiMarzio, Charles; Rajadhyaksha, Milind

2011-01-01

Confocal mosaicing microscopy enables rapid imaging of large areas of fresh tissue, without the processing that is necessary for conventional histology. Mosaicing may offer a means to perform rapid histology at the bedside. A possible barrier toward clinical acceptance is that the mosaics are based on a single mode of grayscale contrast and appear black and white, whereas histology is based on two stains (hematoxylin for nuclei, eosin for cellular cytoplasm and dermis) and appears purple and pink. Toward addressing this barrier, we report advances in digital staining: fluorescence mosaics that show only nuclei, are digitally stained purple and overlaid on reflectance mosaics, which show only cellular cytoplasm and dermis, and are digitally stained pink. With digital staining, the appearance of confocal mosaics mimics the appearance of histology. Using multispectral analysis and color matching functions, red, green, and blue (RGB) components of hematoxylin and eosin stains in tissue were determined. The resulting RGB components were then applied in a linear algorithm to transform fluorescence and reflectance contrast in confocal mosaics to the absorbance contrast seen in pathology. Optimization of staining with acridine orange showed improved quality of digitally stained mosaics, with good correlation to the corresponding histology. PMID:21806269

Disciplined Improvisation: Characteristics of Inquiry in Mindfulness-Based Teaching.

PubMed

Crane, Rebecca S; Stanley, Steven; Rooney, Michael; Bartley, Trish; Cooper, Lucinda; Mardula, Jody

Evidence for the effectiveness of mindfulness-based stress reduction (MBSR) and mindfulness-based cognitive therapy (MBCT) is rapidly growing as interest in this field expands. By contrast, there are few empirical analyses of the pedagogy of MBSR and MBCT. Development of the evidence base concerning the teaching of MBCT or MBSR would support the integrity of the approach in the context of rapid expansion. This paper describes an applied conversation analysis (CA) of the characteristics of inquiry in the MBSR and MBCT teaching process. Audio-recordings of three 8-week MBCT and MBSR classes, with 24, 12, and 6 participants, were transcribed and systematically examined. The study focused on the teacher-led interactive inquiry which takes place in each session after a guided meditation practice. The study describes and analyzes three practices within the inquiry process that can be identified in sequences of talk: turn-taking talk involving questions and reformulations; the development of participant skills in a particular way of describing experience; and talk that constructs intersubjective connection and affiliation within the group. CA enables fine-grained analysis of the interactional work of mindfulness-based inquiry. Inquiry is a process of disciplined improvisation which is both highly specific to the conditions of the moment it took place in and uses repeated and recognizable patterns of interaction.

Microbial genomic island discovery, visualization and analysis.

PubMed

Bertelli, Claire; Tilley, Keith E; Brinkman, Fiona S L

2018-06-03

Horizontal gene transfer (also called lateral gene transfer) is a major mechanism for microbial genome evolution, enabling rapid adaptation and survival in specific niches. Genomic islands (GIs), commonly defined as clusters of bacterial or archaeal genes of probable horizontal origin, are of particular medical, environmental and/or industrial interest, as they disproportionately encode virulence factors and some antimicrobial resistance genes and may harbor entire metabolic pathways that confer a specific adaptation (solvent resistance, symbiosis properties, etc). As large-scale analyses of microbial genomes increases, such as for genomic epidemiology investigations of infectious disease outbreaks in public health, there is increased appreciation of the need to accurately predict and track GIs. Over the past decade, numerous computational tools have been developed to tackle the challenges inherent in accurate GI prediction. We review here the main types of GI prediction methods and discuss their advantages and limitations for a routine analysis of microbial genomes in this era of rapid whole-genome sequencing. An assessment is provided of 20 GI prediction software methods that use sequence-composition bias to identify the GIs, using a reference GI data set from 104 genomes obtained using an independent comparative genomics approach. Finally, we present guidelines to assist researchers in effectively identifying these key genomic regions.

Remote sensing of multimodal transportation systems : research brief.

DOT National Transportation Integrated Search

2016-09-01

Remote Sensing of Multimodal Transportation Systems : Rapid condition monitoring and performance evaluations of the vast and vulnerable transportation infrastructure has been elusive. The framework and models developed in this research will enable th...

