Analysis of Doppler Lidar Data Acquired During the Pentagon Shield Field Campaign

DTIC Science & Technology

2011-04-01

two coherent Doppler lidars deployed during the Pentagon Shield field campaign are analyzed in conjunction with other sensors to characterize the...Observations from two coherent Doppler lidars deployed during the Pentagon Shield field campaign are analyzed in conjunction with other sensors to... coherent Doppler lidars deployed during the Pentagon Shield field campaign are analyzed in conjunction with other sensors to characterize the overall

A Novel Field-Deployable Point-of-Care Diagnostic Test for Cutaneous Leishmaniasis

DTIC Science & Technology

2017-10-01

AWARD NUMBER: W81XWH-14-2-0195 TITLE: A Novel Field-Deployable Point-of-Care Diagnostic Test for Cutaneous Leishmaniasis PRINCIPAL INVESTIGATOR...Field-Deployable Point-of-Care Diagnostic Test for Cutaneous Leishmaniasis 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...Month % completion Aim 1: To use simulated field conditions to optimize and produce the established RPA lateral flow diagnostic test for POC

Ecotoxicological effects of a semi-submerged municipal dump (Castle harbour, Bermuda) on the Calico scallop Argopecten gibbus.

PubMed

Quinn, Brian; Gagné, Francois; Weber, Jean-Philippe; Blaise, Christian

2005-01-01

A biomarker study was undertaken using the Calico scallop Argopecten gibbus to assess the ecotoxicological effects of a semi-submerged municipal dump on the adjacent patch reef lagoon ecosystem (Castle harbour, Bermuda). Caged scallops were deployed in situ for 2 months at various distances from the dump (50 m, 900 m and 2.7 km) and at a reference site (14 km). A suite of biomarkers comprising metallothionein (MT), lipid peroxidation (LPO), vitellin-like proteins (Vn), glutathione S-transferase (GST), DNA strand breaks and condition factor (CF) were investigated in various tissues of the scallop (gill, digestive gland and gonad). Levels of heavy metals were also measured in the whole scallop soft tissue. While there was some variation in response between tissues, in general the results indicated that the dump was negatively impacting scallops deployed in the adjacent marine environment: elevated levels of MT, DNA strand breaks, Vn and GST and reduced condition factor were found for scallops deployed nearest to the dump and at the site 1.5 km from this point source of contamination (Tuckers town) in Castle harbour, with respect to the reference site, North Rock (although this exhibited some degree of metal contamination). The gills from scallops deployed at the dump site were the most responsive tissue, with the highest expression of MT, LPO and DNA damage. This study indicates the potential of the Calico scallop as a convenient bioindicator species in the marine tropical benthos.

Persistent Identifiers for Field Deployments: A Missing Link in the Provenance Chain

NASA Astrophysics Data System (ADS)

Arko, R. A.; Ji, P.; Fils, D.; Shepherd, A.; Chandler, C. L.; Lehnert, K.

2016-12-01

Research in the geosciences is characterized by a wide range of complex and costly field deployments including oceanographic cruises, submersible dives, drilling expeditions, seismic networks, geodetic campaigns, moored arrays, aircraft flights, and satellite missions. Each deployment typically produces a mix of sensor and sample data, spanning a period from hours to decades, that ultimately yields a long tail of post-field products and publications. Publishing persistent, citable identifiers for field deployments will facilitate 1) preservation and reuse of the original field data, 2) reproducibility of the resulting publications, and 3) recognition for both the facilities that operate the platforms and the investigators who secure funding for the experiments. In the ocean domain, sharing unique identifiers for field deployments is a familiar practice. For example, the Biological and Chemical Oceanography Data Management Office (BCO-DMO) routinely links datasets to cruise identifiers published by the Rolling Deck to Repository (R2R) program. In recent years, facilities have started to publish formal/persistent identifiers, typically Digital Object Identifiers (DOIs), for field deployments including seismic networks, oceanographic cruises, and moored arrays. For example, the EarthChem Library (ECL) publishes a DOI for each dataset which, if it derived from an oceanographic research cruise on a US vessel, is linked to a DOI for the cruise published by R2R. Work is underway to create similar links for the IODP JOIDES Resolution Science Operator (JRSO) and the Continental Scientific Drilling Coordination Office (CSDCO). We present results and lessons learned including a draft schema for publishing field deployments as DataCite DOI records; current practice for linking these DOIs with related identifiers such as Open Researcher and Contributor IDs (ORCIDs), Open Funder Registry (OFR) codes, and International Geo Sample Numbers (IGSNs); and consideration of other identifier types for field deployments such as UUIDs and Handles.

Development of Rapid Isothermal Amplification Assays for Detection of Phytophthora spp. in Plant Tissue.

PubMed

Miles, Timothy D; Martin, Frank N; Coffey, Michael D

2015-02-01

Several isothermal amplification techniques recently have been developed that are tolerant of inhibitors present in many plant extracts, which can reduce the need for obtaining purified DNA for running diagnostic assays. One such commercially available technique that has similarities with real-time polymerase chain reaction (PCR) for designing primers and a labeled probe is recombinase polymerase amplification (RPA). This technology was used to develop two simple and rapid approaches for detection of Phytophthora spp.: one genus-specific assay multiplexed with a plant internal control and the other species-specific assays for Phytophthora ramorum and P. kernoviae. All assays were tested for sensitivity (ranging from 3 ng to 1 fg of DNA) and specificity using DNA extracted from more than 136 Phytophthora taxa, 21 Pythium spp., 1 Phytopythium sp., and a wide range of plant species. The lower limit of linear detection using purified DNA was 200 to 300 fg of DNA in all pathogen RPA assays. Six different extraction buffers were tested for use during plant tissue maceration and the assays were validated in the field by collecting 222 symptomatic plant samples from over 50 different hosts. Only 56 samples were culture positive for Phytophthora spp. whereas 91 were positive using the Phytophthora genus-specific RPA test and a TaqMan real-time PCR assay. A technique for the generation of sequencing templates from positive RPA amplifications to confirm species identification was also developed. These RPA assays have added benefits over traditional technologies because they are rapid (results can be obtained in as little as 15 min), do not require DNA extraction or extensive training to complete, use less expensive portable equipment than PCR-based assays, and are significantly more specific than current immunologically based methods. This should provide a rapid, field-deployable capability for pathogen detection that will facilitate point-of-sample collection processing, thereby reducing the time necessary for accurate diagnostics and making management decisions.

Longitudinal analyses of the DNA methylome in deployed military servicemen identify susceptibility loci for post-traumatic stress disorder.

PubMed

Rutten, B P F; Vermetten, E; Vinkers, C H; Ursini, G; Daskalakis, N P; Pishva, E; de Nijs, L; Houtepen, L C; Eijssen, L; Jaffe, A E; Kenis, G; Viechtbauer, W; van den Hove, D; Schraut, K G; Lesch, K-P; Kleinman, J E; Hyde, T M; Weinberger, D R; Schalkwyk, L; Lunnon, K; Mill, J; Cohen, H; Yehuda, R; Baker, D G; Maihofer, A X; Nievergelt, C M; Geuze, E; Boks, M P M

2018-05-01

In order to determine the impact of the epigenetic response to traumatic stress on post-traumatic stress disorder (PTSD), this study examined longitudinal changes of genome-wide blood DNA methylation profiles in relation to the development of PTSD symptoms in two prospective military cohorts (one discovery and one replication data set). In the first cohort consisting of male Dutch military servicemen (n=93), the emergence of PTSD symptoms over a deployment period to a combat zone was significantly associated with alterations in DNA methylation levels at 17 genomic positions and 12 genomic regions. Evidence for mediation of the relation between combat trauma and PTSD symptoms by longitudinal changes in DNA methylation was observed at several positions and regions. Bioinformatic analyses of the reported associations identified significant enrichment in several pathways relevant for symptoms of PTSD. Targeted analyses of the significant findings from the discovery sample in an independent prospective cohort of male US marines (n=98) replicated the observed relation between decreases in DNA methylation levels and PTSD symptoms at genomic regions in ZFP57, RNF39 and HIST1H2APS2. Together, our study pinpoints three novel genomic regions where longitudinal decreases in DNA methylation across the period of exposure to combat trauma marks susceptibility for PTSD.

A fusion of minicircle DNA and nanoparticle delivery technologies facilitates therapeutic genetic engineering of autologous canine olfactory mucosal cells.

PubMed

Delaney, Alexander M; Adams, Christopher F; Fernandes, Alinda R; Al-Shakli, Arwa F; Sen, Jon; Carwardine, Darren R; Granger, Nicolas; Chari, Divya M

2017-06-29

Olfactory ensheathing cells (OECs) promote axonal regeneration and improve locomotor function when transplanted into the injured spinal cord. A recent clinical trial demonstrated improved motor function in domestic dogs with spinal injury following autologous OEC transplantation. Their utility in canines offers promise for human translation, as dogs are comparable to humans in terms of clinical management and genetic/environmental variation. Moreover, the autologous, minimally invasive derivation of OECs makes them viable for human spinal injury investigation. Genetic engineering of transplant populations may augment their therapeutic potential, but relies heavily on viral methods which have several drawbacks for clinical translation. We present here the first proof that magnetic particles deployed with applied magnetic fields and advanced DNA minicircle vectors can safely bioengineer OECs to secrete a key neurotrophic factor, with an efficiency approaching that of viral vectors. We suggest that our alternative approach offers high translational potential for the delivery of augmented clinical cell therapies.

Cross-shore and Vertical Distributions of Invertebrate Larvae Using Autonomous Sampling Coupled with Genetic Analysis

NASA Astrophysics Data System (ADS)

Govindarajan, A.; Pineda, J.; Purcell, M.; Tradd, K.; Packard, G.; Girard, A.; Dennett, M.; Breier, J. A., Jr.

2016-02-01

We present a new method to estimate the distribution of invertebrate larvae relative to environmental variables such as temperature, salinity, and circulation. A large volume in situ filtering system developed for discrete biogeochemical sampling in the deep-sea (the Suspended Particulate Rosette "SUPR" multisampler) was mounted to the autonomous underwater vehicle REMUS 600 for coastal larval and environmental sampling. We describe the results of SUPR-REMUS deployments conducted in Buzzards Bay, Massachusetts (2014) and west of Martha's Vineyard, Massachusetts (2015). We collected discrete samples cross-shore and from surface, middle, and bottom layers of the water column. Samples were preserved for DNA analysis. Our Buzzards Bay deployment targeted barnacle larvae, which are abundant in late winter and early spring. For these samples, we used morphological analysis and DNA barcodes generated by Sanger sequencing to obtain stage and species-specific cross-shore and vertical distributions. We targeted bivalve larvae in our 2015 deployments, and genetic analysis of larvae from these samples is underway. For these samples, we are comparing species barcode data derived from traditional Sanger sequencing of individuals to those obtained from next generation sequencing (NGS) of bulk plankton samples. Our results demonstrate the utility of autonomous sampling combined with DNA barcoding for studying larval distributions and transport dynamics.

Real-Time Label-Free Direct Electronic Monitoring of Topoisomerase Enzyme Binding Kinetics on Graphene.

PubMed

Zuccaro, Laura; Tesauro, Cinzia; Kurkina, Tetiana; Fiorani, Paola; Yu, Hak Ki; Knudsen, Birgitta R; Kern, Klaus; Desideri, Alessandro; Balasubramanian, Kannan

2015-11-24

Monolayer graphene field-effect sensors operating in liquid have been widely deployed for detecting a range of analyte species often under equilibrium conditions. Here we report on the real-time detection of the binding kinetics of the essential human enzyme, topoisomerase I interacting with substrate molecules (DNA probes) that are immobilized electrochemically on to monolayer graphene strips. By monitoring the field-effect characteristics of the graphene biosensor in real-time during the enzyme-substrate interactions, we are able to decipher the surface binding constant for the cleavage reaction step of topoisomerase I activity in a label-free manner. Moreover, an appropriate design of the capture probes allows us to distinctly follow the cleavage step of topoisomerase I functioning in real-time down to picomolar concentrations. The presented results are promising for future rapid screening of drugs that are being evaluated for regulating enzyme activity.

Using SDS-PAGE gel fingerprinting to identify soft-bodied wood-boring insect larvae to species.

PubMed

O'Neill, Mark A; Denos, Mia; Reed, Daniel

2018-03-01

This paper describes the progress that we have made in assessing the feasibility of 'fingerprinting' using imaged SDS-PAGE gels of haemolymph proteins, to identify soft-bodied wood-boring insect larvae such as the Asian longhorn beetle, Anoplophora glabripennis (Motscholsky, 1853) (Coleoptera: Cerambycidae). Because of stringent import restrictions and difficulty in obtaining licences to work with these organisms, we opted to work with four species of scarab beetle, Mecynorhina polyphemus (Fabricius, 1781), Pachnoda sinuata (Fabricius, 1775), Eucidella shiratica (Csiki, 1909) and Eucidella shultzeorum (Kolbe, 1906) which have near identical larval morphologies. We show that this technology when combined with an advanced pattern matching system (Digital Automated Identification SYstem - DAISY) can classify soft-bodied insect larvae that are almost identical morphologically to species at a level of accuracy is in excess of 98%. The study also indicates that the technology copes well with noisy data and small training sets. The experience gained in undertaking this study gives us confidence that we will be able to develop a field deployable system in the medium term. We believe that as a high-throughput identification tool, this technology is superior to competitor technologies (e.g. fingerprinting of imaged DNA gels) in terms of speed, cost and ease of use; and therefore, is suitable for low-cost deployment in the field. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

DNA-based identification of invasive alien species in relation to Canadian federal policy and law, and the basis of rapid-response management.

PubMed

Thomas, Vernon G; Hanner, Robert H; Borisenko, Alex V

2016-11-01

Managing invasive alien species in Canada requires reliable taxonomic identification as the basis of rapid-response management. This can be challenging, especially when organisms are small and lack morphological diagnostic features. DNA-based techniques, such as DNA barcoding, offer a reliable, rapid, and inexpensive toolkit for taxonomic identification of individual or bulk samples, forensic remains, and even environmental DNA. Well suited for this requirement, they could be more broadly deployed and incorporated into the operating policy and practices of Canadian federal departments and should be authorized under these agencies' articles of law. These include Fisheries and Oceans Canada, Canadian Food Inspection Agency, Transport Canada, Environment Canada, Parks Canada, and Health Canada. These efforts should be harmonized with the appropriate provisions of provincial jurisdictions, for example, the Ontario Invasive Species Act. This approach necessitates that a network of accredited, certified laboratories exists, and that updated DNA reference libraries are readily accessible. Harmonizing this approach is vital among Canadian federal agencies, and between the federal and provincial levels of government. Canadian policy and law must also be harmonized with that of the USA when detecting, and responding to, invasive species in contiguous lands and waters. Creating capacity in legislation for use of DNA-based identifications brings the authority to fund, train, deploy, and certify staff, and to refine further developments in this molecular technology.

High-frequency field-deployable isotope analyzer for hydrological applications

Treesearch

Elena S.F. Berman; Manish Gupta; Chris Gabrielli; Tina Garland; Jeffrey J. McDonnell

2009-01-01

A high-frequency, field-deployable liquid water isotope analyzer was developed. The instrument was deployed for 4 contiguous weeks in the H. J. Andrews Experimental Forest Long-term Ecological Research site in western Oregon, where it was used for real-time measurement of the isotope ratios of precipitation and stream water during three large storm events. We were able...

Longitudinal changes of telomere length and epigenetic age related to traumatic stress and post-traumatic stress disorder.

PubMed

Boks, Marco P; van Mierlo, Hans C; Rutten, Bart P F; Radstake, Timothy R D J; De Witte, Lot; Geuze, Elbert; Horvath, Steve; Schalkwyk, Leonard C; Vinkers, Christiaan H; Broen, Jasper C A; Vermetten, Eric

2015-01-01

Several studies have reported an association between traumatic stress and telomere length suggesting that traumatic stress has an impact on ageing at the cellular level. A newly derived tool provides an additional means to investigate cellular ageing by estimating epigenetic age based on DNA methylation profiles. We therefore hypothesise that in a longitudinal study of traumatic stress both indicators of cellular ageing will show increased ageing. We expect that particularly in individuals that developed symptoms of post-traumatic stress disorder (PTSD) increases in these ageing parameters would stand out. From an existing longitudinal cohort study, ninety-six male soldiers were selected based on trauma exposure and the presence of symptoms of PTSD. All military personnel were deployed in a combat zone in Afghanistan and assessed before and 6 months after deployment. The Self-Rating Inventory for PTSD was used to measure the presence of PTSD symptoms, while exposure to combat trauma during deployment was measured with a 19-item deployment experiences checklist. These groups did not differ for age, gender, alcohol consumption, cigarette smoking, military rank, length, weight, or medication use. In DNA from whole blood telomere length was measured and DNA methylation levels were assessed using the Illumina 450K DNA methylation arrays. Epigenetic ageing was estimated using the DNAm age estimator procedure. The association of trauma with telomere length was in the expected direction but not significant (B=-10.2, p=0.52). However, contrary to our expectations, development of PTSD symptoms was associated with the reverse process, telomere lengthening (B=1.91, p=0.018). In concordance, trauma significantly accelerated epigenetic ageing (B=1.97, p=0.032) and similar to the findings in telomeres, development of PTSD symptoms was inversely associated with epigenetic ageing (B=-0.10, p=0.044). Blood cell count, medication and premorbid early life trauma exposure did not confound the results. Overall, in this longitudinal study of military personnel deployed to Afghanistan we show an acceleration of ageing by trauma. However, development of PTSD symptoms was associated with telomere lengthening and reversed epigenetic ageing. These findings warrant further study of a perhaps dysfunctional compensatory cellular ageing reversal in PTSD. Copyright © 2014 Elsevier Ltd. All rights reserved.

Electromagnetic panel deployment and retraction using the geomagnetic field in LEO satellite missions

NASA Astrophysics Data System (ADS)

Inamori, Takaya; Sugawara, Yoshiki; Satou, Yasutaka

2015-12-01

Increasingly, spacecraft are installed with large-area structures that are extended and deployed post-launch. These extensible structures have been applied in several missions for power generation, thermal radiation, and solar propulsion. Here, we propose a deployment and retraction method using the electromagnetic force generated when the geomagnetic field interacts with electric current flowing on extensible panels. The panels are installed on a satellite in low Earth orbit. Specifically, electrical wires placed on the extensible panels generate magnetic moments, which interfere with the geomagnetic field. The resulting repulsive and retraction forces enable panel deployment and retraction. In the proposed method, a satellite realizes structural deployment using simple electrical wires. Furthermore, the satellite can achieve not only deployment but also retraction for avoiding damage from space debris and for agile attitude maneuvers. Moreover, because the proposed method realizes quasi-static deployment and the retraction of panels by electromagnetic forces, low impulsive force is exerted on fragile panels. The electrical wires can also be used to detect the panel deployment and retraction and generate a large magnetic moment for attitude control. The proposed method was assessed in numerical simulations based on multibody dynamics. Simulation results shows that a small cubic satellite with a wire current of 25 AT deployed 4 panels (20 cm × 20 cm) in 500 s and retracted 4 panels in 100 s.

A simple method for verifying the deployment of the TOMS-EP solar arrays

NASA Technical Reports Server (NTRS)

Koppersmith, James R.; Ketchum, Eleanor

1995-01-01

The Total Ozone Mapping Spectrometer-Earth Probe (TOMS-EP) mission relies upon a successful deployment of the spacecraft's solar arrays. Several methods of verification are being employed to ascertain the solar array deployment status, with each requiring differing amounts of data. This paper describes a robust attitude-independent verification method that utilizes telemetry from the coarse Sun sensors (CSS's) and the three-axis magnetometers (TAM's) to determine the solar array deployment status - and it can do so with only a few, not necessarily contiguous, points of data. The method developed assumes that the solar arrays are deployed. Telemetry data from the CSS and TAM are converted to the Sun and magnetic field vectors in spacecraft body coordinates, and the angle between them is calculated. Deployment is indicated if this angle is within a certain error tolerance of the angle between the reference Sun and magnetic field vectors. Although several other methods can indicate a non-deployed state, with this method there is a 70% confidence level in confirming deployment as well as a nearly 100% certainty in confirming a non-deployed state. In addition, the spacecraft attitude (which is not known during the first orbit after launch) is not needed for this algorithm because the angle between the Sun and magnetic field vectors is independent of the spacecraft attitude. This technique can be applied to any spacecraft with a TAM and with CSS's mounted on the solar array(s).

Sensitive Detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by Loop-Mediated Isothermal Amplification

PubMed Central

Lang, Jillian M.; Langlois, Paul; Nguyen, Marian Hanna R.; Triplett, Lindsay R.; Purdie, Laura; Holton, Timothy A.; Djikeng, Appolinaire; Vera Cruz, Casiana M.; Verdier, Valérie

2014-01-01

Molecular diagnostics for crop diseases can enhance food security by enabling the rapid identification of threatening pathogens and providing critical information for the deployment of disease management strategies. Loop-mediated isothermal amplification (LAMP) is a PCR-based tool that allows the rapid, highly specific amplification of target DNA sequences at a single temperature and is thus ideal for field-level diagnosis of plant diseases. We developed primers highly specific for two globally important rice pathogens, Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB) disease, and X. oryzae pv. oryzicola, the causal agent of bacterial leaf streak disease (BLS), for use in reliable, sensitive LAMP assays. In addition to pathovar distinction, two assays that differentiate X. oryzae pv. oryzae by African or Asian lineage were developed. Using these LAMP primer sets, the presence of each pathogen was detected from DNA and bacterial cells, as well as leaf and seed samples. Thresholds of detection for all assays were consistently 104 to 105 CFU ml−1, while genomic DNA thresholds were between 1 pg and 10 fg. Use of the unique sequences combined with the LAMP assay provides a sensitive, accurate, rapid, simple, and inexpensive protocol to detect both BB and BLS pathogens. PMID:24837384

Optimization of multiplexed PCR on an integrated microfluidic forensic platform for rapid DNA analysis.

PubMed

Estes, Matthew D; Yang, Jianing; Duane, Brett; Smith, Stan; Brooks, Carla; Nordquist, Alan; Zenhausern, Frederic

2012-12-07

This study reports the design, prototyping, and assay development of multiplexed polymerase chain reaction (PCR) on a plastic microfluidic device. Amplification of 17 DNA loci is carried out directly on-chip as part of a system for continuous workflow processing from sample preparation (SP) to capillary electrophoresis (CE). For enhanced performance of on-chip PCR amplification, improved control systems have been developed making use of customized Peltier assemblies, valve actuators, software, and amplification chemistry protocols. Multiple enhancements to the microfluidic chip design have been enacted to improve the reliability of sample delivery through the various on-chip modules. This work has been enabled by the encapsulation of PCR reagents into a solid phase material through an optimized Solid Phase Encapsulating Assay Mix (SPEAM) bead-based hydrogel fabrication process. SPEAM bead technology is reliably coupled with precise microfluidic metering and dispensing for efficient amplification and subsequent DNA short tandem repeat (STR) fragment analysis. This provides a means of on-chip reagent storage suitable for microfluidic automation, with the long shelf-life necessary for point-of-care (POC) or field deployable applications. This paper reports the first high quality 17-plex forensic STR amplification from a reference sample in a microfluidic chip with preloaded solid phase reagents, that is designed for integration with up and downstream processing.

Computer-aided dispatch--traffic management center field operational test final detailed test plan : WSDOT deployment

DOT National Transportation Integrated Search

2003-10-01

The purpose of this document is to expand upon the evaluation components presented in "Computer-aided dispatch--traffic management center field operational test final evaluation plan : WSDOT deployment". This document defines the objective, approach,...

Personalized medicine in human space flight: using Omics based analyses to develop individualized countermeasures that enhance astronaut safety and performance.

PubMed

Schmidt, Michael A; Goodwin, Thomas J

2013-01-01

Space flight is one of the most extreme conditions encountered by humans. Advances in Omics methodologies (genomics, transcriptomics, proteomics, and metabolomics) have revealed that unique differences exist between individuals. These differences can be amplified in extreme conditions, such as space flight. A better understanding of individual differences may allow us to develop personalized countermeasure packages that optimize the safety and performance of each astronaut. In this review, we explore the role of "Omics" in advancing our ability to: (1) more thoroughly describe the biological response of humans in space; (2) describe molecular attributes of individual astronauts that alter the risk profile prior to entering the space environment; (3) deploy Omics techniques in the development of personalized countermeasures; and (4) develop a comprehensive Omics-based assessment and countermeasure platform that will guide human space flight in the future. In this review, we advance the concept of personalized medicine in human space flight, with the goal of enhancing astronaut safety and performance. Because the field is vast, we explore selected examples where biochemical individuality might significantly impact countermeasure development. These include gene and small molecule variants associated with: (1) metabolism of therapeutic drugs used in space; (2) one carbon metabolism and DNA stability; (3) iron metabolism, oxidative stress and damage, and DNA stability; and (4) essential input (Mg and Zn) effects on DNA repair. From these examples, we advance the case that widespread Omics profiling should serve as the foundation for aerospace medicine and research, explore methodological considerations to advance the field, and suggest why personalized medicine may become the standard of care for humans in space.

Design of Mechanisms for Deployable, Optical Instruments: Guidelines for Reducing Hysteresis

NASA Technical Reports Server (NTRS)

Lake, Mark S.; Hachkowski, M. Roman

2000-01-01

This paper is intended to facilitate the development of deployable, optical instruments by providing a rational approach for the design, testing, and qualification of high-precision (i.e., low-hysteresis) deployment mechanisms for these instruments. Many of the guidelines included herein come directly from the field of optomechanical engineering, and are, therefore, neither newly developed guidelines, nor are they uniquely applicable to the design of high-precision deployment mechanisms. This paper is to be regarded as a guide to design and not a set of NASA requirements, except as may be defined in formal project specifications. Furthermore, due to the rapid pace of advancement in the field of precision deployment, this paper should be regarded as a preliminary set of guidelines. However, it is expected that this paper, with revisions as experience may indicate to be desirable, might eventually form the basis for a set of uniform design requirements for high-precision deployment mechanisms on future NASA space-based science instruments.

Simple Technique for in Field Samples Collection in the Cases of Skin Rash Illness and Subsequent PCR Detection of Orthopoxviruses and Varicella Zoster Virus

PubMed Central

Magazani, Edmond K.; Garin, Daniel; Muyembe, Jean-Jacques T.; Bentahir, Mostafa; Gala, Jean-Luc

2014-01-01

Background In case of outbreak of rash illness in remote areas, clinically discriminating monkeypox (MPX) from severe form of chickenpox and from smallpox remains a concern for first responders. Objective The goal of the study was therefore to use MPX and chickenpox outbreaks in Democratic Republic of Congo (DRC) as a test case for establishing a rapid and specific diagnosis in affected remote areas. Methods In 2008 and 2009, successive outbreaks of presumed MPX skin rash were reported in Bena Tshiadi, Yangala and Ndesha healthcare districts of the West Kasai province (DRC). Specimens consisting of liquid vesicle dried on filter papers or crusted scabs from healing patients were sampled by first responders. A field analytical facility was deployed nearby in order to carry out a real-time PCR (qPCR) assay using genus consensus primers, consensus orthopoxvirus (OPV) and smallpox-specific probes spanning over the 14 kD fusion protein encoding gene. A PCR-restriction fragment length polymorphism was used on-site as backup method to confirm the presence of monkeypox virus (MPXV) in samples. To complete the differential diagnosis of skin rash, chickenpox was tested in parallel using a commercial qPCR assay. In a post-deployment step, a MPXV-specific pyrosequencing was carried out on all biotinylated amplicons generated on-site in order to confirm the on-site results. Results Whereas MPXV proved to be the agent causing the rash illness outbreak in the Bena Tshiadi, VZV was the causative agent of the disease in Yangala and Ndesha districts. In addition, each on-site result was later confirmed by MPXV-specific pyrosequencing analysis without any discrepancy. Conclusion This experience of rapid on-site dual use DNA-based differential diagnosis of rash illnesses demonstrates the potential of combining tests specifically identifying bioterrorism agents and agents causing natural outbreaks. This opens the way to rapid on-site DNA-based identification of a broad spectrum of causative agents in remote areas. PMID:24841633

Performance characteristics of a low-cost, field-deployable miniature CCD spectrometer

PubMed Central

Coles, Simon; Nimmo, Malcolm; Worsfold, Paul J.

2000-01-01

Miniature spectrometers incorporating array detectors are becoming a viable, low-cost option for field and process deployments. The performance characteristics of one such instrument are reported and compared with those of a conventional benchtop instrument. The parameters investigated were wavelength repeatability, photometric linearity, instrumental noise (photometric precision) and instrumental drift. PMID:18924863

Using SPMDs To Assess Natural Recovery Of PCB-Contaminated Sediments In Lake Hartwell, SC: I. A Field Test Of New In-Situ Deployment Methods

EPA Science Inventory

Results from the field testing of some innovative sampling methods developed to evaluate risk management strategies for polychlorinated biphenyl (PCB) contaminated sediments are presented. Semipermeable membrane devices (SPMDs) were combined with novel deployment methods to quan...

Development of field-deployable instrumentation based on “antigen–antibody” reactions for detection of hemorrhagic disease in ruminants

USDA-ARS?s Scientific Manuscript database

Development of field-deployable methodology utilizing antigen–antibody reactions and the surface Plasmon resonance (SPR) effect to provide a rapid diagnostic test for recognition of the blue tongue virus (BTV) and epizootic hemorrhage disease virus (EHDV) in wild and domestic ruminants is reported. ...

Microspacecraft and Earth observation: Electrical field (ELF) measurement project

NASA Technical Reports Server (NTRS)

Olsen, Tanya; Elkington, Scot; Parker, Scott; Smith, Grover; Shumway, Andrew; Christensen, Craig; Parsa, Mehrdad; Larsen, Layne; Martinez, Ranae; Powell, George

1990-01-01

The Utah State University space system design project for 1989 to 1990 focuses on the design of a global electrical field sensing system to be deployed in a constellation of microspacecraft. The design includes the selection of the sensor and the design of the spacecraft, the sensor support subsystems, the launch vehicle interface structure, on board data storage and communications subsystems, and associated ground receiving stations. Optimization of satellite orbits and spacecraft attitude are critical to the overall mapping of the electrical field and, thus, are also included in the project. The spacecraft design incorporates a deployable sensor array (5 m booms) into a spinning oblate platform. Data is taken every 0.1 seconds by the electrical field sensors and stored on-board. An omni-directional antenna communicates with a ground station twice per day to down link the stored data. Wrap-around solar cells cover the exterior of the spacecraft to generate power. Nine Pegasus launches may be used to deploy fifty such satellites to orbits with inclinations greater than 45 deg. Piggyback deployment from other launch vehicles such as the DELTA 2 is also examined.

Designing DNA nanodevices for compatibility with the immune system of higher organisms

NASA Astrophysics Data System (ADS)

Surana, Sunaina; Shenoy, Avinash R.; Krishnan, Yamuna

2015-09-01

DNA is proving to be a powerful scaffold to construct molecularly precise designer DNA devices. Recent trends reveal their ever-increasing deployment within living systems as delivery devices that not only probe but also program and re-program a cell, or even whole organisms. Given that DNA is highly immunogenic, we outline the molecular, cellular and organismal response pathways that designer nucleic acid nanodevices are likely to elicit in living systems. We address safety issues applicable when such designer DNA nanodevices interact with the immune system. In light of this, we discuss possible molecular programming strategies that could be integrated with such designer nucleic acid scaffolds to either evade or stimulate the host response with a view to optimizing and widening their applications in higher organisms.

Integrated Incident Management System (IIMS) web client application development, deployment and evaluation Staten Island (SI) demonstration project : final report.

DOT National Transportation Integrated Search

2015-09-27

This evaluation report provides background on the development and findings. The aim of the UTRC project was to develop and : deploy Portable IIMS based on Smartphone web applications. Previously, traditional IIMS was deployed in the field vehicles : ...

Longitudinal changes in glucocorticoid receptor exon 1F methylation and psychopathology after military deployment

PubMed Central

Schür, R R; Boks, M P; Rutten, B P F; Daskalakis, N P; de Nijs, L; van Zuiden, M; Kavelaars, A; Heijnen, C J; Joëls, M; Kahn, R S; Geuze, E; Vermetten, E; Vinkers, C H

2017-01-01

Several cross-sectional studies have demonstrated the relevance of DNA methylation of the glucocorticoid receptor exon 1F region (GR-1F) for trauma-related psychopathology. We conducted a longitudinal study to examine GR-1F methylation changes over time in relation to trauma exposure and the development of post-deployment psychopathology. GR-1F methylation (52 loci) was quantified using pyrosequencing in whole blood of 92 military men 1 month before and 6 months after a 4-month deployment period to Afghanistan. GR-1F methylation overall (mean methylation and the number of methylated loci) and functional methylation (methylation at loci associated with GR exon 1F expression) measures were examined. We first investigated the effect of exposure to potentially traumatic events during deployment on these measures. Subsequently, changes in GR-1F methylation were related to changes in mental health problems (total Symptom Checklist-90 score) and posttraumatic stress disorder (PTSD) symptoms (Self-Report Inventory for PTSD). Trauma exposure during deployment was associated with an increase in all methylation measures, but development of mental health problems 6 months after deployment was only significantly associated with an increased functional methylation. Emergence of post-deployment PTSD symptoms was not related to increased functional methylation over time. Pre-deployment methylation levels did not predict post-deployment psychopathology. To our knowledge, this is the first study to prospectively demonstrate trauma-related increases in GR-1F methylation, and it shows that only increases at specific functionally relevant sites predispose for post-deployment psychopathology. PMID:28742078

Loop-mediated isothermal DNA amplification for asymptomatic malaria detection in challenging field settings: Technical performance and pilot implementation in the Peruvian Amazon

PubMed Central

Serra-Casas, Elisa; Manrique, Paulo; Ding, Xavier C.; Carrasco-Escobar, Gabriel; Alava, Freddy; Gave, Anthony; Rodriguez, Hugo; Contreras-Mancilla, Juan; Rosas-Aguirre, Angel; Speybroeck, Niko; González, Iveth J.

2017-01-01

Background Loop-mediated isothermal DNA amplification (LAMP) methodology offers an opportunity for point-of-care (POC) molecular detection of asymptomatic malaria infections. However, there is still little evidence on the feasibility of implementing this technique for population screenings in isolated field settings. Methods Overall, we recruited 1167 individuals from terrestrial (‘road’) and hydric (‘riverine’) communities of the Peruvian Amazon for a cross-sectional survey to detect asymptomatic malaria infections. The technical performance of LAMP was evaluated in a subgroup of 503 samples, using real-time Polymerase Chain Reaction (qPCR) as reference standard. The operational feasibility of introducing LAMP testing in the mobile screening campaigns was assessed based on field-suitability parameters, along with a pilot POC-LAMP assay in a riverine community without laboratory infrastructure. Results LAMP had a sensitivity of 91.8% (87.7–94.9) and specificity of 91.9% (87.8–95.0), and the overall accuracy was significantly better among samples collected during road screenings than riverine communities (p≤0.004). LAMP-based diagnostic strategy was successfully implemented within the field-team logistics and the POC-LAMP pilot in the riverine community allowed for a reduction in the turnaround time for case management, from 12–24 hours to less than 5 hours. Specimens with haemolytic appearance were regularly observed in riverine screenings and could help explaining the hindered performance/interpretation of the LAMP reaction in these communities. Conclusions LAMP-based molecular malaria diagnosis can be deployed outside of reference laboratories, providing similar performance as qPCR. However, scale-up in remote field settings such as riverine communities needs to consider a number of logistical challenges (e.g. environmental conditions, labour-intensiveness in large population screenings) that can influence its optimal implementation. PMID:28982155

New seismic instrumentation packaged for all terrestrial environments (including the quietest observatories!).

NASA Astrophysics Data System (ADS)

Parker, Tim; Devanney, Peter; Bainbridge, Geoff; Townsend, Bruce

2017-04-01

The march to make every type of seismometer, weak to strong motion, reliable and economically deployable in any terrestrial environment continues with the availability of three new sensors and seismic systems including ones with over 200dB of dynamic range. Until recently there were probably 100 pier type broadband sensors for every observatory type pier, not the types of deployments geoscientists are needing to advance science and monitoring capability. Deeper boreholes are now the recognized quieter environments for best observatory class instruments and these same instruments can now be deployed in direct burial environments which is unprecedented. The experiences of facilities in large deployments of broadband seismometers in continental scale rolling arrays proves the utility of packaging new sensors in corrosion resistant casings and designing in the robustness needed to work reliably in temporary deployments. Integrating digitizers and other sensors decreases deployment complexity, decreases acquisition and deployment costs, increases reliability and utility. We'll discuss the informed evolution of broadband pier instruments into the modern integrated field tools that enable economic densification of monitoring arrays along with supporting new ways to approach geoscience research in a field environment.

Evaluation of advanced air bag deployment algorithm performance using event data recorders.

PubMed

Gabler, Hampton C; Hinch, John

2008-10-01

This paper characterizes the field performance of occupant restraint systems designed with advanced air bag features including those specified in the US Federal Motor Vehicle Safety Standard (FMVSS) No. 208 for advanced air bags, through the use of Event Data Recorders (EDRs). Although advanced restraint systems have been extensively tested in the laboratory, we are only beginning to understand the performance of these systems in the field. Because EDRs record many of the inputs to the advanced air bag control module, these devices can provide unique insights into the characteristics of field performance of air bags. The study was based on 164 advanced air bag cases extracted from NASS/CDS 2002-2006 with associated EDR data. In this dataset, advanced driver air bags were observed to deploy with a 50% probability at a longitudinal delta-V of 9 mph for the first stage, and at 26 mph for both inflator stages. In general, advanced air bag performance was as expected, however, the study identified cases of air bag deployments at delta-Vs as low as 3-4 mph, non-deployments at delta-Vs over 26 mph, and possible delayed air bag deployments.

Evaluation of Advanced Air Bag Deployment Algorithm Performance using Event Data Recorders

PubMed Central

Gabler, Hampton C.; Hinch, John

2008-01-01

This paper characterizes the field performance of occupant restraint systems designed with advanced air bag features including those specified in the US Federal Motor Vehicle Safety Standard (FMVSS) No. 208 for advanced air bags, through the use of Event Data Recorders (EDRs). Although advanced restraint systems have been extensively tested in the laboratory, we are only beginning to understand the performance of these systems in the field. Because EDRs record many of the inputs to the advanced air bag control module, these devices can provide unique insights into the characteristics of field performance of air bags. The study was based on 164 advanced air bag cases extracted from NASS/CDS 2002-2006 with associated EDR data. In this dataset, advanced driver air bags were observed to deploy with a 50% probability at a longitudinal delta-V of 9 mph for the first stage, and at 26 mph for both inflator stages. In general, advanced air bag performance was as expected, however, the study identified cases of air bag deployments at delta-Vs as low as 3-4 mph, non-deployments at delta-Vs over 26 mph, and possible delayed air bag deployments. PMID:19026234

Farm Deployable Microbial Bioreactor for Fuel Ethanol Production

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

Okeke, Benedict

Research was conducted to develop a farm and field deployable microbial bioreactor for bioethanol production from biomass. Experiments were conducted to select the most efficient microorganisms for conversion of plant fiber to sugars for fermentation to ethanol. Mixtures of biomass and surface soil samples were collected from selected sites in Alabama black belt counties (Macon, Sumter, Choctaw, Dallas, Montgomery, Lowndes) and other areas within the state of Alabama. Experiments were conducted to determine the effects of culture parameters on key biomass saccharifying enzymes (cellulase, beta-glucosidase, xylanase and beta-xylosidase). A wide-scale sampling of locally-grown fruits in Central Alabama was embarked tomore » isolate potential xylose fermenting microorganisms. Yeast isolates were evaluated for xylose fermentation. Selected microorganisms were characterized by DNA based methods. Factors affecting enzyme production and biomass saccharification were examined and optimized in the laboratory. Methods of biomass pretreatment were compared. Co-production of amylolytic enzymes with celluloytic-xylanolytic enzymes was evaluated; and co-saccharification of a combination of biomass, and starch-rich materials was examined. Simultaneous saccharification and fermentation with and without pre-saccharifcation was studied. Whole culture broth and filtered culture broth simultaneous saccahrifcation and fermentation were compared. A bioreactor system was designed and constructed to employ laboratory results for scale up of biomass saccharification.« less

The deployment of information systems and information technology in field hospitals.

PubMed

Crowe, Ian R J; Naguib, Raouf N G

2010-01-01

Information systems and related technologies continue to develop and have become an integral part of healthcare provision and hospital care in particular. Field hospitals typically operate in the most austere and difficult of conditions and have yet to fully exploit related technologies. This paper addresses those aspects of healthcare informatics, healthcare knowledge management and lean healthcare that can be applied to field hospitals, with a view to improving patient care. The aim is to provide a vision for the deployment of information systems and information technology in field hospitals, using the British Army's field hospital as a representative model.

Training improves reading speed in peripheral vision: is it due to attention?

PubMed

Lee, Hye-Won; Kwon, Miyoung; Legge, Gordon E; Gefroh, Joshua J

2010-06-01

Previous research has shown that perceptual training in peripheral vision, using a letter-recognition task, increases reading speed and letter recognition (S. T. L. Chung, G. E. Legge, & S. H. Cheung, 2004). We tested the hypothesis that enhanced deployment of spatial attention to peripheral vision explains this training effect. Subjects were pre- and post-tested with 3 tasks at 10° above and below fixation-RSVP reading speed, trigram letter recognition (used to construct visual-span profiles), and deployment of spatial attention (measured as the benefit of a pre-cue for target position in a lexical-decision task). Groups of five normally sighted young adults received 4 days of trigram letter-recognition training in upper or lower visual fields, or central vision. A control group received no training. Our measure of deployment of spatial attention revealed visual-field anisotropies; better deployment of attention in the lower field than the upper, and in the lower-right quadrant compared with the other three quadrants. All subject groups exhibited slight improvement in deployment of spatial attention to peripheral vision in the post-test, but this improvement was not correlated with training-related increases in reading speed and the size of visual-span profiles. Our results indicate that improved deployment of spatial attention to peripheral vision does not account for improved reading speed and letter recognition in peripheral vision.

Cable-catenary large antenna concept

NASA Technical Reports Server (NTRS)

Akle, W.

1985-01-01

Deployable to very large diameters (over 1000 ft), while still remaining compatible with a complete satellite system launch by STS, the cable-catenary antenna comprises: 8 radial deployable boom masts; a deployable hub and feed support center mast; balanced front and back, radial and circumferential catenary cabling for highly accurate (mm) surface control; no interfering cabling in the antenna field; and an RF reflecting mesh supported on the front catenaries. Illustrations show the antenna-satellite system deployed and stowed configurations; the antenna deployment sequence; the design analysis logic; the sizing analysis output, and typical parametric design data.

Assessment of DoD’s Central Identification Lab and the Feasibility of Increasing Identification Rates

DTIC Science & Technology

2009-06-01

mtDNA exists in the ancient remains with which the CIL must work . Secondly, mtDNA is wholly maternally inherited as a single unit and allows for...they should be instructed to work for a certain number of days strictly on trying to find maternal -eligible donors. The most important objective of the...In addition to the impact frequent deployments have on the staff’s personal life , impacts on their work in the lab are also significant. First and

Ostreid herpesvirus 1 infection among Pacific oyster (Crassostrea gigas) Spat: relevance of water temperature to virus replication and circulation prior to the onset of mortality.

PubMed

Renault, Tristan; Bouquet, Anne Lise; Maurice, Julien-Thomas; Lupo, Coralie; Blachier, Philippe

2014-09-01

A number of bivalve species worldwide, including the Pacific oyster, Crassostrea gigas, have been affected by mass mortality events associated with herpesviruses, resulting in significant losses. A particular herpesvirus was purified from naturally infected larval Pacific oysters, and its genome was completely sequenced. This virus has been classified as Ostreid herpesvirus 1 (OsHV-1) within the family Malacoherpesviridae. Since 2008, mass mortality outbreaks among C. gigas in Europe have been related to the detection of a variant of OsHV-1 called μVar. Additional data are necessary to better describe mortality events in relation to environmental-parameter fluctuations and OsHV-1 detection. For this purpose, a single batch of Pacific oyster spat was deployed in 4 different locations in the Marennes-Oleron area (France): an oyster pond ("claire"), a shellfish nursery, and two locations in the field. Mortality rates were recorded based on regular observation, and samples were collected to search for and quantify OsHV-1 DNA by real-time PCR. Although similar massive mortality rates were reported at the 4 sites, mortality was detected earlier in the pond and in the nursery than at both field sites. This difference may be related to earlier increases in water temperature. Mass mortality was observed among oysters a few days after increases in the number of PCR-positive oysters and viral-DNA amounts were recorded. An initial increment in the number of PCR-positive oysters was reported at both field sites during the survey in the absence of significant mortality. During this period, the water temperature was below 16°C. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Ostreid Herpesvirus 1 Infection among Pacific Oyster (Crassostrea gigas) Spat: Relevance of Water Temperature to Virus Replication and Circulation Prior to the Onset of Mortality

PubMed Central

Bouquet, Anne Lise; Maurice, Julien-Thomas; Lupo, Coralie; Blachier, Philippe

2014-01-01

A number of bivalve species worldwide, including the Pacific oyster, Crassostrea gigas, have been affected by mass mortality events associated with herpesviruses, resulting in significant losses. A particular herpesvirus was purified from naturally infected larval Pacific oysters, and its genome was completely sequenced. This virus has been classified as Ostreid herpesvirus 1 (OsHV-1) within the family Malacoherpesviridae. Since 2008, mass mortality outbreaks among C. gigas in Europe have been related to the detection of a variant of OsHV-1 called μVar. Additional data are necessary to better describe mortality events in relation to environmental-parameter fluctuations and OsHV-1 detection. For this purpose, a single batch of Pacific oyster spat was deployed in 4 different locations in the Marennes-Oleron area (France): an oyster pond (“claire”), a shellfish nursery, and two locations in the field. Mortality rates were recorded based on regular observation, and samples were collected to search for and quantify OsHV-1 DNA by real-time PCR. Although similar massive mortality rates were reported at the 4 sites, mortality was detected earlier in the pond and in the nursery than at both field sites. This difference may be related to earlier increases in water temperature. Mass mortality was observed among oysters a few days after increases in the number of PCR-positive oysters and viral-DNA amounts were recorded. An initial increment in the number of PCR-positive oysters was reported at both field sites during the survey in the absence of significant mortality. During this period, the water temperature was below 16°C. PMID:24973071

Detection of an enigmatic plethodontid Salamander using Environmental DNA

USGS Publications Warehouse

Pierson, Todd W.; Mckee, Anna; Spear, Stephen F.; Maerz, John C.; Camp, Carlos D.; Glenn, Travis C.

2016-01-01

The isolation and identification of environmental DNA (eDNA) offers a non-invasive and efficient method for the detection of rare and secretive aquatic wildlife, and it is being widely integrated into inventory and monitoring efforts. The Patch-Nosed Salamander (Urspelerpes brucei) is a tiny, recently discovered species of plethodontid salamander known only from headwater streams in a small region of Georgia and South Carolina. Here, we present results of a quantitative PCR-based eDNA assay capable of detecting Urspelerpes in more than 75% of 33 samples from five confirmed streams. We deployed the method at 31 additional streams and located three previously undocumented populations of Urspelerpes. We compare the results of our eDNA assay with our attempt to use aquatic leaf litterbags for the rapid detection of Urspelerpes and demonstrate the relative efficacy of the eDNA assay. We suggest that eDNA offers great potential for use in detecting other aquatic and semi-aquatic plethodontid salamanders.

Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways.

PubMed

Bhatia, Dhiraj; Arumugam, Senthil; Nasilowski, Michel; Joshi, Himanshu; Wunder, Christian; Chambon, Valérie; Prakash, Ved; Grazon, Chloé; Nadal, Brice; Maiti, Prabal K; Johannes, Ludger; Dubertret, Benoit; Krishnan, Yamuna

2016-12-01

Functionalization of quantum dots (QDs) with a single biomolecular tag using traditional approaches in bulk solution has met with limited success. DNA polyhedra consist of an internal void bounded by a well-defined three-dimensional structured surface. The void can house cargo and the surface can be functionalized with stoichiometric and spatial precision. Here, we show that monofunctionalized QDs can be realized by encapsulating QDs inside DNA icosahedra and functionalizing the DNA shell with an endocytic ligand. We deployed the DNA-encapsulated QDs for real-time imaging of three different endocytic ligands-folic acid, galectin-3 (Gal3) and the Shiga toxin B-subunit (STxB). Single-particle tracking of Gal3- or STxB-functionalized QD-loaded DNA icosahedra allows us to monitor compartmental dynamics along endocytic pathways. These DNA-encapsulated QDs, which bear a unique stoichiometry of endocytic ligands, represent a new class of molecular probes for quantitative imaging of endocytic receptor dynamics.

Results of investigation at the Miravalles Geothermal Field, Costa Rica: Part 1, Well logging. Resultados de las investigaciones en el campo geotermico de Miravalles, Costa Rica: Parte 1, Registros de pozos (in EN;SP)

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

Dennis, B.R.; Lawton, R.G.; Kolar, J.D.

The well-logging operations performed in the Miravalles Geothermal Field in Costa Rica were conducted during two separate field trips. The Phase I program provided the deployment of a suite of high-temperature borehole instruments, including the temperature/rabbit, fluid sampler, and three-arm caliper in Well PGM-3. These same tools were deployed in Well PGM-10 along with an additional survey run with a combination fluid velocity/temperature/pressure instrument used to measure thermodynamic properties under flowing well conditions. The Phase II program complemented Phase I with the suite of tools deployed in Wells PGM-5, PGM-11, and PGM-12. 4 refs., 25 figs., 1 tab.

Coping with the challenges of early disaster response: 24 years of field hospital experience after earthquakes.