Influenza A virus hemagglutinin glycosylation compensates for antibody escape fitness costs.

PubMed

Kosik, Ivan; Ince, William L; Gentles, Lauren E; Oler, Andrew J; Kosikova, Martina; Angel, Matthew; Magadán, Javier G; Xie, Hang; Brooke, Christopher B; Yewdell, Jonathan W

2018-01-01

Rapid antigenic evolution enables the persistence of seasonal influenza A and B viruses in human populations despite widespread herd immunity. Understanding viral mechanisms that enable antigenic evolution is critical for designing durable vaccines and therapeutics. Here, we utilize the primerID method of error-correcting viral population sequencing to reveal an unexpected role for hemagglutinin (HA) glycosylation in compensating for fitness defects resulting from escape from anti-HA neutralizing antibodies. Antibody-free propagation following antigenic escape rapidly selected viruses with mutations that modulated receptor binding avidity through the addition of N-linked glycans to the HA globular domain. These findings expand our understanding of the viral mechanisms that maintain fitness during antigenic evolution to include glycan addition, and highlight the immense power of high-definition virus population sequencing to reveal novel viral adaptive mechanisms.

Assembly of Four Diverse Heterocyclic Libraries Enabled by Prins Cyclization, Au-Catalyzed Enyne Cycloisomerization, and Automated Amide Synthesis

PubMed Central

Cui, Jiayue; Chai, David I.; Miller, Christopher; Hao, Jason; Thomas, Christopher; Wang, JingQi; Scheidt, Karl A.; Kozmin, Sergey A.

2013-01-01

We describe a unified synthetic strategy for efficient assembly of four new heterocyclic libraries. The synthesis began by creating a range of structurally diverse pyrrolidinones or piperidinones. Such compounds were obtained in a simple one-flask operation starting with readily available amines, ketoesters, and unsaturated anhydrides. The use of tetrahydropyran-containing ketoesters, which were rapidly assembled by our Prins cyclization protocol, enabled efficient fusion of pyran and piperidinone cores. A newly developed Au(I)-catalyzed cycloisomerization of alkyne-containing enamides further expanded heterocyclic diversity by providing rapid entry into a wide range of bicyclic and tricyclic dienamides. The final stage of the process entailed diversification of each of the initially produced carboxylic acids using a fully automated platform for amide synthesis, which delivered 1872 compounds in high diastereomeric and chemical purity. PMID:22860634

Shock ion acceleration by an ultrashort circularly polarized laser pulse via relativistic transparency in an exploded target.

PubMed

Kim, Young-Kuk; Cho, Myung-Hoon; Song, Hyung Seon; Kang, Teyoun; Park, Hyung Ju; Jung, Moon Youn; Hur, Min Sup

2015-10-01

We investigated ion acceleration by an electrostatic shock in an exploded target irradiated by an ultrashort, circularly polarized laser pulse by means of one- and three-dimensional particle-in-cell simulations. We discovered that the laser field penetrating via relativistic transparency (RT) rapidly heated the upstream electron plasma to enable the formation of a high-speed electrostatic shock. Owing to the RT-based rapid heating and the fast compression of the initial density spike by a circularly polarized pulse, a new regime of the shock ion acceleration driven by an ultrashort (20-40 fs), moderately intense (1-1.4 PW) laser pulse is envisaged. This regime enables more efficient shock ion acceleration under a limited total pulse energy than a linearly polarized pulse with crystal laser systems of λ∼1μm.

Adaptive phenotypic response to climate enabled by epigenetics in a K-strategy species, the fish Leucoraja ocellata (Rajidae)

PubMed Central

Incarnato, Danny; Ward, Ben J.; van Oosterhout, Cock; Bradbury, Ian; Hanson, Mark; Bentzen, Paul