PubMed

Bar-On, Elhanan; Abargel, Avi; Peleg, Kobi; Kreiss, Yitshak

2013-10-01

To propose strategies and recommendations for future planning and deployment of field hospitals after earthquakes by comparing the experience of 4 field hospitals deployed by The Israel Defense Forces (IDF) Medical Corps in Armenia, Turkey, India and Haiti. Quantitative data regarding the earthquakes were collected from published sources; data regarding hospital activity were collected from IDF records; and qualitative information was obtained from structured interviews with key figures involved in the missions. The hospitals started operating between 89 and 262 hours after the earthquakes. Their sizes ranged from 25 to 72 beds, and their personnel numbered between 34 and 100. The number of patients treated varied from 1111 to 2400. The proportion of earthquake-related diagnoses ranged from 28% to 67% (P < .001), with hospitalization rates between 3% and 66% (P < .001) and surgical rates from 1% to 24% (P < .001). In spite of characteristic scenarios and injury patterns after earthquakes, patient caseload and treatment requirements varied widely. The variables affecting the patient profile most significantly were time until deployment, total number of injured, availability of adjacent medical facilities, and possibility of evacuation from the disaster area. When deploying a field hospital in the early phase after an earthquake, a wide variability in patient caseload should be anticipated. Customization is difficult due to the paucity of information. Therefore, early deployment necessitates full logistic self-sufficiency and operational versatility. Also, collaboration with local and international medical teams can greatly enhance treatment capabilities.

How well could existing sensors detect the deployment of a solar radiation management (SRM) geoengineering effort?

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

Hurd, Alan J.

2016-04-29

While the stated reason for asking this question is “to understand better our ability to warn policy makers in the unlikely event of an unanticipated SRM geoengineering deployment or large-scale field experiment”, my colleagues and I felt that motives would be important context because the scale of any meaningful SRM deployment would be so large that covert deployment seems impossible. However, several motives emerged that suggest a less-than-global effort might be important.

Performance-cost evaluation methodology for ITS equipment deployment

DOT National Transportation Integrated Search

2000-09-01

Although extensive Intelligent Transportation Systems (ITS) technology is being deployed in the field, little analysis is being performed to evaluate the benefits of implementation schemes. Benefit analysis is particularly in need for one popular ITS...

Case study: design and implementation of training for scientists deploying to Ebola diagnostic field laboratories in Sierra Leone: October 2014 to February 2016

PubMed Central

Lewis, Suzanna M.; Lansley, Amber; Fraser, Sara; Shieber, Clare; Shah, Sonal; Semper, Amanda; Bailey, Daniel; Busuttil, Jason; Evans, Liz; Carroll, Miles W.; Silman, Nigel J.; Brooks, Tim; Shallcross, Jane A.

2017-01-01

As part of the UK response to the 2013–2016 Ebola virus disease (EVD) epidemic in West Africa, Public Health England (PHE) were tasked with establishing three field Ebola virus (EBOV) diagnostic laboratories in Sierra Leone by the UK Department for International Development (DFID). These provided diagnostic support to the Ebola Treatment Centre (ETC) facilities located in Kerry Town, Makeni and Port Loko. The Novel and Dangerous Pathogens (NADP) Training group at PHE, Porton Down, designed and implemented a pre-deployment Ebola diagnostic laboratory training programme for UK volunteer scientists being deployed to the PHE EVD laboratories. Here, we describe the training, workflow and capabilities of these field laboratories for use in response to disease epidemics and in epidemiological surveillance. We discuss the training outcomes, the laboratory outputs, lessons learned and the legacy value of the support provided. We hope this information will assist in the recruitment and training of staff for future responses and in the design and implementation of rapid deployment diagnostic field laboratories for future outbreaks of high consequence pathogens. This article is part of the themed issue ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’. PMID:28396470

DNA-programmable multiplexing for scalable, renewable redox protein bio-nanoelectronics.

PubMed

Withey, Gary D; Kim, Jin Ho; Xu, Jimmy

2008-11-01

A universal, site-addressable DNA linking strategy is deployed for the programmable assembly of multifunctional, long-lasting redox protein nanoelectronic devices. This addressable linker, the first incorporated into a redox enzyme-nanoelectronic system, promotes versatility and renewability by allowing the reconfiguration and replacement of enzymes at will. The linker is transferable to all redox proteins due to the simple conjugation chemistry involved. The efficacy of this linking strategy is assessed using two model enzymes, glucose oxidase (GOx) and alcohol dehydrogenase (ADH), self-assembled onto separate nanoelectrode regions comprised of a highly ordered carbon nanotube (CNT) array. The sequence-specificity of DNA hybridization provides the means of encoding spatial address to the self-assembling process that conjugates enzymes tagged with single-stranded DNA (ssDNA) to the tips of designated CNTs functionalized with the complementary strands. In this study, we demonstrate the feasibility of multiplexed, scalable, reconfigurable and renewable transduction of redox protein signals by virtue of DNA addressing.

MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs

PubMed Central

Gaultier, Nicolas Paul Eugène; Miller, Dana; Purbojati, Rikky Wenang; Lauro, Federico M.

2017-01-01

Abstract Background: As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. Findings: MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. Conclusions: MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers. PMID:28430964

MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs.

PubMed

Heinle, Cassie Elizabeth; Gaultier, Nicolas Paul Eugène; Miller, Dana; Purbojati, Rikky Wenang; Lauro, Federico M

2017-06-01

As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers. © The Authors 2017. Published by Oxford University Press.

The impact of time and field conditions on brown bear (Ursus arctos) faecal DNA amplification

USGS Publications Warehouse

Murphy, M.A.; Kendall, K.C.; Robinson, A.; Waits, L.P.

2007-01-01

To establish longevity of faecal DNA samples under varying summer field conditions, we collected 53 faeces from captive brown bears (Ursus arctos) on a restricted vegetation diet. Each faeces was divided, and one half was placed on a warm, dry field site while the other half was placed on a cool, wet field site on Moscow Mountain, Idaho, USA. Temperature, relative humidity, and dew point data were collected on each site, and faeces were sampled for DNA extraction at <1, 3, 6, 14, 30, 45, and 60 days. Faecal DNA sample viability was assessed by attempting PCR amplification of a mitochondrial DNA (mtDNA) locus (???150 bp) and a nuclear DNA (nDNA) microsatellite locus (180-200 bp). Time in the field, temperature, and dew point impacted mtDNA and nDNA amplification success with the greatest drop in success rates occurring between 1 and 3 days. In addition, genotyping errors significantly increased over time at both field sites. Based on these results, we recommend collecting samples at frequent transect intervals and focusing sampling efforts during drier portions of the year when possible. ?? 2007 Springer Science+Business Media, Inc.

Mechanism Design Principle for Optical-Precision, Deployable Instruments

NASA Technical Reports Server (NTRS)

Lake, Mark S.; Hachkowski, M. Roman

2000-01-01

The present paper is intended to be a guide for the design of 'microdynamically quiet' deployment mechanisms for optical-precision structures, such as deployable telescope mirrors and optical benches. Many of the guidelines included herein come directly from the field of optomechanical engineering, and are neither newly developed guidelines nor are they uniquely applicable to high-precision deployment mechanisms. However, the application of these guidelines to the design of deployment mechanisms is a rather new practice, so efforts are made herein to illustrate the process through the discussion of specific examples. The present paper summarizes a more extensive set of design guidelines for optical-precision mechanisms that are under development.

Electrophoretic and field-effect graphene for all-electrical DNA array technology.

PubMed

Xu, Guangyu; Abbott, Jeffrey; Qin, Ling; Yeung, Kitty Y M; Song, Yi; Yoon, Hosang; Kong, Jing; Ham, Donhee

2014-09-05

Field-effect transistor biomolecular sensors based on low-dimensional nanomaterials boast sensitivity, label-free operation and chip-scale construction. Chemical vapour deposition graphene is especially well suited for multiplexed electronic DNA array applications, since its large two-dimensional morphology readily lends itself to top-down fabrication of transistor arrays. Nonetheless, graphene field-effect transistor DNA sensors have been studied mainly at single-device level. Here we create, from chemical vapour deposition graphene, field-effect transistor arrays with two features representing steps towards multiplexed DNA arrays. First, a robust array yield--seven out of eight transistors--is achieved with a 100-fM sensitivity, on par with optical DNA microarrays and at least 10 times higher than prior chemical vapour deposition graphene transistor DNA sensors. Second, each graphene acts as an electrophoretic electrode for site-specific probe DNA immobilization, and performs subsequent site-specific detection of target DNA as a field-effect transistor. The use of graphene as both electrode and transistor suggests a path towards all-electrical multiplexed graphene DNA arrays.

Rapidly deployable emergency communication system

DOEpatents

Gladden, Charles A.; Parelman, Martin H.

1979-01-01

A highly versatile, highly portable emergency communication system which permits deployment in a very short time to cover both wide areas and distant isolated areas depending upon mission requirements. The system employs a plurality of lightweight, fully self-contained repeaters which are deployed within the mission area to provide communication between field teams, and between each field team and a mobile communication control center. Each repeater contains a microcomputer controller, the program for which may be changed from the control center by the transmission of digital data within the audible range (300-3,000 Hz). Repeaters are accessed by portable/mobile transceivers, other repeaters, and the control center through the transmission and recognition of digital data code words in the subaudible range.

Venomous adversaries: a reference to snake identification, field safety, and bite-victim first aid for disaster-response personnel deploying into the hurricane-prone regions of North America.

PubMed

Wozniak, Edward J; Wisser, John; Schwartz, Michael

2006-01-01

Each hurricane season, emergency-preparedness deployment teams including but not limited to the Office of Force Readiness and Deployment of the US Public Health Service, Federal Emergency Management Agency, Deployment Medical Assistance Teams, Veterinary Medical Assistance Teams, and the US Army and Air Force National Guard are at risk for deploying into hurricane-stricken areas that harbor indigenous hazards, including those posed by venomous snakes. North America is home to 2 distinct families of venomous snakes: 1) Viperidae, which includes the rattlesnakes, copperheads, and cottonmouths; and 2) Elapidae, in which the only native species are the coral snakes. Although some of these snakes are easily identified, some are not, and many rank among the most feared and misunderstood animals. This article specifically addresses all the native species of venomous snakes that inhabit the hurricane-prone regions of North America and is intended to serve as a reference to snake identification, basic field safety procedures, and the currently recommended first-aid measures for snakebite casualties.

Deep-sea sampling on CMarZ cruises in the Atlantic Ocean - an Introduction

NASA Astrophysics Data System (ADS)

Wiebe, Peter H.; Bucklin, Ann; Madin, Laurence; Angel, Martin V.; Sutton, Tracey; Pagés, Francesc; Hopcroft, Russell R.; Lindsay, Dhugal

2010-12-01

The deep-sea zooplankton assemblage is hypothesized to have high species diversity, with low abundances of each species. However, even rare species may have huge population sizes and play a critical role in the dynamics of deep-sea environments. The Census of Marine Zooplankton (CMarZ) study sought to accurately assess zooplankton diversity in the mesopelagic and bathypelagic zones of the subtropical/tropical of the northwest and eastern sections of the Atlantic Ocean using integrated morphological and molecular analysis of large-volume samples to depths of 5,000 m. The field surveys in April 2006 and November 2007 included scientists and students associated with the CMarZ. The cruise field work entailed at-sea analysis of samples and identification of specimens by expert taxonomists, with at-sea DNA sequencing to determine a barcode (i.e., a short DNA sequence for species recognition) for selected species. Environmental data and zooplankton samples were collected with 1-m 2 and 10-m 2 opening/closing MOCNESS (0-1000 m and 1000-5000 m, respectively), and with either a 0.25-m 2 MOCNESS or a 0.5-m 2 Multi-net above 1000 m. More than 500 species were identified and more than 1000 specimens placed in a queue for barcoding on each cruise; several hundred species were barcoded at sea. For several taxonomic groups, a significant fraction of the region's known species were collected and identified. For example, in the northwest Atlantic 93 of 140 known ostracod species for the Atlantic Ocean were collected, 6 undescribed species were found, and the first DNA barcode for a planktonic ostracod was obtained. The deployment of trawls with fine-mesh nets to sample large volumes at great depths for small zooplankton confirmed that there is considerable species diversity at depth, with more species yet to be discovered.

Part II: Functional delivery of a neurotherapeutic gene to neural stem cells using minicircle DNA and nanoparticles: Translational advantages for regenerative neurology.

PubMed

Fernandes, Alinda R; Chari, Divya M

2016-09-28

Both neurotrophin-based therapy and neural stem cell (NSC)-based strategies have progressed to clinical trials for treatment of neurological diseases and injuries. Brain-derived neurotrophic factor (BDNF) in particular can confer neuroprotective and neuro-regenerative effects in preclinical studies, complementing the cell replacement benefits of NSCs. Therefore, combining both approaches by genetically-engineering NSCs to express BDNF is an attractive approach to achieve combinatorial therapy for complex neural injuries. Current genetic engineering approaches almost exclusively employ viral vectors for gene delivery to NSCs though safety and scalability pose major concerns for clinical translation and applicability. Magnetofection, a non-viral gene transfer approach deploying magnetic nanoparticles and DNA with magnetic fields offers a safe alternative but significant improvements are required to enhance its clinical application for delivery of large sized therapeutic plasmids. Here, we demonstrate for the first time the feasibility of using minicircles with magnetofection technology to safely engineer NSCs to overexpress BDNF. Primary mouse NSCs overexpressing BDNF generated increased daughter neuronal cell numbers post-differentiation, with accelerated maturation over a four-week period. Based on our findings we highlight the clinical potential of minicircle/magnetofection technology for therapeutic delivery of key neurotrophic agents. Copyright © 2016 Elsevier B.V. All rights reserved.

The Rotary Zone Thermal Cycler: A Low-Power System Enabling Automated Rapid PCR

PubMed Central

Bartsch, Michael S.; Renzi, Ronald F.; Van de Vreugde, James L.; Kim, Hanyoup; Knight, Daniel L.; Sinha, Anupama; Branda, Steven S.; Patel, Kamlesh D.

2015-01-01

Advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology (e.g., aliquoting, centrifuging, mixing, and thermal cycling) to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks into contact with a stationary 4-microliter capillary-bound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system that uses low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between-run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, we present preliminary results for rapid single-plex PCR, multiplex short tandem repeat (STR) amplification, and second strand cDNA synthesis. PMID:25826708

Resolving complex chromosome structures during meiosis: versatile deployment of Smc5/6.

PubMed

Verver, Dideke E; Hwang, Grace H; Jordan, Philip W; Hamer, Geert

2016-03-01

The Smc5/6 complex, along with cohesin and condensin, is a member of the structural maintenance of chromosome (SMC) family, large ring-like protein complexes that are essential for chromatin structure and function. Thanks to numerous studies of the mitotic cell cycle, Smc5/6 has been implicated to have roles in homologous recombination, restart of stalled replication forks, maintenance of ribosomal DNA (rDNA) and heterochromatin, telomerase-independent telomere elongation, and regulation of chromosome topology. The nature of these functions implies that the Smc5/6 complex also contributes to the profound chromatin changes, including meiotic recombination, that characterize meiosis. Only recently, studies in diverse model organisms have focused on the potential meiotic roles of the Smc5/6 complex. Indeed, Smc5/6 appears to be essential for meiotic recombination. However, due to both the complexity of the process of meiosis and the versatility of the Smc5/6 complex, many additional meiotic functions have been described. In this review, we provide a clear overview of the multiple functions found so far for the Smc5/6 complex in meiosis. Additionally, we compare these meiotic functions with the known mitotic functions in an attempt to find a common denominator and thereby create clarity in the field of Smc5/6 research.

Identifying species of moths (Lepidoptera) from Baihua Mountain, Beijing, China, using DNA barcodes

PubMed Central

Liu, Xiao F; Yang, Cong H; Han, Hui L; Ward, Robert D; Zhang, Ai-bing

2014-01-01

DNA barcoding has become a promising means for the identification of organisms of all life-history stages. Currently, distance-based and tree-based methods are most widely used to define species boundaries and uncover cryptic species. However, there is no universal threshold of genetic distance values that can be used to distinguish taxonomic groups. Alternatively, DNA barcoding can deploy a “character-based” method, whereby species are identified through the discrete nucleotide substitutions. Our research focuses on the delimitation of moth species using DNA-barcoding methods. We analyzed 393 Lepidopteran specimens belonging to 80 morphologically recognized species with a standard cytochrome c oxidase subunit I (COI) sequencing approach, and deployed tree-based, distance-based, and diagnostic character-based methods to identify the taxa. The tree-based method divided the 393 specimens into 79 taxa (species), and the distance-based method divided them into 84 taxa (species). Although the diagnostic character-based method found only 39 so-identifiable species in the 80 species, with a reduction in sample size the accuracy rate substantially improved. For example, in the Arctiidae subset, all 12 species had diagnostics characteristics. Compared with traditional morphological method, molecular taxonomy performed well. All three methods enable the rapid delimitation of species, although they have different characteristics and different strengths. The tree-based and distance-based methods can be used for accurate species identification and biodiversity studies in large data sets, while the character-based method performs well in small data sets and can also be used as the foundation of species-specific biochips. PMID:25360280

An improved DNA force field for ssDNA interactions with gold nanoparticles

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

Jiang, Xiankai; Huai, Ping; Fan, Chunhai

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones “protecting” hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thusmore » the “protection” by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.« less

An improved DNA force field for ssDNA interactions with gold nanoparticles

NASA Astrophysics Data System (ADS)

Jiang, Xiankai; Gao, Jun; Huynh, Tien; Huai, Ping; Fan, Chunhai; Zhou, Ruhong; Song, Bo

2014-06-01

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones "protecting" hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the "protection" by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

An improved DNA force field for ssDNA interactions with gold nanoparticles.

PubMed

Jiang, Xiankai; Gao, Jun; Huynh, Tien; Huai, Ping; Fan, Chunhai; Zhou, Ruhong; Song, Bo

2014-06-21

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones "protecting" hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the "protection" by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples

USGS Publications Warehouse

Pilliod, David S.; Goldberg, Caren S.; Arkle, Robert S.; Waits, Lisette P.

2013-01-01

Environmental DNA (eDNA) methods for detecting aquatic species are advancing rapidly, but with little evaluation of field protocols or precision of resulting estimates. We compared sampling results from traditional field methods with eDNA methods for two amphibians in 13 streams in central Idaho, USA. We also evaluated three water collection protocols and the influence of sampling location, time of day, and distance from animals on eDNA concentration in the water. We found no difference in detection or amount of eDNA among water collection protocols. eDNA methods had slightly higher detection rates than traditional field methods, particularly when species occurred at low densities. eDNA concentration was positively related to field-measured density, biomass, and proportion of transects occupied. Precision of eDNA-based abundance estimates increased with the amount of eDNA in the water and the number of replicate subsamples collected. eDNA concentration did not vary significantly with sample location in the stream, time of day, or distance downstream from animals. Our results further advance the implementation of eDNA methods for monitoring aquatic vertebrates in stream habitats.

Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

PubMed Central

2015-01-01

Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and subtler conformational properties, including the conformational equilibrium between the BI and BII states, and the A and B forms of DNA. The parametrization efforts were simultaneously guided by gas-phase quantum mechanics (QM) data on small model compounds and condensed-phase experimental data on the hydration and osmotic properties of biologically relevant ions and their solutions, as well as theoretical predictions for ionic distribution around DNA oligomer. In addition, fine-tuning of the internal base parameters was performed to obtain the final DNA model. Notably, the Drude model is shown to more accurately reproduce counterion condensation theory predictions of DNA charge neutralization by the condensed ions as compared to the CHARMM36 additive DNA force field, indicating an improved physical description of the forces dictating the ionic solvation of DNA due to the explicit treatment of electronic polarizability. In combination with the polarizable DNA force field, the availability of Drude polarizable parameters for proteins, lipids, and carbohydrates will allow for simulation studies of heterogeneous biological systems. PMID:24874104

Seismic-monitoring changes and the remote deployment of seismic stations (seismic spider) at Mount St. Helens, 2004-2005: Chapter 7 in A volcano rekindled: the renewed eruption of Mount St. Helens, 2004-2006

USGS Publications Warehouse

McChesney, Patrick J.; Couchman, Marvin R.; Moran, Seth C.; Lockhart, Andrew B.; Swinford, Kelly J.; LaHusen, Richard G.; Sherrod, David R.; Scott, William E.; Stauffer, Peter H.

2008-01-01

The instruments in place at the start of volcanic unrest at Mount St. Helens in 2004 were inadequate to record the large earthquakes and monitor the explosions that occurred as the eruption developed. To remedy this, new instruments were deployed and the short-period seismic network was modified. A new method of establishing near-field seismic monitoring was developed, using remote deployment by helicopter. The remotely deployed seismic sensor was a piezoelectric accelerometer mounted on a surface-coupled platform. Remote deployment enabled placement of stations within 250 m of the active vent.

Army Logistician. Volume 38, Issue 3, May-June 2006

DTIC Science & Technology

2006-06-01

that are deployed or preparing to deploy and those in the process of transforming to a modular design find it difficult to keep abreast of emerging...The Air Force and the Marine Corps have well-defined and -established career fields in con- tracting for their NCOs. Now the Army is developing ...How will field -grade officers in a BCT be developed as logistics officers? How will CSS company commanders be developed ? Will there be a female

Real-time Integration of Biological, Optical and Physical Oceanographic Data from Multiple Vessels and Nearshore Sites using a Wireless Network

DTIC Science & Technology

1997-09-30

field experiments in Puget Sound . Each research vessel will use multi- sensor profiling instrument packages which obtain high-resolution physical...field deployment of the wireless network is planned for May-July, 1998, at Orcas Island, WA. IMPACT We expect that wireless communication systems will...East Sound project to be a first step toward continental shelf and open ocean deployments with the next generation of wireless and satellite

Computer-aided dispatch--traffic management center field operational test final evaluation plan : WSDOT deployment

DOT National Transportation Integrated Search

2003-09-22

This document presents the Evaluation Teams plan for conducting the evaluation of the FOT in Washington State. A companion document exists for the evaluation of the Utah deployment. This plan includes the experimental design for testing hypotheses...

Spatiotemporal variations in metal accumulation, RNA/DNA ratio and energy reserve in Perna viridis transplanted along a marine pollution gradient in Hong Kong.

PubMed

Yeung, Jamius W Y; Zhou, Guang-Jie; Leung, Kenneth M Y

2017-11-30

We examined spatiotemporal variations of metal levels and three growth related biomarkers, i.e., RNA/DNA ratio (RD), total energy reserve (Et) and condition index (CI), in green-lipped mussels Perna viridis transplanted into five locations along a pollution gradient in the marine environment of Hong Kong over 120days of deployment. There were significant differences in metal levels and biomarker responses among the five sites and six time points. Mussels in two clean sites displayed better CI and significantly lower levels of Ag, Cu, Pb and Zn in their tissues than the other sites. Temporal patterns of RD in P. viridis were found to be site-specific. Across all sites, Et decreased in P. viridis over the deployment period, though the rate of decrease varied significantly among the sites. Therefore, temporal variation of biomarkers should be taken to consideration in mussel-watch programs because such information can help discriminate pollution-induced change from natural variation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of a ROV Deployed Video Analysis Tool for Rapid Measurement of Submerged Oil/Gas Leaks

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

Savas, Omer

Expanded deep sea drilling around the globe makes it necessary to have readily available tools to quickly and accurately measure discharge rates from accidental submerged oil/gas leak jets for the first responders to deploy adequate resources for containment. We have developed and tested a field deployable video analysis software package which is able to provide in the field sufficiently accurate flow rate estimates for initial responders in accidental oil discharges in submarine operations. The essence of our approach is based on tracking coherent features at the interface in the near field of immiscible turbulent jets. The software package, UCB_Plume, ismore » ready to be used by the first responders for field implementation. We have tested the tool on submerged water and oil jets which are made visible using fluorescent dyes. We have been able to estimate the discharge rate within 20% accuracy. A high end WINDOWS laptop computer is suggested as the operating platform and a USB connected high speed, high resolution monochrome camera as the imaging device are sufficient for acquiring flow images under continuous unidirectional illumination and running the software in the field. Results are obtained over a matter of minutes.« less

Building a better sticky trap: description of an easy-to-use trap and pole mount for quantifying the abundance of adult aquatic insects

USGS Publications Warehouse

Smith, Joshua T.; Kennedy, Theodore A.; Muehlbauer, Jeffrey D.

2014-01-01

Insect emergence is a fundamental process in freshwaters. It is a critical life-history stage for aquatic insects and provides an important prey resource for terrestrial and aquatic consumers. Sticky traps are increasingly being used to sample these insects. The most common design consists of an acetate sheet coated with a nondrying adhesive that is attached to a wire frame or cylinder. These traps must be prepared at the deployment site, a process that can be time consuming and difficult given the vagaries of field conditions. Our goals were to develop a sturdy, low-cost sticky trap that could be prepared in advance, rapidly deployed and recovered in the field, and used to estimate the flight direction of insects. We used 150-mm Petri dishes with lids. The dishes can be coated cleanly and consistently with Tangle-Trap® adhesive. Deploying traps is simple and requires only a pole set near the body of water being sampled. Four dishes can be attached to the pole using Velcro and aligned in 4 different directions to enable quantification of insect flight direction. After sampling, Petri dishes can be taped closed, packed in boxes, and stored indefinitely. Petri traps are comparable in price to standard acetate sheet traps at ∼US$0.50/directional deployment, but they require more space for storage than acetate sheet traps. However, a major benefit of Petri traps is that field deployment times are ⅓ those of acetate traps. Our study demonstrated that large Petri dishes are an ideal platform for sampling postemergent adult aquatic insects, particularly when the study design involves estimating flight direction and when rapid deployment and recovery of traps is critical.

Advances in damage control resuscitation and surgery: implications on the organization of future military field forces

PubMed Central

Tien, Col Homer; Beckett, Maj Andrew; Garraway, LCol Naisan; Talbot, LCol Max; Pannell, Capt Dylan; Alabbasi, Thamer

2015-01-01

Medical support to deployed field forces is increasingly becoming a shared responsibility among allied nations. National military medical planners face several key challenges, including fiscal restraints, raised expectations of standards of care in the field and a shortage of appropriately trained specialists. Even so, medical services are now in high demand, and the availability of medical support may become the limiting factor that determines how and where combat units can deploy. The influence of medical factors on operational decisions is therefore leading to an increasing requirement for multinational medical solutions. Nations must agree on the common standards that govern the care of the wounded. These standards will always need to take into account increased public expectations regarding the quality of care. The purpose of this article is to both review North Atlantic Treaty Organization (NATO) policies that govern multinational medical missions and to discuss how recent scientific advances in prehospital battlefield care, damage control resuscitation and damage control surgery may inform how countries within NATO choose to organize and deploy their field forces in the future. PMID:26100784

A field-deployable GC-EI-HRTOF-MS for in situ characterization of volatile organic compounds

NASA Astrophysics Data System (ADS)

Lerner, B. M.; Herndon, S. C.; Yacovitch, T. I.; Roscioli, J. R.; Fortner, E.; Knighton, W. B.; Sueper, D.; Isaacman-VanWertz, G. A.; Jayne, J. T.; Worsnop, D. R.

2017-12-01

Previous authors have demonstrated the value of coupling conventional gas chromatograph (GC) separation techniques with the new generation of electron-impact high-resolution time-of-flight mass spectrometry (EI-HR-ToF-MS) detectors for the measurement of halocarbons and semi-volatile organic species. Here, we present new instrumentation, analytical techniques and field data from the deployment of a GC-EI-HR-ToF-MS system in the mini Aerodyne mobile laboratory to sites upwind and downwind of San Antonio, Texas in May 2017. The instrument employed a multi-component adsorbent trap pre-concertation system followed by single-column separation. We will show results from the field work, including inter-comparison with other VOC measurements and characterization of C5-C10 hydrocarbon mixing ratios to distinguish urban and oil/gas emission sources in characterized air. We will discuss practical aspects of deployment of the GC-EI-HRTOF-MS in a mobile laboratory and system performance in the field. Will we also present further development of Aerodyne's TERN software package for chromatographic data analysis to processing of HRTOF-MS datasets.

Tribological Effects on DNA Translocation in a Nanochannel Coated with a Self-Assembled Monolayer

PubMed Central

Luan, Binquan; Afzali, Ali; Harrer, Stefan; Peng, Hongbo; Waggoner, Philip; Polonsky, Stas; Stolovitzky, Gustavo; Martyna, Glenn

2010-01-01

A biomimetic nanochannel coated with a self-assembled monolayer (SAM) can be used for sensing and analyzing biomolecules. The interaction between a transported biomolecule and a SAM governs the mechanically or electrically driven motion of the molecule. To investigate the translocation dynamics of a biomolecule, we performed all-atom molecular dynamics simulations on a single-stranded DNA in a solid-state nanochannel coated with a SAM that consists of octane or octanol polymers. Simulation results demonstrate that the interaction between DNA and a hydrophobic or a hydrophilic SAM is effectively repulsive or adhesive, respectively, resulting in different translocation dynamics of DNA. Therefore, with proper designs of SAMs coated on a channel surface, it is possible to control the translocation dynamics of a biomolecule. This work also demonstrates that traditional tribology methods can be deployed to study a biological or bio-mimetic transport process. PMID:21128651

A Portable, Field-Deployable Analyzer for Isotopic Water Measurements

NASA Astrophysics Data System (ADS)

Berman, E. S.; Gupta, M.; Huang, Y. W.; Lacelle, D.; McKay, C. P.; Fortson, S.

2015-12-01

Water stable isotopes have for many years been used to study the hydrological cycle, catchment hydrology, and polar climate among other applications. Typically, discrete water samples are collected and transported to a laboratory for isotope analysis. Due to the expense and labor associated with such sampling, isotope studies have generally been limited in scope and time-resolution. Field sampling of water isotopes has been shown in recent years to provide dense data sets with the increased time resolution illuminating substantially greater short term variability than is generally observed during discrete sampling. A truly portable instrument also opens the possibility to utilize the instrument as a tool for identifying which water samples would be particularly interesting for further laboratory investigation. To make possible such field measurements of liquid water isotopes, Los Gatos Research has developed a miniaturized, field-deployable liquid water isotope analyzer. The prototype miniature liquid water isotope analyzer (mini-LWIA) uses LGR's patented Off-Axis ICOS (Integrated Cavity Output Spectroscopy) technology in a rugged, Pelican case housing for easy transport and field operations. The analyzer simultaneously measures both δ2H and δ18O from liquid water, with both manual and automatic water introduction options. The laboratory precision for δ2H is 0.6 ‰, and for δ18O is 0.3 ‰. The mini-LWIA was deployed in the high Arctic during the summer of 2015 at Inuvik in the Canadian Northwest Territories. Samples were collected from Sachs Harbor, on the southwest coast of Banks Island, including buried basal ice from the Lurentide Ice Sheet, some ice wedges, and other types of ground ice. Methodology and water analysis results from this extreme field deployment will be presented.

Separation of large DNA molecules by applying pulsed electric field to size exclusion chromatography-based microchip

NASA Astrophysics Data System (ADS)

Azuma, Naoki; Itoh, Shintaro; Fukuzawa, Kenji; Zhang, Hedong

2018-02-01

Through electrophoresis driven by a pulsed electric field, we succeeded in separating large DNA molecules with an electrophoretic microchip based on size exclusion chromatography (SEC), which was proposed in our previous study. The conditions of the pulsed electric field required to achieve the separation were determined by numerical analyses using our originally proposed separation model. From the numerical results, we succeeded in separating large DNA molecules (λ DNA and T4 DNA) within 1600 s, which was approximately half of that achieved under a direct electric field in our previous study. Our SEC-based electrophoresis microchip will be one of the effective tools to meet the growing demand of faster and more convenient separation of large DNA molecules, especially in the field of epidemiological research of infectious diseases.

Next Generation Polar Seismic Instrumentation Challenges

NASA Astrophysics Data System (ADS)

Parker, T.; Beaudoin, B. C.; Gridley, J.; Anderson, K. R.

2011-12-01

Polar region logistics are the limiting factor for deploying deep field seismic arrays. The IRIS PASSCAL Instrument Center, in collaboration with UNAVCO, designed and deployed several systems that address some of the logistical constraints of polar deployments. However, continued logistics' pressures coupled with increasingly ambitious science projects require further reducing the logistics required for deploying both summer and over winter stations. Our focus is to reduce station power requirements and bulk, thereby minimizing the time and effort required to deploy these arrays. We will reduce the weight of the battery bank by incorporating the most applicable new high energy-density battery technology. Using these batteries will require a completely new power management system along with an appropriate smart enclosure. The other aspect will be to integrate the digitizing system with the sensor. Both of these technologies should reduce the install time and shipping volume plus weight while reducing some instrument costs. We will also continue work on an effective Iridium telemetry solution for automated data return. The costs and limitations of polar deep-field science easily justifies a specialized development effort but pays off doubly in that we will continue to leverage the advancements in reduced logistics and increased performance for the benefit of low-latitude seismic research.

Deployment and Performance of the NASA D3R During the GPM OLYMPEx Field Campaign

NASA Technical Reports Server (NTRS)

Chandrasekar, V.; Beauchamp, Robert M.; Chen, Haonan; Vega, Manuel; Schwaller, Mathew; Willie, Delbert; Dabrowski, Aaron; Kumar, Mohit; Petersen, Walter; Wolff, David

2016-01-01

The NASA D3R was successfully deployed and operated throughout the NASA OLYMPEx field campaign. A differential phase based attenuation correction technique has been implemented for D3R observations. Hydrometeor classification has been demonstrated for five distinct classes using Ku-band observations of both convection and stratiform rain. The stratiform rain hydrometeor classification is compared against LDR observations and shows good agreement in identification of mixed-phase hydrometeors in the melting layer.

Clinical Utility of Epstein-Barr Virus DNA Testing in the Treatment of Nasopharyngeal Carcinoma Patients.

PubMed

Kim, Kelly Y; Le, Quynh-Thu; Yom, Sue S; Ng, Raymond H W; Chan, K C Allen; Bratman, Scott V; Welch, John J; Divi, Rao L; Petryshyn, Raymond A; Conley, Barbara A

2017-08-01

Epstein-Barr virus (EBV) DNA analysis has been shown to be useful for early detection, prognostication, and monitoring of treatment response of nasopharyngeal carcinoma (NPC), and the recent literature provides growing evidence of the clinical utility of EBV DNA testing, particularly to inform treatment decisions for NPC patients. Despite the fact that NPC is a rare disease, the NRG Oncology cooperative group has successfully activated a phase 2/3 randomized clinical trial for NPC with international partners and in that process has discovered that the development of a harmonized EBV DNA test is absolutely critical for integration into clinical trials and for future deployment in clinical and central laboratories. In November 2015, the National Cancer Institute (NCI) convened a workshop of international experts in the treatment of NPC and EBV testing to provide a forum for discussing the state of EBV DNA testing and its clinical utility, and to stimulate consideration of future studies and clinical practice guidelines for EBV DNA. This review provides a summary of that discussion. Published by Elsevier Inc.

High-Temperature Superconductors as Electromagnetic Deployment and Support Structures in Spacecraft. [NASA NIAC Phase I

NASA Technical Reports Server (NTRS)

Getliffe, Gwendolyn V.; Inamdar, Niraj K.; Masterson, Rebecca; Miller, David W.

2012-01-01

This report, concluding a one-year NIAC Phase I study, describes a new structural and mechanical technique aimed at reducing the mass and increasing the deployed-to-stowed length and volume ratios of spacecraft systems. This technique uses the magnetic fields generated by electrical current passing through coils of high-temperature superconductors (HTSs) to support spacecraft structures and deploy them to operational configurations from their stowed positions inside a launch vehicle fairing.

Mission Planning System Increment 5 (MPS Inc 5)

DTIC Science & Technology

2016-03-01

DoD - Department of Defense DoDAF - DoD Architecture Framework FD - Full Deployment FDD - Full Deployment Decision FY - Fiscal Year IA...Alternative Selected (Funds First Obligated (FFO)) (O/T) : Mar 2013 / Mar 2013 • MS B (O/T) : Apr 2012 / Apr 2012 • MS C (O/T) : N/A / N/A • FDD (O/T...Deployed Software Intensive Program" as described in the DOD Instruction 5000.02, January 7, 2015. 4. FDD provides approval to field the

A Social Potential Fields Approach for Self-Deployment and Self-Healing in Hierarchical Mobile Wireless Sensor Networks

PubMed Central

González-Parada, Eva; Cano-García, Jose; Aguilera, Francisco; Sandoval, Francisco; Urdiales, Cristina

2017-01-01

Autonomous mobile nodes in mobile wireless sensor networks (MWSN) allow self-deployment and self-healing. In both cases, the goals are: (i) to achieve adequate coverage; and (ii) to extend network life. In dynamic environments, nodes may use reactive algorithms so that each node locally decides when and where to move. This paper presents a behavior-based deployment and self-healing algorithm based on the social potential fields algorithm. In the proposed algorithm, nodes are attached to low cost robots to autonomously navigate in the coverage area. The proposed algorithm has been tested in environments with and without obstacles. Our study also analyzes the differences between non-hierarchical and hierarchical routing configurations in terms of network life and coverage. PMID:28075364

A Social Potential Fields Approach for Self-Deployment and Self-Healing in Hierarchical Mobile Wireless Sensor Networks.

PubMed

González-Parada, Eva; Cano-García, Jose; Aguilera, Francisco; Sandoval, Francisco; Urdiales, Cristina

2017-01-09

Autonomous mobile nodes in mobile wireless sensor networks (MWSN) allow self-deployment and self-healing. In both cases, the goals are: (i) to achieve adequate coverage; and (ii) to extend network life. In dynamic environments, nodes may use reactive algorithms so that each node locally decides when and where to move. This paper presents a behavior-based deployment and self-healing algorithm based on the social potential fields algorithm. In the proposed algorithm, nodes are attached to low cost robots to autonomously navigate in the coverage area. The proposed algorithm has been tested in environments with and without obstacles. Our study also analyzes the differences between non-hierarchical and hierarchical routing configurations in terms of network life and coverage.

Velocity profiles, Reynolds stresses and bed roughness from an autonomous field deployed Acoustic Doppler Velocity Profiler in a mixed sediment tidal estuary

NASA Astrophysics Data System (ADS)

O'Boyle, Louise; Thorne, Peter; Cooke, Richard; Cohbed Team

2014-05-01

Estuaries are among some of the most important global landscapes in terms of population density, ecology and economy. Understanding the dynamics of these natural mixed sediment environments is of particular interest amid growing concerns over sea level rise, climate variations and estuarine response to these changes. Many predictors exist for bed form formation and sand transport in sandy coastal zones; however less work has been published on mixed sediments. This paper details a field study which forms part of the COHBED project aiming to increase understanding of bed forms in a biotic mixed sediment estuarine environment. The study was carried out in the Dee Estuary, in the eastern Irish Sea between England and Wales from the 21st May to 4th June 2013. A state of the art instrumentation frame, known as SEDbed, was deployed at three sites of differing sediment properties and biological makeup within the intertidal zone of the estuary. The SEDbed deployment consisted of a suite of optical and acoustic instrumentation, including an Acoustic Doppler Velocity Profiler (ADVP), Acoustic Doppler Velocimeter (ADV) and a three dimensional acoustic ripple profiler, 3D-ARP. Supplementary field samples and measurements were recorded alongside the frame during each deployment. This paper focuses on the use of new technological developments for the investigation of sediment dynamics. The hydrodynamics at each of the deployment sites are presented including centimetre resolution velocity profiles in the near bed region of the water column, obtained from the ADVP, which is presently the only autonomous field deployed coherent Doppler profiler . Based on these high resolution profiles variations in frictional velocity, bed shear stress and roughness length are calculated. Comparisons are made with theoretical models and with Reynolds stress values obtained from ADV data at a single point within the ADVP profile and from ADVP data itself. Predictions of bed roughness at each deployment site are compared with ripple measurements obtained on site using a three dimensional acoustic ripple profiler, 3D-ARP. These results will later be used to validate laboratory studies in mixed sediments, carried out as part of the COHBED Project, and enable development of new bed from predictors for biotic mixed sediment environments.

Teaching the Toolkit: A Laboratory Series to Demonstrate the Evolutionary Conservation of Metazoan Cell Signaling Pathways

ERIC Educational Resources Information Center

LeClair, Elizabeth E.

2008-01-01

A major finding of comparative genomics and developmental genetics is that metazoans share certain conserved, embryonically deployed signaling pathways that instruct cells as to their ultimate fate. Because the DNA encoding these pathways predates the evolutionary split of most animal groups, it should in principle be possible to clone…

Final test report for advanced traveler information systems (ATIS) and related standards as deployed by the Nebraska department of roads.

DOT National Transportation Integrated Search

2008-03-14

This report contains the results, findings and conclusions generated from the evaluation and field testing of a specific subset of ITS Standards applicable to the center-to-center exchange of advanced traveler information as deployed by the Nebraska ...

A Wireless Communications Laboratory on Cellular Network Planning

ERIC Educational Resources Information Center

Dawy, Z.; Husseini, A.; Yaacoub, E.; Al-Kanj, L.

2010-01-01

The field of radio network planning and optimization (RNPO) is central for wireless cellular network design, deployment, and enhancement. Wireless cellular operators invest huge sums of capital on deploying, launching, and maintaining their networks in order to ensure competitive performance and high user satisfaction. This work presents a lab…

Shape accuracy optimization for cable-rib tension deployable antenna structure with tensioned cables

NASA Astrophysics Data System (ADS)

Liu, Ruiwei; Guo, Hongwei; Liu, Rongqiang; Wang, Hongxiang; Tang, Dewei; Song, Xiaoke

2017-11-01

Shape accuracy is of substantial importance in deployable structures as the demand for large-scale deployable structures in various fields, especially in aerospace engineering, increases. The main purpose of this paper is to present a shape accuracy optimization method to find the optimal pretensions for the desired shape of cable-rib tension deployable antenna structure with tensioned cables. First, an analysis model of the deployable structure is established by using finite element method. In this model, geometrical nonlinearity is considered for the cable element and beam element. Flexible deformations of the deployable structure under the action of cable network and tensioned cables are subsequently analyzed separately. Moreover, the influence of pretension of tensioned cables on natural frequencies is studied. Based on the results, a genetic algorithm is used to find a set of reasonable pretension and thus minimize structural deformation under the first natural frequency constraint. Finally, numerical simulations are presented to analyze the deployable structure under two kinds of constraints. Results show that the shape accuracy and natural frequencies of deployable structure can be effectively improved by pretension optimization.

Supramolecular gel electrophoresis of large DNA fragments.

PubMed

Tazawa, Shohei; Kobayashi, Kazuhiro; Oyoshi, Takanori; Yamanaka, Masamichi

2017-10-01

Pulsed-field gel electrophoresis is a frequent technique used to separate exceptionally large DNA fragments. In a typical continuous field electrophoresis, it is challenging to separate DNA fragments larger than 20 kbp because they migrate at a comparable rate. To overcome this challenge, it is necessary to develop a novel matrix for the electrophoresis. Here, we describe the electrophoresis of large DNA fragments up to 166 kbp using a supramolecular gel matrix and a typical continuous field electrophoresis system. C 3 -symmetric tris-urea self-assembled into a supramolecular hydrogel in tris-boric acid-EDTA buffer, a typical buffer for DNA electrophoresis, and the supramolecular hydrogel was used as a matrix for electrophoresis to separate large DNA fragments. Three types of DNA marker, the λ-Hind III digest (2 to 23 kbp), Lambda DNA-Mono Cut Mix (10 to 49 kbp), and Marker 7 GT (10 to 165 kbp), were analyzed in this study. Large DNA fragments of greater than 100 kbp showed distinct mobility using a typical continuous field electrophoresis system. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of DNA Force Fields in Implicit Solvation

PubMed Central

Gaillard, Thomas; Case, David A.

2011-01-01

DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models. PMID:22043178

Quantification of Plasmodiophora brassicae Using a DNA-Based Soil Test Facilitates Sustainable Oilseed Rape Production

PubMed Central

Wallenhammar, Ann-Charlotte; Gunnarson, Albin; Hansson, Fredrik; Jonsson, Anders

2016-01-01

Outbreaks of clubroot disease caused by the soil-borne obligate parasite Plasmodiophora brassicae are common in oilseed rape (OSR) in Sweden. A DNA-based soil testing service that identifies fields where P. brassicae poses a significant risk of clubroot infection is now commercially available. It was applied here in field surveys to monitor the prevalence of P. brassicae DNA in field soils intended for winter OSR production and winter OSR field experiments. In 2013 in Scania, prior to planting, P. brassicae DNA was detected in 60% of 45 fields on 10 of 18 farms. In 2014, P. brassicae DNA was detected in 44% of 59 fields in 14 of 36 farms, in the main winter OSR producing region in southern Sweden. P. brassicae was present indicative of a risk for >10% yield loss with susceptible cultivars (>1300 DNA copies g soil−1) in 47% and 44% of fields in 2013 and 2014 respectively. Furthermore, P. brassicae DNA was indicative of sites at risk of complete crop failure if susceptible cultivars were grown (>50 000 copies g−1 soil) in 14% and 8% of fields in 2013 and 2014, respectively. A survey of all fields at Lanna research station in western Sweden showed that P. brassicae was spread throughout the farm, as only three of the fields (20%) showed infection levels below the detection limit for P.brassicae DNA, while the level was >50,000 DNA copies g−1 soil in 20% of the fields. Soil-borne spread is of critical importance and soil scraped off footwear showed levels of up to 682 million spores g−1 soil. Soil testing is an important tool for determining the presence of P. brassicae and providing an indication of potential yield loss, e.g., in advisory work on planning for a sustainable OSR crop rotation. This soil test is gaining acceptance as a tool that increases the likelihood of success in precision agriculture and in applied research conducted in commercial oilseed fields and at research stations. The present application highlights the importance of prevention of disease spread by cleaning of farm equipment, footwear, etc. PMID:27135241

Quantification of Plasmodiophora brassicae Using a DNA-Based Soil Test Facilitates Sustainable Oilseed Rape Production.

PubMed

Wallenhammar, Ann-Charlotte; Gunnarson, Albin; Hansson, Fredrik; Jonsson, Anders

2016-04-22

Outbreaks of clubroot disease caused by the soil-borne obligate parasite Plasmodiophora brassicae are common in oilseed rape (OSR) in Sweden. A DNA-based soil testing service that identifies fields where P. brassicae poses a significant risk of clubroot infection is now commercially available. It was applied here in field surveys to monitor the prevalence of P. brassicae DNA in field soils intended for winter OSR production and winter OSR field experiments. In 2013 in Scania, prior to planting, P. brassicae DNA was detected in 60% of 45 fields on 10 of 18 farms. In 2014, P. brassicae DNA was detected in 44% of 59 fields in 14 of 36 farms, in the main winter OSR producing region in southern Sweden. P. brassicae was present indicative of a risk for >10% yield loss with susceptible cultivars (>1300 DNA copies g soil(-1)) in 47% and 44% of fields in 2013 and 2014 respectively. Furthermore, P. brassicae DNA was indicative of sites at risk of complete crop failure if susceptible cultivars were grown (>50 000 copies g(-1) soil) in 14% and 8% of fields in 2013 and 2014, respectively. A survey of all fields at Lanna research station in western Sweden showed that P. brassicae was spread throughout the farm, as only three of the fields (20%) showed infection levels below the detection limit for P.brassicae DNA, while the level was >50,000 DNA copies g(-1) soil in 20% of the fields. Soil-borne spread is of critical importance and soil scraped off footwear showed levels of up to 682 million spores g(-1) soil. Soil testing is an important tool for determining the presence of P. brassicae and providing an indication of potential yield loss, e.g., in advisory work on planning for a sustainable OSR crop rotation. This soil test is gaining acceptance as a tool that increases the likelihood of success in precision agriculture and in applied research conducted in commercial oilseed fields and at research stations. The present application highlights the importance of prevention of disease spread by cleaning of farm equipment, footwear, etc.

Field comparison of optical and clark cell dissolved-oxygen sensors

USGS Publications Warehouse

Fulford, J.M.; Davies, W.J.; Garcia, L.

2005-01-01

Three multi-parameter water-quality monitors equipped with either Clark cell type or optical type dissolved-oxygen sensors were deployed for 30 days in a brackish (salinity <10 parts per thousand) environment to determine the sensitivity of the sensors to biofouling. The dissolved-oxygen sensors compared periodically to a hand-held dissolved oxygen sensor, but were not serviced or cleaned during the deployment. One of the Clark cell sensors and the optical sensor performed similarly during the deployment. The remaining Clark cell sensor was not aged correctly prior to deployment and did not perform as well as the other sensors. All sensors experienced substantial biofouling that gradually degraded the accuracy of the dissolved-oxygen measurement during the last half of the deployment period. Copyright ASCE 2005.

Deployable Mini-Payload Missions Enabled by Small Radioisotope Power Systems (RPSs)

NASA Technical Reports Server (NTRS)

Abelson, Robert D.; Satter, Celeste M.

2005-01-01

Deployable mini-payloads are envisioned as small, simple, standalone instruments that could be deployed from a mother vehicle such as a rover or the proposed Jupiter Icy Moons Orbiter to key points of interest within the solar system. Used in conjunction with a small radioisotope power system (RPS), these payloads could potentially be used for long-duration science missions or as positional beacons for rovers or other spacecraft. The RPS power source would be suitable for deployable mini-payload missions that would take place anywhere there is limited, intermittent, or no solar insolation. This paper introduces two such concepts: (1) a seismic monitoring station deployed by a rover or aerobot, and (2) a passive fields and particles station delivered by a mother spacecraft to Jupiter.

Electrical characterization of gold-DNA-gold structures in presence of an external magnetic field by means of I-V curve analysis.