2016-01-01

The relative importance of genetic versus epigenetic changes in adaptive evolution is a hotly debated topic, with studies showing that some species appear to be able to adapt rapidly without significant genetic change. Epigenetic mechanisms may be particularly important for the evolutionary potential of species with long maturation times and low reproductive potential (‘K-strategists’), particularly when faced with rapidly changing environmental conditions. Here we study the transcriptome of two populations of the winter skate (Leucoraja ocellata), a typical ‘K-strategist’, in Atlantic Canada; an endemic population in the southern Gulf of St Lawrence and a large population on the Scotian Shelf. The endemic population has been able to adapt to a 10°C higher water temperature over short evolutionary time (7000 years), dramatically reducing its body size (by 45%) significantly below the minimum maturation size of Scotian Shelf and other populations of winter skate, as well as exhibiting other adaptations in life history and physiology. We demonstrate that the adaptive response to selection has an epigenetic basis, cataloguing 3653 changes in gene expression that may have enabled this species to rapidly respond to the novel environment. We argue that the epigenetic augmentation of species evolutionary potential (its regulation though gene expression) can enable K-strategists to survive and adapt to different environments, and this mechanism may be particularly important for the persistence of sharks, skates and rays in the light of future climate change. PMID:27853546

Heat Treatment Development for a Rapidly Solidified Heat Resistant Cast Al-Si Alloy

NASA Astrophysics Data System (ADS)

Kasprzak, W.; Chen, D. L.; Shaha, S. K.

2013-07-01

Existing heat treatment standards do not properly define tempers for thin-walled castings that solidified with high solidification rates. Recently emerged casting processes such as vacuum high pressure die casting should not require long solution treatment times due to the fine microstructures arising from rapid solidification rates. The heat treatment studies involving rapidly solidified samples with secondary dendrite arm spacing between 10 and 35 μm were conducted for solution times between 30 min and 9 h and temperatures of 510 and 525 °C and for various aging parameters. The metallurgical analysis revealed that an increase in microstructure refinement could enable a reduction of solution time up to 88%. Solution treatment resulted in the dissolution of Al2Cu and Al5Mg8Si6Cu2, while Fe- and TiZrV-based phases remained partially in the microstructure. The highest strength of approximately 351 ± 9.7 and 309 ± 3.4 MPa for the UTS and YS, respectively, was achieved for a 2-step solution treatment at 510 and 525 °C in the T6 peak aging conditions, i.e., 150 °C for 100 h. The T6 temper did not yield dimensionally stable microstructure since exceeding 250 °C during in-service operation could result in phase transformation corresponding to the over-aging reaction. The microstructure refinement had a statistically stronger effect on the alloy strength than the increase in solutionizing time. Additionally, thermal analysis and dilatometer results were presented to assess the dissolution of phases during solution treatment, aging kinetics as well as dimensional stability.

Rapid Screening of Carboxylic Acids from Waste and Surface Waters by ESI-MS/MS Using Barium Ion Chemistry and On-Line Membrane Sampling.

PubMed

Duncan, Kyle D; Volmer, Dietrich A; Gill, Chris G; Krogh, Erik T

2016-03-01

Negative ion tandem mass spectrometric analysis of aliphatic carboxylic acids often yields only non-diagnostic ([M - H](-)) ions with limited selective fragmentation. However, carboxylates cationized with Ba(2+) have demonstrated efficient dissociation in positive ion mode, providing structurally diagnostic product ions. We report the application of barium adducts followed by collision induced dissociation (CID), to improve selectivity for rapid screening of carboxylic acids in complex aqueous samples. The quantitative MS/MS method presented utilizes common product ions of [M - H + Ba](+) precursor ions. The mechanism of product ion formation is investigated using isotopically labeled standards and a series of structurally related carboxylic acids. The results suggest that hydrogen atoms in the β and γ positions yield common product ions ([BaH](+) and [BaOH](+)). Furthermore, the diagnostic product ion at m/z 196 serves as a qualifying ion for carboxylate species. This methodology has been successfully used in conjunction with condensed phase membrane introduction mass spectrometry (CP-MIMS), with barium acetate added directly to the methanol acceptor phase. The combination enables rapid screening of carboxylic acids directly from acidified water samples (wastewater effluent, spiked natural waters) using a capillary hollow fiber PDMS membrane immersion probe. We have applied this technique for the direct analysis of complex naphthenic acid mixtures spiked into natural surface waters using CP-MIMS. Selectivity at the ionization and tandem mass spectrometry level eliminate isobaric interferences from hydroxylated species present within the samples, which have been observed in negative electrospray ionization.