PubMed

Khatir, Nadia Mahmoudi; Banihashemian, Seyedeh Maryam; Periasamy, Vengadesh; Ritikos, Richard; Abd Majid, Wan Haliza; Abdul Rahman, Saadah

2012-01-01

This work presents an experimental study of gold-DNA-gold structures in the presence and absence of external magnetic fields with strengths less than 1,200.00 mT. The DNA strands, extracted by standard method were used to fabricate a Metal-DNA-Metal (MDM) structure. Its electric behavior when subjected to a magnetic field was studied through its current-voltage (I-V) curve. Acquisition of the I-V curve demonstrated that DNA as a semiconductor exhibits diode behavior in the MDM structure. The current versus magnetic field strength followed a decreasing trend because of a diminished mobility in the presence of a low magnetic field. This made clear that an externally imposed magnetic field would boost resistance of the MDM structure up to 1,000.00 mT and for higher magnetic field strengths we can observe an increase in potential barrier in MDM junction. The magnetic sensitivity indicates the promise of using MDM structures as potential magnetic sensors.

Electrical Characterization of Gold-DNA-Gold Structures in Presence of an External Magnetic Field by Means of I–V Curve Analysis

PubMed Central

Khatir, Nadia Mahmoudi; Banihashemian, Seyedeh Maryam; Periasamy, Vengadesh; Ritikos, Richard; Majid, Wan Haliza Abd; Rahman, Saadah Abdul

2012-01-01

This work presents an experimental study of gold-DNA-gold structures in the presence and absence of external magnetic fields with strengths less than 1,200.00 mT. The DNA strands, extracted by standard method were used to fabricate a Metal-DNA-Metal (MDM) structure. Its electric behavior when subjected to a magnetic field was studied through its current-voltage (I–V) curve. Acquisition of the I–V curve demonstrated that DNA as a semiconductor exhibits diode behavior in the MDM structure. The current versus magnetic field strength followed a decreasing trend because of a diminished mobility in the presence of a low magnetic field. This made clear that an externally imposed magnetic field would boost resistance of the MDM structure up to 1,000.00 mT and for higher magnetic field strengths we can observe an increase in potential barrier in MDM junction. The magnetic sensitivity indicates the promise of using MDM structures as potential magnetic sensors. PMID:22737025

Engaging High School Science Teachers in Field-Based Seismology Research: Opportunities and Challenges

NASA Astrophysics Data System (ADS)

Long, M. D.

2015-12-01

Research experiences for secondary school science teachers have been shown to improve their students' test scores, and there is a substantial body of literature about the effectiveness of RET (Research Experience for Teachers) or SWEPT (Scientific Work Experience Programs for Teachers) programs. RET programs enjoy substantial support, and several opportunities for science teachers to engage in research currently exist. However, there are barriers to teacher participation in research projects; for example, laboratory-based projects can be time consuming and require extensive training before a participant can meaningfully engage in scientific inquiry. Field-based projects can be an effective avenue for involving teachers in research; at its best, earth science field work is a fun, highly immersive experience that meaningfully contributes to scientific research projects, and can provide a payoff that is out of proportion to a relatively small time commitment. In particular, broadband seismology deployments provide an excellent opportunity to provide teachers with field-based research experience. Such deployments are labor-intensive and require large teams, with field tasks that vary from digging holes and pouring concrete to constructing and configuring electronics systems and leveling and orienting seismometers. A recently established pilot program, known as FEST (Field Experiences for Science Teachers) is experimenting with providing one week of summer field experience for high school earth science teachers in Connecticut. Here I report on results and challenges from the first year of the program, which is funded by the NSF-CAREER program and is being run in conjunction with a temporary deployment of 15 seismometers in Connecticut, known as SEISConn (Seismic Experiment for Imaging Structure beneath Connecticut). A small group of teachers participated in a week of field work in August 2015 to deploy seismometers in northern CT; this experience followed a visit of the PI to the classroom of one of the teacher participants during spring 2015 to give a series of talks on Connecticut earthquakes and geology. This presentation will focus on the challenges and opportunities of running small, PI-driven, field-based RET programs.

Tomorrow's vector vaccines for small ruminants.

PubMed

Kyriakis, C S

2015-12-14

Inactivated and attenuated vaccines have contributed to the control or even the eradication of significant animal pathogens. However, these traditional vaccine technologies have limitations and disadvantages. Inactivated vaccines lack efficacy against certain pathogens, while attenuated vaccines are not always as safe. New technology vaccines, namely DNA and recombinant viral vector vaccines, are being developed and tested against pathogens of small ruminants. These vaccines induce both humoral and cellular immune responses, are safe to manufacture and use and can be utilized in strategies for differentiation of infected from vaccinated animals. Although there are more strict regulatory requirements for the safety standards of these vaccines, once a vaccine platform is evaluated and established, effective vaccines can be rapidly produced and deployed in the field to prevent spread of emerging pathogens. The present article offers an introduction to these next generation technologies and examples of vaccines that have been tested against important diseases of sheep and goats. Copyright © 2015 Elsevier B.V. All rights reserved.

Design and Field Test of a WSN Platform Prototype for Long-Term Environmental Monitoring

PubMed Central

Lazarescu, Mihai T.

2015-01-01

Long-term wildfire monitoring using distributed in situ temperature sensors is an accurate, yet demanding environmental monitoring application, which requires long-life, low-maintenance, low-cost sensors and a simple, fast, error-proof deployment procedure. We present in this paper the most important design considerations and optimizations of all elements of a low-cost WSN platform prototype for long-term, low-maintenance pervasive wildfire monitoring, its preparation for a nearly three-month field test, the analysis of the causes of failure during the test and the lessons learned for platform improvement. The main components of the total cost of the platform (nodes, deployment and maintenance) are carefully analyzed and optimized for this application. The gateways are designed to operate with resources that are generally used for sensor nodes, while the requirements and cost of the sensor nodes are significantly lower. We define and test in simulation and in the field experiment a simple, but effective communication protocol for this application. It helps to lower the cost of the nodes and field deployment procedure, while extending the theoretical lifetime of the sensor nodes to over 16 years on a single 1 Ah lithium battery. PMID:25912349

The Field Shower Wastewater Recycling System: Development of a Program of Instruction and Preliminary Analysis of Its Potential Health Implications.

DTIC Science & Technology

1987-02-01

The FSWRS will be used by forces deployed to Theaters of Operations located in water-short areas of the world, and will greatly reduce water supply... operators take ’ A appropriate precautions in handling sulfuric acid and un- . treat.d waters. Although no health hazards are anticipated to result from...field. The FSWRS will be used by forces deployed to Theaters of Operations located in water short areas of the world, and will greatly reduce water

Evaluation of Methods for In-Situ Calibration of Field-Deployable Microphone Phased Arrays

NASA Technical Reports Server (NTRS)

Humphreys, William M.; Lockard, David P.; Khorrami, Mehdi R.; Culliton, William G.; McSwain, Robert G.

2017-01-01

Current field-deployable microphone phased arrays for aeroacoustic flight testing require the placement of hundreds of individual sensors over a large area. Depending on the duration of the test campaign, the microphones may be required to stay deployed at the testing site for weeks or even months. This presents a challenge in regards to tracking the response (i.e., sensitivity) of the individual sensors as a function of time in order to evaluate the health of the array. To address this challenge, two different methods for in-situ tracking of microphone responses are described. The first relies on the use of an aerial sound source attached as a payload on a hovering small Unmanned Aerial System (sUAS) vehicle. The second relies on the use of individually excited ground-based sound sources strategically placed throughout the array pattern. Testing of the two methods was performed in microphone array deployments conducted at Fort A.P. Hill in 2015 and at Edwards Air Force Base in 2016. The results indicate that the drift in individual sensor responses can be tracked reasonably well using both methods. Thus, in-situ response tracking methods are useful as a diagnostic tool for monitoring the health of a phased array during long duration deployments.

A Causal Role for the Cortical Frontal Eye Fields in Microsaccade Deployment

PubMed Central

Dash, Suryadeep; Lomber, Stephen G.

2016-01-01

Microsaccades aid vision by helping to strategically sample visual scenes. Despite the importance of these small eye movements, no cortical area has ever been implicated in their generation. Here, we used unilateral and bilateral reversible inactivation of the frontal eye fields (FEF) to identify a cortical drive for microsaccades. Unexpectedly, FEF inactivation altered microsaccade metrics and kinematics. Such inactivation also impaired microsaccade deployment following peripheral cue onset, regardless of cue side or inactivation configuration. Our results demonstrate that the FEF provides critical top-down drive for microsaccade generation, particularly during the recovery of microsaccades after disruption by sensory transients. Our results constitute the first direct evidence, to our knowledge, for the contribution of any cortical area to microsaccade generation, and they provide a possible substrate for how cognitive processes can influence the strategic deployment of microsaccades. PMID:27509130

A Causal Role for the Cortical Frontal Eye Fields in Microsaccade Deployment.

PubMed

Peel, Tyler R; Hafed, Ziad M; Dash, Suryadeep; Lomber, Stephen G; Corneil, Brian D

2016-08-01

Microsaccades aid vision by helping to strategically sample visual scenes. Despite the importance of these small eye movements, no cortical area has ever been implicated in their generation. Here, we used unilateral and bilateral reversible inactivation of the frontal eye fields (FEF) to identify a cortical drive for microsaccades. Unexpectedly, FEF inactivation altered microsaccade metrics and kinematics. Such inactivation also impaired microsaccade deployment following peripheral cue onset, regardless of cue side or inactivation configuration. Our results demonstrate that the FEF provides critical top-down drive for microsaccade generation, particularly during the recovery of microsaccades after disruption by sensory transients. Our results constitute the first direct evidence, to our knowledge, for the contribution of any cortical area to microsaccade generation, and they provide a possible substrate for how cognitive processes can influence the strategic deployment of microsaccades.

The rotary zone thermal cycler: A low-power system enabling automated rapid PCR

DOE PAGES

Bartsch, Michael S.; Edwards, Harrison S.; Gas Transmission Systems, Walnut Creek, CA; ...

2015-03-31

In this study, advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, portable, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology such as aliquoting, centrifuging, mixing, and thermal cycling to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks intomore » contact with a stationary 4-microliter capillary-bound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We further demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system using low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, preliminary results are presented for rapid single-plex PCR, multiplex short tandem repeat (STR) amplification, and second strand cDNA synthesis.« less

The rotary zone thermal cycler: A low-power system enabling automated rapid PCR

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

Bartsch, Michael S.; Edwards, Harrison S.; Gas Transmission Systems, Walnut Creek, CA

In this study, advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, portable, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology such as aliquoting, centrifuging, mixing, and thermal cycling to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks intomore » contact with a stationary 4-microliter capillary-bound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We further demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system using low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, preliminary results are presented for rapid single-plex PCR, multiplex short tandem repeat (STR) amplification, and second strand cDNA synthesis.« less

Characterizing Microbial Community and Geochemical Dynamics at Hydrothermal Vents Using Osmotically Driven Continuous Fluid Samplers

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

Robidart, Julie C.; Callister, Stephen J.; Song, Peng F.

2013-05-07

Microbes play a key role in mediating all aquatic biogeochemical cycles, and ongoing efforts are aimed at better understanding the relationships between microbial phylogenetic and physiological diversity, and habitat physical and chemical characteristics. Establishing such relationships is facilitated by sampling and studying microbiology and geochemistry at the appropriate spatial and temporal scales, to access information on the past and current environmental state that contributes to observed microbial abundances and activities. A modest number of sampling systems exist to date, few of which can be used in remote, harsh environments such as hydrothermal vents, where the ephemeral nature of venting underscoresmore » the necessity for higher resolution sampling. We have developed a robust, continuous fluid sampling system for co-registered microbial and biogeochemical analyses. The osmosis-powered bio-osmosampling system (BOSS) use no electricity, collects fluids with daily resolution or better, can be deployed in harsh, inaccessible environments and can sample fluids continuously for up to five years. Here we present a series of tests to examine DNA, RNA and protein stability over time, as well as material compatability, via lab experiments. We also conducted two field deployments at deep-sea hydrothermal vents to assess changes in microbial diversity and protein expression as a function of the physico-chemical environment. Our data reveal significant changes in microbial community composition co-occurring with relatively modest changes in the geochemistry. These data additionally provide new insights into the distribution of an enigmatic sulfur oxidizing symbiont in its free-living state. Data from the second deployment reveal differences in the representation of peptides over time, underscoring the utility of the BOSS in meta-proteomic studies. In concert, these data demonstrate the efficacy of this approach, and illustrate the value of using this method to study microbial and geochemical phenomena.« less

SKA2 Methylation is Involved in Cortisol Stress Reactivity and Predicts the Development of Post-Traumatic Stress Disorder (PTSD) After Military Deployment

PubMed Central

Boks, Marco P; Rutten, Bart P F; Geuze, Elbert; Houtepen, Lotte C; Vermetten, Eric; Kaminsky, Zachary; Vinkers, Christiaan H

2016-01-01

Genomic variation in the SKA2 gene has recently been identified as a promising suicide biomarker. In light of its role in glucocorticoid receptor transactivation, we investigated whether SKA2 DNA methylation influences cortisol stress reactivity and is involved in the development of post-traumatic stress disorder (PTSD). Increased SKA2 methylation was significantly associated with lower cortisol stress reactivity in 85 healthy individuals exposed to the Trier Social Stress Test (B=−173.40, t=−2.324, p-value=0.023). Next, we observed that longitudinal decreases in SKA2 methylation after deployment were associated with the emergence of post-deployment PTSD symptoms in a Dutch military cohort (N=93; B=−0.054, t=−3.706, p-value=3.66 × 10−4). In contrast, exposure to traumatic stress during deployment by itself resulted in longitudinal increases in SKA2 methylation (B=0.037, t=4.173, p-value=6.98 × 10−5). Using pre-deployment SKA2 methylation levels and childhood trauma exposure, we found that the previously published suicide prediction rule significantly predicted post-deployment PTSD symptoms (AUC=0.66, 95% CI: 0.53–0.79) with an optimal sensitivity of 0.81 and specificity of 0.91. Permutation analysis using random methylation loci supported these findings. Together, these data establish the importance of SKA2 for cortisol stress responsivity and the development of PTSD and provide further evidence that SKA2 is a promising biomarker for stress-related disorders including PTSD. PMID:26361058

SKA2 Methylation is Involved in Cortisol Stress Reactivity and Predicts the Development of Post-Traumatic Stress Disorder (PTSD) After Military Deployment.

PubMed

Boks, Marco P; Rutten, Bart P F; Geuze, Elbert; Houtepen, Lotte C; Vermetten, Eric; Kaminsky, Zachary; Vinkers, Christiaan H

2016-04-01

Genomic variation in the SKA2 gene has recently been identified as a promising suicide biomarker. In light of its role in glucocorticoid receptor transactivation, we investigated whether SKA2 DNA methylation influences cortisol stress reactivity and is involved in the development of post-traumatic stress disorder (PTSD). Increased SKA2 methylation was significantly associated with lower cortisol stress reactivity in 85 healthy individuals exposed to the Trier Social Stress Test (B=-173.40, t=-2.324, p-value=0.023). Next, we observed that longitudinal decreases in SKA2 methylation after deployment were associated with the emergence of post-deployment PTSD symptoms in a Dutch military cohort (N=93; B=-0.054, t=-3.706, p-value=3.66 × 10(-4)). In contrast, exposure to traumatic stress during deployment by itself resulted in longitudinal increases in SKA2 methylation (B=0.037, t=4.173, p-value=6.98 × 10(-5)). Using pre-deployment SKA2 methylation levels and childhood trauma exposure, we found that the previously published suicide prediction rule significantly predicted post-deployment PTSD symptoms (AUC=0.66, 95% CI: 0.53-0.79) with an optimal sensitivity of 0.81 and specificity of 0.91. Permutation analysis using random methylation loci supported these findings. Together, these data establish the importance of SKA2 for cortisol stress responsivity and the development of PTSD and provide further evidence that SKA2 is a promising biomarker for stress-related disorders including PTSD.

Signal timing on a shoestring

DOT National Transportation Integrated Search

2005-03-01

The conventional approach to signal timing optimization and field deployment requires current traffic flow data, experience with optimization models, familiarity with the signal controller hardware, and knowledge of field operations including signal ...

Signal timing on a shoestring.

DOT National Transportation Integrated Search

2005-03-01

The conventional approach to signal timing optimization and field deployment requires current traffic flow data, experience with optimization models, familiarity with the signal controller hardware, and knowledge of field operations including signal ...

Direct observation of iron-induced conformational changes of mitochondrial DNA by high-resolution field-emission in-lens scanning electron microscopy.

PubMed Central

Yaffee, M; Walter, P; Richter, C; Müller, M

1996-01-01

When respiring rat liver mitochondria are incubated in the presence of Fe(III) gluconate, their DNA (mtDNA) relaxes from the supercoiled to the open circular form dependent on the iron dose. Anaerobiosis or antioxidants fail to completely inhibit the unwinding. High-resolution field-emission in-lens scanning electron microscopy imaging, in concert with backscattered electron detection, pinpoints nanometer-range iron colloids bound to mtDNA isolated from iron-exposed mitochondria. High-resolution field-emission in-lens scanning electron microscopy with backscattered electron detection imaging permits simultaneous detailed visual analysis of DNA topology, iron dose-dependent mtDNA unwinding, and assessment of iron colloid formation on mtDNA strands. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:8643576

Modification of the coil-stretch transition by confinement

NASA Astrophysics Data System (ADS)

Doyle, Patick; Tang, Jing; Jones, Jeremy

2010-03-01

Large double stranded DNA are both a powerful system to study polymer dynamics at the single molecule level and also important molecules for genomic applications. While homogenous electric fields are routinely used to separate DNA in gels, DNA deformation in more complex fields has been less widely studied. We will demonstrate how micro/nanofluidic devices allow for the generation of electric fields with well-defined kinematics for trapping, stretching and then watching DNA relax back to equilibrium. The dimensions of the devices highly confine DNA and subsequently change both their conformation and dynamics. We will show how these confinements effects change the coil-stretch transition of a DNA being electrophoretically stretched in a purely elongational electrical field. We experimentally show that a two-stage coil stretch transition occurs and develop a simple dumbbell model which captures most of the relevant physics. We trace the origin of this phenomena to the modification of the effective spring law due to confinement.

Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements

PubMed Central

Iyer, Lakshminarayan M.; Burroughs, A. Maxwell; Anand, Swadha; de Souza, Robson F.

2017-01-01

ABSTRACT Intense biological conflicts between prokaryotic genomes and their genomic parasites have resulted in an arms race in terms of the molecular “weaponry” deployed on both sides. Using a recursive computational approach, we uncovered a remarkable class of multidomain proteins with 2 to 15 domains in the same polypeptide deployed by viruses and plasmids in such conflicts. Domain architectures and genomic contexts indicate that they are part of a widespread conflict strategy involving proteins injected into the host cell along with parasite DNA during the earliest phase of infection. Their unique feature is the combination of domains with highly disparate biochemical activities in the same polypeptide; accordingly, we term them polyvalent proteins. Of the 131 domains in polyvalent proteins, a large fraction are enzymatic domains predicted to modify proteins, target nucleic acids, alter nucleotide signaling/metabolism, and attack peptidoglycan or cytoskeletal components. They further contain nucleic acid-binding domains, virion structural domains, and 40 novel uncharacterized domains. Analysis of their architectural network reveals both pervasive common themes and specialized strategies for conjugative elements and plasmids or (pro)phages. The themes include likely processing of multidomain polypeptides by zincin-like metallopeptidases and mechanisms to counter restriction or CRISPR/Cas systems and jump-start transcription or replication. DNA-binding domains acquired by eukaryotes from such systems have been reused in XPC/RAD4-dependent DNA repair and mitochondrial genome replication in kinetoplastids. Characterization of the novel domains discovered here, such as RNases and peptidases, are likely to aid in the development of new reagents and elucidation of the spread of antibiotic resistance. IMPORTANCE This is the first report of the widespread presence of large proteins, termed polyvalent proteins, predicted to be transmitted by genomic parasites such as conjugative elements, plasmids, and phages during the initial phase of infection along with their DNA. They are typified by the presence of multiple domains with disparate activities combined in the same protein. While some of these domains are predicted to assist the invasive element in replication, transcription, or protection of their DNA, several are likely to target various host defense systems or modify the host to favor the parasite's life cycle. Notably, DNA-binding domains from these systems have been transferred to eukaryotes, where they have been incorporated into DNA repair and mitochondrial genome replication systems. PMID:28559295

Advances in the in-field detection of microorganisms in ice.

PubMed

Barnett, Megan J; Pearce, David A; Cullen, David C

2012-01-01

The historic view of ice-bound ecosystems has been one of a predominantly lifeless environment, where microorganisms certainly exist but are assumed to be either completely inactive or in a state of long-term dormancy. However, this standpoint has been progressively overturned in the past 20years as studies have started to reveal the importance of microbial life in the functioning of these environments. Our present knowledge of the distribution, taxonomy, and metabolic activity of such microbial life has been derived primarily from laboratory-based analyses of collected field samples. To date, only a restricted range of life detection and characterization techniques have been applied in the field. Specific examples include direct observation and DNA-based techniques (microscopy, specific stains, and community profiling based on PCR amplification), the detection of biomarkers (such as adenosine triphosphate), and measurements of metabolism [through the uptake and incorporation of radiolabeled isotopes or chemical alteration of fluorescent substrates (umbelliferones are also useful here)]. On-going improvements in technology mean that smaller and more robust life detection and characterization systems are continually being designed, manufactured, and adapted for in-field use. Adapting technology designed for other applications is the main source of new methodology, and the range of techniques is currently increasing rapidly. Here we review the current use of technology and techniques to detect and characterize microbial life within icy environments and specifically its deployment to in-field situations. We discuss the necessary considerations, limitations, and adaptations, review emerging technologies, and highlight the future potential. Successful application of these new techniques to in-field studies will certainly generate new insights into the way ice bound ecosystems function. Copyright © 2012 Elsevier Inc. All rights reserved.

Direct observation of λ-DNA molecule reversal movement within microfluidic channels under electric field with single molecule imaging technique

NASA Astrophysics Data System (ADS)

Fengyun, Yang; Kaige, Wang; Dan, Sun; Wei, Zhao; Hai-qing, Wang; Xin, He; Gui-ren, Wang; Jin-tao, Bai

2016-07-01

The electrodynamic characteristics of single DNA molecules moving within micro-/nano-fluidic channels are important in the design of biomedical chips and bimolecular sensors. In this study, the dynamic properties of λ-DNA molecules transferring along the microchannels driven by the external electrickinetic force were systemically investigated with the single molecule fluorescence imaging technique. The experimental results indicated that the velocity of DNA molecules was strictly dependent on the value of the applied electric field and the diameter of the channel. The larger the external electric field, the larger the velocity, and the more significant deformation of DNA molecules. More meaningfully, it was found that the moving directions of DNA molecules had two completely different directions: (i) along the direction of the external electric field, when the electric field intensity was smaller than a certain threshold value; (ii) opposite to the direction of the external electric field, when the electric field intensity was greater than the threshold electric field intensity. The reversal movement of DNA molecules was mainly determined by the competition between the electrophoresis force and the influence of electro-osmosis flow. These new findings will theoretically guide the practical application of fluidic channel sensors and lab-on-chips for precisely manipulating single DNA molecules. Project supported by the National Natural Science Foundation of China (Grant No. 61378083), the International Cooperation Foundation of the National Science and Technology Major Project of the Ministry of Science and Technology of China (Grant No. 2011DFA12220), the Major Research Plan of National Natural Science Foundation of China (Grant No. 91123030), and the Natural Science Foundation of Shaanxi Province of China (Grant Nos. 2010JS110 and 2013SZS03-Z01).

Magnetic-field-induced DNA strand breaks in brain cells of the rat.

PubMed Central

Lai, Henry; Singh, Narendra P

2004-01-01

In previous research, we found that rats acutely (2 hr) exposed to a 60-Hz sinusoidal magnetic field at intensities of 0.1-0.5 millitesla (mT) showed increases in DNA single- and double-strand breaks in their brain cells. Further research showed that these effects could be blocked by pretreating the rats with the free radical scavengers melatonin and N-tert-butyl-alpha-phenylnitrone, suggesting the involvement of free radicals. In the present study, effects of magnetic field exposure on brain cell DNA in the rat were further investigated. Exposure to a 60-Hz magnetic field at 0.01 mT for 24 hr caused a significant increase in DNA single- and double-strand breaks. Prolonging the exposure to 48 hr caused a larger increase. This indicates that the effect is cumulative. In addition, treatment with Trolox (a vitamin E analog) or 7-nitroindazole (a nitric oxide synthase inhibitor) blocked magnetic-field-induced DNA strand breaks. These data further support a role of free radicals on the effects of magnetic fields. Treatment with the iron chelator deferiprone also blocked the effects of magnetic fields on brain cell DNA, suggesting the involvement of iron. Acute magnetic field exposure increased apoptosis and necrosis of brain cells in the rat. We hypothesize that exposure to a 60-Hz magnetic field initiates an iron-mediated process (e.g., the Fenton reaction) that increases free radical formation in brain cells, leading to DNA strand breaks and cell death. This hypothesis could have an important implication for the possible health effects associated with exposure to extremely low-frequency magnetic fields in the public and occupational environments. PMID:15121512

Investigation of wing upper surface flow-field disturbance due to NASA DC-8-72 in-flight inboard thrust-reverser deployment

NASA Technical Reports Server (NTRS)

Hamid, Hedayat U.; Margason, Richard J.; Hardy, Gordon

1995-01-01

An investigation of the wing upper surface flow-field disturbance due to in-flight inboard thrust reverser deployment on the NASA DC-8-72, which was conducted cooperatively by NASA Ames, the Federal Aviation Administration (FAA), McDonnell Douglas, and the Aerospace Industry Association (AIA), is outlined and discussed in detail. The purpose of this flight test was to obtain tufted flow visualization data which demonstrates the effect of thrust reverser deployment on the wing upper surface flow field to determine if the disturbed flow regions could be modeled by computational methods. A total of six symmetric thrust reversals of the two inboard engines were performed to monitor tuft and flow cone patterns as well as the character of their movement at the nominal Mach numbers of 0.55, 0.70, and 0.85. The tufts and flow cones were photographed and video-taped to determine the type of flow field that occurs with and without the thrust reversers deployed. In addition, the normal NASA DC-8 onboard Data Acquisition Distribution System (DADS) was used to synchronize the cameras. Results of this flight test will be presented in two parts. First, three distinct flow patterns associated with the above Mach numbers were sketched from the motion videos and discussed in detail. Second, other relevant aircraft parameters, such as aircraft's angular orientation, altitude, Mach number, and vertical descent, are discussed. The flight test participants' comments were recorded on the videos and the interested reader is referred to the video supplement section of this report for that information.

Using Consumer Electronics and Apps in Industrial Environments - Development of a Framework for Dynamic Feature Deployment and Extension by Using Apps on Field Devices

NASA Astrophysics Data System (ADS)

Schmitt, Mathias

2014-12-01

The aim of this paper is to give a preliminary insight regarding the current work in the field of mobile interaction in industrial environments by using established interaction technologies and metaphors from the consumer goods industry. The major objective is the development and implementation of a holistic app-framework, which enables dynamic feature deployment and extension by using mobile apps on industrial field devices. As a result, field device functionalities can be updated and adapted effectively in accordance with well-known appconcepts from consumer electronics to comply with the urgent requirements of more flexible and changeable factory systems of the future. In addition, a much more user-friendly and utilizable interaction with field devices can be realized. Proprietary software solutions and device-stationary user interfaces can be overcome and replaced by uniform, cross-vendor solutions

Coverage-guaranteed sensor node deployment strategies for wireless sensor networks.

PubMed

Fan, Gaojuan; Wang, Ruchuan; Huang, Haiping; Sun, Lijuan; Sha, Chao

2010-01-01

Deployment quality and cost are two conflicting aspects in wireless sensor networks. Random deployment, where the monitored field is covered by randomly and uniformly deployed sensor nodes, is an appropriate approach for large-scale network applications. However, their successful applications depend considerably on the deployment quality that uses the minimum number of sensors to achieve a desired coverage. Currently, the number of sensors required to meet the desired coverage is based on asymptotic analysis, which cannot meet deployment quality due to coverage overestimation in real applications. In this paper, we first investigate the coverage overestimation and address the challenge of designing coverage-guaranteed deployment strategies. To overcome this problem, we propose two deployment strategies, namely, the Expected-area Coverage Deployment (ECD) and BOundary Assistant Deployment (BOAD). The deployment quality of the two strategies is analyzed mathematically. Under the analysis, a lower bound on the number of deployed sensor nodes is given to satisfy the desired deployment quality. We justify the correctness of our analysis through rigorous proof, and validate the effectiveness of the two strategies through extensive simulation experiments. The simulation results show that both strategies alleviate the coverage overestimation significantly. In addition, we also evaluate two proposed strategies in the context of target detection application. The comparison results demonstrate that if the target appears at the boundary of monitored region in a given random deployment, the average intrusion distance of BOAD is considerably shorter than that of ECD with the same desired deployment quality. In contrast, ECD has better performance in terms of the average intrusion distance when the invasion of intruder is from the inside of monitored region.

Propulsive Small Expendable Deployer System (ProSEDS)

NASA Technical Reports Server (NTRS)

1999-01-01

NASA's Propulsive Small Expendable Deployer System experiment (ProSEDS) will demonstrate the use of an electrodynamic tether, basically a long, thin wire, for propulsion. An electrodynamic tether uses the same principles as electric motors in toys, appliances and computer disk drives, and generators in automobiles and power plants. When electrical current is flowing through the tether, a magnetic field is produced that pushes against the magnetic field of the Earth. For ProSEDS, the current in the tether results by virtue of the voltage generated when the tether moves through the Earth's magnetic field at more than 17,000 mph. This approach can produce drag thrust generating useable power. Since electrodynamic tethers require no propellant, they could substantially reduce the weight of the spacecraft and provide a cost-effective method of reboosting spacecraft. The initial flight of ProSEDS is scheduled to fly aboard an Air Force Delta II rocket in the summer of 2002. In orbit, ProSEDS will deploy from a Delta II second stage. It will be a 3.1-mile (5 kilometer) long, ultrathin base-wire cornected with a 6.2-mile (10 kilometer) long nonconducting tether. This photograph shows Less Johnson, a scientist at MSFC inspecting the nonconducting part of a tether as it exits a deployer similar to the one to be used in the ProSEDS experiment. The ProSEDS experiment is managed by the Space Transportation Directorate at MSFC.

Surgical workload of a foreign medical team after Typhoon Haiyan.

PubMed

Read, David J; Holian, Annette; Moller, Cea-Cea; Poutawera, Vaughan

2016-05-01

On 8 November 2013, Typhoon Haiyan struck the Philippines causing widespread loss of lives and infrastructures. At the request of the Government of the Philippines, the Australian Government deployed a surgical field hospital to the city of Tacloban for 4 weeks. This paper describes the establishment of the hospital, the surgical workload and handover to the local health system upon the end of deployment. A Microsoft excel database was utilized throughout the deployment, recording demographics, relationship to the typhoon and surgical procedure performed. Over the 21 days of surgical activity, the Australian field hospital performed 222 operations upon 131 persons. A mean of 10.8 procedures were performed per day (range 3-20). The majority (70.2%) of procedures were soft tissue surgery. Diabetes was present in 22.9% and 67.9% were typhoon-related. The Australian Medical Assistance Team field hospital adhered to the World Health Organization guidelines for foreign medical teams, in ensuring informed consent, appropriate anaesthesia and surgery, and worked collaboratively with local surgeons, ensuring adequate documentation and clinical handover. This paper describes the experience of a trained, equipped and collaborative surgical foreign medical team in Tacloban in the aftermath of Typhoon Haiyan. Sepsis from foot injuries in diabetic patients constituted an unexpected majority of the workload. New presentations of typhoon-related injuries were presented throughout the deployment. © 2015 Royal Australasian College of Surgeons.

Nano-funnels as electro-osmotic ``tweezers and pistons''

NASA Astrophysics Data System (ADS)

Wang, Yanqian; Panyukov, Sergey; Zhou, Jinsheng; Menard, Laurent D.; Ramsey, J. Michael; Rubinstien, Michael

2014-03-01

An electric field is used to force a DNA molecule into a nano-channel by compensating the free energy penalty that results from the reduced conformational entropy of the confined macromolecule. Narrow nano-channels require high critical electric fields to achieve DNA translocation, leading to short dwell times of DNA in these channels. We demonstrate that nano-funnels integrated with nano-channels reduce the free energy barrier and lower the critical electric field required for DNA translocation. A focused electric field within the funnel increases the electric force on the DNA, compresses the molecule, and increases the osmotic pressure at the nano-channel entrance. This ``electro-osmotic piston'' forces the molecule into the nano-channel at lower electric fields than those observed without the funnel. Appropirately designed nano-funnels can also function as tweezers that allow manipulation of the position of the DNA molecule. The predictions of our theory describing double-stranded DNA behavior in nano-funnel - nano-channel devices are consistent with experimental results. Thanks for the financial support from NSF (DMR-1309892, DMR-1121107, DMR-1122483), NIH (1-P50-HL107168, 1-P01-HL108808-01A1, R01HG02647), NHGRI and CF Foundation.

Acquisition of Oceanographic Measurements from Baleen Whales: Field Deployments of Tags Developed Under Grant ONR (N00014-13-1-0854)

DTIC Science & Technology

2014-09-30

and on blue and humpback whales in Iceland. • To evaluate the reliability and quality of CTD data collected in arctic ice covered waters by slow...swimming bowhead whales and from the open ocean by fast swimming blue and humpback whales . APPROACH Diving ocean predators can act as “real-time...2014: Deployment of tags on bowhead whales in Disko Bay. June-July 2015: Deployment of tags on blue and humpback whales in Iceland. April-December

DNA Immobilization and Hybridization Detection by the Intrinsic Molecular Charge Using Capacitive Field-Effect Sensors Modified with a Charged Weak Polyelectrolyte Layer.

PubMed

Bronder, Thomas S; Poghossian, Arshak; Scheja, Sabrina; Wu, Chunsheng; Keusgen, Michael; Mewes, Dieter; Schöning, Michael J

2015-09-16

Miniaturized setup, compatibility with advanced micro- and nanotechnologies, and ability to detect biomolecules by their intrinsic molecular charge favor the semiconductor field-effect platform as one of the most attractive approaches for the development of label-free DNA chips. In this work, a capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensor covered with a layer-by-layer prepared, positively charged weak polyelectrolyte layer of PAH (poly(allylamine hydrochloride)) was used for the label-free electrical detection of DNA (deoxyribonucleic acid) immobilization and hybridization. The negatively charged probe single-stranded DNA (ssDNA) molecules were electrostatically adsorbed onto the positively charged PAH layer, resulting in a preferentially flat orientation of the ssDNA molecules within the Debye length, thus yielding a reduced charge-screening effect and a higher sensor signal. Each sensor-surface modification step (PAH adsorption, probe ssDNA immobilization, hybridization with complementary target DNA (cDNA), reducing an unspecific adsorption by a blocking agent, incubation with noncomplementary DNA (ncDNA) solution) was monitored by means of capacitance-voltage and constant-capacitance measurements. In addition, the surface morphology of the PAH layer was studied by atomic force microscopy and contact-angle measurements. High hybridization signals of 34 and 43 mV were recorded in low-ionic strength solutions of 10 and 1 mM, respectively. In contrast, a small signal of 4 mV was recorded in the case of unspecific adsorption of fully mismatched ncDNA. The density of probe ssDNA and dsDNA molecules as well as the hybridization efficiency was estimated using the experimentally measured DNA immobilization and hybridization signals and a simplified double-layer capacitor model. The results of field-effect experiments were supported by fluorescence measurements, verifying the DNA-immobilization and hybridization event.

San Diego field operational test of smart call boxes : institutional issues

DOT National Transportation Integrated Search

1997-01-01

Important institutional lessons learned in the course of the San Diego smart call box field operational test are presented. These lessons relate both to the conduct of the field test itself and to requirements for deployment of intelligent transporta...

Applications of Dynamic Deployment of Services in Industrial Automation

NASA Astrophysics Data System (ADS)

Candido, Gonçalo; Barata, José; Jammes, François; Colombo, Armando W.

Service-oriented Architecture (SOA) is becoming a de facto paradigm for business and enterprise integration. SOA is expanding into several domains of application envisioning a unified solution suitable across all different layers of an enterprise infrastructure. The application of SOA based on open web standards can significantly enhance the interoperability and openness of those devices. By embedding a dynamical deployment service even into small field de- vices, it would be either possible to allow machine builders to place built- in services and still allow the integrator to deploy on-the-run the services that best fit his current application. This approach allows the developer to keep his own preferred development language, but still deliver a SOA- compliant application. A dynamic deployment service is envisaged as a fundamental framework to support more complex applications, reducing deployment delays, while increasing overall system agility. As use-case scenario, a dynamic deployment service was implemented over DPWS and WS-Management specifications allowing designing and programming an automation application using IEC61131 languages, and deploying these components as web services into devices.

Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping

PubMed Central

Normanno, Davide; Vanzi, Francesco; Pavone, Francesco Saverio

2008-01-01

Gene expression regulation is a fundamental biological process which deploys specific sets of genomic information depending on physiological or environmental conditions. Several transcription factors (including lac repressor, LacI) are present in the cell at very low copy number and increase their local concentration by binding to multiple sites on DNA and looping the intervening sequence. In this work, we employ single-molecule manipulation to experimentally address the role of DNA supercoiling in the dynamics and stability of LacI-mediated DNA looping. We performed measurements over a range of degrees of supercoiling between −0.026 and +0.026, in the absence of axial stretching forces. A supercoiling-dependent modulation of the lifetimes of both the looped and unlooped states was observed. Our experiments also provide evidence for multiple structural conformations of the LacI–DNA complex, depending on torsional constraints. The supercoiling-dependent modulation demonstrated here adds an important element to the model of the lac operon. In fact, the complex network of proteins acting on the DNA in a living cell constantly modifies its topological and mechanical properties: our observations demonstrate the possibility of establishing a signaling pathway from factors affecting DNA supercoiling to transcription factors responsible for the regulation of specific sets of genes. PMID:18310101

Deployment Health Surveillance

DTIC Science & Technology

2004-06-01

executing a rigorous pre- and post- deployment health screening program. Our healthcare providers practice preventive medicine, promote healthy lifestyles ...individual responsibility for their health and fitness. This includes avoidance of unhealthy behaviors like alcohol abuse and cigarette smoking...due to accident or disease. The basic principles of disease prevention in the field really haven’t changed much. Hand washing, food sanitation

Quick survey of avirulence genes in field isolates of Magnaporthe oryzae in the past 60 years

USDA-ARS?s Scientific Manuscript database

Avirulence (AVR) genes in Magnaporthe oryzae determine deployment of effective corresponding resistance (R) genes. Instability of AVR genes is the major cause for resistance breakdown. Information on the presence or absence (P/A) of AVR genes can be used as a predictor of the stability of deployed R...

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

PubMed

Lemkul, Justin A; MacKerell, Alexander D

2017-05-09

Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.

Power Hardware-in-the-Loop Evaluation of PV Inverter Grid Support on Hawaiian Electric Feeders: Preprint

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

Nelson, Austin; Prabakar, Kumaraguru; Nagarajan, Adarsh

As more grid-connected photovoltaic (PV) inverters become compliant with evolving interconnections requirements, there is increased interest from utilities in understanding how to best deploy advanced grid-support functions (GSF) in the field. One efficient and cost-effective method to examine such deployment options is to leverage power hardware-in-the-loop (PHIL) testing methods. Two Hawaiian Electric feeder models were converted to real-time models in the OPAL-RT real-time digital testing platform, and integrated with models of GSF capable PV inverters that were modeled from characterization test data. The integrated model was subsequently used in PHIL testing to evaluate the effects of different fixed power factormore » and volt-watt control settings on voltage regulation of the selected feeders. The results of this study were provided as inputs for field deployment and technical interconnection requirements for grid-connected PV inverters on the Hawaiian Islands.« less

Fabrication system, method and apparatus for microelectromechanical devices

NASA Technical Reports Server (NTRS)

Johnson, A. David (Inventor); Busta, Heinz H. (Inventor); Nowicki, Ronald S. (Inventor)

1999-01-01

A fabrication system and method of fabrication for producing microelectromechanical devices such as field-effect displays using thin-film technology. A spacer is carried at its proximal end on the surface of a substrate having field-effect emitters with the spacer being enabled for tilting movement from a nested position to a deployed position which is orthogonal to the plane of the substrate. An actuator is formed with one end connected with the substrate and another end connected with spacer. The actuator is made of a shape memory alloy material which contracts when heated through the material's phase-change transition temperature. Contraction of the actuator exerts a pulling force on the spacer which is tilted to the deployed position. A plurality of the spacers are distributed over the area of the display. A glass plate having a phosphor-coated surface is fitted over the distal ends of the deployed spacer.

Advanced Opto-Electronics (LIDAR and Microsensor Development)

NASA Technical Reports Server (NTRS)

Vanderbilt, Vern C. (Technical Monitor); Spangler, Lee H.

2005-01-01

Our overall intent in this aspect of the project were to establish a collaborative effort between several departments at Montana State University for developing advanced optoelectronic technology for advancing the state-of-the-art in optical remote sensing of the environment. Our particular focus was on development of small systems that can eventually be used in a wide variety of applications that might include ground-, air-, and space deployments, possibly in sensor networks. Specific objectives were to: 1) Build a field-deployable direct-detection lidar system for use in measurements of clouds, aerosols, fish, and vegetation; 2) Develop a breadboard prototype water vapor differential absorption lidar (DIAL) system based on highly stable, tunable diode laser technology developed previously at MSU. We accomplished both primary objectives of this project, in developing a field-deployable direct-detection lidar and a breadboard prototype of a water vapor DIAL system. Paper summarizes each of these accomplishments.

DNA-informed breeding of rosaceous crops: promises, progress and prospects

PubMed Central

Peace, Cameron P

2017-01-01

Crops of the Rosaceae family provide valuable contributions to rural economies and human health and enjoyment. Sustained solutions to production challenges and market demands can be met with genetically improved new cultivars. Traditional rosaceous crop breeding is expensive and time-consuming and would benefit from improvements in efficiency and accuracy. Use of DNA information is becoming conventional in rosaceous crop breeding, contributing to many decisions and operations, but only after past decades of solved challenges and generation of sufficient resources. Successes in deployment of DNA-based knowledge and tools have arisen when the ‘chasm’ between genomics discoveries and practical application is bridged systematically. Key steps are establishing breeder desire for use of DNA information, adapting tools to local breeding utility, identifying efficient application schemes, accessing effective services in DNA-based diagnostics and gaining experience in integrating DNA information into breeding operations and decisions. DNA-informed germplasm characterization for revealing identity and relatedness has benefitted many programs and provides a compelling entry point to reaping benefits of genomics research. DNA-informed germplasm evaluation for predicting trait performance has enabled effective reallocation of breeding resources when applied in pioneering programs. DNA-based diagnostics is now expanding from specific loci to genome-wide considerations. Realizing the full potential of this expansion will require improved accuracy of predictions, multi-trait DNA profiling capabilities, streamlined breeding information management systems, strategies that overcome plant-based features that limit breeding progress and widespread training of current and future breeding personnel and allied scientists. PMID:28326185

Trapping and breaking of in vivo nicked DNA during pulsed-field gel electrophoresis

PubMed Central

Khan, Sharik R.; Kuzminov, Andrei

2013-01-01

Pulsed field gel electrophoresis (PFGE) offers a high-resolution approach to quantify chromosomal fragmentation in bacteria, measured as percent of chromosomal DNA entering the gel. The degree of separation in PFG depends upon the size of DNA, as well as various conditions of electrophoresis, such as electric field strength (FS), time of electrophoresis, switch time and buffer composition. Here we describe a new parameter, the structural integrity of the sample DNA itself, that influences its migration through PFGs. We show that sub-chromosomal fragments containing both spontaneous and DNA damage-induced nicks are prone to breakage during PFGE. Such breakage at single strand interruptions results in artefactual decrease in molecular weight of linear DNA making accurate determination of the number of double strand breaks difficult. While breakage of nicked sub-chromosomal fragments is FS-independent, some high molecular weight sub-chromosomal fragments are also trapped within wells under the standard PFGE conditions. This trapping can be minimized by lowering the field strength and increasing the time of electrophoresis. We discuss how breakage of nicked DNA may be mechanistically linked to trapping. Our results suggest how to optimize conditions for PFGE when quantifying chromosomal fragmentation induced by DNA damage. PMID:23770235

HLA Typing for Bone Marrow Transplantation

DTIC Science & Technology

2011-07-21

Confirmatory Testing DC Donor Center DIY Do it yourself DNA Deoxyribonucleic Acid DOD Department of Defense D/R Donor/Recipient EBMT European...testing information is complete, thus allowing for report card analysis earlier in the process. • Deployed functionality to allow cord banks the ability...inventory was labeled with a new Report Card Status: “PreOrder Condition”). • Developed features to support Local IDs and International Society Blood

New Generator Technology

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

Nielsen, Roy S.

2015-02-17

New generator technology project is driven by the need to be able to remotely deploy generator technology where it is needed, when it is needed. Both the military and aid programs that provide assistance after disasters could use the ability to deploy energy generation that fits the needs of the situation. Currently, pre-specified generators are deployed, sometime more than half way around the world to provide electricity. Through our Phase-I to Phase III DARPA grant, we will provide a mechanism where a 3d print station and raw materials could be shipped to a deployment site and remotely deployed personnel. Thesemore » remote personnel can collaborate with engineers at a home location where 3d print plans can be optimized for the remote purpose. The plans can then be sent electronically to the remote location for printing, much like NASA sent the plans for a socket wrench to the International Space Station for printing in . If multiple generators need to be deployed at different remote locations, within miles of each other the printer rig can be moved to print the generators where they are needed. 3d printing is growing in the field of manufacturing. 3d printing has matured to the point where many types of materials are now available for many types of manufacturing. Both magnetic and electrically conductive material materials have recently been developed which can now lead to 3d printing of engines and generators. Our project will provide a successful printer rig that can be remotely deployed, to print a generator design in the field as well as provide a process for deploying the printed generator as well. This Systems Engineering Management Plan(SEMP) will provide the planning required for a Phase I DARPA grant that may also include goals for Phase II and Phase II grants. The SEMP provides a proposed project schedule, references, system engineering processes, specialty engineering system deployment and product support sections. Each section will state how our company will provide the necessary services to make this project succeed.« less

Electrostatic field of the large fragment of Escherichia coli DNA polymerase I.

PubMed

Warwicker, J; Ollis, D; Richards, F M; Steitz, T A

1985-12-05

The electrostatic field of the large fragment of Escherichia coli DNA polymerase I (Klenow fragment) has been calculated by the finite difference procedure on a 2 A grid. The potential field is substantially negative at physiological pH (reflecting the net negative charge at this pH). The largest regions of positive potential are in the deep crevice of the C-terminal domain, which is the proposed binding site for the DNA substrate. Within the crevice, the electrostatic potential has a partly helical form. If the DNA is positioned to fulfil stereochemical requirements, then the positive potential generally follows the major groove and (to a lesser extent) the negative potential is in the minor groove. Such an arrangement could stabilize DNA configurations related by screw symmetry. The histidine residues of the Klenow fragment give the positive field of the groove a sensitivity to relatively small pH changes around neutrality. We suggest that the histidine residues could change their ionization states in response to DNA binding, and that this effect could contribute to the protein-DNA binding energy.

Rule-Based vs. Behavior-Based Self-Deployment for Mobile Wireless Sensor Networks

PubMed Central

Urdiales, Cristina; Aguilera, Francisco; González-Parada, Eva; Cano-García, Jose; Sandoval, Francisco

2016-01-01

In mobile wireless sensor networks (MWSN), nodes are allowed to move autonomously for deployment. This process is meant: (i) to achieve good coverage; and (ii) to distribute the communication load as homogeneously as possible. Rather than optimizing deployment, reactive algorithms are based on a set of rules or behaviors, so nodes can determine when to move. This paper presents an experimental evaluation of both reactive deployment approaches: rule-based and behavior-based ones. Specifically, we compare a backbone dispersion algorithm with a social potential fields algorithm. Most tests are done under simulation for a large number of nodes in environments with and without obstacles. Results are validated using a small robot network in the real world. Our results show that behavior-based deployment tends to provide better coverage and communication balance, especially for a large number of nodes in areas with obstacles. PMID:27399709

DNA nanotechnology

NASA Astrophysics Data System (ADS)

Seeman, Nadrian C.; Sleiman, Hanadi F.

2018-01-01

DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

Recovery Based Nanowire Field-Effect Transistor Detection of Pathogenic Avian Influenza DNA

NASA Astrophysics Data System (ADS)

Lin, Chih-Heng; Chu, Chia-Jung; Teng, Kang-Ning; Su, Yi-Jr; Chen, Chii-Dong; Tsai, Li-Chu; Yang, Yuh-Shyong

2012-02-01

Fast and accurate diagnosis is critical in infectious disease surveillance and management. We proposed a DNA recovery system that can easily be adapted to DNA chip or DNA biosensor for fast identification and confirmation of target DNA. This method was based on the re-hybridization of DNA target with a recovery DNA to free the DNA probe. Functionalized silicon nanowire field-effect transistor (SiNW FET) was demonstrated to monitor such specific DNA-DNA interaction using high pathogenic strain virus hemagglutinin 1 (H1) DNA of avian influenza (AI) as target. Specific electric changes were observed in real-time for AI virus DNA sensing and device recovery when nanowire surface of SiNW FET was modified with complementary captured DNA probe. The recovery based SiNW FET biosensor can be further developed for fast identification and further confirmation of a variety of influenza virus strains and other infectious diseases.

Rapid concentration of deoxyribonucleic acid via Joule heating induced temperature gradient focusing in poly-dimethylsiloxane microfluidic channel.

PubMed

Ge, Zhengwei; Wang, Wei; Yang, Chun

2015-02-09

This paper reports rapid microfluidic electrokinetic concentration of deoxyribonucleic acid (DNA) with the Joule heating induced temperature gradient focusing (TGF) by using our proposed combined AC and DC electric field technique. A peak of 480-fold concentration enhancement of DNA sample is achieved within 40s in a simple poly-dimethylsiloxane (PDMS) microfluidic channel of a sudden expansion in cross-section. Compared to a sole DC field, the introduction of an AC field can reduce DC field induced back-pressure and produce sufficient Joule heating effects, resulting in higher concentration enhancement. Within such microfluidic channel structure, negative charged DNA analytes can be concentrated at a location where the DNA electrophoretic motion is balanced with the bulk flow driven by DC electroosmosis under an appropriate temperature gradient field. A numerical model accounting for a combined AC and DC field and back-pressure driven flow effects is developed to describe the complex Joule heating induced TGF processes. The experimental observation of DNA concentration phenomena can be explained by the numerical model. Copyright © 2014 Elsevier B.V. All rights reserved.

Total Quality Management (TQM) in Self-Financed Technical Institutions: A Quality Function Deployment (QFD) and Force Field Analysis Approach

ERIC Educational Resources Information Center

Thakkar, Jitesh; Deshmukh, S. G.; Shastree, Anil

2006-01-01

Purpose: To explore the potential for adoption of TQM in self-financed technical institutions in the light of new demands and challenges posed by customers/students and society. Design/methodology/approach: The paper presents use of quality function deployment (QFD) which prioritizes technical requirements and correlates them with various…

Pest Management Practices for the Military: Novel Field Studies to Develop Methods to Protect Deployed Troops from Mosquito, Filth/Biting Flies, and Sand Fly Vectors

USDA-ARS?s Scientific Manuscript database

New techniques that we developed to protect deployed military troops from the threat of vector-borne diseases and are also applicable for use by civilian mosquito control program use are described. Techniques illustrated included (1) novel military personal protection methods, (2) barrier treatments...

Effect of a magnetic field on the track structure of low-energy electrons: a Monte Carlo study

NASA Astrophysics Data System (ADS)

Bug, M. U.; Gargioni, E.; Guatelli, S.; Incerti, S.; Rabus, H.; Schulte, R.; Rosenfeld, A. B.

2010-10-01

The increasing use of MRI-guided radiation therapy evokes the necessity to investigate the potential impact of a magnetic field on the biological effectiveness of therapeutic radiation beams. While it is known that a magnetic field, applied during irradiation, can improve the macroscopic absorbed dose distribution of electrons in the tumor region, effects on the microscopic distribution of energy depositions and ionizations have not yet been investigated. An effect on the number of ionizations in a DNA segment, which is related to initial DNA damage in form of complex strand breaks, could be beneficial in radiation therapy. In this work we studied the effects of a magnetic field on the pattern of ionizations at nanometric level by means of Monte Carlo simulations using the Geant4-DNA toolkit. The track structure of low-energy electrons in the presence of a uniform static magnetic field of strength up to 14 T was calculated for a simplified DNA segment model in form of a water cylinder. In the case that no magnetic field is applied, nanodosimetric results obtained with Geant4-DNA were compared with those from the PTB track structure code. The obtained results suggest that any potential enhancement of complexity of DNA strand breaks induced by irradiation in a magnetic field is not related to modifications of the low-energy secondary electrons track structure.

Deploying a Proximal Sensing Cart to Identify Drought-Adaptive Traits in Upland Cotton for High-Throughput Phenotyping

PubMed Central

Thompson, Alison L.; Thorp, Kelly R.; Conley, Matthew; Andrade-Sanchez, Pedro; Heun, John T.; Dyer, John M.; White, Jeffery W.

2018-01-01

Field-based high-throughput phenotyping is an emerging approach to quantify difficult, time-sensitive plant traits in relevant growing conditions. Proximal sensing carts represent an alternative platform to more costly high-clearance tractors for phenotyping dynamic traits in the field. A proximal sensing cart and specifically a deployment protocol, were developed to phenotype traits related to drought tolerance in the field. The cart-sensor package included an infrared thermometer, ultrasonic transducer, multi-spectral reflectance sensor, weather station, and RGB cameras. The cart deployment protocol was evaluated on 35 upland cotton (Gossypium hirsutum L.) entries grown in 2017 at Maricopa, AZ, United States. Experimental plots were grown under well-watered and water-limited conditions using a (0,1) alpha lattice design and evaluated in June and July. Total collection time of the 0.87 hectare field averaged 2 h and 27 min and produced 50.7 MB and 45.7 GB of data from the sensors and RGB cameras, respectively. Canopy temperature, crop water stress index (CWSI), canopy height, normalized difference vegetative index (NDVI), and leaf area index (LAI) differed among entries and showed an interaction with the water regime (p < 0.05). Broad-sense heritability (H2) estimates ranged from 0.097 to 0.574 across all phenotypes and collections. Canopy cover estimated from RGB images increased with counts of established plants (r = 0.747, p = 0.033). Based on the cart-derived phenotypes, three entries were found to have improved drought-adaptive traits compared to a local adapted cultivar. These results indicate that the deployment protocol developed for the cart and sensor package can measure multiple traits rapidly and accurately to characterize complex plant traits under drought conditions. PMID:29868041

The specific host plant DNA detection suggests a potential migration of Apolygus lucorum from cotton to mungbean fields

PubMed Central

Bao, Wei-Fang; Yang, Fan; Xu, Bin; Yang, Yi-Zhong

2017-01-01

The polyphagous mirid bug Apolygus lucorum (Heteroptera: Miridae) has more than 200 species of host plants and is an insect pest of important agricultural crops, including cotton (Gossypium hirsutum) and mungbean (Vigna radiata). Previous field trials have shown that A. lucorum adults prefer mungbean to cotton plants, indicating the considerable potential of mungbean as a trap crop in cotton fields. However, direct evidence supporting the migration of A. lucorum adults from cotton to mungbean is lacking. We developed a DNA-based polymerase chain reaction (PCR) approach to reveal the movement of A. lucorum between neighboring mungbean and cotton fields. Two pairs of PCR primers specific to cotton or mungbean were designed to target the trnL-trnF region of chloroplast DNA. Significant differences in the detectability half-life (DS50) were observed between these two host plants, and the mean for cotton (8.26 h) was approximately two times longer than that of mungbean (4.38 h), requiring weighted mean calculations to compare the detectability of plant DNA in the guts of field-collected bugs. In field trials, cotton DNA was detected in the guts of the adult A. lucorum individuals collected in mungbean plots, and the cotton DNA detection rate decreased successively from 5 to 15 m away from the mungbean-cotton midline. In addition to the specific detection of cotton- and mungbean-fed bugs, both cotton and mungbean DNA were simultaneously detected within the guts of single individuals caught from mungbean fields. This study successfully established a tool for molecular gut-content analyses and clearly demonstrated the movement of A. lucorum adults from cotton to neighboring mungbean fields, providing new insights into understanding the feeding characteristics and landscape-level ecology of A. lucorum under natural conditions. PMID:28586352

DNA Nanotechnology for Cancer Therapy

PubMed Central

Kumar, Vinit; Palazzolo, Stefano; Bayda, Samer; Corona, Giuseppe; Toffoli, Giuseppe; Rizzolio, Flavio

2016-01-01

DNA nanotechnology is an emerging and exciting field, and represents a forefront frontier for the biomedical field. The specificity of the interactions between complementary base pairs makes DNA an incredible building material for programmable and very versatile two- and three-dimensional nanostructures called DNA origami. Here, we analyze the DNA origami and DNA-based nanostructures as a drug delivery system. Besides their physical-chemical nature, we dissect the critical factors such as stability, loading capability, release and immunocompatibility, which mainly limit in vivo applications. Special attention was dedicated to highlighting the boundaries to be overcome to bring DNA nanostructures closer to the bedside of patients. PMID:27022418

Temporal and spatial variability of aeolian sand transport: Implications for field measurements

NASA Astrophysics Data System (ADS)

Ellis, Jean T.; Sherman, Douglas J.; Farrell, Eugene J.; Li, Bailiang

2012-01-01

Horizontal variability is often cited as one source of disparity between observed and predicted rates of aeolian mass flux, but few studies have quantified the magnitude of this variability. Two field projects were conducted to evaluate meter-scale spatial and temporal in the saltation field. In Shoalhaven Heads, NSW, Australia a horizontal array of passive-style sand traps were deployed on a beach for 600 or 1200 s across a horizontal span of 0.80 m. In Jericoacoara, Brazil, traps spanning 4 m were deployed for 180 and 240 s. Five saltation sensors (miniphones) spaced 1 m apart were also deployed at Jericoacoara. Spatial variation in aeolian transport rates over small spatial and short temporal scales was substantial. The measured transport rates ( Q) obtained from the passive traps ranged from 0.70 to 32.63 g/m/s. When considering all traps, the coefficient of variation ( CoV) values ranged from 16.6% to 67.8%, and minimum and maximum range of variation coefficient ( RVC) values were 106.1% to 152.5% and 75.1% to 90.8%, respectively. The miniphone Q and CoV averaged 47.1% and 4.1% for the 1260 s data series, which was subsequently sub-sampled at 60-630 s intervals to simulate shorter deployment times. A statistically significant ( p < 0.002), inverselinear relationship was found between sample duration and CoV and between Q and CoV, the latter relationship also considering data from previous studies.

Applications of Sunphotometry to Aerosol Extinction and Surface Anisotropy

NASA Technical Reports Server (NTRS)

Tsay, S. C.; Holben, B. N.; Privette, J. L.

2005-01-01

Support cost-sharing of a newly developed sunphotometer in field deployment for aerosol studies. This is a cost-sharing research to deploy a newly developed sun-sky-surface photometer for studying aerosol extinction and surface anisotropy at the ARM SGP, TWP, and NSA-AAO CART sites and in many field campaigns. Atmospheric aerosols affect the radiative energy balance of the Earth, both directly by perturbing the incoming/outgoing radiation fields and indirectly by influencing the properties/processes of clouds and reactive greenhouse gases. The surface bidirectional reflectance distribution function (BRDF) also plays a crucial role in the radiative energy balance, since the BRDF is required to determine (1) the spectral and spectrally-averaged surface albedo, and (2) the top-of-the-atmosphere (TOA) angular distribution of radiance field. Therefore, the CART sites provide an excellent, albeit unique, opportunity to collect long-term climatic data in characterizing aerosol properties and various types of surface anisotropy.

Mobile phone tools for field-based health care workers in low-income countries.

PubMed

Derenzi, Brian; Borriello, Gaetano; Jackson, Jonathan; Kumar, Vikram S; Parikh, Tapan S; Virk, Pushwaz; Lesh, Neal

2011-01-01

In low-income regions, mobile phone-based tools can improve the scope and efficiency of field health workers. They can also address challenges in monitoring and supervising a large number of geographically distributed health workers. Several tools have been built and deployed in the field, but little comparison has been done to help understand their effectiveness. This is largely because no framework exists in which to analyze the different ways in which the tools help strengthen existing health systems. In this article we highlight 6 key functions that health systems currently perform where mobile tools can provide the most benefit. Using these 6 health system functions, we compare existing applications for community health workers, an important class of field health workers who use these technologies, and discuss common challenges and lessons learned about deploying mobile tools. © 2011 Mount Sinai School of Medicine.

Field deployment of a scope for growth assay involving Gammarus pulex, a freshwater benthic invertebrate.

PubMed

Maltby, L; Naylor, C; Calow, P

1990-06-01

Scope for growth (SfG) is a measure of the energy balance of an animal (i.e., the difference between energy intake and metabolic output). The SfG of marine invertebrates, particularly the mussel Mytilus edulis, has been successfully used as the basis of a field bioassay to detect a range of stresses both natural (temperature, food, salinity) and anthropogenic (hydrocarbons, sewage sludge). SfG of the freshwater amphipod Gammarus pulex was found to be a sensitive indicator of stress under laboratory conditions and here we describe the field deployment of this technique and present data from three field trials. In every case, SfG was reduced at the downstream polluted site compared with that at an upstream reference site. This reduction in SfG was the result of a decrease in energy intake (absorption) rather than an increase in energy expenditure (respiration).

The establishment and application of direct coupled electrostatic-structural field model in electrostatically controlled deployable membrane antenna

NASA Astrophysics Data System (ADS)

Gu, Yongzhen; Duan, Baoyan; Du, Jingli

2018-05-01

The electrostatically controlled deployable membrane antenna (ECDMA) is a promising space structure due to its low weight, large aperture and high precision characteristics. However, it is an extreme challenge to describe the coupled field between electrostatic and membrane structure accurately. A direct coupled method is applied to solve the coupled problem in this paper. Firstly, the membrane structure and electrostatic field are uniformly described by energy, considering the coupled problem is an energy conservation phenomenon. Then the direct coupled electrostatic-structural field governing equilibrium equations are obtained by energy variation approach. Numerical results show that the direct coupled method improves the computing efficiency by 36% compared with the traditional indirect coupled method with the same level accuracy. Finally, the prototype has been manufactured and tested and the ECDMA finite element simulations show good agreement with the experiment results as the maximum surface error difference is 6%.

Social Learning Strategies: Bridge-Building between Fields.

PubMed

Kendal, Rachel L; Boogert, Neeltje J; Rendell, Luke; Laland, Kevin N; Webster, Mike; Jones, Patricia L

2018-07-01

While social learning is widespread, indiscriminate copying of others is rarely beneficial. Theory suggests that individuals should be selective in what, when, and whom they copy, by following 'social learning strategies' (SLSs). The SLS concept has stimulated extensive experimental work, integrated theory, and empirical findings, and created impetus to the social learning and cultural evolution fields. However, the SLS concept needs updating to accommodate recent findings that individuals switch between strategies flexibly, that multiple strategies are deployed simultaneously, and that there is no one-to-one correspondence between psychological heuristics deployed and resulting population-level patterns. The field would also benefit from the simultaneous study of mechanism and function. SLSs provide a useful vehicle for bridge-building between cognitive psychology, neuroscience, and evolutionary biology. Copyright © 2018. Published by Elsevier Ltd.

Timing matters: error-prone gap filling and translesion synthesis in immunoglobulin gene hypermutation

PubMed Central

Sale, Julian E.; Batters, Christopher; Edmunds, Charlotte E.; Phillips, Lara G.; Simpson, Laura J.; Szüts, Dávid

2008-01-01

By temporarily deferring the repair of DNA lesions encountered during replication, the bypass of DNA damage is critical to the ability of cells to withstand genomic insults. Damage bypass can be achieved either by recombinational mechanisms that are generally accurate or by a process called translesion synthesis. Translesion synthesis involves replacing the stalled replicative polymerase with one of a number of specialized DNA polymerases whose active sites are able to tolerate a distorted or damaged DNA template. While this property allows the translesion polymerases to synthesize across damaged bases, it does so with the trade-off of an increased mutation rate. The deployment of these enzymes must therefore be carefully regulated. In addition to their important role in general DNA damage tolerance and mutagenesis, the translesion polymerases play a crucial role in converting the products of activation induced deaminase-catalysed cytidine deamination to mutations during immunoglobulin gene somatic hypermutation. In this paper, we specifically consider the control of translesion synthesis in the context of the timing of lesion bypass relative to replication fork progression and arrest at sites of DNA damage. We then examine how recent observations concerning the control of translesion synthesis might help refine our view of the mechanisms of immunoglobulin gene somatic hypermutation. PMID:19008194

Chondroitin sulfate-polyethylenimine copolymer-coated superparamagnetic iron oxide nanoparticles as an efficient magneto-gene carrier for microRNA-encoding plasmid DNA delivery

NASA Astrophysics Data System (ADS)

Lo, Yu-Lun; Chou, Han-Lin; Liao, Zi-Xian; Huang, Shih-Jer; Ke, Jyun-Han; Liu, Yu-Sheng; Chiu, Chien-Chih; Wang, Li-Fang

2015-04-01

MicroRNA-128 (miR-128) is an attractive therapeutic molecule with powerful glioblastoma regulation properties. However, miR-128 lacks biological stability and leads to poor delivery efficacy in clinical applications. In our previous study, we demonstrated two effective transgene carriers, including polyethylenimine (PEI)-decorated superparamagnetic iron oxide nanoparticles (SPIONs) as well as chemically-conjugated chondroitin sulfate-PEI copolymers (CPs). In this contribution, we report optimized conditions for coating CPs onto the surfaces of SPIONs, forming CPIOs, for magneto-gene delivery systems. The optimized weight ratio of the CPs and SPIONs is 2 : 1, which resulted in the formation of a stable particle as a good transgene carrier. The hydrodynamic diameter of the CPIOs is ~136 nm. The gel electrophoresis results demonstrate that the weight ratio of CPIO/DNA required to completely encapsulate pDNA is >=3. The in vitro tests of CPIO/DNA were done in 293 T, CRL5802, and U87-MG cells in the presence and absence of an external magnetic field. The magnetofection efficiency of CPIO/DNA was measured in the three cell lines with or without fetal bovine serum (FBS). CPIO/DNA exhibited remarkably improved gene expression in the presence of the magnetic field and 10% FBS as compared with a gold non-viral standard, PEI/DNA, and a commercial magnetofection reagent, PolyMag/DNA. In addition, CPIO/DNA showed less cytotoxicity than PEI/DNA and PolyMag/DNA against the three cell lines. The transfection efficiency of the magnetoplex improved significantly with an assisted magnetic field. In miR-128 delivery, a microRNA plate array and fluorescence in situ hybridization were used to demonstrate that CPIO/pMIRNA-128 indeed expresses more miR-128 with the assisted magnetic field than without. In a biodistribution test, CPIO/Cy5-DNA showed higher accumulation at the tumor site where an external magnet is placed nearby.MicroRNA-128 (miR-128) is an attractive therapeutic molecule with powerful glioblastoma regulation properties. However, miR-128 lacks biological stability and leads to poor delivery efficacy in clinical applications. In our previous study, we demonstrated two effective transgene carriers, including polyethylenimine (PEI)-decorated superparamagnetic iron oxide nanoparticles (SPIONs) as well as chemically-conjugated chondroitin sulfate-PEI copolymers (CPs). In this contribution, we report optimized conditions for coating CPs onto the surfaces of SPIONs, forming CPIOs, for magneto-gene delivery systems. The optimized weight ratio of the CPs and SPIONs is 2 : 1, which resulted in the formation of a stable particle as a good transgene carrier. The hydrodynamic diameter of the CPIOs is ~136 nm. The gel electrophoresis results demonstrate that the weight ratio of CPIO/DNA required to completely encapsulate pDNA is >=3. The in vitro tests of CPIO/DNA were done in 293 T, CRL5802, and U87-MG cells in the presence and absence of an external magnetic field. The magnetofection efficiency of CPIO/DNA was measured in the three cell lines with or without fetal bovine serum (FBS). CPIO/DNA exhibited remarkably improved gene expression in the presence of the magnetic field and 10% FBS as compared with a gold non-viral standard, PEI/DNA, and a commercial magnetofection reagent, PolyMag/DNA. In addition, CPIO/DNA showed less cytotoxicity than PEI/DNA and PolyMag/DNA against the three cell lines. The transfection efficiency of the magnetoplex improved significantly with an assisted magnetic field. In miR-128 delivery, a microRNA plate array and fluorescence in situ hybridization were used to demonstrate that CPIO/pMIRNA-128 indeed expresses more miR-128 with the assisted magnetic field than without. In a biodistribution test, CPIO/Cy5-DNA showed higher accumulation at the tumor site where an external magnet is placed nearby. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr01404b

DNA barcoding for biosecurity: case studies from the UK plant protection program.

PubMed

Hodgetts, Jennifer; Ostojá-Starzewski, Jozef C; Prior, Thomas; Lawson, Rebecca; Hall, Jayne; Boonham, Neil

2016-11-01

Since its conception, DNA barcoding has seen a rapid uptake within the research community. Nevertheless, as with many new scientific tools, progression towards the point of routine deployment within diagnostic laboratories has been slow. In this paper, we discuss the application of DNA barcoding in the Defra plant health diagnostic laboratories, where DNA barcoding is used primarily for the identification of invertebrate pests. We present a series of case studies that demonstrate the successful application of DNA barcoding but also reveal some potential limitations to expanded use. The regulated plant pest, Bursephalenchus xylophilus, and one of its vectors, Monochamus alternatus, were found in dining chairs. Some traded wood products are potentially high risk, allowing the movement of longhorn beetles; Trichoferus campestris, Leptura quadrifasciata, and Trichoferus holosericeus were found in a wooden cutlery tray, a railway sleeper, and a dining chair, respectively. An outbreak of Meloidogyne fallax was identified in Allium ampeloprasum and in three weed species. Reference sequences for UK native psyllids were generated to enable the development of rapid diagnostics to be used for monitoring following the release of Aphalara itadori as a biological control agent for Fallopia japonica.

[Application of new technologies in the design, manufacture and use of technology deployment of field medical units and establishments].

PubMed

Iakovlev, S V; Sidorov, V A; Korniushko, I G; Medvedev, V R; Matveev, A G

2011-11-01

Presented data is about attendance means of deployment of field medical units and pieces of army-level medical services and disaster medicine Defense Ministry did not ensure compliance with requirements to create optimal conditions for highly effective work of the medical staff, placing the wounded, the use of modern aids and appliances. The prospects of creation of mobile unit for high-availability modular pre-fabricated on the basis of tent structures, pneumoconstructions and removable habitable bodies, containers, tents, pneumocovers till 2020 are analyzed. Livelihood systems provide armor protection against fragments, bullets, flames, damaging factors of chemical and biological weapons.

The acoustic field of singing humpback whales in the vertical plane

NASA Astrophysics Data System (ADS)

Au, Whitlow W. L.; Pack, Adam A.; Lammers, Marc O.; Herman, Louis; Andrews, Kimberly; Deakos, Mark

2003-04-01

A vertical array of five hydrophones was used to measure the acoustic field of singing humpback whales. Once a singer was located, two swimmers with snorkel gear were deployed to determine the orientation of the whale and to position the boat so that the array could be deployed in front of the whale at a minimum standoff distance of 10 m. The spacing of the hydrophones was 7 m with the deepest hydrophone deployed at depth of 35 m. An 8-channel TASCAM recorder having a bandwidth of 24 kHz was used to record the hydrophone signals. The location of the singer was determined by computing the time of arrival differences between the hydrophone signals. The maximum source level varied between individual units in a song, with values between 180 and 190 dB. The acoustic field determined by considering the relative intensity of higher frequency harmonics in the signals indicate that the sounds are projected in the horizontal direction with the singer's head canted downward 45 to 60°. High-frequency harmonics extended beyond 24 kHz, suggesting that humpback whales may have an upper frequency limit of hearing as high as 24 kHz.

Genome-wide map of Apn1 binding sites under oxidative stress in Saccharomyces cerevisiae.

PubMed

Morris, Lydia P; Conley, Andrew B; Degtyareva, Natalya; Jordan, I King; Doetsch, Paul W

2017-11-01

The DNA is cells is continuously exposed to reactive oxygen species resulting in toxic and mutagenic DNA damage. Although the repair of oxidative DNA damage occurs primarily through the base excision repair (BER) pathway, the nucleotide excision repair (NER) pathway processes some of the same lesions. In addition, damage tolerance mechanisms, such as recombination and translesion synthesis, enable cells to tolerate oxidative DNA damage, especially when BER and NER capacities are exceeded. Thus, disruption of BER alone or disruption of BER and NER in Saccharomyces cerevisiae leads to increased mutations as well as large-scale genomic rearrangements. Previous studies demonstrated that a particular region of chromosome II is susceptible to chronic oxidative stress-induced chromosomal rearrangements, suggesting the existence of DNA damage and/or DNA repair hotspots. Here we investigated the relationship between oxidative damage and genomic instability utilizing chromatin immunoprecipitation combined with DNA microarray technology to profile DNA repair sites along yeast chromosomes under different oxidative stress conditions. We targeted the major yeast AP endonuclease Apn1 as a representative BER protein. Our results indicate that Apn1 target sequences are enriched for cytosine and guanine nucleotides. We predict that BER protects these sites in the genome because guanines and cytosines are thought to be especially susceptible to oxidative attack, thereby preventing large-scale genome destabilization from chronic accumulation of DNA damage. Information from our studies should provide insight into how regional deployment of oxidative DNA damage management systems along chromosomes protects against large-scale rearrangements. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi.

PubMed

Krüger, Manuela; Stockinger, Herbert; Krüger, Claudia; Schüssler, Arthur

2009-01-01

* At present, molecular ecological studies of arbuscular mycorrhizal fungi (AMF) are only possible above species level when targeting entire communities. To improve molecular species characterization and to allow species level community analyses in the field, a set of newly designed AMF specific PCR primers was successfully tested. * Nuclear rDNA fragments from diverse phylogenetic AMF lineages were sequenced and analysed to design four primer mixtures, each targeting one binding site in the small subunit (SSU) or large subunit (LSU) rDNA. To allow species resolution, they span a fragment covering the partial SSU, whole internal transcribed spacer (ITS) rDNA region and partial LSU. * The new primers are suitable for specifically amplifying AMF rDNA from material that may be contaminated by other organisms (e.g., samples from pot cultures or the field), characterizing the diversity of AMF species from field samples, and amplifying a SSU-ITS-LSU fragment that allows phylogenetic analyses with species level resolution. * The PCR primers can be used to monitor entire AMF field communities, based on a single rDNA marker region. Their application will improve the base for deep sequencing approaches; moreover, they can be efficiently used as DNA barcoding primers.

Frequency and Voltage Dependence of the Dielectrophoretic Trapping of Short Lengths of DNA and dCTP in a Nanopipette

PubMed Central

Ying, Liming; White, Samuel S.; Bruckbauer, Andreas; Meadows, Lisa; Korchev, Yuri E.; Klenerman, David

2004-01-01

The study of the properties of DNA under high electric fields is of both fundamental and practical interest. We have exploited the high electric fields produced locally in the tip of a nanopipette to probe the motion of double- and single-stranded 40-mer DNA, a 1-kb single-stranded DNA, and a single-nucleotide triphosphate (dCTP) just inside and outside the pipette tip at different frequencies and amplitudes of applied voltages. We used dual laser excitation and dual color detection to simultaneously follow two fluorophore-labeled DNA sequences with millisecond time resolution, significantly faster than studies to date. A strong trapping effect was observed during the negative half cycle for all DNA samples and also the dCTP. This effect was maximum below 1 Hz and decreased with higher frequency. We assign this trapping to strong dielectrophoresis due to the high electric field and electric field gradient in the pipette tip. Dielectrophoresis in electrodeless tapered nanostructures has potential applications for controlled mixing and manipulation of short lengths of DNA and other biomolecules, opening new possibilities in miniaturized biological analysis. PMID:14747337

Microwave-field-driven acoustic modes in DNA.

PubMed Central

Edwards, G S; Davis, C C; Saffer, J D; Swicord, M L

1985-01-01

The direct coupling of a microwave field to selected DNA molecules is demonstrated using standard dielectrometry. The absorption is resonant with a typical lifetime of 300 ps. Such a long lifetime is unexpected for DNA in aqueous solution at room temperature. Resonant absorption at fundamental and harmonic frequencies for both supercoiled circular and linear DNA agrees with an acoustic mode model. Our associated acoustic velocities for linear DNA are very close to the acoustic velocity of the longitudinal acoustic mode independently observed on DNA fibers using Brillouin spectroscopy. The difference in acoustic velocities for supercoiled circular and linear DNA is discussed in terms of solvent shielding of the nonbonded potentials in DNA. Images FIGURE 5 FIGURE 6 FIGURE 7 PMID:3893557

Return to contingency: developing a coherent strategy for future R2E/R3 land medical capabilities.

PubMed

Ingram, Mike; Mahan, J

2015-03-01

Key to deploying forces in the future will be the provision of a rapidly deployable Deployed Hospital Capability. Developing this capability has been the focus of 34 Field Hospital and 2nd Medical Brigade over the last 18 months and this paper describes a personal account of this development work to date. Future contingent Deployed Hospital Capability must meet the requirements of Defence; that is to be rapidly deployable delivering a hospital standard of care. The excellence seen in clinical delivery on recent operations is intensive; in personnel, equipment, infrastructure and sustainment. The challenge in developing a coherent capability has been in balancing the clinical capability and capacity against strategic load in light of recent advances in battlefield medicine. This paper explores the issues encountered and solutions found to date in reconstituting a Very High Readiness Deployed Hospital Capability. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Equine behavioral enrichment toys as tools for non-invasive recovery of viral and host DNA.

PubMed

Seeber, Peter A; Soilemetzidou, Sanatana E; East, Marion L; Walzer, Chris; Greenwood, Alex D

2017-09-01

Direct collection of samples from wildlife can be difficult and sometimes impossible. Non-invasive remote sampling for the purpose of DNA extraction is a potential tool for monitoring the presence of wildlife at the individual level, and for identifying the pathogens shed by wildlife. Equine herpesviruses (EHV) are common pathogens of equids that can be fatal if transmitted to other mammals. Transmission usually occurs by nasal aerosol discharge from virus-shedding individuals. The aim of this study was to validate a simple, non-invasive method to track EHV shedding in zebras and to establish an efficient protocol for genotyping individual zebras from environmental DNA (eDNA). A commercially available horse enrichment toy was deployed in captive Grévy's, mountain, and plains zebra enclosures and swabbed after 4-24 hr. Using eDNA extracted from these swabs four EHV strains (EHV-1, EHV-7, wild ass herpesvirus and zebra herpesvirus) were detected by PCR and confirmed by sequencing, and 12 of 16 zebras present in the enclosures were identified as having interacted with the enrichment toy by mitochondrial DNA amplification and sequencing. We conclude that, when direct sampling is difficult or prohibited, non-invasive sampling of eDNA can be a useful tool to determine the genetics of individuals or populations and for detecting pathogen shedding in captive wildlife. © 2017 Wiley Periodicals, Inc.

Profiling Nematode Communities in Unmanaged Flowerbed and Agricultural Field Soils in Japan by DNA Barcode Sequencing

PubMed Central

Morise, Hisashi; Miyazaki, Erika; Yoshimitsu, Shoko; Eki, Toshihiko

2012-01-01

Soil nematodes play crucial roles in the soil food web and are a suitable indicator for assessing soil environments and ecosystems. Previous nematode community analyses based on nematode morphology classification have been shown to be useful for assessing various soil environments. Here we have conducted DNA barcode analysis for soil nematode community analyses in Japanese soils. We isolated nematodes from two different environmental soils of an unmanaged flowerbed and an agricultural field using the improved flotation-sieving method. Small subunit (SSU) rDNA fragments were directly amplified from each of 68 (flowerbed samples) and 48 (field samples) isolated nematodes to determine the nucleotide sequence. Sixteen and thirteen operational taxonomic units (OTUs) were obtained by multiple sequence alignment from the flowerbed and agricultural field nematodes, respectively. All 29 SSU rDNA-derived OTUs (rOTUs) were further mapped onto a phylogenetic tree with 107 known nematode species. Interestingly, the two nematode communities examined were clearly distinct from each other in terms of trophic groups: Animal predators and plant feeders were markedly abundant in the flowerbed soils, in contrast, bacterial feeders were dominantly observed in the agricultural field soils. The data from the flowerbed nematodes suggests a possible food web among two different trophic nematode groups and plants (weeds) in the closed soil environment. Finally, DNA sequences derived from the mitochondrial cytochrome oxidase c subunit 1 (COI) gene were determined as a DNA barcode from 43 agricultural field soil nematodes. These nematodes were assigned to 13 rDNA-derived OTUs, but in the COI gene analysis were assigned to 23 COI gene-derived OTUs (cOTUs), indicating that COI gene-based barcoding may provide higher taxonomic resolution than conventional SSU rDNA-barcoding in soil nematode community analysis. PMID:23284767

Environmental Assessment/Overseas Environmental Assessment for the F-35 Joint Strike Fighter Initial Operational Test and Evaluation

DTIC Science & Technology

2009-09-01

NAS Lemoore; Yolk Field ANGB; Alpena 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF 18. NUMBER 19a. NAME OF RESPONSIBLE PERSON a. REPORT...Currently identified preferred locations for conducting deployment demonstrations are Alpena Combat Readiness Training Center (CRTC), Michigan; Edwards...3-5 3.1.3 Deployment Demonstration Locations .............................................................3-5 3.1.3.1 Alpena Combat Range Test

Nonstrategic Nuclear Weapons

DTIC Science & Technology

2017-02-21

missiles; cruise missiles; and gravity bombs . In contrast with the longer-range “strategic” nuclear weapons, these weapons had a lower profile in policy...States sought to deploy dual-capable aircraft and nuclear bombs at bases on the territories of NATO members in eastern Europe. Neither NATO, as an...ballistic missiles; cruise missiles; and gravity bombs . The United States deployed these weapons with its troops in the field, aboard aircraft, on

Deployment Considerations for Low-cost Air Quality Sensor Networks; Examining Spatial Variability of Gas-Phase Pollutants Around a Building in Los Angeles

NASA Astrophysics Data System (ADS)

Collier-Oxandale, A. M.; Hannigan, M.; Casey, J. G.; Johnston, J.; Coffey, E.; Thorson, J.

2017-12-01

The field of low-cost air quality sensing technologies is growing rapidly through the continual development of new sensors, increased research into sensor performance, and more and more community groups utilizing sensors to investigate local issues. However, as this technology is still in an exploratory phase, there are few `best-practices' available to serve as guidelines for these projects and the standardization of some procedures could benefit the research community as a whole. For example, deployment considerations such as where and how to place a monitor at a given location are often determined by accessibility and safety, power-requirements, and what is an ideal for sampling the target pollutant. Using data from multiple gas-phase sensors, we will examine the importance of siting considerations for low-cost monitoring systems. During a sampling campaign in Los Angeles, a subset of monitors was deployed at one field site to explore the variability in air quality sensor data around a single building. The site is a three story, multi-family housing unit in a primarily residential neighborhood that is near two major roadways and other potential sources of pollution. Five low-cost monitors were co-located prior to and following the field deployment. During the approximately 2.5-month deployment, these monitors were placed at various heights above street level, on different sides of the building, and on the roof. In our analysis, we will examine how monitor placement affects a sensor's ability to detect local verses more regional trends and how this building-scale spatial variability changes over time. Additionally, examining data from VOC sensors (quantified for methane and total non-methane hydrocarbon signals) and O3 sensors will allow us to compare the variability of primary and secondary pollutants. An outcome of this analysis may include guidelines or `best practices' for siting sensors that could aid in ensuring the collection of high quality field data. These may be particularly useful in community-based projects where monitor siting is typically a collaborative process.

Acadia National Park ITS field operational test : visitor survey

DOT National Transportation Integrated Search

2003-02-01

In 2002, as part of the Acadia National Park Field Operational Test, Intelligent Transportation Systems (ITS) components were deployed to help visitors travel around Mount Desert Island and in Acadia National Park. Using data from surveys of visitors...

Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests.

PubMed

Lee, Ping-Shin; Gan, Han Ming; Clements, Gopalasamy Reuben; Wilson, John-James

2016-11-01

Mammal diversity assessments based on DNA derived from invertebrates have been suggested as alternatives to assessments based on traditional methods; however, no study has field-tested both approaches simultaneously. In Peninsular Malaysia, we calibrated the performance of mammal DNA derived from blowflies (Diptera: Calliphoridae) against traditional methods used to detect species. We first compared five methods (cage trapping, mist netting, hair trapping, scat collection, and blowfly-derived DNA) in a forest reserve with no recent reports of megafauna. Blowfly-derived DNA and mist netting detected the joint highest number of species (n = 6). Only one species was detected by multiple methods. Compared to the other methods, blowfly-derived DNA detected both volant and non-volant species. In another forest reserve, rich in megafauna, we calibrated blowfly-derived DNA against camera traps. Blowfly-derived DNA detected more species (n = 11) than camera traps (n = 9), with only one species detected by both methods. The rarefaction curve indicated that blowfly-derived DNA would continue to detect more species with greater sampling effort. With further calibration, blowfly-derived DNA may join the list of traditional field methods. Areas for further investigation include blowfly feeding and dispersal biology, primer biases, and the assembly of a comprehensive and taxonomically-consistent DNA barcode reference library.

A simplified field protocol for genetic sampling of birds using buccal swabs

USGS Publications Warehouse

Vilstrup, Julia T.; Mullins, Thomas D.; Miller, Mark P.; McDearman, Will; Walters, Jeffrey R.; Haig, Susan M.

2018-01-01

DNA sampling is an essential prerequisite for conducting population genetic studies. For many years, blood sampling has been the preferred method for obtaining DNA in birds because of their nucleated red blood cells. Nonetheless, use of buccal swabs has been gaining favor because they are less invasive yet still yield adequate amounts of DNA for amplifying mitochondrial and nuclear markers; however, buccal swab protocols often include steps (e.g., extended air-drying and storage under frozen conditions) not easily adapted to field settings. Furthermore, commercial extraction kits and swabs for buccal sampling can be expensive for large population studies. We therefore developed an efficient, cost-effective, and field-friendly protocol for sampling wild birds after comparing DNA yield among 3 inexpensive buccal swab types (2 with foam tips and 1 with a cotton tip). Extraction and amplification success was high (100% and 97.2% respectively) using inexpensive generic swabs. We found foam-tipped swabs provided higher DNA yields than cotton-tipped swabs. We further determined that omitting a drying step and storing swabs in Longmire buffer increased efficiency in the field while still yielding sufficient amounts of DNA for detailed population genetic studies using mitochondrial and nuclear markers. This new field protocol allows time- and cost-effective DNA sampling of juveniles or small-bodied birds for which drawing blood may cause excessive stress to birds and technicians alike.

Structural DNA Nanotechnology: Artificial Nanostructures for Biomedical Research.

PubMed

Ke, Yonggang; Castro, Carlos; Choi, Jong Hyun

2018-06-04

Structural DNA nanotechnology utilizes synthetic or biologic DNA as designer molecules for the self-assembly of artificial nanostructures. The field is founded upon the specific interactions between DNA molecules, known as Watson-Crick base pairing. After decades of active pursuit, DNA has demonstrated unprecedented versatility in constructing artificial nanostructures with significant complexity and programmability. The nanostructures could be either static, with well-controlled physicochemical properties, or dynamic, with the ability to reconfigure upon external stimuli. Researchers have devoted considerable effort to exploring the usability of DNA nanostructures in biomedical research. We review the basic design methods for fabricating both static and dynamic DNA nanostructures, along with their biomedical applications in fields such as biosensing, bioimaging, and drug delivery.

Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens

PubMed Central

Rey, Jean-François; Barrett, Luke G.; Thrall, Peter H.

2018-01-01

Genetically-controlled plant resistance can reduce the damage caused by pathogens. However, pathogens have the ability to evolve and overcome such resistance. This often occurs quickly after resistance is deployed, resulting in significant crop losses and a continuing need to develop new resistant cultivars. To tackle this issue, several strategies have been proposed to constrain the evolution of pathogen populations and thus increase genetic resistance durability. These strategies mainly rely on varying different combinations of resistance sources across time (crop rotations) and space. The spatial scale of deployment can vary from multiple resistance sources occurring in a single cultivar (pyramiding), in different cultivars within the same field (cultivar mixtures) or in different fields (mosaics). However, experimental comparison of the efficiency (i.e. ability to reduce disease impact) and durability (i.e. ability to limit pathogen evolution and delay resistance breakdown) of landscape-scale deployment strategies presents major logistical challenges. Therefore, we developed a spatially explicit stochastic model able to assess the epidemiological and evolutionary outcomes of the four major deployment options described above, including both qualitative resistance (i.e. major genes) and quantitative resistance traits against several components of pathogen aggressiveness: infection rate, latent period duration, propagule production rate, and infectious period duration. This model, implemented in the R package landsepi, provides a new and useful tool to assess the performance of a wide range of deployment options, and helps investigate the effect of landscape, epidemiological and evolutionary parameters. This article describes the model and its parameterisation for rust diseases of cereal crops, caused by fungi of the genus Puccinia. To illustrate the model, we use it to assess the epidemiological and evolutionary potential of the combination of a major gene and different traits of quantitative resistance. The comparison of the four major deployment strategies described above will be the objective of future studies. PMID:29649208

Intra-urban spatial variability of surface ozone in Riverside, CA: viability and validation of low-cost sensors

NASA Astrophysics Data System (ADS)

Sadighi, Kira; Coffey, Evan; Polidori, Andrea; Feenstra, Brandon; Lv, Qin; Henze, Daven K.; Hannigan, Michael

2018-03-01

Sensor networks are being more widely used to characterize and understand compounds in the atmosphere like ozone (O3). This study employs a measurement tool, called the U-Pod, constructed at the University of Colorado Boulder, to investigate spatial and temporal variability of O3 in a 200 km2 area of Riverside County near Los Angeles, California. This tool contains low-cost sensors to collect ambient data at non-permanent locations. The U-Pods were calibrated using a pre-deployment field calibration technique; all the U-Pods were collocated with regulatory monitors. After collocation, the U-Pods were deployed in the area mentioned. A subset of pods was deployed at two local regulatory air quality monitoring stations providing validation for the collocation calibration method. Field validation of sensor O3 measurements to minute-resolution reference observations resulted in R2 and root mean squared errors (RMSEs) of 0.95-0.97 and 4.4-5.9 ppbv, respectively. Using the deployment data, ozone concentrations were observed to vary on this small spatial scale. In the analysis based on hourly binned data, the median R2 values between all possible U-Pod pairs varied from 0.52 to 0.86 for ozone during the deployment. The medians of absolute differences were calculated between all possible pod pairs, 21 pairs total. The median values of those median absolute differences for each hour of the day varied between 2.2 and 9.3 ppbv for the ozone deployment. Since median differences between U-Pod concentrations during deployment are larger than the respective root mean square error values, we can conclude that there is spatial variability in this criteria pollutant across the study area. This is important because it means that citizens may be exposed to more, or less, ozone than they would assume based on current regulatory monitoring.

Characteristics and oxidative stress on rats and traffic policemen of ambient fine particulate matter from Shenyang.

PubMed

Ma, Mingyue; Li, Shuyin; Jin, Huanrong; Zhang, Yumin; Xu, Jia; Chen, Dongmei; Kuimin, Chen; Yuan, Zhou; Xiao, Chunling

2015-09-01

Fine particulate matter (PM2.5) pollution is becoming serious in China. This study aimed to investigate the impact of PM2.5 on DNA damage in Shenyang city. The concentration and composition of PM2.5 in traffic policemen's working sites including fields and indoor offices were obtained. Blood samples of field and office policemen were collected to detect DNA damage by Comet assay. Rats were used to further analyzing the oxidative DNA damage. The average concentration of PM2.5 in exposed group was significantly higher than that in control group. Composition analysis revealed that toxic heavy metal and polycyclic aromatic hydrocarbon substances were main elements of this PM2.5. DNA damage in field policemen was significantly higher than those in non-field group. Moreover, animal studies confirmed the oxidative DNA damage induced by PM2.5. Taken together, high DNA damages are found in the Shenyang traffic policemen and rats exposed to high level of airborne PM2.5. Copyright © 2015 Elsevier B.V. All rights reserved.

Tilted hexagonal post arrays: DNA electrophoresis in anisotropic media

PubMed Central

Chen, Zhen; Dorfman, Kevin D.

2013-01-01

Using Brownian dynamics simulations, we show that DNA electrophoresis in a hexagonal array of micron-sized posts changes qualitatively when the applied electric field vector is not coincident with the lattice vectors of the array. DNA electrophoresis in such “tilted” post arrays is superior to the standard “un-tilted” approach; while the time required to achieve a resolution of unity in a tilted post array is similar to an un-tilted array at a low electric field strengths, this time (i) decreases exponentially with electric field strength in a tilted array and (ii) increases exponentially with electric field strength in an un-tilted array. Although the DNA dynamics in a post array are complicated, the electrophoretic mobility results indicate that the “free path”, i.e., the average distance of ballistic trajectories of point sized particles launched from random positions in the unit cell until they intersect the next post, is a useful proxy for the detailed DNA trajectories. The analysis of the free path reveals a fundamental connection between anisotropy of the medium and DNA transport therein that goes beyond simply improving the separation device. PMID:23868490

Cost-Effective, Insitu Field Measurements for Determining the Water Retention Quantification onBehavior of Individual Right-of-Way Bioswales

NASA Astrophysics Data System (ADS)

Wang, S.; McGillis, W. R.; Hu, R.; Culligan, P. J.

2017-12-01

Green infrastructure (GI) interventions, such as right-of-way bioswales, are being implemented in many urban areas, including New York City, to help mitigate the negative impacts of stormwater runoff. To understand the storm water retention capacity of bioswales, hydrological models, at scales ranging from the tributary area of a single right-of-way bioswale to an entire watershed, are often invoked. The validation and calibration of these models is, however, currently hampered by lack of extensive field measurements that quantify bioswale stormwater retention behaviors for different storm sizes and bioswale configurations. To overcome this problem, three field methods to quantify the water retention capacity of individual bioswales were developed. The methods are potentially applicable to other applications concerned with quantifying flow regimes in urban area. Precise measurements with high time resolutions and low environmental impacts are desired for gauging the hydraulic performance of bioswales, and similar GI configurations. To satisfy these requirements, an in-field measurement method was developed which involved the deployment of acoustic water-level sensors to measure the upstream and downstream water levels of flow into and out of a bioswale located in the Bronx areas of New York City. The measurements were made during several individual storm events. To provide reference flow rates to enable accurate calibration of the acoustic water level measurements, two other conductometry-based methods, which made use of YSI sensors and injected calcium chloride solutions, were also developed and deployed simultaneously with the water level measurements. The suite of data gathered by these methods enabled the development of a relationship between stage-discharge and rainfall intensity, which was then used to obtain the upstream and downstream hydrographs for the individual bioswale for the different storm events. This presentation will describe in detail the developed field methods, and will present results arising from the deployment of the methods, including results on the stormwater infiltration quantity and infiltration rate of the studied bioswale. The field methods are easily deployed at other bioswales sites and for other similar GI configurations.

Versatile and Programmable DNA Logic Gates on Universal and Label-Free Homogeneous Electrochemical Platform.

PubMed

Ge, Lei; Wang, Wenxiao; Sun, Ximei; Hou, Ting; Li, Feng

2016-10-04

Herein, a novel universal and label-free homogeneous electrochemical platform is demonstrated, on which a complete set of DNA-based two-input Boolean logic gates (OR, NAND, AND, NOR, INHIBIT, IMPLICATION, XOR, and XNOR) is constructed by simply and rationally deploying the designed DNA polymerization/nicking machines without complicated sequence modulation. Single-stranded DNA is employed as the proof-of-concept target/input to initiate or prevent the DNA polymerization/nicking cyclic reactions on these DNA machines to synthesize numerous intact G-quadruplex sequences or binary G-quadruplex subunits as the output. The generated output strands then self-assemble into G-quadruplexes that render remarkable decrease to the diffusion current response of methylene blue and, thus, provide the amplified homogeneous electrochemical readout signal not only for the logic gate operations but also for the ultrasensitive detection of the target/input. This system represents the first example of homogeneous electrochemical logic operation. Importantly, the proposed homogeneous electrochemical logic gates possess the input/output homogeneity and share a constant output threshold value. Moreover, the modular design of DNA polymerization/nicking machines enables the adaptation of these homogeneous electrochemical logic gates to various input and output sequences. The results of this study demonstrate the versatility and universality of the label-free homogeneous electrochemical platform in the design of biomolecular logic gates and provide a potential platform for the further development of large-scale DNA-based biocomputing circuits and advanced biosensors for multiple molecular targets.

Centrifugal LabTube platform for fully automated DNA purification and LAMP amplification based on an integrated, low-cost heating system.

PubMed

Hoehl, Melanie M; Weißert, Michael; Dannenberg, Arne; Nesch, Thomas; Paust, Nils; von Stetten, Felix; Zengerle, Roland; Slocum, Alexander H; Steigert, Juergen

2014-06-01

This paper introduces a disposable battery-driven heating system for loop-mediated isothermal DNA amplification (LAMP) inside a centrifugally-driven DNA purification platform (LabTube). We demonstrate LabTube-based fully automated DNA purification of as low as 100 cell-equivalents of verotoxin-producing Escherichia coli (VTEC) in water, milk and apple juice in a laboratory centrifuge, followed by integrated and automated LAMP amplification with a reduction of hands-on time from 45 to 1 min. The heating system consists of two parallel SMD thick film resistors and a NTC as heating and temperature sensing elements. They are driven by a 3 V battery and controlled by a microcontroller. The LAMP reagents are stored in the elution chamber and the amplification starts immediately after the eluate is purged into the chamber. The LabTube, including a microcontroller-based heating system, demonstrates contamination-free and automated sample-to-answer nucleic acid testing within a laboratory centrifuge. The heating system can be easily parallelized within one LabTube and it is deployable for a variety of heating and electrical applications.

Imagining Sisyphus happy: DNA barcoding and the unnamed majority.

PubMed

Blaxter, Mark

2016-09-05

The vast majority of life on the Earth is physically small, and is classifiable as micro- or meiobiota. These organisms are numerically dominant and it is likely that they are also abundantly speciose. By contrast, the vast majority of taxonomic effort has been expended on 'charismatic megabionts': larger organisms where a wealth of morphology has facilitated Linnaean species definition. The hugely successful Linnaean project is unlikely to be extensible to the totality of approximately 10 million species in a reasonable time frame and thus alternative toolkits and methodologies need to be developed. One such toolkit is DNA barcoding, particularly in its metabarcoding or metagenetics mode, where organisms are identified purely by the presence of a diagnostic DNA sequence in samples that are not processed for morphological identification. Building on secure Linnaean foundations, classification of unknown (and unseen) organisms to molecular operational taxonomic units (MOTUs) and deployment of these MOTUs in biodiversity science promises a rewarding resolution to the Sisyphean task of naming all the world's species.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

Molecular dynamics simulations of polarizable DNA in crystal environment

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Baucom, Jason; Darden, Thomas A.; Sagui, Celeste

We have investigated the role of the electrostatic description and cell environment in molecular dynamics (MD) simulations of DNA. Multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)2 have been carried out using two different force fields: a traditional description based on atomic point charges and a polarizable force field. For the time scales probed, and given the ?right? distribution of divalent ions, the latter performs better than the nonpolarizable force field. In particular, by imposing the experimental unit cell environment, an initial configuration with ideal B-DNA duplexes in the unit cell acquires sequence-dependent features that very closely resemble the crystallographic ones. Simultaneously, the all-atom root-mean-square coordinates deviation (RMSD) with respect to the crystallographic structure is seen to decay. At later times, the polarizable force field is able to maintain this lower RMSD, while the nonpolarizable force field starts to drift away.