Miniaturized Embryo Array for Automated Trapping, Immobilization and Microperfusion of Zebrafish Embryos

PubMed Central

Akagi, Jin; Khoshmanesh, Khashayar; Evans, Barbara; Hall, Chris J.; Crosier, Kathryn E.; Cooper, Jonathan M.; Crosier, Philip S.; Wlodkowic, Donald

2012-01-01

Zebrafish (Danio rerio) has recently emerged as a powerful experimental model in drug discovery and environmental toxicology. Drug discovery screens performed on zebrafish embryos mirror with a high level of accuracy the tests usually performed on mammalian animal models, and fish embryo toxicity assay (FET) is one of the most promising alternative approaches to acute ecotoxicity testing with adult fish. Notwithstanding this, automated in-situ analysis of zebrafish embryos is still deeply in its infancy. This is mostly due to the inherent limitations of conventional techniques and the fact that metazoan organisms are not easily susceptible to laboratory automation. In this work, we describe the development of an innovative miniaturized chip-based device for the in-situ analysis of zebrafish embryos. We present evidence that automatic, hydrodynamic positioning, trapping and long-term immobilization of single embryos inside the microfluidic chips can be combined with time-lapse imaging to provide real-time developmental analysis. Our platform, fabricated using biocompatible polymer molding technology, enables rapid trapping of embryos in low shear stress zones, uniform drug microperfusion and high-resolution imaging without the need of manual embryo handling at various developmental stages. The device provides a highly controllable fluidic microenvironment and post-analysis eleuthero-embryo stage recovery. Throughout the incubation, the position of individual embryos is registered. Importantly, we also for first time show that microfluidic embryo array technology can be effectively used for the analysis of anti-angiogenic compounds using transgenic zebrafish line (fli1a:EGFP). The work provides a new rationale for rapid and automated manipulation and analysis of developing zebrafish embryos at a large scale. PMID:22606275

Rapid Analysis of Pharmacology for Infectious Diseases

PubMed Central

Hopkins, Andrew L; Bickerton, G. Richard; Carruthers, Ian M; Boyer, Stephen K; Rubin, Harvey; Overington, John P

2011-01-01

Pandemic, epidemic and endemic infectious diseases are united by a common problem: how do we rapidly and cost-effectively identify potential pharmacological interventions to treat infections? Given the large number of emerging and neglected infectious diseases and the fact that they disproportionately afflict the poorest members of the global society, new ways of thinking are required to develop high productivity discovery systems that can be applied to a large number of pathogens. The growing availability of parasite genome data provides the basis for developing methods to prioritize, a priori potential drug targets and analyze the pharmacological landscape of an infectious disease. Thus the overall objective of infectious disease informatics is to enable the rapid generation of plausible, novel medical hypotheses of test-able pharmacological experiments, by uncovering undiscovered relationships in the wealth of biomedical literature and databases that were collected for other purposes. In particular our goal is to identify potential drug targets present in a pathogen genome and prioritize which pharmacological experiments are most likely to discover drug-like lead compounds rapidly against a pathogen (i.e. which specific compounds and drug targets should be screened, in which assays and where they can be sourced). An integral part of the challenge is the development and integration of methods to predict druggability, essentiality, synthetic lethality and polypharmocology in pathogen genomes, while simultaneously integrating the inevitable issues of chemical tractability and the potential for acquired drug resistance from the start. PMID:21401504

Wearable Flexible and Stretchable Glove Biosensor for On-Site Detection of Organophosphorus Chemical Threats

DTIC Science & Technology

2017-03-03

finger enables rapid on-site detection of organophosphate (OP) nerve-agent compounds on suspicious surfaces and agricultural products following their...used as pesticides in agricultural and domestic settings.21,22 These OP neurotoxins severely affect the nervous system and lead to rapid death. Due to...The “on-hand” detection of different OP chemical agents on a variety of surfaces and agricultural foodstuffs demonstrate that the new wireless glove

Early Detection of Clinically Significant Prostate Cancer Using Ultrasonic Acoustic Radiation Force Impulse (ARFI) Imaging

DTIC Science & Technology

2017-10-01

Toolkit for rapid 3D visualization and image volume interpretation, followed by automated transducer positioning in a user-selected image plane for... Toolkit (IGSTK) to enable rapid 3D visualization and image volume interpretation followed by automated transducer positioning in the user-selected... careers in science, technology, and the humanities. What do you plan to do during the next reporting period to accomplish the goals? If this