"Warrant" Revisited: Integrating Mathematics Teachers' Pedagogical and Epistemological Considerations into Toulmin's Model for Argumentation

ERIC Educational Resources Information Center

Nardi, Elena; Biza, Irene; Zachariades, Theodossios

2012-01-01

In this paper, we propose an approach to analysing teacher arguments that takes into account field dependence--namely, in Toulmin's sense, the dependence of warrants deployed in an argument on the field of activity to which the argument relates. Freeman, to circumvent issues that emerge when we attempt to determine the field(s) that an argument…

Arctic Glass: Innovative Consumer Technology in Support of Arctic Research

NASA Astrophysics Data System (ADS)

Ruthkoski, T.

2015-12-01

The advancement of cyberinfrastructure on the North Slope of Alaska is drastically limited by location-specific conditions, including: unique geophysical features, remoteness of location, and harsh climate. The associated cost of maintaining this unique cyberinfrastructure also becomes a limiting factor. As a result, field experiments conducted in this region have historically been at a technological disadvantage. The Arctic Glass project explored a variety of scenarios where innovative consumer-grade technology was leveraged as a lightweight, rapidly deployable, sustainable, alternatives to traditional large-scale Arctic cyberinfrastructure installations. Google Glass, cloud computing services, Internet of Things (IoT) microcontrollers, miniature LIDAR, co2 sensors designed for HVAC systems, and portable network kits are several of the components field-tested at the Toolik Field Station as part of this project. Region-specific software was also developed, including a multi featured, voice controlled Google Glass application named "Arctic Glass". Additionally, real-time sensor monitoring and remote control capability was evaluated through the deployment of a small cluster of microcontroller devices. Network robustness was analyzed as the devices delivered streams of abiotic data to a web-based dashboard monitoring service in near real time. The same data was also uploaded synchronously by the devices to Amazon Web Services. A detailed overview of solutions deployed during the 2015 field season, results from experiments utilizing consumer sensors, and potential roles consumer technology could play in support of Arctic science will be discussed.

Flux Chamber Measurements of Methane Emissions and Stable Isotope Composition from an Arctic Wetland Using Field-Deployed Real-Time CRDS Vs Lab Measurements

NASA Astrophysics Data System (ADS)

Thompson, H. A.; Stern, J. C.; Graham, H. V.; Pratt, L. M.; White, J. R.

2014-12-01

The emission of CH4 from Arctic landscapes under warming climate is an important feedback in Earth's climate system. Studies of CH4 flux from Arctic wetlands have been growing in recent years, but few provide details on biogeochemical controls. Stable isotopic measurements help elucidate methane production and consumption pathways and offer important understanding about dynamics of CH4 cycling in Arctic systems. In order to demonstrate the possible instrumental approaches to measuring methane dynamics of wetlands in the Arctic, a fringing wetland of a small lake near the Russell Glacier in Southwestern Greenland was outfitted with static flux chambers and instrumented with a field-deployable Cavity Ring Down Spectrometer (CRDS) to measure real-time concentrations of CH4 and CO2 and their stable carbon isotopes. Several different wetland plant communities were included in the flux chamber experiments and field tests were conducted during several weeks in July 2014. Analytical measurements by CRDS were compared to batch samples analyzed in the laboratory using both Off-Axis Integrated Cavity Output Spectroscopy (ICOS) and Gas Chromatography-Combustion-Isotope Ratio Mass Spectrometry (GC-C-IRMS) with cryogenic pre-concentration. Results from flux chamber deployments will be presented and comparisons between the real-time field measurements and laboratory instrumental techniques will be evaluated.

Gastrointestinal Infections in Deployed Forces in the Middle East Theater: An Historical 60 Year Perspective

PubMed Central

Riddle, Mark S.; Savarino, Stephen J.; Sanders, John W.

2015-01-01

Infectious diarrhea has been among the most common maladies of military deployments throughout time. The U.S. military experienced a significant burden from this disease in the middle eastern and north African campaigns of World War II (WWII). This article compares patterns of disease experienced in WWII with the recent military deployments to the same region for Operation Iraqi Freedom and Operation Enduring Freedom (OIF/OEF). Remarkable similarities in the prevalence and risk factors were noted, which belie the assumed improvements in prevention against these infections. In both campaigns, peaks of diarrhea occurred shortly after arrival of new personnel, which were seasonally associated and were linked to initial lapses in field sanitation and hygiene. It is important to reassess current strategies, especially, in light of emerging evidence of the chronic sequelae of these common infections to include a reemphasis on or reexamination of vaccine development, rapid field diagnostics, treatment algorithms, and antimicrobial prophylaxis. PMID:26350450

Smoking and deployment: perspectives of junior-enlisted U.S. Air Force and U.S. Army personnel and their supervisors.

PubMed

Poston, Walker S C; Taylor, Jennifer E; Hoffman, Kevin M; Peterson, Alan L; Lando, Harry A; Shelton, Suzanne; Haddock, C Keith

2008-05-01

Smoking during deployments is a growing problem, particularly among junior-enlisted personnel, who have the highest smoking rates in the military. Few studies have examined reasons for smoking initiation among never smokers, relapse among former smokers, or increased smoking frequency among current smokers. We conducted 24 focus groups at four Air Force and two Army installations (N = 189) to examine the extent of smoking during deployment and to elucidate factors thought to contribute to new initiation, relapse, and increased smoking in a sample of junior-enlisted personnel and their supervisors. Important reasons for smoking included: (1) managing stress, boredom, anxiety, and sleep deprivation; (2) lack of alternate activities and privileges; (3) the perception that dangers in the field trumps the health impact of smoking; and (4) the role of the military environment in encouraging smoking. In addition, the phenomenon of new initiation and relapse to smoking in the field was discussed.

Completing the Link between Exposure Science and Toxicology for Improved Environmental Health Decision Making: The Aggregate Exposure Pathway Framework

EPA Science Inventory

Driven by major scientific advances in analytical methods, biomonitoring, computation, and a newly articulated vision for a greater impact in public health, the field of exposure science is undergoing a rapid transition from a field of observation to a field of prediction. Deploy...

DNA curvature and flexibility in vitro and in vivo

PubMed Central

Peters, Justin P.; Maher, L. James

2014-01-01

It has been more than 50 years since the elucidation of the structure of double-helical DNA. Despite active research and progress in DNA biology and biochemistry, much remains to be learned in the field of DNA biophysics. Predicting the sequence-dependent curvature and flexibility of DNA is difficult. Applicability of the conventional worm-like chain polymer model of DNA has been challenged. The fundamental forces responsible for the remarkable resistance of DNA to bending and twisting remain controversial. The apparent “softening” of DNA measured in vivo in the presence of kinking proteins and superhelical strain is incompletely understood. New methods and insights are being applied to these problems. This review places current work on DNA biophysics in historical context and illustrates the ongoing interplay between theory and experiment in this exciting field. PMID:20478077

Cloud Environment Automation: from infrastructure deployment to application monitoring

NASA Astrophysics Data System (ADS)

Aiftimiei, C.; Costantini, A.; Bucchi, R.; Italiano, A.; Michelotto, D.; Panella, M.; Pergolesi, M.; Saletta, M.; Traldi, S.; Vistoli, C.; Zizzi, G.; Salomoni, D.

2017-10-01

The potential offered by the cloud paradigm is often limited by technical issues, rules and regulations. In particular, the activities related to the design and deployment of the Infrastructure as a Service (IaaS) cloud layer can be difficult to apply and time-consuming for the infrastructure maintainers. In this paper the research activity, carried out during the Open City Platform (OCP) research project [1], aimed at designing and developing an automatic tool for cloud-based IaaS deployment is presented. Open City Platform is an industrial research project funded by the Italian Ministry of University and Research (MIUR), started in 2014. It intends to research, develop and test new technological solutions open, interoperable and usable on-demand in the field of Cloud Computing, along with new sustainable organizational models that can be deployed for and adopted by the Public Administrations (PA). The presented work and the related outcomes are aimed at simplifying the deployment and maintenance of a complete IaaS cloud-based infrastructure.

Swarm Deployable Boom Assembly (DBA) Development of a Deployable Magnetometer Boom for the Swarm Spacecraft

NASA Astrophysics Data System (ADS)

McMahon, Paul; Jung, Hans-Juergen; Edwards, Jeff

2013-09-01

The Swarm programme consists of 3 magnetically clean satellites flying in close formation designed to measure the Earth's magnetic field using 2 Magnetometers mounted on a 4.3m long deployable boom.Deployment is initiated by releasing 3 HDRMs, once released the boom oscillates back and forth on a pair of pivots, similar to a restaurant kitchen door hinge, for around 120 seconds before coming to rest on 3 kinematic mounts which are used to provide an accurate reference location in the deployed position. Motion of the boom is damped through a combination of friction, spring hysteresis and flexing of the 120+ cables crossing the hinge. Considerable development work and accurate numerical modelling of the hinge motion was required to predict performance across a wide temperature range and ensure that during the 1st overshoot the boom did not damage itself, the harness or the spacecraft.Due to the magnetic cleanliness requirements of the spacecraft no magnetic materials could be used in the design of the hardware.

Space Shuttle to deploy Magellan planetary science mission

NASA Technical Reports Server (NTRS)

1989-01-01

The objectives of Space Shuttle Mission STS-30 are described along with major flight activities, prelaunch and launch operations, trajectory sequence of events, and landing and post-landing operations. The primary objective of STS-30 is to successfully deploy the Magellan spacecraft into low earth orbit. Following deployment, Magellan will be propelled to its Venus trajectory by an Inertial Upper Stage booster. The objectives of the Magellan mission are to obtain radar images of more than 70 percent of Venus' surface, a near-global topographic map, and near-global gravity field data. Secondary STS-30 payloads include the Fluids Experiment Apparatus (FEA) and the Mesoscale Lightning Experiment (MLE).

Brady's Geothermal Field - Map of DAS, Nodal, Vibroseis and Reftek Station Deployment

DOE Data Explorer

Kurt Feigl

2016-10-15

Map of DAS, nodal, vibroseis and Reftek stations during March 2016 deployment. The plot on the left has nodal stations labeled; the plot on the right has vibroseis observations labeled. Stations are shown in map-view using Brady's rotated X-Y coordinates with side plots denoting elevation with respect to the WGS84 ellipsoid. Blue circles denote vibroseis data, x symbols denote DAS (cyan for horizontal and magenta for vertical), black asterisks denote Reftek data, and red plus signs denote nodal data. This map can be found on UW-Madison's askja server at /PoroTomo/DATA/MAPS/Deployment_Stations.pdf

Utility-Scale Photovoltaic Deployment Scenarios of the Western United States: Implications for Solar Energy Zones in Nevada

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

Frew, Bethany; Mai, Trieu; Krishnan, Venkat

2016-12-01

In this study, we use the National Renewable Energy Laboratory's (NREL's) Regional Energy Deployment System (ReEDS) capacity expansion model to estimate utility-scale photovoltaic (UPV) deployment trends from present day through 2030. The analysis seeks to inform the U.S. Bureau of Land Management's (BLM's) planning activities related to UPV development on federal lands in Nevada as part of the Resource Management Plan (RMP) revision for the Las Vegas and Pahrump field offices. These planning activities include assessing the demand for new or expanded additional Solar Energy Zones (SEZ), per the process outlined in BLM's Western Solar Plan process.

Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics

PubMed Central

Ben Imeddourene, Akli; Elbahnsi, Ahmad; Guéroult, Marc; Oguey, Christophe; Foloppe, Nicolas; Hartmann, Brigitte

2015-01-01

The accurate prediction of the structure and dynamics of DNA remains a major challenge in computational biology due to the dearth of precise experimental information on DNA free in solution and limitations in the DNA force-fields underpinning the simulations. A new generation of force-fields has been developed to better represent the sequence-dependent B-DNA intrinsic mechanics, in particular with respect to the BI ↔ BII backbone equilibrium, which is essential to understand the B-DNA properties. Here, the performance of MD simulations with the newly updated force-fields Parmbsc0εζOLI and CHARMM36 was tested against a large ensemble of recent NMR data collected on four DNA dodecamers involved in nucleosome positioning. We find impressive progress towards a coherent, realistic representation of B-DNA in solution, despite residual shortcomings. This improved representation allows new and deeper interpretation of the experimental observables, including regarding the behavior of facing phosphate groups in complementary dinucleotides, and their modulation by the sequence. It also provides the opportunity to extensively revisit and refine the coupling between backbone states and inter base pair parameters, which emerges as a common theme across all the complementary dinucleotides. In sum, the global agreement between simulations and experiment reveals new aspects of intrinsic DNA mechanics, a key component of DNA-protein recognition. PMID:26657165

Using occupancy modelling to compare environmental DNA to traditional field methods for regional-scale monitoring of an endangered aquatic species.

PubMed

Schmelzle, Molly C; Kinziger, Andrew P

2016-07-01

Environmental DNA (eDNA) monitoring approaches promise to greatly improve detection of rare, endangered and invasive species in comparison with traditional field approaches. Herein, eDNA approaches and traditional seining methods were applied at 29 research locations to compare method-specific estimates of detection and occupancy probabilities for endangered tidewater goby (Eucyclogobius newberryi). At each location, multiple paired seine hauls and water samples for eDNA analysis were taken, ranging from two to 23 samples per site, depending upon habitat size. Analysis using a multimethod occupancy modelling framework indicated that the probability of detection using eDNA was nearly double (0.74) the rate of detection for seining (0.39). The higher detection rates afforded by eDNA allowed determination of tidewater goby occupancy at two locations where they have not been previously detected and at one location considered to be locally extirpated. Additionally, eDNA concentration was positively related to tidewater goby catch per unit effort, suggesting eDNA could potentially be used as a proxy for local tidewater goby abundance. Compared to traditional field sampling, eDNA provided improved occupancy parameter estimates and can be applied to increase management efficiency across a broad spatial range and within a diversity of habitats. © 2015 John Wiley & Sons Ltd.

Genotoxicity in native fish associated with agricultural runoff events

USGS Publications Warehouse

Whitehead, Andrew; Kuivila, Kathryn; Orlando, James L.; Kotelevtsev, S.; Anderson, Susan L.

2004-01-01

The primary objective of the present study was to test whether agricultural chemical runoff was associated with in-stream genotoxicity in native fish. Using Sacramento sucker (Catostomus occidentalis), we combined field-caging experiments in an agriculturally dominated watershed with controlled laboratory exposures to field-collected water samples, and we coupled genotoxicity biomarker measurements in fish with bacterial mutagenicity analysis of water samples. We selected DNA strand breakage as a genotoxicity biomarker and Ames Salmonella mutagenicity tests as a second, supporting indicator of genotoxicity. Data from experiments conducted during rainfall runoff events following winter application of pesticides in 2000 and 2001 indicated that DNA strand breaks were significantly elevated in fish exposed to San Joaquin River (CA, USA) water (38.8, 28.4, and 53.6% DNA strand breakage in year 2000 field, year 2000 lab, and year 2001 field exposures, respectively) compared with a nearby reference site (15.4, 8.7, and 12.6% DNA strand breakage in year 2000 field, year 2000 lab, and year 2001 field exposures, respectively). Time-course measurements in field experiments supported a linkage between induction of DNA strand breakage and the timing of agricultural runoff. San Joaquin River water also caused significant reversion mutation in two Ames Salmonella tester strains. Salmonella mutagenicity corroborated in-stream effects, further strengthening a causal relationship between runoff events and genotoxicity. Potentially responsible agents are discussed in the context of timing of runoff events in the field, concordance between laboratory and field exposures, pesticide application patterns in the drainage, and analytical chemistry data.

Single DNA imaging and length quantification through a mobile phone microscope

NASA Astrophysics Data System (ADS)

Wei, Qingshan; Luo, Wei; Chiang, Samuel; Kappel, Tara; Mejia, Crystal; Tseng, Derek; Chan, Raymond Yan L.; Yan, Eddie; Qi, Hangfei; Shabbir, Faizan; Ozkan, Haydar; Feng, Steve; Ozcan, Aydogan

2016-03-01

The development of sensitive optical microscopy methods for the detection of single DNA molecules has become an active research area which cultivates various promising applications including point-of-care (POC) genetic testing and diagnostics. Direct visualization of individual DNA molecules usually relies on sophisticated optical microscopes that are mostly available in well-equipped laboratories. For POC DNA testing/detection, there is an increasing need for the development of new single DNA imaging and sensing methods that are field-portable, cost-effective, and accessible for diagnostic applications in resource-limited or field-settings. For this aim, we developed a mobile-phone integrated fluorescence microscopy platform that allows imaging and sizing of single DNA molecules that are stretched on a chip. This handheld device contains an opto-mechanical attachment integrated onto a smartphone camera module, which creates a high signal-to-noise ratio dark-field imaging condition by using an oblique illumination/excitation configuration. Using this device, we demonstrated imaging of individual linearly stretched λ DNA molecules (48 kilobase-pair, kbp) over 2 mm2 field-of-view. We further developed a robust computational algorithm and a smartphone app that allowed the users to quickly quantify the length of each DNA fragment imaged using this mobile interface. The cellphone based device was tested by five different DNA samples (5, 10, 20, 40, and 48 kbp), and a sizing accuracy of <1 kbp was demonstrated for DNA strands longer than 10 kbp. This mobile DNA imaging and sizing platform can be very useful for various diagnostic applications including the detection of disease-specific genes and quantification of copy-number-variations at POC settings.

Preservation of RNA and DNA from mammal samples under field conditions.

PubMed

Camacho-Sanchez, Miguel; Burraco, Pablo; Gomez-Mestre, Ivan; Leonard, Jennifer A

2013-07-01

Ecological and conservation genetics require sampling of organisms in the wild. Appropriate preservation of the collected samples, usually by cryostorage, is key to the quality of the genetic data obtained. Nevertheless, cryopreservation in the field to ensure RNA and DNA stability is not always possible. We compared several nucleic acid preservation solutions appropriate for field sampling and tested them on rat (Rattus rattus) blood, ear and tail tip, liver, brain and muscle. We compared the efficacy of a nucleic acid preservation (NAP) buffer for DNA preservation against 95% ethanol and Longmire buffer, and for RNA preservation against RNAlater (Qiagen) and Longmire buffer, under simulated field conditions. For DNA, the NAP buffer was slightly better than cryopreservation or 95% ethanol, but high molecular weight DNA was preserved in all conditions. The NAP buffer preserved RNA as well as RNAlater. Liver yielded the best RNA and DNA quantity and quality; thus, liver should be the tissue preferentially collected from euthanized animals. We also show that DNA persists in nonpreserved muscle tissue for at least 1 week at ambient temperature, although degradation is noticeable in a matter of hours. When cryopreservation is not possible, the NAP buffer is an economical alternative for RNA preservation at ambient temperature for at least 2 months and DNA preservation for at least 10 months. © 2013 John Wiley & Sons Ltd.

Military deployment toxicology: a program manager's perspective.

PubMed

Knechtges, P L

2000-02-01

The Persian Gulf War drew attention to the potential hazards of chemicals that personnel may encounter during military operations and deployments overseas. During the War, the oil well fires of Kuwait highlighted the military threat of industrial chemicals in the area of operations. Following the War, the occurrence of Gulf War Illnesses brought home concerns and suspicions regarding "low level" and "mixed" exposures to chemicals. The public's concern and attention resulted in numerous institutional responses to the real and perceived problems of health risks during military deployments. These institutional responses ranged in scope from a Presidential Review Directive to the initiative known as the Deployment Toxicology Research, Development, Testing and Evaluation (RDT&E) Program. Most institutions, however, seem to agree that additional research is needed to assess the health risks from chemical exposures during military deployments. Establishing and managing an effective RDT&E program in risk assessment for deployed forces is a challenging enterprise. The Deployment Toxicology RDT&E Program was conceived utilizing the military's acquisition framework, an effective methodology with a proven record of fielding of new technologies. Based on a series of structured meetings with military representatives that would utilize new risk assessment tools, a hierarchical set of plans was developed to identify and prioritize end products. The challenge ahead for the Deployment Toxicology RDT&E Program is to execute these plans, provide the necessary oversight, and transition the results into successful product development.

Cavity Attenuated Phase Shift (CAPS) Method for Airborne Aerosol Light Extinction Measurement: Instrument Validation and First Results from Field Deployment

NASA Astrophysics Data System (ADS)

Petzold, A.; Perim de Faria, J.; Berg, M.; Bundke, U.; Freedman, A.

2015-12-01

Monitoring the direct impact of aerosol particles on climate requires the continuous measurement of aerosol optical parameters like the aerosol extinction coefficient on a regular basis. Remote sensing and ground-based networks are well in place (e.g., AERONET, ACTRIS), whereas the regular in situ measurement of vertical profiles of atmospheric aerosol optical properties remains still an important challenge in quantifying climate change. The European Research Infrastructure IAGOS (In-service Aircraft for a Global Observing System; www.iagos.org) responds to the increasing requests for long-term, routine in situ observational data by using commercial passenger aircraft as measurement platform. However, scientific instrumentation for the measurement of atmospheric constituents requires major modifications before being deployable aboard in-service passenger aircraft. Recently, a compact and robust family of optical instruments based on the cavity attenuated phase shift (CAPS) technique has become available for measuring aerosol light extinction. While this technique was successfully deployed for ground-based atmospheric measurements under various conditions, its suitability for operation aboard aircraft in the free and upper free troposphere still has to be demonstrated. In this work, the modifications of a CAPS PMex instrument for measuring aerosol light extinction on aircraft, the results from subsequent laboratory tests for evaluating the modified instrument prototype, and first results from a field deployment aboard a research aircraft will be covered. In laboratory studies, the instrument showed excellent agreement (deviation < 5%) with theoretical values calculated from Rayleigh scattering cross-sections, when operated on pressurized air and CO2 at ambient and low pressure (~200 hPa). For monodisperse and polydisperse aerosols, reference aerosol extinction coefficients were calculated from measured size distributions and agreed with the CAPS PMex instrument response within 10% deviation. During the field deployment, aerosol extinction coefficients and associated aerosol size distributions have been measured and will be presented as comparison studies between measured and calculated data.

Radiological Monitoring Equipment For Real-Time Quantification Of Area Contamination In Soils And Facility Decommissioning

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

M. V. Carpenter; Jay A. Roach; John R Giles

2005-09-01

The environmental restoration industry offers several sys¬tems that perform scan-type characterization of radiologically contaminated areas. The Idaho National Laboratory (INL) has developed and deployed a suite of field systems that rapidly scan, characterize, and analyse radiological contamination in surface soils. The base system consists of a detector, such as sodium iodide (NaI) spectrometers, a global positioning system (GPS), and an integrated user-friendly computer interface. This mobile concept was initially developed to provide precertifica¬tion analyses of soils contaminated with uranium, thorium, and radium at the Fernald Closure Project, near Cincinnati, Ohio. INL has expanded the functionality of this basic system tomore » create a suite of integrated field-deployable analytical systems. Using its engineering and radiation measurement expertise, aided by computer hardware and software support, INL has streamlined the data acquisition and analysis process to provide real-time information presented on wireless screens and in the form of coverage maps immediately available to field technicians. In addition, custom software offers a user-friendly interface with user-selectable alarm levels and automated data quality monitoring functions that validate the data. This system is deployed from various platforms, depending on the nature of the survey. The deployment platforms include a small all-terrain vehicle used to survey large, relatively flat areas, a hand-pushed unit for areas where manoeuvrability is important, an excavator-mounted system used to scan pits and trenches where personnel access is restricted, and backpack- mounted systems to survey rocky shoreline features and other physical settings that preclude vehicle-based deployment. Variants of the base system include sealed proportional counters for measuring actinides (i.e., plutonium-238 and americium-241) in building demolitions, soil areas, roadbeds, and process line routes at the Miamisburg Closure Project near Dayton, Ohio. In addition, INL supports decontamination operations at the Oak Ridge National Laboratory.« less

A Descriptive Analysis of Dental Conditions Occurring During Conflicts, Deployments, and Field Training Exercises

DTIC Science & Technology

1999-12-01

Infection of an extraction site (dry socket, localized osteitis). Apical abscess /periapical abscess - Collection of purulent exudate around the area...conditions for deployment data were 5.79% higher than the rate during conflicts. Caries, third molar complications, periapical abscesses , and endodontics are...restorations and fractured teeth. The "Periodontal" category was grouped to include periodontal abscess , acute necrotizing gingivitis (ANUG), and

Gypsy moth (Lepidoptera: Lymantriidae) flight behavior and phenology based on field-deployed automated pheromone-baited traps

Treesearch

Patrick C. Tobin; Kenneth T. Klein; Donna S. Leonard

2009-01-01

Populations of the gypsy moth, Lymantria dispar (L.), are extensively monitored in the United States through the use of pheromone-baited traps.We report on use of automated pheromone-baited traps that use a recording sensor and data logger to record the unique date-time stamp of males as they enter the trap.We deployed a total of 352 automated traps...

The Role of Mass Spectrometry-Based Metabolomics in Medical Countermeasures Against Radiation

PubMed Central

Patterson, Andrew D.; Lanz, Christian; Gonzalez, Frank J.; Idle, Jeffrey R.

2013-01-01

Radiation metabolomics can be defined as the global profiling of biological fluids to uncover latent, endogenous small molecules whose concentrations change in a dose-response manner following exposure to ionizing radiation. In response to the potential threat of nuclear or radiological terrorism, the Center for High-Throughput Minimally Invasive Radiation Biodosimetry (CMCR) was established to develop field-deployable biodosimeters based, in principle, on rapid analysis by mass spectrometry of readily and easily obtainable biofluids. In this review, we briefly summarize radiation biology and key events related to actual and potential nuclear disasters, discuss the important contributions the field of mass spectrometry has made to the field of radiation metabolomics, and summarize current discovery efforts to use mass spectrometry-based metabolomics to identify dose-responsive urinary constituents, and ultimately to build and deploy a noninvasive high-throughput biodosimeter. PMID:19890938

First insights into macro- and meiofaunal colonisation patterns on paired wood/slate substrata at Atlantic deep-sea hydrothermal vents

NASA Astrophysics Data System (ADS)

Cuvelier, Daphne; Beesau, Julie; Ivanenko, Viatcheslav N.; Zeppilli, Daniela; Sarradin, Pierre-Marie; Sarrazin, Jozée

2014-05-01

In 2006, paired wood and slate panels, each equipped with a temperature probe, were deployed on three different localities on and around the Eiffel Tower edifice (Lucky Strike vent field, Mid-Atlantic Ridge) within close proximity of visible hydrothermal activity. Recovery of these panels took place in 2008. For this two-year deployment period, the composition of colonising organisms (both macro-and meiofauna) was assessed, along with image analyses of the deployment sites in 2006 and 2008. Very few significant differences in colonisation between organic (wood) and inorganic (slate) panels were revealed. Rather, the locality of deployment and the local environmental conditions and hydrothermal activity were found to influence taxonomic composition. Variability in microhabitat conditions and biological interactions were hypothesised to interact jointly in shaping new faunal communities on the colonisation substrata.

­The Carnegie Quick Deploy Box (QDB) for use with broadband and intermediate period sensors

NASA Astrophysics Data System (ADS)

Wagner, L. S.; Roman, D.; Bartholomew, T.; Golden, S.; Schleigh, B.

2017-12-01

Recent data processing advances have increased the call for dense recordings of teleseismic data. However, traditional broadband field installations typically comprise 1) a sensor vault 2) a field box to hold the recording and power systems, and 3) a solar panel mount. The construction of these installations is time consuming and requires bulky construction materials, limiting the number of stations that can be installed from a single vehicle without repeated trips to a storage facility. Depending on the deployment location, watertight containers for both vault and field box can be difficult to find, resulting in a loss of data due to flooding. Recent technological improvements have made possible the direct burial of sensors (no vault required) and a reduction in the size of the solar panels needed to run a station. With support from the Brinson Foundation, we take advantage of these advances to create a field box/shipping container that will greatly simplify these types of seismic deployments. The goal of the Carnegie Quick Deploy Box (QDB) is to have everything needed for an intermediate period station install (except battery and shovel) contained in a single box for shipment, and to be able to leave everything (except the shovel) in that box when the station is deployed. The box is small enough ( 13"x13"x21") and lightweight enough (< 35 lbs) to be checked as airline luggage. The solar panel mount can be attached securely to the top of the box, but it can also be pole mounted with U-bolts or hose clamps. The sensor can be direct-buried. The sensor cable and solar panel cable plug into watertight bulkhead-fitted plugs on the outside of the box that are in turn plugged into the digitizer and power regulator inside the box. Our prototype boxes (Pelican Cases) have proved watertight when submerged for days. This equipment has been tested in Alaska in winter and Nicaragua in summer without failure due to flooding or power. The cost for parts for a single box (not including sensor cable, sensor, or digitizer) is $500. The setup is simple, and can be completed in a matter of minutes once the sensor is installed. QDBs such as ours will make possible a dramatic increase in the number of stations that can be installed, while also significantly decreasing the cost of deployment per station by reducing vehicle time, fuel, personnel time, and shipping costs.

Medical Surveillance Monthly Report (MSMR). Volume 22, Number 6, June 2015

DTIC Science & Technology

2015-06-01

and then plateaued (with marked year-to-year variability) through 2010 (Figure 2). women and among those who were not deployed within the fi rst...acids were extracted with the QIAamp stool DNA kit (QIAGEN, USA). For the respiratory samples, detection and characterization of human infl uenza...research by the Walter Reed Army Institute of Research Division of Human Subjects Protection. Some of the authors are military service members. Th is

High-throughput DNA separation in nanofilter arrays.

PubMed

Choi, Sungup; Kim, Ju Min; Ahn, Kyung Hyun; Lee, Seung Jong

2014-08-01

We numerically investigated the dynamics of short double-stranded DNA molecules moving through a deep-shallow alternating nanofilter, by utilizing Brownian dynamics simulation. We propose a novel mechanism for high-throughput DNA separation with a high electric field, which was originally predicted by Laachi et al. [Phys. Rev. Lett. 2007, 98, 098106]. In this work, we show that DNA molecules deterministically move along different electrophoretic streamlines according to their length, owing to geometric constraint at the exit of the shallow region. Consequently, it is more probable that long DNA molecules pass over a deep well region without significant lateral migration toward the bottom of the deep well, which is in contrast to the long dwelling time for short DNA molecules. We investigated the dynamics of DNA passage through a nanofilter facilitating electrophoretic field kinematics. The statistical distribution of the DNA molecules according to their size clearly corroborates our assumption. On the other hand, it was also found that the tapering angle between the shallow and deep regions significantly affects the DNA separation performance. The current results show that the nonuniform field effect combined with geometric constraint plays a key role in nanofilter-based DNA separation. We expect that our results will be helpful in designing and operating nanofluidics-based DNA separation devices and in understanding the polymer dynamics in confined geometries. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

LASER FLUORESCENCE EEM PROBE FOR CONE PENETROMETER POLLUTION ANALYSIS

EPA Science Inventory

A fiber optic LIF (Laser induced fluorescence) EEM (Excitation emission matrix) instrument for CPT deployment has been successfully developed and field tested. The system employs a Nd: YAG laser and Raman shifter as a rugged field portable excitation source. This excitation sou...

On Efficient Deployment of Wireless Sensors for Coverage and Connectivity in Constrained 3D Space.

PubMed

Wu, Chase Q; Wang, Li

2017-10-10

Sensor networks have been used in a rapidly increasing number of applications in many fields. This work generalizes a sensor deployment problem to place a minimum set of wireless sensors at candidate locations in constrained 3D space to k -cover a given set of target objects. By exhausting the combinations of discreteness/continuousness constraints on either sensor locations or target objects, we formulate four classes of sensor deployment problems in 3D space: deploy sensors at Discrete/Continuous Locations (D/CL) to cover Discrete/Continuous Targets (D/CT). We begin with the design of an approximate algorithm for DLDT and then reduce DLCT, CLDT, and CLCT to DLDT by discretizing continuous sensor locations or target objects into a set of divisions without sacrificing sensing precision. Furthermore, we consider a connected version of each problem where the deployed sensors must form a connected network, and design an approximation algorithm to minimize the number of deployed sensors with connectivity guarantee. For performance comparison, we design and implement an optimal solution and a genetic algorithm (GA)-based approach. Extensive simulation results show that the proposed deployment algorithms consistently outperform the GA-based heuristic and achieve a close-to-optimal performance in small-scale problem instances and a significantly superior overall performance than the theoretical upper bound.

Packing and deploying Soft Origami to and from cylindrical volumes with application to automotive airbags

PubMed Central

Nelson, Todd G.; Zimmerman, Trent K.; Fernelius, Janette D.; Magleby, Spencer P.; Howell, Larry L.

2016-01-01

Packing soft-sheet materials of approximately zero bending stiffness using Soft Origami (origami patterns applied to soft-sheet materials) into cylindrical volumes and their deployment via mechanisms or internal pressure (inflation) is of interest in fields including automobile airbags, deployable heart stents, inflatable space habitats, and dirigible and parachute packing. This paper explores twofold patterns, the ‘flasher’ and the ‘inverted-cone fold’, for packing soft-sheet materials into cylindrical volumes. Two initial packing methods and mechanisms are examined for each of the flasher and inverted-cone fold patterns. An application to driver’s side automobile airbags is performed, and deployment tests are completed to compare the influence of packing method and origami pattern on deployment performance. Following deployment tests, two additional packing methods for the inverted-cone fold pattern are explored and applied to automobile airbags. It is shown that modifying the packing method (using different methods to impose the same base pattern on the soft-sheet material) can lead to different deployment performance. In total, two origami patterns and six packing methods are examined, and the benefits of using Soft Origami patterns and packing methods are discussed. Soft Origami is presented as a viable method for efficiently packing soft-sheet materials into cylindrical volumes. PMID:27703707

Stent deployment protocol for optimized real-time visualization during endovascular neurosurgery.

PubMed

Silva, Michael A; See, Alfred P; Dasenbrock, Hormuzdiyar H; Ashour, Ramsey; Khandelwal, Priyank; Patel, Nirav J; Frerichs, Kai U; Aziz-Sultan, Mohammad A

2017-05-01

Successful application of endovascular neurosurgery depends on high-quality imaging to define the pathology and the devices as they are being deployed. This is especially challenging in the treatment of complex cases, particularly in proximity to the skull base or in patients who have undergone prior endovascular treatment. The authors sought to optimize real-time image guidance using a simple algorithm that can be applied to any existing fluoroscopy system. Exposure management (exposure level, pulse management) and image post-processing parameters (edge enhancement) were modified from traditional fluoroscopy to improve visualization of device position and material density during deployment. Examples include the deployment of coils in small aneurysms, coils in giant aneurysms, the Pipeline embolization device (PED), the Woven EndoBridge (WEB) device, and carotid artery stents. The authors report on the development of the protocol and their experience using representative cases. The stent deployment protocol is an image capture and post-processing algorithm that can be applied to existing fluoroscopy systems to improve real-time visualization of device deployment without hardware modifications. Improved image guidance facilitates aneurysm coil packing and proper positioning and deployment of carotid artery stents, flow diverters, and the WEB device, especially in the context of complex anatomy and an obscured field of view.

Packing and deploying Soft Origami to and from cylindrical volumes with application to automotive airbags

NASA Astrophysics Data System (ADS)

Bruton, Jared T.; Nelson, Todd G.; Zimmerman, Trent K.; Fernelius, Janette D.; Magleby, Spencer P.; Howell, Larry L.

2016-09-01

Packing soft-sheet materials of approximately zero bending stiffness using Soft Origami (origami patterns applied to soft-sheet materials) into cylindrical volumes and their deployment via mechanisms or internal pressure (inflation) is of interest in fields including automobile airbags, deployable heart stents, inflatable space habitats, and dirigible and parachute packing. This paper explores twofold patterns, the `flasher' and the `inverted-cone fold', for packing soft-sheet materials into cylindrical volumes. Two initial packing methods and mechanisms are examined for each of the flasher and inverted-cone fold patterns. An application to driver's side automobile airbags is performed, and deployment tests are completed to compare the influence of packing method and origami pattern on deployment performance. Following deployment tests, two additional packing methods for the inverted-cone fold pattern are explored and applied to automobile airbags. It is shown that modifying the packing method (using different methods to impose the same base pattern on the soft-sheet material) can lead to different deployment performance. In total, two origami patterns and six packing methods are examined, and the benefits of using Soft Origami patterns and packing methods are discussed. Soft Origami is presented as a viable method for efficiently packing soft-sheet materials into cylindrical volumes.

Packing and deploying Soft Origami to and from cylindrical volumes with application to automotive airbags.

PubMed

Bruton, Jared T; Nelson, Todd G; Zimmerman, Trent K; Fernelius, Janette D; Magleby, Spencer P; Howell, Larry L

2016-09-01

Packing soft-sheet materials of approximately zero bending stiffness using Soft Origami (origami patterns applied to soft-sheet materials) into cylindrical volumes and their deployment via mechanisms or internal pressure (inflation) is of interest in fields including automobile airbags, deployable heart stents, inflatable space habitats, and dirigible and parachute packing. This paper explores twofold patterns, the 'flasher' and the 'inverted-cone fold', for packing soft-sheet materials into cylindrical volumes. Two initial packing methods and mechanisms are examined for each of the flasher and inverted-cone fold patterns. An application to driver's side automobile airbags is performed, and deployment tests are completed to compare the influence of packing method and origami pattern on deployment performance. Following deployment tests, two additional packing methods for the inverted-cone fold pattern are explored and applied to automobile airbags. It is shown that modifying the packing method (using different methods to impose the same base pattern on the soft-sheet material) can lead to different deployment performance. In total, two origami patterns and six packing methods are examined, and the benefits of using Soft Origami patterns and packing methods are discussed. Soft Origami is presented as a viable method for efficiently packing soft-sheet materials into cylindrical volumes.

Low Density Supersonic Decelerator Parachute Decelerator System

NASA Technical Reports Server (NTRS)

Gallon, John C.; Clark, Ian G.; Rivellini, Tommaso P.; Adams, Douglas S.; Witkowski, Allen

2013-01-01

The Low Density Supersonic Decelerator Project has undertaken the task of developing and testing a large supersonic ringsail parachute. The parachute under development is intended to provide mission planners more options for parachutes larger than the Mars Science Laboratory's 21.5m parachute. During its development, this new parachute will be taken through a series of tests in order to bring the parachute to a TRL-6 readiness level and make the technology available for future Mars missions. This effort is primarily focused on two tests, a subsonic structural verification test done at sea level atmospheric conditions and a supersonic flight behind a blunt body in low-density atmospheric conditions. The preferred method of deploying a parachute behind a decelerating blunt body robotic spacecraft in a supersonic flow-field is via mortar deployment. Due to the configuration constraints in the design of the test vehicle used in the supersonic testing it is not possible to perform a mortar deployment. As a result of this limitation an alternative deployment process using a ballute as a pilot is being developed. The intent in this alternate approach is to preserve the requisite features of a mortar deployment during canopy extraction in a supersonic flow. Doing so will allow future Mars missions to either choose to mortar deploy or pilot deploy the parachute that is being developed.

Field Data on Head Injuries in Side Airbag Vehicles in Lateral Impact

PubMed Central

Yoganandan, Narayan; Pintar, Frank A.; Gennarelli, Thomas A.

2005-01-01

Field data on side airbag deployments in lateral crashes and head injuries have largely remained anecdotal. Consequently, the purpose of this research was to report head injuries in lateral motor vehicle impacts. Data from the National Automotive Sampling System files were extracted from side impacts associated with side airbag deployments. Matched pairs with similar vehicle characteristics but without side airbags were also extracted. All data were limited to the United States Federal Motor vehicle Safety Standards FMVSS 214 compliant vehicles so that the information may be more effectively used in the future. In this study, some fundamental analyses are presented regarding occupant- and vehicle-related parameters. PMID:16179147

A field-deployable compound-specific isotope analyzer based on quantum cascade laser and hollow waveguide

NASA Astrophysics Data System (ADS)

Wu, Sheng; Deev, Andrei

2013-01-01

A field deployable Compound Specific Isotope Analyzer (CSIA) coupled with capillary chromatogrpahy based on Quantum Cascade (QC) lasers and Hollow Waveguide (HWG) with precision and chemical resolution matching mature Mass Spectroscopy has been achieved in our laboratory. The system could realize 0.3 per mil accuracy for 12C/13C for a Gas Chromatography (GC) peak lasting as short as 5 seconds with carbon molar concentration in the GC peak less than 0.5%. Spectroscopic advantages of HWG when working with QC lasers, i.e. single mode transmission, noiseless measurement and small sample volume, are compared with traditional free space and multipass spectroscopy methods.

Detection of influenza A virus using carbon nanotubes field effect transistor based DNA sensor

NASA Astrophysics Data System (ADS)

Tran, Thi Luyen; Nguyen, Thi Thuy; Huyen Tran, Thi Thu; Chu, Van Tuan; Thinh Tran, Quang; Tuan Mai, Anh

2017-09-01

The carbon nanotubes field effect transistor (CNTFET) based DNA sensor was developed, in this paper, for detection of influenza A virus DNA. Number of factors that influence the output signal and analytical results were investigated. The initial probe DNA, decides the available DNA strands on CNTs, was 10 μM. The hybridization time for defined single helix was 120 min. The hybridization temperature was set at 30 °C to get a net change in drain current of the DNA sensor without altering properties of any biological compounds. The response time of the DNA sensor was less than one minute with a high reproducibility. In addition, the DNA sensor has a wide linear detection range from 1 pM to 10 nM, and a very low detection limit of 1 pM. Finally, after 7-month storage in 7.4 pH buffer, the output signal of DNA sensor recovered 97%.

U.S. Army Annual Injury Epidemiology Report 2007

DTIC Science & Technology

2009-09-30

IPP) analyses, field investigations, and evaluations completed in 2007 are also presented. Topics included the examination of predictors of injuries...from non-deployment-related analyses, field investigations, and evaluations completed in 2007 by the Injury Prevention Program at U.S. Army Center for...injuries will be higher in the summer and should follow the work/rest recommendations and water replacement guidelines in Field Manual 21-10, Field

Free-solution electrophoretic separations of DNA–drag-tag conjugates on glass microchips with no polymer network and no loss of resolution at increased electric field strength

PubMed Central

Albrecht, Jennifer Coyne; Kerby, Matthew B.; Niedringhaus, Thomas P.; Lin, Jennifer S.; Wang, Xiaoxiao; Barron, Annelise E.

2012-01-01

Here, we demonstrate the potential for high-resolution electrophoretic separations of ssDNA-protein conjugates in borosilicate glass microfluidic chips, with no sieving media and excellent repeatability. Using polynucleotides of two different lengths conjugated to moderately cationic protein polymer drag-tags, we measured separation efficiency as a function of applied electric field. In excellent agreement with prior theoretical predictions of Slater et al., resolution is found to remain constant as applied field is increased up to 700 V/cm, the highest field we were able to apply. This remarkable result illustrates the fundamentally different physical limitations of Free-Solution Conjugate Electrophoresis (FSCE)-based DNA separations relative to matrix-based DNA electrophoresis. Single-stranded DNA separations in “gels” have always shown rapidly declining resolution as the field strength is increased; this is especially true for ssDNA > 400 bases in length. FSCE’s ability to decouple DNA peak resolution from applied electric field suggests the future possibility of ultra-rapid FSCE sequencing on chips. We investigated sources of peak broadening for FSCE separations on borosilicate glass microchips, using six different protein polymer drag-tags. For drag-tags with four or more positive charges, electrostatic and adsorptive interactions with pHEA-coated microchannel walls led to appreciable band-broadening, while much sharper peaks were seen for bioconjugates with nearly charge-neutral protein drag-tags. PMID:21500207

One simple DNA extraction device and its combination with modified visual loop-mediated isothermal amplification for rapid on-field detection of genetically modified organisms.

PubMed

Zhang, Miao; Liu, Yinan; Chen, Lili; Quan, Sheng; Jiang, Shimeng; Zhang, Dabing; Yang, Litao

2013-01-02

Quickness, simplicity, and effectiveness are the three major criteria for establishing a good molecular diagnosis method in many fields. Herein we report a novel detection system for genetically modified organisms (GMOs), which can be utilized to perform both on-field quick screening and routine laboratory diagnosis. In this system, a newly designed inexpensive DNA extraction device was used in combination with a modified visual loop-mediated isothermal amplification (vLAMP) assay. The main parts of the DNA extraction device included a silica gel membrane filtration column and a modified syringe. The DNA extraction device could be easily operated without using other laboratory instruments, making it applicable to an on-field GMO test. High-quality genomic DNA (gDNA) suitable for polymerase chain reaction (PCR) and isothermal amplification could be quickly isolated from plant tissues using this device within 15 min. In the modified vLAMP assay, a microcrystalline wax encapsulated detection bead containing SYBR green fluorescent dye was introduced to avoid dye inhibition and cross-contaminations from post-LAMP operation. The system was successfully applied and validated in screening and identification of GM rice, soybean, and maize samples collected from both field testing and the Grain Inspection, Packers, and Stockyards Administration (GIPSA) proficiency test program, which demonstrated that it was well-adapted to both on-field testing and/or routine laboratory analysis of GMOs.

Ni-DNA-based nanowires and nanodevices

NASA Astrophysics Data System (ADS)

Chang, Chia-Ching; Yuan, Chiun-Jye; Jian, Wen-Bin; Chen, Yu-Chang; di Ventra, Massimiliano

DNA is a highly versatile biopolymer that has been a recent focus in the field of nanomachines and nanoelectronics. DNA exhibits high stability, adjustable conductance, self-organizing capability, programmability and vast information storage. It is an ideal material in the applications of nanodevices, nanoelectronics, and molecular computing. Low conductance of native DNA renders applications difficult. However, doping with nickel ions tunes the DNA into a conducting polymer. Further studies showed that nickel ions containing DNA (Ni-DNA) nanowires exhibit characteristics of memristor and memcapacitor making them a potential mass information storage system. In summary, Ni-DNA has promising applications in a variety of fields, including nanoelectronics, biosensors and memcomputing. This study was supported in part by the Ministry of Science and Technology (MOST), Taiwan (ROC) MOST 103-2112-M-009-011 -MY3, and MOST 105-2627-M-009-006.

Comparison of Haemophilus parasuis reference strains and field isolates by using random amplified polymorphic DNA and protein profiles

PubMed Central

2012-01-01

Background Haemophilus parasuis is the causative agent of Glässer’s disease and is a pathogen of swine in high-health status herds. Reports on serotyping of field strains from outbreaks describe that approximately 30% of them are nontypeable and therefore cannot be traced. Molecular typing methods have been used as alternatives to serotyping. This study was done to compare random amplified polymorphic DNA (RAPD) profiles and whole cell protein (WCP) lysate profiles as methods for distinguishing H. parasuis reference strains and field isolates. Results The DNA and WCP lysate profiles of 15 reference strains and 31 field isolates of H. parasuis were analyzed using the Dice and neighbor joining algorithms. The results revealed unique and reproducible DNA and protein profiles among the reference strains and field isolates studied. Simpson’s index of diversity showed significant discrimination between isolates when three 10mer primers were combined for the RAPD method and also when both the RAPD and WCP lysate typing methods were combined. Conclusions The RAPD profiles seen among the reference strains and field isolates did not appear to change over time which may reflect a lack of DNA mutations in the genes of the samples. The recent field isolates had different WCP lysate profiles than the reference strains, possibly because the number of passages of the type strains may affect their protein expression. PMID:22703293

Dielectrophoretic Isolation and Detection of cfc-DNA Nanoparticulate Biomarkers and Virus from Blood

PubMed Central

Sonnenberg, Avery; Marciniak, Jennifer Y.; McCanna, James; Krishnan, Rajaram; Rassenti, Laura; Kipps, Thomas J.; Heller, Michael J.

2015-01-01

Dielectrophoretic (DEP) microarray devices allow important cellular nanoparticulate biomarkers and virus to be rapidly isolated, concentrated and detected directly from clinical and biological samples. A variety of sub-micron nanoparticulate entities including cell free circulating (cfc) DNA, mitochondria and virus can be isolated into DEP high-field areas on microelectrodes, while blood cells and other micron-size entities become isolated into DEP low-field areas between the microelectrodes. The nanoparticulate entities are held in the DEP high-field areas while cells are washed away along with proteins and other small molecules which are not affected by the DEP electric fields. DEP carried out on 20 µL of whole blood obtained from Chronic Lymphocytic Leukemia (CLL) patients showed a considerable amount of SYBR Green stained DNA fluorescent material concentrated in the DEP high-field regions. Whole blood obtained from healthy individuals showed little or no fluorescent DNA materials in the DEP high-field regions. Fluorescent T7 bacteriophage virus could be isolated directly from blood samples, and fluorescently stained mitochondria could be isolated from biological buffer samples. Using newer DEP microarray devices, high molecular weight (hmw) DNA could be isolated from serum and detected at levels as low as 8–16 ng/mL. PMID:23436471

Effects of field-of-view restrictions on speed and accuracy of manoeuvring.

PubMed

Toet, Alexander; Jansen, Sander E M; Delleman, Nico J

2007-12-01

Effects of field-of-view restrictions on the speed and accuracy of participants performing a real-world manoeuvring task through an obstacled environment were investigated. Although field-of-view restrictions are known to affect human behaviour and to degrade performance for a range of different tasks, the relationship between human manoeuvring performance and field-of-view size is not known. This knowledge is essential to evaluate a trade-off between human performance, cost, and ergonomic aspects of field-of-view limiting devises like head-mounted displays and night vision goggles which are frequently deployed for tasks involving human motion through environments with obstacles. In this study the speed and accuracy of movement were measured in 15 participants (8 men, 7 women, 22.9 +/- 2.8 yr. of age) traversing a course formed by three wall segments for different field-of-view restrictions. Analysis showed speed decreased linearly with decreasing field-of-view extent, while accuracy was consistently reduced for all restricted field-of-view conditions. Present results may be used to evaluate cost and performance trade-offs for field-of-view restricting devices deployed to perform time-limited human-locomotion tasks in complex structured environments, such as night-vision goggles and head-mounted displays.

Electrostatic coupling between DNA and its counterions modulates the observed translational diffusion coefficients.

PubMed

Stellwagen, Earle; Stellwagen, Nancy C

2015-09-01

Free solution capillary electrophoresis (CE) is a useful technique for measuring the translational diffusion coefficients of charged analytes. The measurements are relatively fast if the polarity of the electric field is reversed to drive the analyte back and forth past the detection window during each run. We have tested the validity of the resulting diffusion coefficients using double-stranded DNA molecules ranging in size from 20 to 960 base pairs as the model system. The diffusion coefficients of small DNAs are equal to values in the literature measured by other techniques. However, the diffusion coefficients of DNA molecules larger than ∼30 base pairs are anomalously high and deviate increasingly from the literature values with increasing DNA molar mass. The anomalously high diffusion coefficients are due to electrostatic coupling between the DNA and its counterions. As a result, the measured diffusion coefficients vary with the diffusion coefficient of the counterion, as well as with cation concentration and electric field strength. These effects can be reduced or eliminated by measuring apparent diffusion coefficients of the DNA at several different electric field strengths and extrapolating the results to zero electric field.

Tilted hexagonal post arrays: DNA electrophoresis in anisotropic media.

PubMed

Chen, Zhen; Dorfman, Kevin D

2014-02-01

Using Brownian dynamics simulations, we show that DNA electrophoresis in a hexagonal array of micron-sized posts changes qualitatively when the applied electric field vector is not coincident with the lattice vectors of the array. DNA electrophoresis in such "tilted" post arrays is superior to the standard "un-tilted" approach; while the time required to achieve a resolution of unity in a tilted post array is similar to an un-tilted array at a low-electric field strengths, this time (i) decreases exponentially with electric field strength in a tilted array and (ii) increases exponentially with electric field strength in an un-tilted array. Although the DNA dynamics in a post array are complicated, the electrophoretic mobility results indicate that the "free path," i.e. the average distance of ballistic trajectories of point-sized particles launched from random positions in the unit cell until they intersect the next post, is a useful proxy for the detailed DNA trajectories. The analysis of the free path reveals a fundamental connection between anisotropy of the medium and DNA transport therein that goes beyond simply improving the separation device. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simulations of DNA stretching by flow field in microchannels with complex geometry.

PubMed

Huang, Chiou-De; Kang, Dun-Yen; Hsieh, Chih-Chen

2014-01-01

Recently, we have reported the experimental results of DNA stretching by flow field in three microchannels (C. H. Lee and C. C. Hsieh, Biomicrofluidics 7(1), 014109 (2013)) designed specifically for the purpose of preconditioning DNA conformation for easier stretching. The experimental results do not only demonstrate the superiority of the new devices but also provides detailed observation of DNA behavior in complex flow field that was not available before. In this study, we use Brownian dynamics-finite element method (BD-FEM) to simulate DNA behavior in these microchannels, and compare the results against the experiments. Although the hydrodynamic interaction (HI) between DNA segments and between DNA and the device boundaries was not included in the simulations, the simulation results are in fairly good agreement with the experimental data from either the aspect of the single molecule behavior or from the aspect of ensemble averaged properties. The discrepancy between the simulation and the experimental results can be explained by the neglect of HI effect in the simulations. Considering the huge savings on the computational cost from neglecting HI, we conclude that BD-FEM can be used as an efficient and economic designing tool for developing new microfluidic device for DNA manipulation.

Food and drinking water hygiene and intestinal protozoa in deployed German soldiers.

PubMed

Frickmann, Hagen; Schwarz, Norbert G; Wiemer, Dorothea F; Fischer, Marcellus; Tannich, Egbert; Scheid, Patrick L; Müller, Martin; Schotte, Ulrich; Bock, Wolfgang; Hagen, Ralf M

2013-03-01

This report analyzes the occurrence of Cryptosporidium spp., E. histolytica, and G. intestinalis in stool of returnees from military deployments and the impact of hygiene precautions. Between 2007 and 2010, stool samples of 830 returnees that were obtained 8-12 weeks after military deployments in Afghanistan, Uzbekistan, the Balkans, Democratic Republic of the Congo/Gabonese Republic, and Sudan and 292 control samples from non-deployed soldiers were analyzed by PCR for Cryptosporidium spp., E. histolytica, G. intestinalis, and the commensal indicator of fecal contamination E. dispar. Data on hygiene precautions were available. The soldiers were questioned regarding gastrointestinal and general symptoms. Among 1122 stool samples, 18 were positive for G. intestinalis, 10 for E. dispar, and no-one for Cryptosporidium spp. and E. histolytica. An increased risk of acquiring chronic parasitic infections in comparison with non-deployed controls was demonstrated only for G. intestinalis in Sudan, where standardized food and drinking water hygiene precautions could not be implemented. Standard food and drinking water hygiene precautions in the context of screened military field camps proved to be highly reliable in preventing food-borne and water-borne chronic infections and colonization by intestinal protozoa, leading to detection proportions similar to those in non-deployed controls.

Accuracy of vaginal symptom self-diagnosis algorithms for deployed military women.

PubMed

Ryan-Wenger, Nancy A; Neal, Jeremy L; Jones, Ashley S; Lowe, Nancy K

2010-01-01

Deployed military women have an increased risk for development of vaginitis due to extreme temperatures, primitive sanitation, hygiene and laundry facilities, and unavailable or unacceptable healthcare resources. The Women in the Military Self-Diagnosis (WMSD) and treatment kit was developed as a field-expedient solution to this problem. The primary study aims were to evaluate the accuracy of women's self-diagnosis of vaginal symptoms and eight diagnostic algorithms and to predict potential self-medication omission and commission error rates. Participants included 546 active duty, deployable Army (43.3%) and Navy (53.6%) women with vaginal symptoms who sought healthcare at troop medical clinics on base.In the clinic lavatory, women conducted a self-diagnosis using a sterile cotton swab to obtain vaginal fluid, a FemExam card to measure positive or negative pH and amines, and the investigator-developed WMSD Decision-Making Guide. Potential self-diagnoses were "bacterial infection" (bacterial vaginosis [BV] and/or trichomonas vaginitis [TV]), "yeast infection" (candida vaginitis [CV]), "no infection/normal," or "unclear." The Affirm VPIII laboratory reference standard was used to detect clinically significant amounts of vaginal fluid DNA for organisms associated with BV, TV, and CV. Women's self-diagnostic accuracy was 56% for BV/TV and 69.2% for CV. False-positives would have led to a self-medication commission error rate of 20.3% for BV/TV and 8% for CV. Potential self-medication omission error rates due to false-negatives were 23.7% for BV/TV and 24.8% for CV. The positive predictive value of diagnostic algorithms ranged from 0% to 78.1% for BV/TV and 41.7% for CV. The algorithms were based on clinical diagnostic standards. The nonspecific nature of vaginal symptoms, mixed infections, and a faulty device intended to measure vaginal pH and amines explain why none of the algorithms reached the goal of 95% accuracy. The next prototype of the WMSD kit will not include nonspecific vaginal signs and symptoms in favor of recently available point-of-care devices that identify antigens or enzymes of the causative BV, TV, and CV organisms.

Appendix I1-2 to Wind HUI Initiative 1: Field Campaign Report

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

John Zack; Deborah Hanley; Dora Nakafuji

This report is an appendix to the Hawaii WindHUI efforts to dev elop and operationalize short-term wind forecasting and wind ramp event forecasting capabilities. The report summarizes the WindNET field campaign deployment experiences and challenges. As part of the WindNET project on the Big Island of Hawaii, AWS Truepower (AWST) conducted a field campaign to assess the viability of deploying a network of monitoring systems to aid in local wind energy forecasting. The data provided at these monitoring locations, which were strategically placed around the Big Island of Hawaii based upon results from the Oahu Wind Integration and Transmission Studymore » (OWITS) observational targeting study (Figure 1), provided predictive indicators for improving wind forecasts and developing responsive strategies for managing real-time, wind-related system events. The goal of the field campaign was to make measurements from a network of remote monitoring devices to improve 1- to 3-hour look ahead forecasts for wind facilities.« less

Exposure assessment of microwave ovens and impact on total exposure in WLANs

PubMed Central

Plets, David; Verloock, Leen; Van Den Bossche, Matthias; Tanghe, Emmeric; Joseph, Wout; Martens, Luc

2016-01-01

In situ exposure of electric fields of 11 microwave ovens is assessed in an occupational environment and in an office. Measurements as a function of distance without load and with a load of 275 ml of tap water were performed at distances of <1 m. The maximal measured field was 55.2 V m−1 at 5 cm from the oven (without load), which is 2.5 and 1.1 times below the International Commission on Non-Ionizing Radiation Protection reference level for occupational exposure and general public exposure, respectively. For exposure at distances of >1 m, a model of the electric field in a realistic environment is proposed. In an office scenario, switching on a microwave oven increases the median field strength from 91 to 145 mV m−1 (+91 %) in a traditional Wireless Local Area Network (WLAN) deployment and from 44 to 92 mV m−1 (+109 %) in an exposure-optimised WLAN deployment. PMID:25956787

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

PubMed

Yoo, Jejoong; Wilson, James; Aksimentiev, Aleksei

2016-10-01

Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA-DNA interactions. In the simulations performed using the two standard models, Ca(2+) ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc2 and CaCl2 solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca(2+) ions in the simulations of Ca(2+) -mediated DNA-DNA interactions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter-DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca(2+) to DNA phosphate is strong enough to affect the direction of the electric field-driven translocation of DNA through a solid-state nanopore. To address these shortcomings of the standard Ca(2+) model, we introduce a custom model of a hydrated Ca(2+) ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca(2+) can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 752-763, 2016. © 2016 Wiley Periodicals, Inc.

DNA electrophoresis in agarose gels: effects of field and gel concentration on the exponential dependence of reciprocal mobility on DNA length.

PubMed

Rill, Randolph L; Beheshti, Afshin; Van Winkle, David H

2002-08-01

Electrophoretic mobilities of DNA molecules ranging in length from 200 to 48 502 base pairs (bp) were measured in agarose gels with concentrations T = 0.5% to 1.3% at electric fields from E = 0.71 to 5.0 V/cm. This broad data set determines a range of conditions over which the new interpolation equation nu(L) = (beta+alpha(1+exp(-L/gamma))(-1) can be used to relate mobility to length with high accuracy. Mobility data were fit with chi(2) > 0.999 for all gel concentrations and fields ranging from 2.5 to 5 V/cm, and for lower fields at low gel concentrations. Analyses using so-called reptation plots (Rousseau, J., Drouin, G., Slater, G. W., Phys. Rev. Lett. 1997, 79, 1945-1948) indicate that this simple exponential relation is obeyed well when there is a smooth transition from the Ogston sieving regime to the reptation regime with increasing DNA length. Deviations from this equation occur when DNA migration is hindered, apparently by entropic-trapping, which is favored at low fields and high gel concentrations in the ranges examined.

Artist's Concept of Propulsive Small Expendable Deployer System (ProSEDS)

NASA Technical Reports Server (NTRS)

1999-01-01

Pictured is an artist's concept of NASA's Propulsive Small Expendable Deployer System experiment (ProSEDS). ProSEDS will demonstrate the use of an electrodynamic tether, basically a long, thin wire, for propulsion. An electrodynamic tether uses the same principles as electric motors in toys, appliances and computer disk drives, and generators in automobiles and power plants. When electrical current is flowing through the tether, a magnetic field is produced that pushes against the magnetic field of the Earth. For ProSEDS, the current in the tether results by virtue of the voltage generated when the tether moves through the Earth's magnetic field at more than 17,000 mph. This approach can produce drag thrust generating useable power. Since electrodynamic tethers require no propellant, they could substantially reduce the weight of the spacecraft and provide a cost-effective method of reboosting spacecraft. The initial flight of ProSEDS is scheduled to fly aboard an Air Force Delta II rocket in summer of 2002. In orbit, ProSEDS will deploy from a Delta II second stage. It will be a 3.1-mile (5 kilometer) long, ultrathin base-wire tether cornected with a 6.2-mile (10 kilometer) long nonconducting tether. The ProSEDS experiment is managed by the Space Transportation Directorate at the Marshall Space Flight Center.

Active Time-Domain Reflectometry for Unattended Safeguards Systems FY15 Report

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

Tedeschi, Jonathan R.; Smith, Leon E.; Moore, David E.

2015-09-01

The International Atomic Energy Agency (IAEA) continues to expand its use of unattended measurement systems. An increasing number of systems and an expanding family of instruments create challenges in terms of deployment efficiency and the implementation of data authentication measures. In collaboration with the IAEA, tamper-indicating measures to address data-transmission authentication challenges with unattended safeguards systems are under investigation. Pacific Northwest National Laboratory (PNNL) is studying the viability of active time-domain reflectometry (TDR) along two parallel but interconnected paths: (1) swept-frequency TDR as the highly flexible, laboratory gold standard to which field-deployable options can be compared, and (2) a low-costmore » commercially available spread-spectrum TDR technology as one option for field implementation. This report describes PNNL’s FY15 progress in the viability study including: an overview of the TDR methods under investigation; description of the testing configurations and mock tampering scenarios; results from a preliminary sensitivity comparison of the two TDR methods; demonstration of a quantitative metric for estimating field performance that acknowledges the need for high detection probability while minimizing false alarms. FY15 progress reported here sets the stage for a rigorous comparison of the candidate TDR methods, over a range of deployment scenarios and perturbing effects typical of IAEA unattended monitoring systems.« less

All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model

PubMed Central

Savelyev, Alexey; MacKerell, Alexander D.

2014-01-01

Presented is a first generation atomistic force field for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting QM data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude force field yields stable DNA duplexes on the 100 ns time scale and satisfactorily reproduces (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII sub-states of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive force field, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA. PMID:24752978

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.

Israel and Iran: A Dangerous Rivalry

DTIC Science & Technology

2011-01-01

and Knesset view the Islamic Republic as “a bitter ideological enemy that is deter- mined to bring about the physical annihilation of Israel”; only...entirely different set of values. . . . Iran sends children into mine fields. Iran denies the Holocaust. Iran openly calls for Israel’s destruction...compromise on sovereignty by having U.S. troops deployed here.” Quoted in Barbara Opall -Rome, “U.S. to Deploy Radar, Troops In Israel,” Defense News

Laser Remote Sensing at NASA

NASA Technical Reports Server (NTRS)

Barnes, Norman P.

2005-01-01

NASA is developing active remote sensors to monitor the health of Planet Earth and for exploration of other planets. Development and deployment of these remote sensors can have a huge economic impact. Lasers for these active remote sensors span the spectral range from the ultraviolet to the mid infrared spectral regions. Development activities range from quantum mechanical modeling and prediction of new laser materials to the design, development, and demonstration be deployed in the field.

ALFA MHK Biological Monitoring Stationary deployment

DOE Data Explorer

Horne, John

2016-10-01

Acoustic backscatter data from a WBAT operating at 70kHz deployed at PMEC-SETS from April to September of 2016. 180 pings were collected at 1Hz every two hours, as part of the Advanced Laboratory and Field Arrays (ALFA) for Marine Energy project. Data was subject to preliminary processing (noise removal, a threshold of -75dB was applied, surface turbulence and data below 0.5m from the bottom was removed).

All-Atom MD Simulation of DNA Condensation Using Ab Initio Derived Force Field Parameters of Cobalt(III)-Hexammine.

PubMed

Sun, Tiedong; Mirzoev, Alexander; Korolev, Nikolay; Lyubartsev, Alexander P; Nordenskiöld, Lars

2017-08-24

It is well established that the presence of the trivalent cobalt(III)-hexammine cation (CoHex 3+ ) at submillimolar concentrations leads to bundling (condensation) of double-stranded DNA molecules, which is caused by DNA-DNA attraction induced by the multivalent counterions. However, the detailed mechanism of this process is still not fully understood. Furthermore, in all-atom molecular dynamics (MD) simulations, spontaneous aggregation of several DNA oligonucleotides in the presence of CoHex 3+ has previously not been demonstrated. In order to obtain a rigorous description of CoHex 3+ -nucleic acid interactions and CoHex 3+ -induced DNA condensation to be used in MD simulations, we have derived optimized force field parameters of the CoHex 3+ ion. They were obtained from Car-Parrinello molecular dynamics simulation of a single CoHex 3+ ion in the presence of 125 water molecules. The new set of force field parameters reproduces the experimentally known transition of DNA from B- to A-form, and qualitatively describes changes of DNA and RNA persistence lengths. We then carried out a 2 μs long atomistic simulation of four DNA oligomers each consisting of 36 base pairs in the presence of CoHex 3+ . We demonstrate that, in this system, DNA molecules display attractive interactions and aggregate into bundle-like structures. This behavior depends critically on the details of the CoHex 3+ interaction with DNA. A control simulation with a similar setup but in the presence of Mg 2+ does not induce DNA-DNA attraction, which is also in agreement with experiment.

Chondroitin sulfate-polyethylenimine copolymer-coated superparamagnetic iron oxide nanoparticles as an efficient magneto-gene carrier for microRNA-encoding plasmid DNA delivery.

PubMed

Lo, Yu-Lun; Chou, Han-Lin; Liao, Zi-Xian; Huang, Shih-Jer; Ke, Jyun-Han; Liu, Yu-Sheng; Chiu, Chien-Chih; Wang, Li-Fang

2015-05-14

MicroRNA-128 (miR-128) is an attractive therapeutic molecule with powerful glioblastoma regulation properties. However, miR-128 lacks biological stability and leads to poor delivery efficacy in clinical applications. In our previous study, we demonstrated two effective transgene carriers, including polyethylenimine (PEI)-decorated superparamagnetic iron oxide nanoparticles (SPIONs) as well as chemically-conjugated chondroitin sulfate-PEI copolymers (CPs). In this contribution, we report optimized conditions for coating CPs onto the surfaces of SPIONs, forming CPIOs, for magneto-gene delivery systems. The optimized weight ratio of the CPs and SPIONs is 2 : 1, which resulted in the formation of a stable particle as a good transgene carrier. The hydrodynamic diameter of the CPIOs is ∼136 nm. The gel electrophoresis results demonstrate that the weight ratio of CPIO/DNA required to completely encapsulate pDNA is ≥3. The in vitro tests of CPIO/DNA were done in 293 T, CRL5802, and U87-MG cells in the presence and absence of an external magnetic field. The magnetofection efficiency of CPIO/DNA was measured in the three cell lines with or without fetal bovine serum (FBS). CPIO/DNA exhibited remarkably improved gene expression in the presence of the magnetic field and 10% FBS as compared with a gold non-viral standard, PEI/DNA, and a commercial magnetofection reagent, PolyMag/DNA. In addition, CPIO/DNA showed less cytotoxicity than PEI/DNA and PolyMag/DNA against the three cell lines. The transfection efficiency of the magnetoplex improved significantly with an assisted magnetic field. In miR-128 delivery, a microRNA plate array and fluorescence in situ hybridization were used to demonstrate that CPIO/pMIRNA-128 indeed expresses more miR-128 with the assisted magnetic field than without. In a biodistribution test, CPIO/Cy5-DNA showed higher accumulation at the tumor site where an external magnet is placed nearby.

Regulation of DNA conformations and dynamics in flows with hybrid field microfluidics.

PubMed

Ren, Fangfang; Zu, Yingbo; Kumar Rajagopalan, Kartik; Wang, Shengnian

2012-01-01

Visualizing single DNA dynamics in flow provides a wealth of physical insights in biophysics and complex flow study. However, large signal fluctuations, generated from diversified conformations, deformation history dependent dynamics and flow induced stochastic tumbling, often frustrate its wide adoption in single molecule and polymer flow study. We use a hybrid field microfluidic (HFM) approach, in which an electric field is imposed at desired locations and appropriate moments to balance the flow stress on charged molecules, to effectively regulate the initial conformations and the deformation dynamics of macromolecules in flow. With λ-DNA and a steady laminar shear flow as the model system, we herein studied the performance of HFM on regulating DNA trapping, relaxation, coil-stretch transition, and accumulation. DNA molecules were found to get captured in the focused planes when motions caused by flow, and the electric field were balanced. The trapped macromolecules relaxed in two different routes while eventually became more uniform in size and globule conformations. When removing the electric field, the sudden stretching dynamics of DNA molecules exhibited a more pronounced extension overshoot in their transient response under a true step function of flow stress while similar behaviors to what other pioneering work in steady shear flow. Such regulation strategies could be useful to control the conformations of other important macromolecules (e.g., proteins) and help better reveal their molecular dynamics.

Early disaster response in Haiti: the Israeli field hospital experience.

PubMed

Kreiss, Yitshak; Merin, Ofer; Peleg, Kobi; Levy, Gad; Vinker, Shlomo; Sagi, Ram; Abargel, Avi; Bartal, Carmi; Lin, Guy; Bar, Ariel; Bar-On, Elhanan; Schwaber, Mitchell J; Ash, Nachman

2010-07-06

The earthquake that struck Haiti in January 2010 caused an estimated 230,000 deaths and injured approximately 250,000 people. The Israel Defense Forces Medical Corps Field Hospital was fully operational on site only 89 hours after the earthquake struck and was capable of providing sophisticated medical care. During the 10 days the hospital was operational, its staff treated 1111 patients, hospitalized 737 patients, and performed 244 operations on 203 patients. The field hospital also served as a referral center for medical teams from other countries that were deployed in the surrounding areas. The key factor that enabled rapid response during the early phase of the disaster from a distance of 6000 miles was a well-prepared and trained medical unit maintained on continuous alert. The prompt deployment of advanced-capability field hospitals is essential in disaster relief, especially in countries with minimal medical infrastructure. The changing medical requirements of people in an earthquake zone dictate that field hospitals be designed to operate with maximum flexibility and versatility regarding triage, staff positioning, treatment priorities, and hospitalization policies. Early coordination with local administrative bodies is indispensable.

DNA Polymerase Eta and Chemotherapeutic Agents

PubMed Central

2011-01-01

Abstract The discovery of human DNA polymerase eta (pol η) has a major impact on the fields of DNA replication/repair fields. Since the discovery of human pol η, a number of new DNA polymerases with the ability to bypass various DNA lesions have been discovered. Among these polymerases, pol η is the most extensively studied lesion bypass polymerase with a defined major biological function, that is, to replicate across the cyclobutane pyrimidine dimers introduced by UV irradiation. Cyclobutane pyrimidine dimer is a major DNA lesion that causes distortion of DNA structure and block the replicative DNA polymerases during DNA replication process. Genetic defects in the pol η gene, Rad30, results in a disease called xeroderma pigmentosum variant. This review focuses on the overall properties of pol η and the mechanism that involved in regulating its activity in cells. In addition, the role of pol η in the action of DNA-targeting anticancer compounds is also discussed. Antioxid. Redox Signal. 14, 2521–2529. PMID:21050139

Divergent dispersion behavior of ssDNA fragments during microchip electrophoresis in pDMA and LPA entangled polymer networks

PubMed Central

Fredlake, Christopher P.; Hert, Daniel G.; Niedringhaus, Thomas P.; Lin, Jennifer S.; Barron, Annelise E.

2015-01-01

Resolution of DNA fragments separated by electrophoresis in polymer solutions (“matrices”) is determined by both the spacing between peaks and the width of the peaks. Prior research on the development of high-performance separation matrices has been focused primarily on optimizing DNA mobility and matrix selectivity, and gave less attention to peak broadening. Quantitative data are rare for peak broadening in systems in which high electric field strengths are used (> 150 V/cm), which is surprising since capillary and microchip-based systems commonly run at these field strengths. Here, we report results for a study of band broadening behavior for ssDNA fragments on a glass microfluidic chip, for electric field strengths up to 320 V/cm. We compare dispersion coefficients obtained in a poly(N,N-dimethylacrylamide) (pDMA) separation matrix that was developed for chip-based DNA sequencing with a commercially available linear polyacrylamide (LPA) matrix commonly used in capillaries. Much larger DNA dispersion coefficients were measured in the LPA matrix as compared to the pDMA matrix, and the dependences of dispersion coefficient on DNA size and electric field strength were found to differ quite starkly in the two matrices. These observations lead us to propose that DNA migration mechanisms differ substantially in our custom pDMA matrix compared to the commercially available LPA matrix. We discuss the implications of these results in terms of developing optimal matrices for specific separation (microchip or capillary) platforms. PMID:22648809

Tethered Satellite System (TSS-1R)-Post Flight (STS-75) Engineering Performance Report

NASA Technical Reports Server (NTRS)

Lavoie, Anthony R.

1996-01-01

The first mission of the Tethered Satellite deployer was flown onboard Atlantis in 1992 during the Space Transportation System (STS) flight STS-46. Due to a mechanical interference with the level wind mechanism the satellite was only Deployed to 256 m rather than the planned 20,000 m. Other problems were also experienced during the STS-46 flight and several modifications were made to the Deployer and Satellite. STS-75 was a reflight of the Tethered Satellite System 1 (TSS-1) designated as Tethered Satellite System 1 Reflight (TSS-1 R) onboard Columbia. As on STS-46, the TSS payload consisted of the Deployer, the Satellite, 3 cargo bay mounted experiments: Shuttle Electrodynamic Tether System (SETS), Shuttle Potential and Return Electron Experiment (SPREE), Deployer Core Equipment (DCORE) 4 Satellite mounted experiments: Research on Electrodynamics Tether Effects (RETE), Research on Orbital Plasma Electrodynamics (ROPE), Satellite Core Instruments (SCORE), Tether Magnetic Field Experiment (TEMAG) and an aft flight deck camera: Tether Optical Phenomena Experiment (TOP). Following successful pre-launch, launch and pre-deployment orbital operations, the Deployer deployed the Tethered Satellite to 19,695 m at which point the tether broke within the Satellite Deployment Boom (SDB). The planned length for On-Station I (OST1) was 20,700 m The Satellite flew away from the Orbiter with the tether attached. The satellite was "safed" and placed in a limited power mode via the RF link. The Satellite was contacted periodically during overflights of ground stations. Cargo bay science activities continued for the period of time allocated to TSS-1 R operations.

Oxyanion flux characterization using passive flux meters: Development and field testing of surfactant-modified granular activated carbon

NASA Astrophysics Data System (ADS)

Lee, Jimi; Rao, P. S. C.; Poyer, Irene C.; Toole, Robyn M.; Annable, M. D.; Hatfield, K.

2007-07-01

We report here on the extension of Passive Flux Meter (PFM) applications for measuring fluxes of oxyanions in groundwater, and present results for laboratory and field studies. Granular activated carbon, with and without impregnated silver (GAC and SI-GAC, respectively), was modified with a cationic surfactant, hexadecyltrimethylammonium (HDTMA), to enhance the anion exchange capacity (AEC). Langmuir isotherm sorption maxima for oxyanions measured in batch experiments were in the following order: perchlorate >> chromate > selenate, consistent with their selectivity. Linear sorption isotherms for several alcohols suggest that surfactant modification of GAC and SI-GAC reduced (˜ 30-45%) sorption of alcohols by GAC. Water and oxyanion fluxes (perchlorate and chromate) measured by deploying PFMs packed with surfactant-modified GAC (SM-GAC) or surfactant-modified, silver-impregnated GAC (SM-SI-GAC) in laboratory flow chambers were in close agreement with the imposed fluxes. The use of SM-SI-GAC as a PFM sorbent was evaluated at a field site with perchlorate contamination of a shallow unconfined aquifer. PFMs packed with SM-SI-GAC were deployed in three existing monitoring wells with a perchlorate concentration range of ˜ 2.5 to 190 mg/L. PFM-measured, depth-averaged, groundwater fluxes ranged from 1.8 to 7.6 cm/day, while depth-averaged perchlorate fluxes varied from 0.22 to 1.7 g/m 2/day. Groundwater and perchlorate flux distributions measured in two PFM deployments closely matched each other. Depth-averaged Darcy fluxes measured with PFMs were in line with an estimate from a borehole dilution test, but much smaller than those based on hydraulic conductivity and head gradients; this is likely due to flow divergence caused by well-screen clogging. Flux-averaged perchlorate concentrations measured with PFM deployments matched concentrations in groundwater samples taken from one well, but not in two other wells, pointing to the need for additional field testing. Use of the surfactant-modified GACs for measuring fluxes of other anions of environmental interest is discussed.

Oxyanion flux characterization using passive flux meters: development and field testing of surfactant-modified granular activated carbon.

PubMed

Lee, Jimi; Rao, P S C; Poyer, Irene C; Toole, Robyn M; Annable, M D; Hatfield, K

2007-07-17

We report here on the extension of Passive Flux Meter (PFM) applications for measuring fluxes of oxyanions in groundwater, and present results for laboratory and field studies. Granular activated carbon, with and without impregnated silver (GAC and SI-GAC, respectively), was modified with a cationic surfactant, hexadecyltrimethylammonium (HDTMA), to enhance the anion exchange capacity (AEC). Langmuir isotherm sorption maxima for oxyanions measured in batch experiments were in the following order: perchlorate>chromate>selenate, consistent with their selectivity. Linear sorption isotherms for several alcohols suggest that surfactant modification of GAC and SI-GAC reduced (approximately 30-45%) sorption of alcohols by GAC. Water and oxyanion fluxes (perchlorate and chromate) measured by deploying PFMs packed with surfactant-modified GAC (SM-GAC) or surfactant-modified, silver-impregnated GAC (SM-SI-GAC) in laboratory flow chambers were in close agreement with the imposed fluxes. The use of SM-SI-GAC as a PFM sorbent was evaluated at a field site with perchlorate contamination of a shallow unconfined aquifer. PFMs packed with SM-SI-GAC were deployed in three existing monitoring wells with a perchlorate concentration range of approximately 2.5 to 190 mg/L. PFM-measured, depth-averaged, groundwater fluxes ranged from 1.8 to 7.6 cm/day, while depth-averaged perchlorate fluxes varied from 0.22 to 1.7 g/m2/day. Groundwater and perchlorate flux distributions measured in two PFM deployments closely matched each other. Depth-averaged Darcy fluxes measured with PFMs were in line with an estimate from a borehole dilution test, but much smaller than those based on hydraulic conductivity and head gradients; this is likely due to flow divergence caused by well-screen clogging. Flux-averaged perchlorate concentrations measured with PFM deployments matched concentrations in groundwater samples taken from one well, but not in two other wells, pointing to the need for additional field testing. Use of the surfactant-modified GACs for measuring fluxes of other anions of environmental interest is discussed.

Functional consequences of inducible genetic elements from the p53 SOS response in a mammalian organ system.

PubMed

Guthrie, O'neil W

2017-10-01

In response to DNA damage from ultraviolet (UV) radiation, bacteria deploy the SOS response in order to limit cell death. This bacterial SOS response is characterized by an increase in the recA gene that transactivates expression of multiple DNA repair genes. The current series of experiments demonstrate that a mammalian organ system (the cochlea) that is not evolutionarily conditioned to UV radiation can elicit SOS responses that are reminiscent of that of bacteria. This mammalian SOS response is characterized by an increase in the p53 gene with activation of multiple DNA repair genes that harbor p53 response elements in their promoters. Furthermore, the experimental results provide support for the notion of a convergent trigger paradox, where independent SOS triggers facilitate disparate physiologic sequelae (loss vs. recovery of function). Therefore, it is proposed that the mammalian SOS response is multifunctional and manipulation of this endogenous response could be exploited in future biomedical interventions. Copyright © 2017 Elsevier Inc. All rights reserved.

DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species.

PubMed

Yu, Min; Jiao, Lichao; Guo, Juan; Wiedenhoeft, Alex C; He, Tuo; Jiang, Xiaomei; Yin, Yafang

2017-12-01

ITS2+ trnH - psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens. The increase in illegal logging and timber trade of CITES-listed tropical species necessitates the development of unambiguous identification methods at the species level. For these methods to be fully functional and deployable for law enforcement, they must work using wood or wood products. DNA barcoding of wood has been promoted as a promising tool for species identification; however, the main barrier to extensive application of DNA barcoding to wood is the lack of a comprehensive and reliable DNA reference library of barcodes from wood. In this study, xylarium wood specimens of nine Dalbergia species were selected from the Wood Collection of the Chinese Academy of Forestry and DNA was then extracted from them for further PCR amplification of eight potential DNA barcode sequences (ITS2, matK, trnL, trnH-psbA, trnV-trnM1, trnV-trnM2, trnC-petN, and trnS-trnG). The barcodes were tested singly and in combination for species-level discrimination ability by tree-based [neighbor-joining (NJ)] and distance-based (TaxonDNA) methods. We found that the discrimination ability of DNA barcodes in combination was higher than any single DNA marker among the Dalbergia species studied, with the best two-marker combination of ITS2+trnH-psbA analyzed with NJ trees performing the best (100% accuracy). These barcodes are relatively short regions (<350 bp) and amplification reactions were performed with high success (≥90%) using wood as the source material, a necessary factor to apply DNA barcoding to timber trade. The present results demonstrate the feasibility of using vouchered xylarium specimens to build DNA barcoding reference databases.

GEOS axial booms

NASA Technical Reports Server (NTRS)

Schmidt, G. K.

1979-01-01

A booms and mechanisms subsystem was designed, developed, and qualified for the geostationary scientific satellite GEOS. Part of this subsystem consist of four axial booms consisting of one pair of 1 m booms and one pair of 2.5 m booms. Each of these booms is carrying one bird cage electric field sensor. Alignment accuracy requirements led to a telescopic type solution. Deployment is performed by pressurized nitrogen. At deployment in orbit two of these booms showed some anomalies and one of these two deployed only about 80%. Following this malfunction a detailed failure investigation was performed resulting in a design modification of some critical components as release mechanism, guide sleeves of the telescopic elements, and pressure system.

Taking it to the streets: delivering on deployment.

PubMed

Carr, Dafna; Welch, Vickie; Fabik, Trish; Hirji, Nadir; O'Connor, Casey

2009-01-01

From inception to deployment, the Wait Time Information System (WTIS) project faced significant challenges associated with time, scope and complexity. It involved not only the creation and deployment of two large-scale province-wide systems (the WTIS and Ontario's Client Registry/Enterprise Master Patient Index) within aggressive time frames, but also the active engagement of 82 Ontario hospitals, scores of healthcare leaders and several thousand clinicians who would eventually be using the new technology and its data. The provincial WTIS project team (see Figure 1) also had to be able to adapt and evolve their planning in an environment that was changing day-by-day. This article looks at the factors that allowed the team to take the WTIS out to the field and shares the approach, processes and tools used to deploy this complex and ambitious information management and information technology (IM/IT) initiative.

Development of a Strain Energy Deployable Boom for the Space Technology 5 Mission

NASA Technical Reports Server (NTRS)

Meyers, Stew; Sturm, James

2004-01-01

The Space Technology 5 (ST5) mission is one of a series of technology demonstration missions for the New Millennium Program. This mission will fly three fully functional 25-kilogram micro-class spacecraft in formation through the Earth's magnetosphere; the primary science instrument is a very sensitive magnetometer. The constraints of a 25-kg Micosat resulted in a spin stabilized, octagonal spacecraft that is 30 cm tall by 50 cm diameter and has state-of-the-art solar cells on all eight sides. A non-magnetic boom was needed to place the magnetometer as far from the spacecraft and its residual magnetic fields as possible. The ST-5 spacecraft is designed to be spun up and released from its deployer with the boom and magnetometer stowed for later release. The deployer is the topic of another paper. This paper describes the development efforts and resulting self-deploying magnetometer boom.

Development of a Strain Energy Deployable Boom for the Space Technology 5 Mission

NASA Technical Reports Server (NTRS)

Meyers, Stew; Sturm, James

2004-01-01

The Space Technology 5 (ST5) mission is one of a series of technology demonstration missions for the New Millennium Program. This mission will fly three fully functional 25 kilogram micro class spacecraft in formation through the Earth s magnetosphere; the primary science instrument is a very sensitive magnetometer. The constraints of a 25 kg "Micosat" resulted in a spin stabilized, octagonal spacecraft that is 30 cm tall by 50 cm diameter and has state of the art solar cells on all eight sides. A non-magnetic boom was needed to place the magnetometer as far from the spacecraft and its residual magnetic fields as possible. The ST-5 spacecraft is designed to be spun up and released from its deployer with the boom and magnetometer stowed for later release. The deployer is the topic of another paper, This paper describes the development efforts and resulting self-deploying magnetometer boom.

Security-by-Experiment: Lessons from Responsible Deployment in Cyberspace.

PubMed

Pieters, Wolter; Hadžiosmanović, Dina; Dechesne, Francien

2016-06-01

Conceiving new technologies as social experiments is a means to discuss responsible deployment of technologies that may have unknown and potentially harmful side-effects. Thus far, the uncertain outcomes addressed in the paradigm of new technologies as social experiments have been mostly safety-related, meaning that potential harm is caused by the design plus accidental events in the environment. In some domains, such as cyberspace, adversarial agents (attackers) may be at least as important when it comes to undesirable effects of deployed technologies. In such cases, conditions for responsible experimentation may need to be implemented differently, as attackers behave strategically rather than probabilistically. In this contribution, we outline how adversarial aspects are already taken into account in technology deployment in the field of cyber security, and what the paradigm of new technologies as social experiments can learn from this. In particular, we show the importance of adversarial roles in social experiments with new technologies.

Field-deployable sniffer for 2,4-dinitrotoluene detection.

PubMed

Albert, K J; Myrick, M L; Brown, S B; James, D L; Milanovich, F P; Walt, D R

2001-08-01

A field-deployable instrument has been developed to detect low-level 2,4-dinitrotoluene (2,4-DNT) vapors. The system is based on previously developed artificial nose technology and employs an array of sensory materials attached to the distal tips of an optical fiber bundle. Both semiselective and nonspecific, cross-reactive sensors were employed. Each sensor within the array responds differentially to vapor exposure so the array's fluorescence response patterns are unique for each analyte. The instrument is computationally "trained" to discriminate target response patterns from nontarget and background environments. This detection system has been applied to detect 2,4-DNT, an analyte commonly detected on the soil surface above buried 2,4,6-trinitrotoluene (TNT) land mines, in spiked soil and aqueous and ground samples. The system has been characterized and demonstrated the ability to detect 120 ppb 2,4-DNT vapor in blind (unknown) humidified samples during a supervised field test.

Environmental DNA as a Tool for Inventory and Monitoring of Aquatic Vertebrates

DTIC Science & Technology

2017-07-01

geomorphic calculations and description of each reach. Methods Channel Surveys We initially selected reaches based on access and visual indicators...WA 99164 I-2 Environmental DNA lab protocol: designing species-specific qPCR assays Species-specific surveys should use quantitative polymerase...to traditional field sampling with respect to sensitivity, detection probabilities, and cost efficiency. Compared to field surveys , eDNA sampling

High mobility organic field-effect transistor based on water-soluble deoxyribonucleic acid via spray coating

NASA Astrophysics Data System (ADS)

Shi, Wei; Han, Shijiao; Huang, Wei; Yu, Junsheng

2015-01-01

High mobility organic field-effect transistors (OFETs) by inserting water-soluble deoxyribonucleic acid (DNA) buffer layer between electrodes and pentacene film through spray coating process were fabricated. Compared with the OFETs incorporated with DNA in the conventional organic solvents of ethanol and methanol: water mixture, the water-soluble DNA based OFET exhibited an over four folds enhancement of field-effect mobility from 0.035 to 0.153 cm2/Vs. By characterizing the surface morphology and the crystalline structure of pentacene active layer through atomic force microscope and X-ray diffraction, it was found that the adoption of water solvent in DNA solution, which played a key role in enhancing the field-effect mobility, was ascribed to both the elimination of the irreversible organic solvent-induced bulk-like phase transition of pentacene film and the diminution of a majority of charge trapping at interfaces in OFETs.

Label-free detection of DNA hybridization using carbon nanotube network field-effect transistors

NASA Astrophysics Data System (ADS)

Star, Alexander; Tu, Eugene; Niemann, Joseph; Gabriel, Jean-Christophe P.; Joiner, C. Steve; Valcke, Christian

2006-01-01

We report carbon nanotube network field-effect transistors (NTNFETs) that function as selective detectors of DNA immobilization and hybridization. NTNFETs with immobilized synthetic oligonucleotides have been shown to specifically recognize target DNA sequences, including H63D single-nucleotide polymorphism (SNP) discrimination in the HFE gene, responsible for hereditary hemochromatosis. The electronic responses of NTNFETs upon single-stranded DNA immobilization and subsequent DNA hybridization events were confirmed by using fluorescence-labeled oligonucleotides and then were further explored for label-free DNA detection at picomolar to micromolar concentrations. We have also observed a strong effect of DNA counterions on the electronic response, thus suggesting a charge-based mechanism of DNA detection using NTNFET devices. Implementation of label-free electronic detection assays using NTNFETs constitutes an important step toward low-cost, low-complexity, highly sensitive and accurate molecular diagnostics. hemochromatosis | SNP | biosensor

Enhanced Stability of DNA Nanostructures by Incorporation of Unnatural Base Pairs.

PubMed

Liu, Qing; Liu, Guocheng; Wang, Ting; Fu, Jing; Li, Rujiao; Song, Linlin; Wang, Zhen-Gang; Ding, Baoquan; Chen, Fei

2017-11-03

Self-assembled DNA nanostructures hold great promise in the fields of nanofabrication, biosensing and nanomedicine. However, the inherent low stability of the DNA double helices, formed by weak interactions, largely hinders the assembly and functions of DNA nanostructures. In this study, we redesigned and constructed a six-arm DNA junction by incorporation of the unnatural base pairs 5-Me-isoC/isoG and A/2-thioT into the double helices. They not only retained the structural integrity of the DNA nanostructure, but also showed enhanced thermal stability and resistance to T7 Exonuclease digestion. This research may expand the applications of DNA nanostructures in nanofabrication and biomedical fields, and furthermore, the genetic alphabet expansion with unnatural base pairs may enable us to construct more complicated and diversified self-assembled DNA nanostructures. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Close encounters with DNA

PubMed Central

Maffeo, C.; Yoo, J.; Comer, J.; Wells, D. B.; Luan, B.; Aksimentiev, A.

2014-01-01

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena and we review the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field. PMID:25238560

Relationship Between Frequency and Deflection Angle in the DNA Prism

PubMed Central

Chen, Zhen; Dorfman, Kevin D.

2013-01-01

The DNA prism is a modification of the standard pulsed-field electrophoresis protocol to provide a continuous separation, where the DNA are deflected at an angle that depends on their molecular weight. The standard switchback model for the DNA prism predicts a monotonic increase in the deflection angle as a function of the frequency for switching the field until a plateau regime is reached. However, experiments indicate that the deflection angle achieves a maximum value before decaying to a size-independent value at high frequencies. Using Brownian dynamics simulations, we show that the maximum in the deflection angle is related to the reorientation time for the DNA and the decay in deflection angle at high frequencies is due to inadequate stretching. The generic features of the dependence of the deflection angle on molecular weight, switching frequency, and electric field strength explain a number of experimental phenomena. PMID:23410375

Close encounters with DNA.

PubMed

Maffeo, C; Yoo, J; Comer, J; Wells, D B; Luan, B; Aksimentiev, A

2014-10-15

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.

Study on the three-station typical network deployments of workspace Measurement and Positioning System

NASA Astrophysics Data System (ADS)

Xiong, Zhi; Zhu, J. G.; Xue, B.; Ye, Sh. H.; Xiong, Y.

2013-10-01

As a novel network coordinate measurement system based on multi-directional positioning, workspace Measurement and Positioning System (wMPS) has outstanding advantages of good parallelism, wide measurement range and high measurement accuracy, which makes it to be the research hotspots and important development direction in the field of large-scale measurement. Since station deployment has a significant impact on the measurement range and accuracy, and also restricts the use-cost, the optimization method of station deployment was researched in this paper. Firstly, positioning error model was established. Then focusing on the small network consisted of three stations, the typical deployments and error distribution characteristics were studied. Finally, through measuring the simulated fuselage using typical deployments at the industrial spot and comparing the results with Laser Tracker, some conclusions are obtained. The comparison results show that under existing prototype conditions, I_3 typical deployment of which three stations are distributed in a straight line has an average error of 0.30 mm and the maximum error is 0.50 mm in the range of 12 m. Meanwhile, C_3 typical deployment of which three stations are uniformly distributed in the half-circumference of an circle has an average error of 0.17 mm and the maximum error is 0.28 mm. Obviously, C_3 typical deployment has a higher control effect on precision than I_3 type. The research work provides effective theoretical support for global measurement network optimization in the future work.

Evaluation of fatigue-prone details using a low-cost thermoelastic stress analysis system.

DOT National Transportation Integrated Search

2016-11-01

This study was designed to develop a novel approach for in situ evaluation of stress fields in the vicinity of fatigue-prone details on highway bridges using a low-cost microbolometer thermal imager. : The method was adapted into a field-deployable i...

Measuring the impact of complete streets projects : preliminary field testing : final report.

DOT National Transportation Integrated Search

2016-12-01

This report describes a field study that sought to assess the impact of Complete Streets (CS) projects in Buffalo, NY. Multiple data collection tools were deployed to capture a diversity of impacts on 8 street corridors where CS projects have been im...

3D Extended Logging for Geothermal Resources: Field Trials with the Geo-Bilt System

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

Mallan, R; Wilt, M; Kirkendall, B

2002-05-29

Geo-BILT (Geothermal Borehole Induction Logging Tool) is an extended induction logging tool designed for 3D resistivity imaging around a single borehole. The tool was developed for deployment in high temperature geothermal wells under a joint program funded by the California Energy Commission, Electromagnetic Instruments (EMI) and the U.S. Department of Energy. EM1 was responsible for tool design and manufacture, and numerical modeling efforts were being addressed at Lawrence Livermore Laboratory (LLNL) and other contractors. The field deployment was done by EM1 and LLNL. The tool operates at frequencies from 2 to 42 kHz, and its design features a series ofmore » three-component magnetic sensors offset at 2 and 5 meters from a three-component magnetic source. The combined package makes it possible to do 3D resistivity imaging, deep into the formation, from a single well. The manufacture and testing of the tool was completed in spring of 2001, and the initial deployment of Geo-BILT occurred in May 2001 at the Lost Hills oil field in southern California at leases operated by Chevron USA. This site was chosen for the initial field test because of the favorable geological conditions and the availability of a number of wells suitable for tool deployment. The second deployment occurred in April 2002 at the Dixie Valley geothermal field, operated by Caithness Power LLC, in central Nevada. This constituted the first test in a high temperature environment. The Chevron site features a fiberglass-cased observation well in the vicinity of a water injector. The injected water, which is used for pressure maintenance and for secondary sweep of the heavy oil formation, has a much lower resistivity than the oil bearing formation. This, in addition to the non-uniform flow of this water, creates a 3D resistivity structure, which is analogous to conditions produced from flowing fractures adjacent to geothermal boreholes. Therefore, it is an excellent site for testing the 3D capability of the tool in a low risk environment. The Dixie Valley site offered an environment where the tool could locate near-well fractures associated with steam development. The Lost Hills field measurements yielded a data set suitable for 3D imaging. The Geo-BLT data corresponded to existing conventional logging data and showed clear indications, in several depth intervals, of near-well 3D structure. Subsequent 3D inversion of these data produced a model consistent with non-planar water flow in specific layers. The Dixie Valley measurements identified structures associated with dike intrusions and water inflow at particular depths. Preliminary analysis suggests these structures are steeply dipping, which is consistent with the geology.« less

Development of a molecular method for testing the effectiveness of UV systems on-site.

PubMed

Nizri, Limor; Vaizel-Ohayon, Dalit; Ben-Amram, Hila; Sharaby, Yehonatan; Halpern, Malka; Mamane, Hadas

2017-12-15

We established a molecular method for quantifying ultraviolet (UV) disinfection efficacy using total bacterial DNA in a water sample. To evaluate UV damage to the DNA, we developed the "DNA damage" factor, which is a novel cultivation-independent approach that reveals UV-exposure efficiency by applying a simple PCR amplification method. The study's goal was to prove the feasibility of this method for demonstrating the efficiency of UV systems in the field using flow-through UV reactors. In laboratory-based experiments using seeded bacteria, the DNA damage tests demonstrated a good correlation between PCR products and UV dose. In the field, natural groundwater sampled before and after being subjected to the full-scale UV reactors was filtered, and the DNA extracted from the filtrate was subjected to PCR amplification for a 900-bp fragment of the 16S rRNA gene with initial DNA concentrations of 0.1 and 1 ng/μL. In both cases, the UV dose predicted and explained a significant proportion of the variance in the log inactivation ratio and DNA damage factor. Log inactivation ratio was very low, as expected in groundwater due to low initial bacterial counts, whereas the DNA damage factor was within the range of values obtained in the laboratory-based experiments. Consequently, the DNA damage factor reflected the true performance of the full-scale UV system during operational water flow by using the indigenous bacterial array present in a water sample. By applying this method, we were able to predict with high confidence, the UV reactor inactivation potential. For method validation, laboratory and field iterations are required to create a practical field calibration curve that can be used to determine the expected efficiency of the full-scale UV system in the field under actual operation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Office of Naval Research Graduate Traineeship Award in Ocean Acoustics for Ankita Deepak Jain

DTIC Science & Technology

2012-09-30

Ziegesar, O., “Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific,” Molecular Ecology 7(6): 695-707 (1998) ...ocean, and correlating measured noise with local wind speed. Mexican waters of the North Pacific Ocean are known to be wintering grounds for humpback ... whales [10]. During this experiment, many marine mammal vocalizations were recorded by the deployed hydrophones. We are in the process of

Biological Response to the Dynamic Spectral-Polarized Underwater Light Field

DTIC Science & Technology

2011-09-30

www.bio.utexas.edu/research/cummingslab/ LONG-TERM GOALS Camouflage in marine environments requires matching all of the background optical ...polarized light field in near-shore and near-surface environments (2) Characterize the biological camouflage response of organisms to these dynamic optical ...field will be measured by the simultaneous deployment of a comprehensive optical suite including underwater video-polarimetry (Cummings), inherent

Effective Use of Personal Assistants for Students with Disabilities: Lessons Learned from the 2014 Accessible Geoscience Field Trip

ERIC Educational Resources Information Center

Hendricks, Julie E.; Atchison, Christopher L.; Feig, Anthony D.

2017-01-01

In 2014, the Geological Society of America sponsored an Accessible Field Trip, designed to demonstrate best practices in accommodating a wide variety of participants with disabilities during a field experience. During the trip, an aide was deployed to assist two student participants with sensory disabilities, one with low vision and the other with…

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline.

PubMed

Reid, Jeffrey G; Carroll, Andrew; Veeraraghavan, Narayanan; Dahdouli, Mahmoud; Sundquist, Andreas; English, Adam; Bainbridge, Matthew; White, Simon; Salerno, William; Buhay, Christian; Yu, Fuli; Muzny, Donna; Daly, Richard; Duyk, Geoff; Gibbs, Richard A; Boerwinkle, Eric

2014-01-29

Massively parallel DNA sequencing generates staggering amounts of data. Decreasing cost, increasing throughput, and improved annotation have expanded the diversity of genomics applications in research and clinical practice. This expanding scale creates analytical challenges: accommodating peak compute demand, coordinating secure access for multiple analysts, and sharing validated tools and results. To address these challenges, we have developed the Mercury analysis pipeline and deployed it in local hardware and the Amazon Web Services cloud via the DNAnexus platform. Mercury is an automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. By taking advantage of cloud computing and with Mercury implemented on the DNAnexus platform, we have demonstrated a powerful combination of a robust and fully validated software pipeline and a scalable computational resource that, to date, we have applied to more than 10,000 whole genome and whole exome samples.

Blocking and guiding adult sea lamprey with pulsed direct current from vertical electrodes

USGS Publications Warehouse

Johnson, Nicholas S.; Thompson, Henry T.; Holbrook, Christopher M.; Tix, John A.

2014-01-01

Controlling the invasion front of aquatic nuisance species is of high importance to resource managers. We tested the hypothesis that adult sea lamprey (Petromyzon marinus), a destructive invasive species in the Laurentian Great Lakes, would exhibit behavioral avoidance to dual-frequency pulsed direct current generated by vertical electrodes and that the electric field would not injure or kill sea lamprey or non-target fish. Laboratory and in-stream experiments demonstrated that the electric field blocked sea lamprey migration and directed sea lamprey into traps. Rainbow trout (Oncorhynchus mykiss) and white sucker (Catostomus commersoni), species that migrate sympatrically with sea lamprey, avoided the electric field and had minimal injuries when subjected to it. Vertical electrodes are advantageous for fish guidance because (1) the electric field produced varies minimally with depth, (2) the electric field is not grounded, reducing power consumption to where portable and remote deployments powered by solar, wind, hydro, or a small generator are feasible, and (3) vertical electrodes can be quickly deployed without significant stream modification allowing rapid responses to new invasions. Similar dual-frequency pulsed direct current fields produced from vertical electrodes may be advantageous for blocking or trapping other invasive fish or for guiding valued fish around dams.

DNA nanotechnology and its applications in biomedical research.

PubMed

Sun, Lifan; Yu, Lu; Shen, Wanqiu

2014-09-01

DNA nanotechnology, which uses DNA as a material to self-assemble designed nanostructures, including DNA 2D arrays, 3D nanostructures, DNA nanotubes and DNA nanomechanical devices, has showed great promise in biomedical applications. Various DNA nanostructures have been used for protein characterization, enzyme assembly, biosensing, drug delivery and biomimetic assemblies. In this review, we will present recent advances of DNA nanotechnology and its applications in biomedical research field.

Systematic random sampling of the comet assay.

PubMed

McArt, Darragh G; Wasson, Gillian R; McKerr, George; Saetzler, Kurt; Reed, Matt; Howard, C Vyvyan

2009-07-01

The comet assay is a technique used to quantify DNA damage and repair at a cellular level. In the assay, cells are embedded in agarose and the cellular content is stripped away leaving only the DNA trapped in an agarose cavity which can then be electrophoresed. The damaged DNA can enter the agarose and migrate while the undamaged DNA cannot and is retained. DNA damage is measured as the proportion of the migratory 'tail' DNA compared to the total DNA in the cell. The fundamental basis of these arbitrary values is obtained in the comet acquisition phase using fluorescence microscopy with a stoichiometric stain in tandem with image analysis software. Current methods deployed in such an acquisition are expected to be both objectively and randomly obtained. In this paper we examine the 'randomness' of the acquisition phase and suggest an alternative method that offers both objective and unbiased comet selection. In order to achieve this, we have adopted a survey sampling approach widely used in stereology, which offers a method of systematic random sampling (SRS). This is desirable as it offers an impartial and reproducible method of comet analysis that can be used both manually or automated. By making use of an unbiased sampling frame and using microscope verniers, we are able to increase the precision of estimates of DNA damage. Results obtained from a multiple-user pooled variation experiment showed that the SRS technique attained a lower variability than that of the traditional approach. The analysis of a single user with repetition experiment showed greater individual variances while not being detrimental to overall averages. This would suggest that the SRS method offers a better reflection of DNA damage for a given slide and also offers better user reproducibility.

P-Hint-Hunt: a deep parallelized whole genome DNA methylation detection tool.

PubMed

Peng, Shaoliang; Yang, Shunyun; Gao, Ming; Liao, Xiangke; Liu, Jie; Yang, Canqun; Wu, Chengkun; Yu, Wenqiang

2017-03-14

The increasing studies have been conducted using whole genome DNA methylation detection as one of the most important part of epigenetics research to find the significant relationships among DNA methylation and several typical diseases, such as cancers and diabetes. In many of those studies, mapping the bisulfite treated sequence to the whole genome has been the main method to study DNA cytosine methylation. However, today's relative tools almost suffer from inaccuracies and time-consuming problems. In our study, we designed a new DNA methylation prediction tool ("Hint-Hunt") to solve the problem. By having an optimal complex alignment computation and Smith-Waterman matrix dynamic programming, Hint-Hunt could analyze and predict the DNA methylation status. But when Hint-Hunt tried to predict DNA methylation status with large-scale dataset, there are still slow speed and low temporal-spatial efficiency problems. In order to solve the problems of Smith-Waterman dynamic programming and low temporal-spatial efficiency, we further design a deep parallelized whole genome DNA methylation detection tool ("P-Hint-Hunt") on Tianhe-2 (TH-2) supercomputer. To the best of our knowledge, P-Hint-Hunt is the first parallel DNA methylation detection tool with a high speed-up to process large-scale dataset, and could run both on CPU and Intel Xeon Phi coprocessors. Moreover, we deploy and evaluate Hint-Hunt and P-Hint-Hunt on TH-2 supercomputer in different scales. The experimental results illuminate our tools eliminate the deviation caused by bisulfite treatment in mapping procedure and the multi-level parallel program yields a 48 times speed-up with 64 threads. P-Hint-Hunt gain a deep acceleration on CPU and Intel Xeon Phi heterogeneous platform, which gives full play of the advantages of multi-cores (CPU) and many-cores (Phi).

Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp.

PubMed

Williams, Maggie R; Stedtfeld, Robert D; Engle, Cathrine; Salach, Paul; Fakher, Umama; Stedtfeld, Tiffany; Dreelin, Erin; Stevenson, R Jan; Latimore, Jo; Hashsham, Syed A

2017-01-01

Loop-mediated isothermal amplification (LAMP) of aquatic invasive species environmental DNA (AIS eDNA) was used for rapid, sensitive, and specific detection of Dreissena sp. relevant to the Great Lakes (USA) basin. The method was validated for two uses including i) direct amplification of eDNA using a hand filtration system and ii) confirmation of the results after DNA extraction using a conventional thermal cycler run at isothermal temperatures. Direct amplification eliminated the need for DNA extraction and purification and allowed detection of target invasive species in grab or concentrated surface water samples, containing both free DNA as well as larger cells and particulates, such as veligers, eggs, or seeds. The direct amplification method validation was conducted using Dreissena polymorpha and Dreissena bugensis and uses up to 1 L grab water samples for high target abundance (e.g., greater than 10 veligers (larval mussels) per L for Dreissena sp.) or 20 L samples concentrated through 35 μm nylon screens for low target abundance, at less than 10 veligers per liter water. Surface water concentrate samples were collected over a period of three years, mostly from inland lakes in Michigan with the help of a network of volunteers. Field samples collected from 318 surface water locations included i) filtered concentrate for direct amplification validation and ii) 1 L grab water sample for eDNA extraction and confirmation. Though the extraction-based protocol was more sensitive (resulting in more positive detections than direct amplification), direct amplification could be used for rapid screening, allowing for quicker action times. For samples collected between May and August, results of eDNA direct amplification were consistent with known presence/absence of selected invasive species. A cross-platform smartphone application was also developed to disseminate the analyzed results to volunteers. Field tests of the direct amplification protocol using a portable device (Gene-Z) showed the method could be used in the field to obtain results within one hr (from sample to result). Overall, the direct amplification has the potential to simplify the eDNA-based monitoring of multiple aquatic invasive species. Additional studies are warranted to establish quantitative correlation between eDNA copy number, veliger, biomass or organismal abundance in the field.

Isothermal amplification of environmental DNA (eDNA) for direct field-based monitoring and laboratory confirmation of Dreissena sp.

PubMed Central

Stedtfeld, Robert D.; Engle, Cathrine; Salach, Paul; Fakher, Umama; Stedtfeld, Tiffany; Dreelin, Erin; Stevenson, R. Jan; Latimore, Jo; Hashsham, Syed A.

2017-01-01

Loop-mediated isothermal amplification (LAMP) of aquatic invasive species environmental DNA (AIS eDNA) was used for rapid, sensitive, and specific detection of Dreissena sp. relevant to the Great Lakes (USA) basin. The method was validated for two uses including i) direct amplification of eDNA using a hand filtration system and ii) confirmation of the results after DNA extraction using a conventional thermal cycler run at isothermal temperatures. Direct amplification eliminated the need for DNA extraction and purification and allowed detection of target invasive species in grab or concentrated surface water samples, containing both free DNA as well as larger cells and particulates, such as veligers, eggs, or seeds. The direct amplification method validation was conducted using Dreissena polymorpha and Dreissena bugensis and uses up to 1 L grab water samples for high target abundance (e.g., greater than 10 veligers (larval mussels) per L for Dreissena sp.) or 20 L samples concentrated through 35 μm nylon screens for low target abundance, at less than 10 veligers per liter water. Surface water concentrate samples were collected over a period of three years, mostly from inland lakes in Michigan with the help of a network of volunteers. Field samples collected from 318 surface water locations included i) filtered concentrate for direct amplification validation and ii) 1 L grab water sample for eDNA extraction and confirmation. Though the extraction-based protocol was more sensitive (resulting in more positive detections than direct amplification), direct amplification could be used for rapid screening, allowing for quicker action times. For samples collected between May and August, results of eDNA direct amplification were consistent with known presence/absence of selected invasive species. A cross-platform smartphone application was also developed to disseminate the analyzed results to volunteers. Field tests of the direct amplification protocol using a portable device (Gene-Z) showed the method could be used in the field to obtain results within one hr (from sample to result). Overall, the direct amplification has the potential to simplify the eDNA-based monitoring of multiple aquatic invasive species. Additional studies are warranted to establish quantitative correlation between eDNA copy number, veliger, biomass or organismal abundance in the field. PMID:29036210

2009 Goose Bay Experiment Ocean Measurements. Part 1; Data

NASA Technical Reports Server (NTRS)

Jacob, S. Daniel; LeVine, David M.

2010-01-01

During late February and early March 2009, a field experiment was performed using the NASA P3 over the Labrador Sea. During this experiment, expendable probes deployed from the aircraft acquired ocean mixed layer temperature, salinity and currents Probes were deployed during three flights of the four. Overall 7 AXBTs, 15 AXCTDs and 7 AXCPs were deployed with a success rate of nearly 70%. This is much lower than expected based on prior experience deploying from other aircraft. But given the difficulties associated with the Pneumatic Sonobuoy Launch Tube mechanism on the NASA P3, this rate likely can be improved significantly by using a different deployment mechanism. Additionally, two sets of collocated measurements of AXBTs, AXCPs and AXCTDs were made to verify the drop rates and measurements of the old AXBTs. While there were differences in the measurements, the old AXCTDs are performing well. The expendable data from the experiment are compared to the Argo profiles in the region to check for consistency. Comparisons indicate all the expendable probes acquired useful data and are well within the range of values measured by Argo floats.

An efficient genetic algorithm for maximum coverage deployment in wireless sensor networks.

PubMed

Yoon, Yourim; Kim, Yong-Hyuk

2013-10-01

Sensor networks have a lot of applications such as battlefield surveillance, environmental monitoring, and industrial diagnostics. Coverage is one of the most important performance metrics for sensor networks since it reflects how well a sensor field is monitored. In this paper, we introduce the maximum coverage deployment problem in wireless sensor networks and analyze the properties of the problem and its solution space. Random deployment is the simplest way to deploy sensor nodes but may cause unbalanced deployment and therefore, we need a more intelligent way for sensor deployment. We found that the phenotype space of the problem is a quotient space of the genotype space in a mathematical view. Based on this property, we propose an efficient genetic algorithm using a novel normalization method. A Monte Carlo method is adopted to design an efficient evaluation function, and its computation time is decreased without loss of solution quality using a method that starts from a small number of random samples and gradually increases the number for subsequent generations. The proposed genetic algorithms could be further improved by combining with a well-designed local search. The performance of the proposed genetic algorithm is shown by a comparative experimental study. When compared with random deployment and existing methods, our genetic algorithm was not only about twice faster, but also showed significant performance improvement in quality.

Field deployable microcantilever based chemical sensing: discrimination between H2O, DMMP and Toluene

NASA Astrophysics Data System (ADS)

Thoreson, E. J.; Stievater, T. H.; Rabinovich, W. S.; Ferraro, M. S.; Papanicolaou, N. A.; Bass, R.; Boos, J. B.; Stepnowski, J. L.; McGill, R. A.

2008-10-01

Low cost passive detection of Chemical Warfare Agents (CWA) and being able to distinguish them from interferents is of great interest in the protection of human capital. If CWA sensors could be made cheaply enough, they could be deployed profusely throughout the environment intended for protection. NRL (Naval Research Labs) has demonstrated a small sensor with potentially very low unit cost and compatible with high volume production which has the ability to distinguish between H2O, DMMP, and Toluene. Additionally, they have measured concentrations as low as 17 ppb passively in a package the size of a quarter. Using the latest MEMS technology coupled with advanced chemical identification algorithms we propose a development path for a low cost, highly integrated chemical sensor capable of detecting CWA's, Explosives, VOC's (Volatile Organic Chemicals), and TIC's (Toxic Industrial Chemicals). ITT AES (Advanced Engineering & Sciences) has partnered with NRL (Naval Research Labs) to develop this ``microharp'' technology into a field deployable sensor that will be capable of remote communication with a central server.

Power Hardware-in-the-Loop Evaluation of PV Inverter Grid Support on Hawaiian Electric Feeders

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

Nelson, Austin A; Prabakar, Kumaraguru; Nagarajan, Adarsh

As more grid-connected photovoltaic (PV) inverters become compliant with evolving interconnections requirements, there is increased interest from utilities in understanding how to best deploy advanced grid-support functions (GSF) in the field. One efficient and cost-effective method to examine such deployment options is to leverage power hardware-in-the-loop (PHIL) testing methods, which combine the fidelity of hardware tests with the flexibility of computer simulation. This paper summarizes a study wherein two Hawaiian Electric feeder models were converted to real-time models using an OPAL-RT real-time digital testing platform, and integrated with models of GSF capable PV inverters based on characterization test data. Themore » integrated model was subsequently used in PHIL testing to evaluate the effects of different fixed power factor and volt-watt control settings on voltage regulation of the selected feeders using physical inverters. Selected results are presented in this paper, and complete results of this study were provided as inputs for field deployment and technical interconnection requirements for grid-connected PV inverters on the Hawaiian Islands.« less

A compact neutron scatter camera for field deployment

DOE PAGES

Goldsmith, John E. M.; Gerling, Mark D.; Brennan, James S.

2016-08-23

Here, we describe a very compact (0.9 m high, 0.4 m diameter, 40 kg) battery operable neutron scatter camera designed for field deployment. Unlike most other systems, the configuration of the sixteen liquid-scintillator detection cells are arranged to provide omnidirectional (4π) imaging with sensitivity comparable to a conventional two-plane system. Although designed primarily to operate as a neutron scatter camera for localizing energetic neutron sources, it also functions as a Compton camera for localizing gamma sources. In addition to describing the radionuclide source localization capabilities of this system, we demonstrate how it provides neutron spectra that can distinguish plutonium metalmore » from plutonium oxide sources, in addition to the easier task of distinguishing AmBe from fission sources.« less

Calibration and Vegetation Field Spectra Collection for the 2000 AVIRIS Hawaii Deployment

NASA Technical Reports Server (NTRS)

Dennison, Philip E.; Gardner, Margaret E.; Roberts, Dar A.; Green, Robert O.

2001-01-01

As part of the April 2000 Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) Hawaii deployment, two researchers from the University of California, Santa Barbara, were sent to Hawaii to collect supporting field data. The primary goal of the fieldwork was to obtain spectra of bright targets to be used for retrieving surface reflectance from AVIRIS imagery. Secondary goals included recording the spectra of dominant vegetation, marking the position of homogeneous land cover for use as potential image endmembers (PIEs), and recording firsthand impressions of cover types. Primary and secondary goals were met. Spectra were recorded for 12 calibration targets on 5 islands and spectra were obtained for 61 vegetation species. Twenty PIEs were located, and video was used to document cover at 56 locations.

Analysis of apple beverages treated with high-power ultrasound: a quality function deployment approach.

PubMed

Režek Jambrak, Anet; Šimunek, Marina; Grbeš, Franjo; Mandura, Ana; Djekic, Ilija

2018-04-01

The objective of this paper was to demonstrate application of quality function deployment in analysing effects of high power ultrasound on quality properties of apple juices and nectars. In order to develop a quality function deployment model, joint with instrumental analysis of treated samples, a field survey was performed to identify consumer preferences towards quality characteristics of juices/nectar. Based on field research, the three most important characteristics were 'taste' and 'aroma' with 28.5% of relative absolute weight importance, followed by 'odour' (16.9%). The quality function deployment model showed that the top three 'quality scores' for apple juice were treatments with amplitude 90 µm, 9 min treatment time and sample temperature 40 °C; 60 µm, 9 min, 60 °C; and 90 µm, 6 min, 40 °C. For nectars, the top three were treatments 120 µm, 9 min, 20 °C; 60 µm, 9 min, 60 °C; and A2.16 60 µm, 9 min, 20 °C. This type of quality model enables a more complex measure of large scale of different quality parameters. Its simplicity should be understood as its practical advantage and, as such, this tool can be a part of design quality when using novel preservation technologies. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Tether deployment monitoring system, phase 2

NASA Technical Reports Server (NTRS)

1989-01-01

An operational Tether Deployment Monitoring System (TEDEMS) was constructed that would show system functionality in a terrestrial environment. The principle function of the TEDEMS system is the launching and attachment of reflective targets onto the tether during its deployment. These targets would be tracked with a radar antenna that was pointed towards the targets by a positioning system. A spring powered launcher for the targets was designed and fabricated. An instrumentation platform and launcher were also developed. These modules are relatively heavy and will influence tether deployment scenarios, unless they are released with a velocity and trajectory closely matching that of the tether. Owing to the tracking range limitations encountered during field trails of the Radar system, final TEDEMS system integration was not completed. The major module not finished was the system control computer. The lack of this device prevented any subsystem testing or field trials to be conducted. Other items only partially complete were the instrumentation platform launcher and modules and the radar target launcher. The work completed and the tests performed suggest that the proposed system continues to be a feasible approach to tether monitoring, although additional effort is still necessary to increase the range at which modules can be detected. The equipment completed and tested, to the extent stated, is available to NASA for use on any future program that requires tether tracking capability.

Scalable Parallel Methods for Analyzing Metagenomics Data at Extreme Scale

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

Daily, Jeffrey A.

2015-05-01

The field of bioinformatics and computational biology is currently experiencing a data revolution. The exciting prospect of making fundamental biological discoveries is fueling the rapid development and deployment of numerous cost-effective, high-throughput next-generation sequencing technologies. The result is that the DNA and protein sequence repositories are being bombarded with new sequence information. Databases are continuing to report a Moore’s law-like growth trajectory in their database sizes, roughly doubling every 18 months. In what seems to be a paradigm-shift, individual projects are now capable of generating billions of raw sequence data that need to be analyzed in the presence of alreadymore » annotated sequence information. While it is clear that data-driven methods, such as sequencing homology detection, are becoming the mainstay in the field of computational life sciences, the algorithmic advancements essential for implementing complex data analytics at scale have mostly lagged behind. Sequence homology detection is central to a number of bioinformatics applications including genome sequencing and protein family characterization. Given millions of sequences, the goal is to identify all pairs of sequences that are highly similar (or “homologous”) on the basis of alignment criteria. While there are optimal alignment algorithms to compute pairwise homology, their deployment for large-scale is currently not feasible; instead, heuristic methods are used at the expense of quality. In this dissertation, we present the design and evaluation of a parallel implementation for conducting optimal homology detection on distributed memory supercomputers. Our approach uses a combination of techniques from asynchronous load balancing (viz. work stealing, dynamic task counters), data replication, and exact-matching filters to achieve homology detection at scale. Results for a collection of 2.56M sequences show parallel efficiencies of ~75-100% on up to 8K cores, representing a time-to-solution of 33 seconds. We extend this work with a detailed analysis of single-node sequence alignment performance using the latest CPU vector instruction set extensions. Preliminary results reveal that current sequence alignment algorithms are unable to fully utilize widening vector registers.« less

Magnetic studies of Co2+, Ni2+, and Zn2+-modified DNA double-crossover lattices

NASA Astrophysics Data System (ADS)

Dugasani, Sreekantha Reddy; Oh, Young Hoon; Gnapareddy, Bramaramba; Park, Tuson; Kang, Won Nam; Park, Sung Ha

2018-01-01

We fabricated divalent-metal-ion-modified DNA double-crossover (DX) lattices on a glass substrate and studied their magnetic characteristics as a function of ion concentrations [Co2+], [Ni2+] and [Zn2+]. Up to certain critical concentrations, the DNA DX lattices with ions revealed discrete S-shaped hysteresis, i.e. characteristics of strong ferromagnetism, with significant changes in the coercive field, remanent magnetization, and susceptibility. Induced magnetic dipoles formed by metal ions in DNA duplex in the presence of a magnetic field imparted ferromagnetic behaviour. By considering hysteresis and the magnitude of magnetization in a magnetization-magnetic field curve, Co2+-modified DNA DX lattices showed a relatively strong ferromagnetic nature with an increasing (decreasing) trend of coercive field and remanent magnetization when [Co2+] ≤ 1 mM ([Co2+] > 1 mM). In contrast, Ni2+ and Zn2+-modified DNA DX lattices exhibited strong and weak ferromagnetic behaviours at lower (≤1 mM for Ni2+ and ≤0.5 mM for Zn2+) and higher (>1 mM for Ni2+ and >0.5 mM for Zn2+) concentrations of ions, respectively. About 1 mM of [Co2+], [Ni2+] and [Zn2+] in DNA DX lattices was of special interest with regard to physical characteristics and was identified to be an optimum concentration of each ion. Finally, we measured the temperature-dependent magnetic characteristics of the metal-ion-modified DNA DX lattices. Nonzero magnetization and inverse susceptibility with almost constant values were observed between 25 and 300 K, with no indication of a magnetic transition. This indicated that the magnetic Curie temperatures of Co2+, Ni2+ and Zn2+-modified DNA DX lattices were above 300 K.

Evolution and inheritance of animal mitochondrial DNA: rules and exceptions.

PubMed

Ladoukakis, Emmanuel D; Zouros, Eleftherios

2017-12-01

Mitochondrial DNA (mtDNA) has been studied intensely for "its own" merit. Its role for the function of the cell and the organism remains a fertile field, its origin and evolution is an indispensable part of the evolution of life and its interaction with the nuclear DNA is among the most important cases of genome synergism and co-evolution. Also, mtDNA was proven one of the most useful tools in population genetics and molecular phylogenetics. In this article we focus on animal mtDNA and discuss briefly how our views about its structure, function and transmission have changed, how these changes affect the information we have accumulated through its use in the fields of phylogeny and population structure and what are the most important questions that remain open for future research.

Experimental analysis of a TEM plane transmission line for DNA studies at 900 MHz EM fields

NASA Astrophysics Data System (ADS)

Belloni, F.; Doria, D.; Lorusso, A.; Nassisi, V.; Velardi, L.; Alifano, P.; Monaco, C.; Talà, A.; Tredici, M.; Rainò, A.

2006-07-01

A suitable plane transmission line was developed and its behaviour analysed at 900 MHz radiofrequency fields to study DNA mutability and the repair of micro-organisms. In this work, utilizing such a device, we investigated the behaviour of DNA mutability and repair of Escherichia coli strains. The transmission line was very simple and versatile in changing its characteristic resistance and field intensity by varying its sizes. In the absence of cell samples inside the transmission line, the relative modulation of the electric and/or magnetic field was ±31% with respect to the mean values, allowing the processing of more samples at different exposure fields in a single run. A slight decrease in spontaneous mutability to rifampicin-resistance of the E. coli JC411 strain was demonstrated in mismatch-repair proficient samples exposed to the radio-frequency fields during their growth on solid medium.

DNA Everywhere. A Guide for Simplified Environmental Genomic DNA Extraction Suitable for Use in Remote Areas

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

Gabrielle N. Pecora; Francine C. Reid; Lauren M. Tom

2016-05-01

Collecting field samples from remote or geographically distant areas can be a financially and logistically challenging. With participation of a local organization where the samples are originated from, gDNA samples can be extracted from the field and shipped to a research institution for further processing and analysis. The ability to set up gDNA extraction capabilities in the field can drastically reduce cost and time when running long-term microbial studies with a large sample set. The method outlined here has developed a compact and affordable method for setting up a “laboratory” and extracting and shipping gDNA samples from anywhere in themore » world. This white paper explains the process of setting up the “laboratory”, choosing and training individuals with no prior scientific experience how to perform gDNA extractions and safe methods for shipping extracts to any research institution. All methods have been validated by the Andersen group at Lawrence Berkeley National Laboratory using the Berkeley Lab PhyloChip.« less

Design of Dual-Road Transportable Portal Monitoring System for Visible Light and Gamma-Ray Imaging

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

Karnowski, Thomas Paul; Cunningham, Mark F; Goddard Jr, James Samuel

2010-01-01

The use of radiation sensors as portal monitors is increasing due to heightened concerns over the smuggling of fissile material. Transportable systems that can detect significant quantities of fissile material that might be present in vehicular traffic are of particular interest, especially if they can be rapidly deployed to different locations. To serve this application, we have constructed a rapid-deployment portal monitor that uses visible-light and gamma-ray imaging to allow simultaneous monitoring of multiple lanes of traffic from the side of a roadway. The system operation uses machine vision methods on the visible-light images to detect vehicles as they entermore » and exit the field of view and to measure their position in each frame. The visible-light and gamma-ray cameras are synchronized which allows the gamma-ray imager to harvest gamma-ray data specific to each vehicle, integrating its radiation signature for the entire time that it is in the field of view. Thus our system creates vehicle-specific radiation signatures and avoids source confusion problems that plague non-imaging approaches to the same problem. Our current prototype instrument was designed for measurement of upto five lanes of freeway traffic with a pair of instruments, one on either side of the roadway. Stereoscopic cameras are used with a third alignment camera for motion compensation and are mounted on a 50 deployable mast. In this paper we discuss the design considerations for the machine-vision system, the algorithms used for vehicle detection and position estimates, and the overall architecture of the system. We also discuss system calibration for rapid deployment. We conclude with notes on preliminary performance and deployment.« less

Design of dual-road transportable portal monitoring system for visible light and gamma-ray imaging

NASA Astrophysics Data System (ADS)

Karnowski, Thomas P.; Cunningham, Mark F.; Goddard, James S.; Cheriyadat, Anil M.; Hornback, Donald E.; Fabris, Lorenzo; Kerekes, Ryan A.; Ziock, Klaus-Peter; Bradley, E. Craig; Chesser, J.; Marchant, W.

2010-04-01

The use of radiation sensors as portal monitors is increasing due to heightened concerns over the smuggling of fissile material. Transportable systems that can detect significant quantities of fissile material that might be present in vehicular traffic are of particular interest, especially if they can be rapidly deployed to different locations. To serve this application, we have constructed a rapid-deployment portal monitor that uses visible-light and gamma-ray imaging to allow simultaneous monitoring of multiple lanes of traffic from the side of a roadway. The system operation uses machine vision methods on the visible-light images to detect vehicles as they enter and exit the field of view and to measure their position in each frame. The visible-light and gamma-ray cameras are synchronized which allows the gamma-ray imager to harvest gamma-ray data specific to each vehicle, integrating its radiation signature for the entire time that it is in the field of view. Thus our system creates vehicle-specific radiation signatures and avoids source confusion problems that plague non-imaging approaches to the same problem. Our current prototype instrument was designed for measurement of upto five lanes of freeway traffic with a pair of instruments, one on either side of the roadway. Stereoscopic cameras are used with a third "alignment" camera for motion compensation and are mounted on a 50' deployable mast. In this paper we discuss the design considerations for the machine-vision system, the algorithms used for vehicle detection and position estimates, and the overall architecture of the system. We also discuss system calibration for rapid deployment. We conclude with notes on preliminary performance and deployment.

Simple method of DNA stretching on glass substrate for fluorescence image and spectroscopy

NASA Astrophysics Data System (ADS)

Neupane, Guru P.; Dhakal, Krishna P.; Lee, Hyunsoo; Guthold, Martin; Joseph, Vincent S.; Hong, Jong-Dal; Kim, Jeongyong

2013-05-01

Study of biological molecule DNA has contributed to developing many breaking thoughts and wide applications in multidisciplinary fields, such as genomic, medical, sensing and forensic fields. Stretching of DNA molecules is an important supportive tool for AFM or spectroscopic studies of DNA in a single molecular level. In this article, we established a simple method of DNA stretching (to its full length) that occurred on a rotating negatively-charged surface of glass substrate. The isolation of a single DNA molecule was attained by the two competitive forces on DNA molecules, that is, the electrostatic attraction developed between the positively charged YOYO-1 stained DNA and the negatively charged substrate, and the centrifugal force of the rotating substrate, which separates the DNA aggregates into the single molecule. Density of stretched DNA molecules was controlled by selecting the specific parameters such as spinning time and rates, loading volume of DNA-dye complex solution etc. The atomic force microscopy image exhibited a single DNA molecule on the negatively-charged substrate in an isolated state. Further, the photoluminescence spectra of a single DNA molecule stained with YOYO-1 were achieved using the method developed in the present study, which is strongly believed to effectively support the spectroscopic analysis of DNA in a single molecular level.

DNA methylation-based age prediction from various tissues and body fluids

PubMed Central

Jung, Sang-Eun; Shin, Kyoung-Jin; Lee, Hwan Young

2017-01-01

Aging is a natural and gradual process in human life. It is influenced by heredity, environment, lifestyle, and disease. DNA methylation varies with age, and the ability to predict the age of donor using DNA from evidence materials at a crime scene is of considerable value in forensic investigations. Recently, many studies have reported age prediction models based on DNA methylation from various tissues and body fluids. Those models seem to be very promising because of their high prediction accuracies. In this review, the changes of age-associated DNA methylation and the age prediction models for various tissues and body fluids were examined, and then the applicability of the DNA methylation-based age prediction method to the forensic investigations was discussed. This will improve the understandings about DNA methylation markers and their potential to be used as biomarkers in the forensic field, as well as the clinical field. PMID:28946940

Biological Response to the Dynamic Spectral-Polarized Underwater Light Field

DTIC Science & Technology

2012-09-30

deployment of a comprehensive optical suite including underwater video- polarimetry (full Stokes vector video-imaging camera custom-built Cummings; and...During field operations, we couple polarimetry measurements of live, free-swimming animals in their environments with a full suite of optical...Seibel, Ahmed). We also restrain live, awake animals to take polarimetry measurements (in the field and laboratory) under a complete set of

Self-assembly of multiferroic core-shell particulate nanocomposites through DNA-DNA hybridization and magnetic field directed assembly of superstructures

NASA Astrophysics Data System (ADS)

Sreenivasulu, Gollapudi; Lochbiler, Thomas A.; Panda, Manashi; Srinivasan, Gopalan; Chavez, Ferman A.

2016-04-01

Multiferroic composites of ferromagnetic and ferroelectric phases are of importance for studies on mechanical strain mediated coupling between the magnetic and electric subsystems. This work is on DNA-assisted self-assembly of superstructures of such composites with nanometer periodicity. The synthesis involved oligomeric DNA-functionalized ferroelectric and ferromagnetic nanoparticles, 600 nm BaTiO3 (BTO) and 200 nm NiFe2O4 (NFO), respectively. Mixing BTO and NFO particles, possessing complementary DNA sequences, resulted in the formation of ordered core-shell heteronanocomposites held together by DNA hybridization. The composites were imaged by scanning electron microscopy and scanning microwave microscopy. The presence of heteroassemblies along with core-shell architecture is clearly observed. The reversible nature of the DNA hybridization allows for restructuring the composites into mm-long linear chains and 2D-arrays in the presence of a static magnetic field and ring-like structures in a rotating-magnetic field. Strong magneto-electric (ME) coupling in as-assembled composites is evident from static magnetic field H induced polarization and low-frequency magnetoelectric voltage coefficient measurements. Upon annealing the nanocomposites at high temperatures, evidence for the formation of bulk composites with excellent cross-coupling between the electric and magnetic subsystems is obtained by H-induced polarization and low-frequency ME voltage coefficient. The ME coupling strength in the self-assembled composites is measured to be much stronger than in bulk composites with randomly distributed NFO and BTO prepared by direct mixing and sintering.

Application of the CometChip platform to assess DNA damage in field-collected blood samples from turtles.

PubMed

Sykora, Peter; Chiari, Ylenia; Heaton, Andrew; Moreno, Nickolas; Glaberman, Scott; Sobol, Robert W

2018-05-01

DNA damage has been linked to genomic instability and the progressive breakdown of cellular and organismal homeostasis, leading to the onset of disease and reduced longevity. Insults to DNA from endogenous sources include base deamination, base hydrolysis, base alkylation, and metabolism-induced oxidative damage that can lead to single-strand and double-strand DNA breaks. Alternatively, exposure to environmental pollutants, radiation or ultra-violet light, can also contribute to exogenously derived DNA damage. We previously validated a novel, high through-put approach to measure levels of DNA damage in cultured mammalian cells. This new CometChip Platform builds on the classical single cell gel electrophoresis or comet methodology used extensively in environmental toxicology and molecular biology. We asked whether the CometChip Platform could be used to measure DNA damage in samples derived from environmental field studies. To this end, we determined that nucleated erythrocytes from multiple species of turtle could be successfully evaluated in the CometChip Platform to quantify levels of DNA damage. In total, we compared levels of DNA damage in 40 animals from two species: the box turtle (Terrapene carolina) and the red-eared slider (Trachemys scripta elegans). Endogenous levels of DNA damage were identical between the two species, yet we did discover some sex-linked differences and changes in DNA damage accumulation. Based on these results, we confirm that the CometChip Platform allows for the measurement of DNA damage in a large number of samples quickly and accurately, and is particularly adaptable to environmental studies using field-collected samples. Environ. Mol. Mutagen. 59:322-333, 2018. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Integrated Field Testing of Fuel Cells and Micro-Turbines

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

Jerome R. Temchin; Stephen J. Steffel

A technical and economic evaluation of the prospects for the deployment of distributed generation on Long Beach Island, New Jersey concluded that properly sited DG would defer upgrading of the electric power grid for 10 years. This included the deployment of fuel cells or microturbines as well as reciprocating engines. The implementation phase of this project focused on the installation of a 120 kW CHP microturbine system at the Harvey Cedars Bible Conference in Harvey Cedars, NJ. A 1.1 MW generator powered by a gas-fired reciprocating engine for additional grid support was also installed at a local substation. This reportmore » contains installation and operation issues as well as the utility perspective on DG deployment.« less

DNA Sequencing Technologies within the Chemical and Biological Defense Enterprise: How to Position the Department of Defense to Maximize the Use of These Emerging Technologies - JUPITR

DTIC Science & Technology

2015-07-01

sharing, the Pathosphere.org open-system architecture is now deployed and available on the Amazon cloud . The site has over 100 users from...SUPPLEMENTARY NOTES 14. ABSTRACT: To generate accurate and actionable disease data that can be integrated into the broader Department of Defense...PREFACE The work described in this report was authorized under the Joint United States Forces Korea Portal and Integrated Threat Recognition

Analysis of DNA Double-Strand Breaks and Cytotoxicity after 7 Tesla Magnetic Resonance Imaging of Isolated Human Lymphocytes

PubMed Central

Guttek, Karina; Hartig, Roland; Godenschweger, Frank; Roggenbuck, Dirk; Ricke, Jens; Reinhold, Dirk; Speck, Oliver

2015-01-01

The global use of magnetic resonance imaging (MRI) is constantly growing and the field strengths increasing. Yet, only little data about harmful biological effects caused by MRI exposure are available and published research analyzing the impact of MRI on DNA integrity reported controversial results. This in vitro study aimed to investigate the genotoxic and cytotoxic potential of 7 T ultra-high-field MRI on isolated human peripheral blood mononuclear cells. Hence, unstimulated mononuclear blood cells were exposed to 7 T static magnetic field alone or in combination with maximum permissible imaging gradients and radiofrequency pulses as well as to ionizing radiation during computed tomography and γ-ray exposure. DNA double-strand breaks were quantified by flow cytometry and automated microscopy analysis of immunofluorescence stained γH2AX. Cytotoxicity was studied by CellTiter-Blue viability assay and [3H]-thymidine proliferation assay. Exposure of unstimulated mononuclear blood cells to 7 T static magnetic field alone or combined with varying gradient magnetic fields and pulsed radiofrequency fields did not induce DNA double-strand breaks, whereas irradiation with X- and γ-rays led to a dose-dependent induction of γH2AX foci. The viability assay revealed a time- and dose-dependent decrease in metabolic activity only among samples exposed to γ-radiation. Further, there was no evidence for altered proliferation response after cells were exposed to 7 T MRI or low doses of ionizing radiation (≤ 0.2 Gy). These findings confirm the acceptance of MRI as a safe non-invasive diagnostic imaging tool, but whether MRI can induce other types of DNA lesions or DNA double-strand breaks during altered conditions still needs to be investigated. PMID:26176601

Architectures and methodologies for future deployment of multi-site Zettabyte-Exascale data handling platforms

NASA Astrophysics Data System (ADS)

Acín, V.; Bird, I.; Boccali, T.; Cancio, G.; Collier, I. P.; Corney, D.; Delaunay, B.; Delfino, M.; dell'Agnello, L.; Flix, J.; Fuhrmann, P.; Gasthuber, M.; Gülzow, V.; Heiss, A.; Lamanna, G.; Macchi, P.-E.; Maggi, M.; Matthews, B.; Neissner, C.; Nief, J.-Y.; Porto, M. C.; Sansum, A.; Schulz, M.; Shiers, J.

2015-12-01

Several scientific fields, including Astrophysics, Astroparticle Physics, Cosmology, Nuclear and Particle Physics, and Research with Photons, are estimating that by the 2020 decade they will require data handling systems with data volumes approaching the Zettabyte distributed amongst as many as 1018 individually addressable data objects (Zettabyte-Exascale systems). It may be convenient or necessary to deploy such systems using multiple physical sites. This paper describes the findings of a working group composed of experts from several

Habitat Demonstration Unit Medical Operations Workstation Upgrades

NASA Technical Reports Server (NTRS)

Trageser, Katherine H.

2011-01-01

This paper provides an overview of the design and fabrication associated with upgrades for the Medical Operations Workstation in the Habitat Demonstration Unit. The work spanned a ten week period. The upgrades will be used during the 2011 Desert Research and Technology Studies (Desert RATS) field campaign. Upgrades include a deployable privacy curtain system, a deployable tray table, an easily accessible biological waste container, reorganization and labeling of the medical supplies, and installation of a retractable camera. All of the items were completed within the ten week period.

Pathfinder

NASA Image and Video Library

1999-03-01

NASA's Propulsive Small Expendable Deployer System experiment (ProSEDS) will demonstrate the use of an electrodynamic tether, basically a long, thin wire, for propulsion. An electrodynamic tether uses the same principles as electric motors in toys, appliances and computer disk drives, and generators in automobiles and power plants. When electrical current is flowing through the tether, a magnetic field is produced that pushes against the magnetic field of the Earth. For ProSEDS, the current in the tether results by virtue of the voltage generated when the tether moves through the Earth's magnetic field at more than 17,000 mph. This approach can produce drag thrust generating useable power. Since electrodynamic tethers require no propellant, they could substantially reduce the weight of the spacecraft and provide a cost-effective method of reboosting spacecraft. The initial flight of ProSEDS is scheduled to fly aboard an Air Force Delta II rocket in the summer of 2002. In orbit, ProSEDS will deploy from a Delta II second stage. It will be a 3.1-mile (5 kilometer) long, ultrathin base-wire cornected with a 6.2-mile (10 kilometer) long nonconducting tether. This photograph shows Less Johnson, a scientist at MSFC inspecting the nonconducting part of a tether as it exits a deployer similar to the one to be used in the ProSEDS experiment. The ProSEDS experiment is managed by the Space Transportation Directorate at MSFC.

Evaluation and Comparison of Methods for Measuring Ozone ...

EPA Pesticide Factsheets

Ambient evaluations of the various ozone and NO2 methods were conducted during field intensive studies as part of the NASA DISCOVER-AQ project conducted during July 2011 near Baltimore, MD; January – February 2013 in the San Juaquin valley, CA; September 2013 in Houston, TX; and July – August 2014 near Denver, CO. During field intensive studies, instruments were calibrated according to manufacturers’ operation manuals and in accordance with FRM requirements listed in 40 CFR 50. During the ambient evaluation campaigns, nightly automated zero and span checks were performed to monitor the validity of the calibration and control for drifts or variations in the span and/or zero response. Both the calibration gas concentrations and the nightly zero and span gas concentrations were delivered using a dynamic dilution calibration system (T700U/T701H, Teledyne API). The analyzers were housed within a temperature-controlled shelter during the sampling campaigns. A glass inlet with sampling height located approximately 5 m above ground level and a subsequent sampling manifold were shared by all instruments. Data generated by all analyzers were collected and logged using a field deployable data acquisition system (Envidas Ultimate). A summary of instruments used during DISCOVER-AQ deployment are listed in Table 1. Figure 1 shows a typical DISCOVER-AQ site (Houston 2013) where EPA (and others) instrumentation was deployed. Under the Clean Air Act, the U.S. EPA has estab

Doppler lidar characterization of the boundary layer for aircraft mass-balance estimates of greenhouse gas emissions

NASA Astrophysics Data System (ADS)

Hardesty, R.; Brewer, A.; Banta, R. M.; Senff, C. J.; Sandberg, S. P.; Alvarez, R. J.; Weickmann, A. M.; Sweeney, C.; Karion, A.; Petron, G.; Frost, G. J.; Trainer, M.

2012-12-01

Aircraft-based mass balance approaches are often used to estimate greenhouse gas emissions from distributed sources such as urban areas and oil and gas fields. A scanning Doppler lidar, which measures range-resolved wind and aerosol backscatter information, can provide important information on mixing and transport processes in the planetary boundary layer for these studies. As part of the Uintah Basin Winter Ozone Study, we deployed a high resolution Doppler lidar to characterize winds and turbulence, atmospheric mixing, and mixing layer depth in the oil and gas fields near Vernal, Utah. The lidar observations showed evolution of the horizontal wind field, vertical mixing and aerosol structure for each day during the 5-week deployment. This information was used in conjunction with airborne in situ observations of methane and carbon dioxide to compute methane fluxes and estimate basin-wide methane emissions. A similar experiment incorporating a lidar along with a radar wind profiler and instrumented aircraft was subsequently carried out in the vicinity of the Denver-Julesburg Basin in Colorado. Using examples from these two studies we discuss the use of Doppler lidar in conjunction with other sources of wind information and boundary layer structure for mass-balance type studies. Plans for a one-year deployment of a Doppler lidar as part of the Indianapolis Flux experiment to estimate urban-scale greenhouse gas emissions near are also presented.

Supporting the joint warfighter by development, training, and fielding of man-portable UGVs

NASA Astrophysics Data System (ADS)

Ebert, Kenneth A.; Stratton, Benjamin V.

2005-05-01

The Robotic Systems Pool (RSP), sponsored by the Joint Robotics Program (JRP), is an inventory of small robotic systems, payloads, and components intended to expedite the development and integration of technology into effective, supportable, fielded robotic assets. The RSP loans systems to multiple users including the military, first-responders, research organizations, and academia. These users provide feedback in their specific domain, accelerating research and development improvements of robotic systems, which in turn allow the joint warfighter to benefit from such changes more quickly than from traditional acquisition cycles. Over the past year, RSP assets have been used extensively for pre-deployment operator and field training of joint Explosive Ordnance Disposal (EOD) teams, and for the training of Navy Reservist repair technicians. These Reservists are part of the Robotic Systems Combat Support Platoon (RSCSP), attached to Space and Naval Warfare Systems Center, San Diego. The RSCSP maintains and repairs RSP assets and provides deployable technical support for users of robotic systems. Currently, a small team from the RSCSP is deployed at Camp Victory repairing and maintaining man-portable unmanned ground vehicles (UGVs) used by joint EOD teams in Operation Iraqi Freedom. The focus of this paper is to elaborate on the RSP and RSCSP and their role as invaluable resources for spiral development in the robotics community by gaining first-hand technical feedback from the warfighter and other users.

Novel Sensor for the In Situ Measurement of Uranium Fluxes

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

Hatfield, Kirk

2015-02-10

The goal of this project was to develop a sensor that incorporates the field-tested concepts of the passive flux meter to provide direct in situ measures of flux for uranium and groundwater in porous media. Measurable contaminant fluxes [J] are essentially the product of concentration [C] and groundwater flux or specific discharge [q ]. The sensor measures [J] and [q] by changes in contaminant and tracer amounts respectively on a sorbent. By using measurement rather than inference from static parameters, the sensor can directly advance conceptual and computational models for field scale simulations. The sensor was deployed in conjunction withmore » DOE in obtaining field-scale quantification of subsurface processes affecting uranium transport (e.g., advection) and transformation (e.g., uranium attenuation) at the Rifle IFRC Site in Rifle, Colorado. Project results have expanded our current understanding of how field-scale spatial variations in fluxes of uranium, groundwater and salient electron donor/acceptors are coupled to spatial variations in measured microbial biomass/community composition, effective field-scale uranium mass balances, attenuation, and stability. The coupling between uranium, various nutrients and micro flora can be used to estimate field-scale rates of uranium attenuation and field-scale transitions in microbial communities. This research focuses on uranium (VI), but the sensor principles and design are applicable to field-scale fate and transport of other radionuclides. Laboratory studies focused on sorbent selection and calibration, along with sensor development and validation under controlled conditions. Field studies were conducted at the Rifle IFRC Site in Rifle, Colorado. These studies were closely coordinated with existing SBR (formerly ERSP) projects to complement data collection. Small field tests were conducted during the first two years that focused on evaluating field-scale deployment procedures and validating sensor performance under controlled field conditions. In the third and fourth year a suite of larger field studies were conducted. For these studies, the uranium flux sensor was used with uranium speciation measurements and molecular-biological tools to characterize microbial community and active biomass at synonymous wells distributed in a large grid. These field efforts quantified spatial changes in uranium flux and field-scale rates of uranium attenuation (ambient and stimulated), uranium stability, and quantitatively assessed how fluxes and effective reaction rates were coupled to spatial variations in microbial community and active biomass. Analyses of data from these field experiments were used to generate estimates of Monod kinetic parameters that are ‘effective’ in nature and optimal for modeling uranium fate and transport at the field-scale. This project provided the opportunity to develop the first sensor that provides direct measures of both uranium (VI) and groundwater flux. A multidisciplinary team was assembled to include two geochemists, a microbiologist, and two quantitative contaminant hydrologists. Now that the project is complete, the sensor can be deployed at DOE sites to evaluate field-scale uranium attenuation, source behavior, the efficacy of remediation, and off-site risk. Because the sensor requires no power, it can be deployed at remote sites for periods of days to months. The fundamental science derived from this project can be used to advance the development of predictive models for various transport and attenuation processes in aquifers. Proper development of these models is critical for long-term stewardship of contaminated sites in the context of predicting uranium source behavior, remediation performance, and off-site risk.« less

Threading dynamics of a polymer through parallel pores: Potential applications to DNA size separation

NASA Astrophysics Data System (ADS)

Åkerman, Björn

1997-04-01

DNA orientation measurements by linear dichroism (LD) spectroscopy and single molecule imaging by fluorescence microscopy are used to investigate the effect of DNA size (71-740 kilo base pairs) and field strength E (1-5.9 V/cm) on the conformation dynamics during the field-driven threading of DNA molecules through a set of parallel pores in agarose gels, with average pore radii between 380 Å and 1400 Å. Locally relaxed but globally oriented DNA molecules are subjected to a perpendicular field, and the observed LD time profile is compared with a recent theory for the threading [D. Long and J.-L. Viovy, Phys. Rev. E 53, 803 (1996)] which assumes the same initial state. As predicted the DNA is driven by the ends into a U-form, leading to an overshoot in the LD. The overshoot-time scales as E-(1.2-1.4) as predicted, but grows more slowly with DNA size than the predicted linear dependence. For long molecules loops form initially in the threading process but are finally consumed by the ends, and the process of transfer of DNA segments, from the loops to the arms of the U, leads to a shoulder in the LD as predicted. The critical size below which loops do not form (as indicated by the LD shoulder being absent) is between 71 and 105 kbp (0.5% agarose, 5.9 V/cm), and considerably larger than predicted because in the initial state the DNA molecules are housed in gel cavities with effective pore sizes about four times larger than the average pore size. From the data, the separation of DNA by exploiting the threading dynamics in pulsed fields [D. Long et al., CR Acad. Sci. Paris, Ser. IIb 321, 239 (1995)] is shown to be feasible in principle in an agarose-based system.

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.

Optical Voltage Sensing Using DNA Origami

PubMed Central

2018-01-01

We explore the potential of DNA nanotechnology for developing novel optical voltage sensing nanodevices that convert a local change of electric potential into optical signals. As a proof-of-concept of the sensing mechanism, we assembled voltage responsive DNA origami structures labeled with a single pair of FRET dyes. The DNA structures were reversibly immobilized on a nanocapillary tip and underwent controlled structural changes upon application of an electric field. The applied field was monitored through a change in FRET efficiency. By exchanging the position of a single dye, we could tune the voltage sensitivity of our DNA origami structure, demonstrating the flexibility and versatility of our approach. The experimental studies were complemented by coarse-grained simulations that characterized voltage-dependent elastic deformation of the DNA nanostructures and the associated change in the distance between the FRET pair. Our work opens a novel pathway for determining the mechanical properties of DNA origami structures and highlights potential applications of dynamic DNA nanostructures as voltage sensors. PMID:29430924

The value of cell-free DNA for molecular pathology.

PubMed

Stewart, Caitlin M; Kothari, Prachi D; Mouliere, Florent; Mair, Richard; Somnay, Saira; Benayed, Ryma; Zehir, Ahmet; Weigelt, Britta; Dawson, Sarah-Jane; Arcila, Maria E; Berger, Michael F; Tsui, Dana Wy

2018-04-01

Over the past decade, advances in molecular biology and genomics techniques have revolutionized the diagnosis and treatment of cancer. The technological advances in tissue profiling have also been applied to the study of cell-free nucleic acids, an area of increasing interest for molecular pathology. Cell-free nucleic acids are released from tumour cells into the surrounding body fluids and can be assayed non-invasively. The repertoire of genomic alterations in circulating tumour DNA (ctDNA) is reflective of both primary tumours and distant metastatic sites, and ctDNA can be sampled multiple times, thereby overcoming the limitations of the analysis of single biopsies. Furthermore, ctDNA can be sampled regularly to monitor response to treatment, to define the evolution of the tumour genome, and to assess the acquisition of resistance and minimal residual disease. Recently, clinical ctDNA assays have been approved for guidance of therapy, which is an exciting first step in translating cell-free nucleic acid research tests into clinical use for oncology. In this review, we discuss the advantages of cell-free nucleic acids as analytes in different body fluids, including blood plasma, urine, and cerebrospinal fluid, and their clinical applications in solid tumours and haematological malignancies. We will also discuss practical considerations for clinical deployment, such as preanalytical factors and regulatory requirements. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

High mobility organic field-effect transistor based on water-soluble deoxyribonucleic acid via spray coating

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

Shi, Wei; Han, Shijiao; Huang, Wei

High mobility organic field-effect transistors (OFETs) by inserting water-soluble deoxyribonucleic acid (DNA) buffer layer between electrodes and pentacene film through spray coating process were fabricated. Compared with the OFETs incorporated with DNA in the conventional organic solvents of ethanol and methanol: water mixture, the water-soluble DNA based OFET exhibited an over four folds enhancement of field-effect mobility from 0.035 to 0.153 cm{sup 2}/Vs. By characterizing the surface morphology and the crystalline structure of pentacene active layer through atomic force microscope and X-ray diffraction, it was found that the adoption of water solvent in DNA solution, which played a key role inmore » enhancing the field-effect mobility, was ascribed to both the elimination of the irreversible organic solvent-induced bulk-like phase transition of pentacene film and the diminution of a majority of charge trapping at interfaces in OFETs.« less

The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol–chloroform–isoamyl alcohol DNA extraction

PubMed Central

Renshaw, Mark A; Olds, Brett P; Jerde, Christopher L; McVeigh, Margaret M; Lodge, David M

2015-01-01

Current research targeting filtered macrobial environmental DNA (eDNA) often relies upon cold ambient temperatures at various stages, including the transport of water samples from the field to the laboratory and the storage of water and/or filtered samples in the laboratory. This poses practical limitations for field collections in locations where refrigeration and frozen storage is difficult or where samples must be transported long distances for further processing and screening. This study demonstrates the successful preservation of eDNA at room temperature (20 °C) in two lysis buffers, CTAB and Longmire's, over a 2-week period of time. Moreover, the preserved eDNA samples were seamlessly integrated into a phenol–chloroform–isoamyl alcohol (PCI) DNA extraction protocol. The successful application of the eDNA extraction to multiple filter membrane types suggests the methods evaluated here may be broadly applied in future eDNA research. Our results also suggest that for many kinds of studies recently reported on macrobial eDNA, detection probabilities could have been increased, and at a lower cost, by utilizing the Longmire's preservation buffer with a PCI DNA extraction. PMID:24834966

Air Quality and Meteorological Boundary Conditions during the MCMA-2003 Field Campaign

NASA Astrophysics Data System (ADS)

Sosa, G.; Arriaga, J.; Vega, E.; Magaña, V.; Caetano, E.; de Foy, B.; Molina, L. T.; Molina, M. J.; Ramos, R.; Retama, A.; Zaragoza, J.; Martínez, A. P.; Márquez, C.; Cárdenas, B.; Lamb, B.; Velasco, E.; Allwine, E.; Pressley, S.; Westberg, H.; Reyes, R.

2004-12-01

A comprehensive field campaign to characterize photochemical smog in the Mexico City Metropolitan Area (MCMA) was conducted during April 2003. An important number of equipment was deployed all around the urban core and its surroundings to measure gas and particles composition from the various sources and receptor sites. In addition to air quality measurements, meteorology variables were also taken by regular weather meteorological stations, tethered balloons, radiosondes, sodars and lidars. One important issue with regard to the field campaign was the characterization of the boundary conditions in order to feed meteorological and air quality models. Four boundary sites were selected to measure continuously criteria pollutants, VOC and meteorological variables at surface level. Vertical meteorological profiles were measured at three other sites : radiosondes in Tacubaya site were launched every six hours daily; tethered balloons were launched at CENICA and FES-Cuautitlan sites according to the weather conditions, and one sodar was deployed at UNAM site in the south of the city. Additionally to these measurements, two fixed meteorological monitoring networks deployed along the city were available to complement these measurements. In general, we observed that transport of pollutants from the city to the boundary sites changes every day, according to the coupling between synoptic and local winds. This effect were less important at elevated sites such as Cerro de la Catedral and ININ, where synoptic wind were more dominant during the field campaign. Also, local sources nearby boundary sites hide the influence of pollution coming from the city some days, particularly at the La Reforma site.

An agronomic field-scale sensor network for monitoring soil water and temperature variation

NASA Astrophysics Data System (ADS)

Brown, D. J.; Gasch, C.; Brooks, E. S.; Huggins, D. R.; Campbell, C. S.; Cobos, D. R.

2014-12-01

Environmental sensor networks have been deployed in a variety of contexts to monitor plant, air, water and soil properties. To date, there have been relatively few such networks deployed to monitor dynamic soil properties in cropped fields. Here we report on experience with a distributed soil sensor network that has been deployed for seven years in a research farm with ongoing agronomic field operations. The Washington State University R. J. Cook Agronomy Farm (CAF), Pullman, WA, USA has recently been designated a United States Department of Agriculture (USDA) Long-Term Agro-Ecosystem Research (LTAR) site. In 2007, 12 geo-referenced locations at CAF were instrumented, then in 2009 this network was expended to 42 locations distributed across the 37-ha farm. At each of this locations, Decagon 5TE probes (Decagon Devices Inc., Pullman, WA, USA) were installed at five depths (30, 60, 90, 120, and 150 cm), with temperature and volumetric soil moisture content recorded hourly. Initially, data loggers were wirelessly connected to a data station that could be accessed through a cell connection, but due to the logistics of agronomic field operations, we later buried the dataloggers at each site and now periodically download data via local radio transmission. In this presentation, we share our experience with the installation, maintenance, calibration and data processing associated with an agronomic soil monitoring network. We also present highlights of data derived from this network, including seasonal fluctuations of soil temperature and volumetric water content at each depth, and how these measurements are influenced by crop type, soil properties, landscape position, and precipitation events.

Pattern mining of user interaction logs for a post-deployment usability evaluation of a radiology PACS client.

PubMed

Jorritsma, Wiard; Cnossen, Fokie; Dierckx, Rudi A; Oudkerk, Matthijs; van Ooijen, Peter M A

2016-01-01

To perform a post-deployment usability evaluation of a radiology Picture Archiving and Communication System (PACS) client based on pattern mining of user interaction log data, and to assess the usefulness of this approach compared to a field study. All user actions performed on the PACS client were logged for four months. A data mining technique called closed sequential pattern mining was used to automatically extract frequently occurring interaction patterns from the log data. These patterns were used to identify usability issues with the PACS. The results of this evaluation were compared to the results of a field study based usability evaluation of the same PACS client. The interaction patterns revealed four usability issues: (1) the display protocols do not function properly, (2) the line measurement tool stays active until another tool is selected, rather than being deactivated after one use, (3) the PACS's built-in 3D functionality does not allow users to effectively perform certain 3D-related tasks, (4) users underuse the PACS's customization possibilities. All usability issues identified based on the log data were also found in the field study, which identified 48 issues in total. Post-deployment usability evaluation based on pattern mining of user interaction log data provides useful insights into the way users interact with the radiology PACS client. However, it reveals few usability issues compared to a field study and should therefore not be used as the sole method of usability evaluation. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

ULTIMATE: a deployable multiple integral field unit for Subaru

NASA Astrophysics Data System (ADS)

Ellis, S. C.; Zhelem, Ross; Brown, David; Staszak, Nicholas F.; Lidman, Chris; Nataf, David M.; Casey, Andrew R.; Xavier, Pascal; Sheinis, Andrew; Gillingham, Peter; Tims, Julia; Lawrence, Jon; Bryant, Julia; Sharp, Rob

2016-08-01

ULTIMATE is an instrument concept under development at the AAO, for the Subaru Telescope, which will have the unique combination of ground layer adaptive optics feeding multiple deployable integral field units. This will allow ULTIMATE to probe unexplored parameter space, enabling science cases such as the evolution of galaxies at z 0:5 to 1.5, and the dark matter content of the inner part of our Galaxy. ULTIMATE will use Starbugs to position between 7 and 13 IFUs over a 14 × 8 arcmin field-of-view, pro- vided by a new wide-field corrector. All Starbugs can be positioned simultaneously, to an accuracy of better than 5 milli-arcsec within the typical slew-time of the telescope, allowing for very efficient re-configuration between observations. The IFUs will feed either the near-infrared nuMOIRCS or the visible/ near-infrared PFS spectrographs, or both. Future possible upgrades include the possibility of purpose built spectrographs and incorporating OH suppression using fibre Bragg gratings. We describe the science case and resulting design requirements, the baseline instrument concept, and the expected performance of the instrument.

Multifaceted contributions: health workers and smallpox eradication in India.

PubMed

Bhattacharya, Sanjoy

2008-01-01

Smallpox eradication in South Asia was a result of the efforts of many grades of health-workers. Working from within the confines of international organisations and government structures, the role of the field officials, who were of various nationalities and also drawn from the cities and rural enclaves of the countries in these regions, was crucial to the development and deployment of policies. However, the role of these personnel is often downplayed in official histories and academic histories, which highlight instead the roles played by a handful of senior officials within the World Health Organization and the federal governments in the sub-continent. This article attempts to provide a more rounded assessment of the complex situation in the field. In this regard, an effort is made to underline the great usefulness of the operational flexibility displayed by field officers, wherein lessons learnt in the field were made an integral part of deploying local campaigns; careful engagement with the communities being targeted, as well as the employment of short term workers from amongst them, was an important feature of this work.

Comparison of on-site field measured inorganic arsenic in rice with laboratory measurements using a field deployable method: Method validation.

PubMed

Mlangeni, Angstone Thembachako; Vecchi, Valeria; Norton, Gareth J; Raab, Andrea; Krupp, Eva M; Feldmann, Joerg

2018-10-15

A commercial arsenic field kit designed to measure inorganic arsenic (iAs) in water was modified into a field deployable method (FDM) to measure iAs in rice. While the method has been validated to give precise and accurate results in the laboratory, its on-site field performance has not been evaluated. This study was designed to test the method on-site in Malawi in order to evaluate its accuracy and precision in determination of iAs on-site by comparing with a validated reference method and giving original data on inorganic arsenic in Malawian rice and rice-based products. The method was validated by using the established laboratory-based HPLC-ICPMS. Statistical tests indicated there were no significant differences between on-site and laboratory iAs measurements determined using the FDM (p = 0.263, ά = 0.05) and between on-site measurements and measurements determined using HPLC-ICP-MS (p = 0.299, ά = 0.05). This method allows quick (within 1 h) and efficient screening of rice containing iAs concentrations on-site. Copyright © 2018 Elsevier Ltd. All rights reserved.

FInd Gas Source

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

Travis, Bryan; Sauer, Jeremy; Dubey, Manvendra

2017-02-24

FIGS is a neural network software that ingests real time synchronized field data on environmental flow fields and turbulence and gas concentration variations at high frequency and uses an error minimization algorithm to locate the gas source and quantify its strength. The software can be interfaced with atmospheric, oceanic and subsurface instruments in a variety of platforms stationary or mobile (e.g. cars, UAVs, submersible vehicles or boreholes) and used to find gas sources by smart use of data and phenomenology. FIGS can be trained by phenomenological model of the flow fields in the environment of interest and/or be calibrated bymore » controlled release. After initial deployment the FIGS learning will grow with time as it accumulates data on source quantification. FIGS can be installed on any computer from small beagle-bones for field deployment/end-use to PC/MACs/main-frame for training/analysis. FIGS has been trained (using LANL's high resolution atmospheric simulations) and calibrated, tested and evaluated in the field and shown to perform well in finding and quantifying methane leaks at 10-100m scales at well pads by ingesting atmospheric measurements. The code is applicable to gas and particle source location at large scales.« less

Mitochondrial DNA and Cancer Epidemiology Workshop

Cancer.gov

A workshop to review the state-of-the science in the mitochondrial DNA field and its use in cancer epidemiology, and to develop a concept for a research initiative on mitochondrial DNA and cancer epidemiology.

Protocol for collecting eDNA samples from streams [Version 2.3

Treesearch

K. J. Carim; T. Wilcox; M. K. Young; K. S. McKelvey; M. K. Schwartz

2015-01-01

Throughout the 2014 field season, we had over two dozen biologist throughout the western US collect over 300 samples for eDNA analysis with paired controls. Control samples were collected by filtering 0.5 L of distilled water. No samples had any evidence of field contamination. This method of sampling verifies the cleanliness of the field equipment, as well as the...

MODIS airborne simulator visible and near-infrared calibration, 1992 ASTEX field experiment. Calibration version: ASTEX King 1.0

NASA Technical Reports Server (NTRS)

Arnold, G. Thomas; Fitzgerald, Michael; Grant, Patrick S.; King, Michael D.

1994-01-01

Calibration of the visible and near-infrared (near-IR) channels of the MODIS Airborne Simulator (MAS) is derived from observations of a calibrated light source. For the 1992 Atlantic Stratocumulus Transition Experiment (ASTEX) field deployment, the calibrated light source was the NASA Goddard 48-inch integrating hemisphere. Tests during the ASTEX deployment were conducted to calibrate the hemisphere and then the MAS. This report summarizes the ASTEX hemisphere calibration, and then describes how the MAS was calibrated from the hemisphere data. All MAS calibration measurements are presented and determination of the MAS calibration coefficients (raw counts to radiance conversion) is discussed. In addition, comparisons to an independent MAS calibration by Ames personnel using their 30-inch integrating sphere is discussed.

[The influence of electromagnetic fields on flora and fauna].

PubMed

Rochalska, Małgorzata

2009-01-01

This paper presents the influence of natural and artificial electromagnetic fields (EMF) on fauna and flora. The mechanisms of Earth's magnetic field detection and the use of this skill by migratory animals to faultlessly reach the destination of their travel are discussed, as well as the positive effects of electric and magnetic fields on plants relative to their physiology, yielding and health. EMF influence on social insects and animal organisms, including possible DNA damages and DNA repair systems, is presented. The influence of high frequency electromagnetic fields on birds nesting is also discussed.

Time to Spread Your Wings: A Review of the Avian Ancient DNA Field

PubMed Central

Grealy, Alicia; Rawlence, Nicolas J.

2017-01-01

Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of “avian ancient DNA” by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions. Applying aDNA analysis with more practical outcomes in mind (such as managing conservation) is another increasingly popular trend among studies that utilise avian aDNA, but the majority of these have yet to influence management policy. We find that while there have been advances in extracting aDNA from a variety of avian substrates including eggshell, feathers, and coprolites, there is a bias in the temporal focus; the majority of the ca. 150 studies reviewed here obtained aDNA from late Holocene (100–1000 yBP) material, with few studies investigating Pleistocene-aged material. In addition, we identify and discuss several other issues within the field that require future attention. With more than one quarter of Holocene bird extinctions occurring in the last several hundred years, it is more important than ever to understand the mechanisms driving the evolution and extinction of bird species through the use of aDNA. PMID:28718817

Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer

PubMed Central

Johnson, Sarah S.; Zaikova, Elena; Goerlitz, David S.; Bai, Yu; Tighe, Scott W.

2017-01-01

The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epidemics. Here, we demonstrate the application of offline DNA sequencing of environmental samples using a hand-held nanopore sequencer in a remote field location: the McMurdo Dry Valleys, Antarctica. Sequencing was performed using a MK1B MinION sequencer from Oxford Nanopore Technologies (ONT; Oxford, United Kingdom) that was equipped with software to operate without internet connectivity. One-direction (1D) genomic libraries were prepared using portable field techniques on DNA isolated from desiccated microbial mats. By adequately insulating the sequencer and laptop, it was possible to run the sequencing protocol for up to 2½ h under arduous conditions. PMID:28337073

Wide Field Spectroscopy of Diffusing and Interacting DNA Using Tunable Nanoscale Geometries

NASA Astrophysics Data System (ADS)

Scott, Shane; Leith, Jason; Brandao, Hugo; Sehayek, Simon; Hofkirchner, Alexander; Laurin, Jill; Berard, Daniel; Verge, Alexander; Wiseman, Paul; Leslie, Sabrina

2015-03-01

It remains an outstanding challenge to directly image interacting and diffusing biomolecules under physiological conditions. Many biochemical questions can be posed in the form: Does A interact with B? What are the energetics, kinetics, stoichiometry, and cooperativity of this interaction? To tackle this challenge, we use tunable nanoscale confinement to perform wide-field imaging of interacting DNA molecules in free solution, under an extended range of reagent concentrations and interaction rates. We present the integration of ``Convex Lens-induced Confinement (CLiC)'' microscopy with image correlation analysis, simultaneously suppressing background fluorescence and extending imaging times. The measured DNA-DNA interactions would be inaccessible to standard techniques but are important for developing a mechanistic understanding of life-preserving processes such as DNA transcription. NSERC.

Injury risk to restrained children exposed to deployed first- and second-generation air bags in frontal crashes.

PubMed

Arbogast, Kristy B; Durbin, Dennis R; Kallan, Michael J; Elliott, Michael R; Winston, Flaura K

2005-04-01

To estimate the risk of serious nonfatal injuries in frontal crashes among belted children seated in the right front seat of vehicles in which second-generation passenger air bags deployed compared with that of belted children seated in the right front seat of vehicles in which first-generation passenger air bags deployed. We enrolled a probability sample of 1781 seat belt-restrained occupants aged 3 through 15 years seated in the right front seat, exposed to deployed passenger air bags in frontal crashes involving insured vehicles in 3 large US regions, between December 1, 1998, and November 30, 2002. A telephone interview was conducted with the driver of the vehicle using a previously validated instrument. The study sample was weighted according to each subject's probability of selection, with analyses conducted on the weighted sample. Main Outcome Measure Risk of serious injury (Abbreviated Injury Scale score of > or =2 injuries and facial lacerations). The risk of serious injury for restrained children in the right front seat exposed to deployed second-generation passenger air bags was 9.9%, compared with 14.9% for similar children exposed to deployed first-generation passenger air bags (adjusted odds ratio, 0.59; 95% confidence interval, 0.36-0.97). This study provides evidence based on field data that the risk of injury to children exposed to deploying second-generation passenger air bags is reduced compared with earlier designs.

Moving environmental DNA methods from concept to practice for monitoring aquatic macroorganisms

USGS Publications Warehouse

Goldberg, Caren S.; Strickler, Katherine M.; Pilliod, David S.

2015-01-01

The discovery that macroorganisms can be detected from their environmental DNA (eDNA) in aquatic systems has immense potential for the conservation of biological diversity. This special issue contains 11 papers that review and advance the field of eDNA detection of vertebrates and other macroorganisms, including studies of eDNA production, transport, and degradation; sample collection and processing to maximize detection rates; and applications of eDNA for conservation using citizen scientists. This body of work is an important contribution to the ongoing efforts to take eDNA detection of macroorganisms from technical breakthrough to established, reliable method that can be used in survey, monitoring, and research applications worldwide. While the rapid advances in this field are remarkable, important challenges remain, including consensus on best practices for collection and analysis, understanding of eDNA diffusion and transport, and avoidance of inhibition in sample collection and processing. Nonetheless, as demonstrated in this special issue, eDNA techniques for research and monitoring are beginning to realize their potential for contributing to the conservation of biodiversity globally.

Part I: Minicircle vector technology limits DNA size restrictions on ex vivo gene delivery using nanoparticle vectors: Overcoming a translational barrier in neural stem cell therapy.

PubMed

Fernandes, Alinda R; Chari, Divya M

2016-09-28

Genetically engineered neural stem cell (NSC) transplant populations offer key benefits in regenerative neurology, for release of therapeutic biomolecules in ex vivo gene therapy. NSCs are 'hard-to-transfect' but amenable to 'magnetofection'. Despite the high clinical potential of this approach, the low and transient transfection associated with the large size of therapeutic DNA constructs is a critical barrier to translation. We demonstrate for the first time that DNA minicircles (small DNA vectors encoding essential gene expression components but devoid of a bacterial backbone, thereby reducing construct size versus conventional plasmids) deployed with magnetofection achieve the highest, safe non-viral DNA transfection levels (up to 54%) reported so far for primary NSCs. Minicircle-functionalized magnetic nanoparticle (MNP)-mediated gene delivery also resulted in sustained gene expression for up to four weeks. All daughter cell types of engineered NSCs (neurons, astrocytes and oligodendrocytes) were transfected (in contrast to conventional plasmids which usually yield transfected astrocytes only), offering advantages for targeted cell engineering. In addition to enhancing MNP functionality as gene delivery vectors, minicircle technology provides key benefits from safety/scale up perspectives. Therefore, we consider the proof-of-concept of fusion of technologies used here offers high potential as a clinically translatable genetic modification strategy for cell therapy. Copyright © 2016 Elsevier B.V. All rights reserved.

Implementation of Novel Design Features for qPCR-Based eDNA Assessment

PubMed Central

Veldhoen, Nik; Hobbs, Jared; Ikonomou, Georgios; Hii, Michael; Lesperance, Mary; Helbing, Caren C.

2016-01-01

Environmental stewardship requires timely, accurate information related to the status of a given ecosystem and the species that occupy it. Recent advances in the application of the highly sensitive real-time quantitative polymerase chain reaction (qPCR) towards identification of constituents within environmental DNA (eDNA) now allow targeted detection of the presence of species-specific biological material within a localized geographic region. However, as with all molecular techniques predicated on the specificity and sensitivity of the PCR assay, careful validation of each eDNA qPCR assay in development must be performed both under controlled laboratory conditions and when challenged with field-derived eDNA samples. Such a step-wise approach forms the basis for incorporation of innovative qPCR design features that strengthen the implementation and interpretation of the eDNA assay. This includes empirical determination that the qPCR assay is refractory to the presence of human DNA and the use of a tripartite assay approach comprised of 1) a primer set targeting plant chloroplast that evaluates the presence of amplifiable DNA from field samples to increase confidence in a negative result, 2) an animal group primer set to increase confidence in the assay result, and 3) a species-specific primer set to assess presence of DNA from the target species. To demonstrate this methodology, we generated eDNA assays specific for the North American bullfrog (Lithobates (Rana) catesbeiana) and the Rocky Mountain tailed frog (Ascaphus montanus) and characterized each with respect to detection sensitivity and specificity with demonstrated performance in a field survey scenario. The qPCR design features presented herein address specific challenges of eDNA assays thereby increasing their interpretative power. PMID:27802293

The development of expertise using an intelligent computer-aided training system

NASA Technical Reports Server (NTRS)

Johnson, Debra Steele

1991-01-01

An initial examination was conducted of an Intelligent Tutoring System (ITS) developed for use in industry. The ITS, developed by NASA, simulated a satellite deployment task. More specifically, the PD (Payload Assist Module Deployment)/ICAT (Intelligent Computer Aided Training) System simulated a nominal Payload Assist Module (PAM) deployment. The development of expertise on this task was examined using three Flight Dynamics Officer (FDO) candidates who has no previous experience with this task. The results indicated that performance improved rapidly until Trial 5, followed by more gradual improvements through Trial 12. The performance dimensions measured included performance speed, actions completed, errors, help required, and display fields checked. Suggestions for further refining the software and for deciding when to expose trainees to more difficult task scenarios are discussed. Further, the results provide an initial demonstration of the effectiveness of the PD/ICAT system in training the nominal PAM deployment task and indicate the potential benefits of using ITS's for training other FDO tasks.

The development of expertise on an intelligent tutoring system

NASA Technical Reports Server (NTRS)

Johnson, Debra Steele

1989-01-01

An initial examination was conducted of an Intelligent Tutoring System (ITS) developed for use in industry. The ITS, developed by NASA, simulated a satellite deployment task. More specifically, the PD (Payload Assist Module Deployment)/ICAT (Intelligent Computer Aided Training) System simulated a nominal Payload Assist Module (PAM) deployment. The development of expertise on this task was examined using three Flight Dynamics Officer (FDO) candidates who had no previous experience with this task. The results indicated that performance improved rapidly until Trial 5, followed by more gradual improvements through Trial 12. The performance dimensions measured included performance speed, actions completed, errors, help required, and display fields checked. Suggestions for further refining the software and for deciding when to expose trainees to more difficult task scenarios are discussed. Further, the results provide an initial demonstration of the effectiveness of the PD/ICAT system in training the nominal PAM deployment task and indicate the potential benefits of using ITS's for training other FDO tasks.

Photodegradation of polyaromatic hydrocarbons in passive air samplers: Field testing different deployment chambers

USGS Publications Warehouse

Bartkow, M.E.; Kennedy, K.E.; Huckins, J.N.; Holling, N.; Komarova, T.; Muller, J.F.

2006-01-01

Semi-permeable membrane devices (SPMDs) were loaded with deuterated anthracene and pyrene as performance reference compounds (PRCs) and deployed at a test site in four different chambers (open and closed box chamber, bowl chamber and cage chamber) for 29 days. The losses of PRCs and the uptake of polyaromatic hydrocarbons (PAHs) from the ambient air were quantified. UV-B levels measured in each deployment chamber indicated that SPMDs would be exposed to the most UV-B in the cage chamber and open box chamber. Significantly less PAHs were quantified in SPMDs deployed in the cage chamber and open box chamber compared to samplers from the other two chambers, suggesting that photodegradation of PAHs had occurred. The loss of PRCs confirmed these results but also showed that photodegradation was occurring in the closed box chamber. The bowl chamber appears to provide the best protection from the influence of direct photodegradation. ?? 2006 Elsevier Ltd. All rights reserved.

The UIST image slicing integral field unit

NASA Astrophysics Data System (ADS)

Ramsay Howat, S.; Todd, S.; Wells, M.; Hastings, P.

2006-06-01

The UKIRT Imager Spectrometer (UIST) contains a deployable integral field unit which is one of the most popular modes of this common-user instrument. In this paper, we review all aspects of the UIST IFU from the design and production of the aluminium mirrors to the integration with the telescope system during commissioning. Reduction of the integral field data is fully supported by the UKIRT data reduction pipeline, ORAC-DR.

Treatment for Uncomplicated Plasmodium falciparum Malaria in French Soldiers Deployed in Sub-Saharan Africa: Gaps Between Policy and Field Practice.

PubMed

Perisse, Anne; Velut, Guillaume; Javelle, Emilie; Loarer, Gwion; Michel, Remy; Simon, F

2018-02-07

Malaria prevention and treatment are big challenges for the French forces deployed in sub-Saharan Africa. Since December 2013, 1,800 French soldiers have been deployed at any one time in the Central African Republic in the framework of "Operation Sangaris" and European Union Force (EUFOR). Over the 2014-2015 period, about 500 cases of malaria were notified in these troops during the operation or after their return (annual incidence: 13.4 p.100 person-year). The recommendation to use dihydroartemisinin-piperaquine (DHA-PQ) as the first-line treatment for French soldiers suffering from uncomplicated Plasmodium falciparum malaria in endemic areas is not always followed in practice in the field by French military general practitioners (GPs). We conduced a retrospective Knowledge-Attitude-Practice study by self-administered questionnaire, to all military French doctors who were in mission in Central African Republic from January 2014 to July 2015 to try to understand what were the reasons for the GP not to prescribe DHA-PQ on the field. Thirty-six GPs (53%) answered to the questionnaire. Eighty-three percent of them knew about the recommendation to use DHA-PQ for un uncomplicated Pf malaria. Fifty-eight percent had a favorable attitude toward DHA-PQ. The factors associated with the prescription of another drug (Atovaquone-proguanil) were: the habit (odds ratio [OR] 0.1, confidence interval (CI) 0-0.6], the fact that Atovaquone-proguanil is more practical to use [OR 0.01, CI 0-0.1]. In practice, only 37.5% prescribed DHA-PQ the most of the time during their mission. Factors associated with a non-favorable attitude toward DHA-PQ were: the necessity to calculate a QTc interval during the treatment [OR 0.2, confidence interval 0-0.9], and the fact that DHA-PQ must be taken on an empty stomach [OR 0.3, CI 0.1-0.8]. GP who received a formation before their mission about malaria and treatment had a favorable attitude toward DHA-PQ. There is very satisfactory knowledge by the military GPs stationed in the Central African Republic on both the recommendations and prescription of antimalarial drugs. The present study highlights some difficulties in implementing the recommendations in an operational context, notably factors limiting the prescription of DHA-PQ during military deployment (need for ECG monitoring, empty stomach, and lack of habit). Proposals can be made to improve the efficacy, tolerance, and practicability of malaria treatment in the field. The main focus should be a more flexible application of the French DHA-PQ risk management plan in the field, specific training and communication about DHA-PQ use, the generalization of ECG printing equipment in the field, and the switch from DHA-PQ to an alternative artemisinin-based combination therapy during deployments in malaria-endemic areas. © Association of Military Surgeons of the United States 2018. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

In vivo conformation of mitochondrial DNA revealed by pulsed-field gel electrophoresis in the true slime mold, Physarum polycephalum.

PubMed

Sakurai, R; Sasaki, N; Takano, H; Abe, T; Kawano, S

2000-04-28

Pulsed-field gel electrophoresis (PFGE) was used to examine the in vivo and in vitro conformations of Physarum polycephalum mitochondrial DNA (mtDNA). We used plugs containing isolated mitochondria, isolated mitochondrial nucleoids (mt-nuclei), and isolated mtDNA, in addition to whole cells. The mtDNA contained in the myxamoebae, plasmodia, isolated mitochondria, and isolated mt-nuclei was circular, but most of the isolated mtDNA had been site-specifically fragmented and linearized during DNA preparation and storage under low ionic strength conditions. Restriction mapping of Physarum mtDNA by the direct digestion of the isolated mt-nuclei from two different strains, DP89 x AI16 and KM88 x AI16, resulted in the circular form. A linear mitochondrial plasmid, mF, is known to promote mitochondrial fusion and integration of itself into the mtDNA in Physarum. Linearization of mtDNA by the integration of the mF plasmid was demonstrated when we used PFGE to analyze isolated mitochondria from the plasmodial strain DP89 x NG7 carrying the mF plasmid (mF+). The PFGE system can be used not only to determine whether the form of mtDNA is linear or circular but also to analyze the dynamic conformational changes of mtDNA.

Investigation of hydrologic and biogeochemical controls on arsenic mobilization using distributed sensing at a field site in Munshiganj, Bangladesh

NASA Astrophysics Data System (ADS)

Ramanathan, N.; Estrin, D.; Harmon, T.; Harvey, C.; Jay, J.; Kohler, E.; Rothenberg, S.

2006-12-01

The presence of arsenic in the groundwater has led to the largest environmental poisoning in history; tens of millions of people in the Ganges Delta continue to drink groundwater that is dangerously contaminated with arsenic. A current working hypothesis is that arsenic is mobilized in the near surface environment where sediments are weathered by seasonal changes in the redox state that drive a cycle of pyrite oxidation and iron oxide reduction. In order to test the supporting hypothesis that subsurface geochemical changes may be induced by agricultural activity, we deployed 42 wirelessly networked ion-selective electrodes, including calcium, ammonium, nitrate, ORP, chloride, carbonate, and pH in a rice paddy in the Munshiganj district of Bangladesh in January of 2006. Each sensor was connected to an MDA300 sensor board and Mica2 wireless transceiver and computational device. Over a period of 11 days, we observed clear diel, and diurnal trends in 4 of the electrodes (calcium, ammonium, chloride and carbonate). The trends may be due to hydrological changes, or geochemical changes induced either by photosynthesis in the overlying water (which then infiltrated to the depth of the sensors) or in the root zone of rice plants. While the spatiotemporally dense measurements from wireless sensor networks enable scientists to ask new questions and elucidate complex relationships in heterogeneous physical environments such as soil, there are many practical issues to address in order to collect data usable for scientific purposes. For example, in response to a stream of faults in one of our sensor network deployments, we designed Sympathy to enable users to find and fix problems impacting the quantity of data collected in the field. Sympathy detects packet loss experienced at the base station and systematically assigns blame to faulty components in the network for remediation, replacing the prior policy of ad-hoc node rebooting and battery replacements. Sympathy has been deployed in many habitat monitoring sensor networks. While using Sympathy at our Bangladesh field site we received 80% of the sensor data expected at the base station, upon returning, post-deployment analysis revealed that 42% of these sensor data were potentially faulty. Due to the remote location of the deployment, we were unable to go back and validate the questionable segments of the data set, forcing us to discard potentially interesting information. In addition to being undesirable, this response is often avoidable as well. Even simple actions such as checking sensor connections and quickly validating sensors in the field could have increased our confidence in the quality of the data, minimizing doubts that data observations were simply caused by badly behaving hardware. To improve data quality, we have designed a system called Confidence, which continuously monitors data collected at a base-station to identify faulty data and notify the user in the field of actions they can take to validate the data or remediate the sensor fault. Augmenting a sensor network deployment with Confidence and Sympathy enables users in the identification and remediation of faults impacting the quality and quantity of data respectively.

Recent Advances in the Tempest UAS for In-Situ Measurements in Highly-Dynamic Environments

NASA Astrophysics Data System (ADS)

Argrow, B. M.; Frew, E.; Houston, A. L.; Weiss, C.

2014-12-01

The spring 2010 deployment of the Tempest UAS during the VORTEX2 field campaign verified that a small UAS, supported by a customized mobile communications, command, and control (C3) architecture, could simultaneously satisfy Federal Aviation Administration (FAA) airspace requirements, and make in-situ thermodynamic measurements in supercell thunderstorms. A multi-hole airdata probe was recently integrated into the Tempest UAS airframe and verification flights were made in spring 2013 to collect in-situ wind measurements behind gust fronts produced by supercell thunderstorms in northeast Colorado. Using instantaneous aircraft attitude estimates from the autopilot, the in-situ measurements were converted to inertial wind estimates, and estimates of uncertainty in the wind measurements was examined. To date, the limited deployments of the Tempest UAS have primarily focused on addressing the engineering and regulatory requirements to conduct supercell research, and the Tempest UAS team of engineers and meteorologists is preparing for deployments with the focus on collecting targeted data for meteorological exploration and hypothesis testing. We describe the recent expansion of the operations area and altitude ceiling of the Tempest UAS, engineering issues for accurate inertial wind estimates, new concepts of operation that include the simultaneous deployment of multiple aircraft with mobile ground stations, and a brief description of our current effort to develop a capability for the Tempest UAS to perform autonomous path planning to maximize energy harvesting from the local wind field for increased endurance.

Deploying the ODIS robot in Iraq and Afghanistan

NASA Astrophysics Data System (ADS)

Smuda, Bill; Schoenherr, Edward; Andrusz, Henry; Gerhart, Grant

2005-05-01

The wars in Iraq and Afghanistan have shown the importance of robotic technology as a force multiplier and a tool for moving soldiers out of harms way. Situations on the ground make soldiers performing checkpoint operations easy targets for snipers and suicide bombers. Robotics technology reduces risk to soldiers and other personnel at checkpoints. Early user involvement in innovative and aggressive development and acquisition strategies are the key to moving robotic and associated technology into the hands of the user. This paper updates activity associated with rapid development of the Omni-Directional Inspection System (ODIS) robot for under vehicle inspection and reports on our field experience with robotics in Iraq and Afghanistan. In February of 2004, two TARDEC Engineers departed for a mission to Iraq and Afghanistan with ten ODIS Robots. Six robots were deployed in the Green Zone in Baghdad. Two Robots were deployed at Kandahar Army Airfield and two were deployed at Bagram Army Airfield in Afghanistan. The TARDEC Engineers who performed this mission trained the soldiers and provided initial on site support. They also trained Exponent employees assigned to the Rapid Equipping Force in ODIS repair. We will discuss our initial deployment, lessons learned and future plans.

Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

PubMed

van der Vaart, Arjan

2015-05-01

Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

Self-assembly of multiferroic core-shell particulate nanocomposites through DNA-DNA hybridization and magnetic field directed assembly of superstructures

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

Sreenivasulu, Gollapudi; Srinivasan, Gopalan, E-mail: srinivas@oakland.edu, E-mail: chavez@oakland.edu; Lochbiler, Thomas A.

Multiferroic composites of ferromagnetic and ferroelectric phases are of importance for studies on mechanical strain mediated coupling between the magnetic and electric subsystems. This work is on DNA-assisted self-assembly of superstructures of such composites with nanometer periodicity. The synthesis involved oligomeric DNA-functionalized ferroelectric and ferromagnetic nanoparticles, 600 nm BaTiO{sub 3} (BTO) and 200 nm NiFe{sub 2}O{sub 4} (NFO), respectively. Mixing BTO and NFO particles, possessing complementary DNA sequences, resulted in the formation of ordered core-shell heteronanocomposites held together by DNA hybridization. The composites were imaged by scanning electron microscopy and scanning microwave microscopy. The presence of heteroassemblies along with core-shellmore » architecture is clearly observed. The reversible nature of the DNA hybridization allows for restructuring the composites into mm-long linear chains and 2D-arrays in the presence of a static magnetic field and ring-like structures in a rotating-magnetic field. Strong magneto-electric (ME) coupling in as-assembled composites is evident from static magnetic field H induced polarization and low-frequency magnetoelectric voltage coefficient measurements. Upon annealing the nanocomposites at high temperatures, evidence for the formation of bulk composites with excellent cross-coupling between the electric and magnetic subsystems is obtained by H-induced polarization and low-frequency ME voltage coefficient. The ME coupling strength in the self-assembled composites is measured to be much stronger than in bulk composites with randomly distributed NFO and BTO prepared by direct mixing and sintering.« less

DNA-templated photonic arrays and assemblies: design principles and future opportunities.

PubMed

Su, Wu; Bonnard, Vanessa; Burley, Glenn A

2011-07-11

Molecular photonics is a rapidly developing and multi-disciplinary field of research involving the construction of molecular assemblies comprising photoactive building blocks that are responsive to a light stimulus. A salient challenge in this field is the controlled assembly of these building blocks with nanoscale precision. DNA exhibits considerable promise as an architecture for the templated assembly of photoactive materials. In this Concept Article we describe the progress that has been made in the area of DNA photonics, in which DNA acts as a platform for the construction of optoelectronic assemblies, thin films and devices. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DNA repair: a changing geography? (1964-2008).

PubMed

Maisonobe, Marion; Giglia-Mari, Giuseppina; Eckert, Denis

2013-07-01

This article aims to explain the current state of DNA Repair studies' global geography by focusing on the genesis of the community. Bibliometric data is used to localize scientific activities related to DNA Repair at the city level. The keyword "DNA Repair" was introduced first by American scientists. It started to spread after 1964 that is to say, after P. Howard-Flanders (Yale University), P. Hanawalt (Stanford University) and R. Setlow (Oak Ridge Laboratories) found evidence for Excision Repair mechanisms. It was the first stage in the emergence of an autonomous scientific community. In this article, we will try to assess to what extent the geo-history of this scientific field is determinant in understanding its current geography. In order to do so, we will localize the places where the first "DNA Repair" publications were signed fifty years ago and the following spatial diffusion process, which led to the current geography of the field. Then, we will focus on the evolution of the research activity of "early entrants" in relation to the activity of "latecomers". This article is an opportunity to share with DNA Repair scientists some research results of a dynamic field in Science studies: spatial scientometrics. Copyright © 2013 Elsevier B.V. All rights reserved.

Development and evaluation of an open-source, low-cost distributed sensor network for environmental monitoring applications

NASA Astrophysics Data System (ADS)

Gunawardena, N.; Pardyjak, E. R.; Stoll, R.; Khadka, A.

2018-02-01

Over the last decade there has been a proliferation of low-cost sensor networks that enable highly distributed sensor deployments in environmental applications. The technology is easily accessible and rapidly advancing due to the use of open-source microcontrollers. While this trend is extremely exciting, and the technology provides unprecedented spatial coverage, these sensors and associated microcontroller systems have not been well evaluated in the literature. Given the large number of new deployments and proposed research efforts using these technologies, it is necessary to quantify the overall instrument and microcontroller performance for specific applications. In this paper, an Arduino-based weather station system is presented in detail. These low-cost energy-budget measurement stations, or LEMS, have now been deployed for continuous measurements as part of several different field campaigns, which are described herein. The LEMS are low-cost, flexible, and simple to maintain. In addition to presenting the technical details of the LEMS, its errors are quantified in laboratory and field settings. A simple artificial neural network-based radiation-error correction scheme is also presented. Finally, challenges and possible improvements to microcontroller-based atmospheric sensing systems are discussed.

VIRUS: first deployment of the massively replicated fiber integral field spectrograph for the upgraded Hobby-Eberly Telescope

NASA Astrophysics Data System (ADS)

Hill, Gary J.; Tuttle, Sarah E.; Vattiat, Brian L.; Lee, Hanshin; Drory, Niv; Kelz, Andreas; Ramsey, Jason; Peterson, Trent W.; DePoy, D. L.; Marshall, J. L.; Gebhardt, Karl; Chonis, Taylor; Dalton, Gavin; Farrow, Daniel; Good, John M.; Haynes, Dionne M.; Indahl, Briana L.; Jahn, Thomas; Kriel, Hermanus; Montesano, Francesco; Nicklas, Harald; Noyola, Eva; Prochaska, Travis; Allen, Richard D.; Bender, Ralf; Blanc, Guillermo; Fabricius, Maximilian H.; Finkelstein, Steve; Landriau, Martin; MacQueen, Phillip J.; Roth, M. M.; Savage, R. D.; Snigula, Jan M.; Anwad, Heiko

2016-08-01

The Visible Integral-field Replicable Unit Spectrograph (VIRUS) consists of 156 identical spectrographs (arrayed as 78 pairs) fed by 35,000 fibers, each 1.5 arcsec diameter, at the focus of the upgraded 10 m Hobby-Eberly Telescope (HET). VIRUS has a fixed bandpass of 350-550 nm and resolving power R 700. VIRUS is the first example of industrial-scale replication applied to optical astronomy and is capable of surveying large areas of sky, spectrally. The VIRUS concept offers significant savings of engineering effort, cost, and schedule when compared to traditional instruments. The main motivator for VIRUS is to map the evolution of dark energy for the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX‡), using 0.8M Lyman-alpha emitting galaxies as tracers. The VIRUS array is undergoing staged deployment during 2016 and 2017. It will provide a powerful new facility instrument for the HET, well suited to the survey niche of the telescope, and will open up large spectroscopic surveys of the emission line universe for the first time. We will review the production, lessons learned in reaching volume production, characterization, and first deployment of this massive instrument.

UAV Deployment Exercise for Mapping Purposes: Evaluation of Emergency Response Applications.

PubMed

Boccardo, Piero; Chiabrando, Filiberto; Dutto, Furio; Tonolo, Fabio Giulio; Lingua, Andrea

2015-07-02

Exploiting the decrease of costs related to UAV technology, the humanitarian community started piloting the use of similar systems in humanitarian crises several years ago in different application fields, i.e., disaster mapping and information gathering, community capacity building, logistics and even transportation of goods. Part of the author's group, composed of researchers in the field of applied geomatics, has been piloting the use of UAVs since 2006, with a specific focus on disaster management application. In the framework of such activities, a UAV deployment exercise was jointly organized with the Regional Civil Protection authority, mainly aimed at assessing the operational procedures to deploy UAVs for mapping purposes and the usability of the acquired data in an emergency response context. In the paper the technical features of the UAV platforms will be described, comparing the main advantages/disadvantages of fixed-wing versus rotor platforms. The main phases of the adopted operational procedure will be discussed and assessed especially in terms of time required to carry out each step, highlighting potential bottlenecks and in view of the national regulation framework, which is rapidly evolving. Different methodologies for the processing of the acquired data will be described and discussed, evaluating the fitness for emergency response applications.

Rickettsial infection among military personnel deployed in Northern Sri Lanka.

PubMed

Premaratna, Ranjan; Ariyaratna, Nimalka; Attanayake, Champaka; Bandara, Wijesinghe; Chandrasena, Nilmini; de Silva, H Janaka

2014-12-20

Military personnel deployed in field actvities report on frequent tick bites. Therefore they may run the risk of exposure to rickettsial organisms. In order to assess the risk of exposure to rickettsial organisms, two groups of military personnel who were deployed in field activities of Nothern Sri Lanka were investigated. The first group was studied in order to assess the sero-prevalence of rickettsioses and consisted of soldiers who were admitted following injuries during field activities. The second group was studied to identify the incidence of acute rickettsioses during their acute febrile presentations. They were tested with IFA-IgG against spotted fever group rickettsioses (SFG), scrub typhus (ST) and murine typhus. In the first group, 48/57 (84%) military personnel had serological evidence of exposure to rickettsioses (in all, IFA-IgG titer ≥ 1:128): 33/50 (66%) to SFG rickettsioses, 1/50 (2%) to ST and 14/50 (28%) had mixed titers for both (in all, titers were higher for SFG). While all of them were in military uniform most of the time and frequently slept on scrub land, 35/57 (61.4%) had never used insect repellents and none were on doxycycline prophylaxis. 48/57 (84%) had experienced tick bites during field activity. In the second group, there were 49 who presented with acute febrile illness with a mean duration of 8.5 days (SD 3.2). 33/49 (67.3%) were serologically positive for acute rickettsioses (IgG ≥1:256); 26 (79%) due to ST and 7 (21%) due to SFG rickettsioses, Exposure to rickettsial disease was common among soldiers who were deployed in Northern Sri Lanka. Scrub typhus was the predominent species accounting for acute febrile illness. Further studies are needed to understand the reasons for very high sero-prevalence for SFG rickettsioses with no anticedent febrile illness. Use of preventive measures was not satisfactory. The high sero-prevelence of SFG rickettsioses is likely to interfere with serological diagnosis of acute SFG rickettsioses in this population.

Deployable Integral Field Units, Multislits, and Image Slicer for the Goodman Imaging Spectrograph on the SOAR Telescope

NASA Astrophysics Data System (ADS)

Cecil, Gerald N.; Moffett, A. J.; Cui, Y.; Eckert, K. D.; McBride, J.; Kannappan, S.; Keller, K.; Barlow, B. N.; Dunlap, B.; Bland-Hawthorn, J.

2010-01-01

The Goodman Imager-Spectrograph on the 4.1m SOAR telescope has operated on Cerro Pachon, Chile with volume-phase holographic gratings in long-slit mode since its commissioning in 2008. Recently, UNC graduate students played key roles to implement robust upgrades for multi-object spectroscopy that will soon be available to US astronomers through the NOAO time share on SOAR: • Multislits over 3x5 arcmin, generated on PCB solder stencils with exceptional sharpness compared to conventional laser cuts, initially to survey globular clusters for pulsating hot sub-dwarfs • An image slicer to obtain 3 simultaneous parallel spectra 70-arcsec long, 1- or 2-arcsec wide, spanning 320-750 nm to map stellar and gaseous emission and mass over the 1500 galaxies in the RESOLVE survey underway on SOAR • Four integral field units, each composed of 5-arcsec diameter, fused bundles of 0.5-arcsec diameter thin-clad optical fiber, independently deployed over a 10x5 arcmin field targeted by an EMCCD also used for Lucky Imaging. Initially will study aperture effects in single fiber surveys, extragalactic globular clusters, and demonstrate technology prior to deployment on larger telescopes • New wheels supporting a large set of existing narrow-band and Sloan filters • A trombone-style atmospheric dispersion compensator that corrects the full 12-arcmin diameter science field down to 30 deg elevation. Working in UNC's Goodman Laboratory for Astronomical Instrumentation, students employed SolidWorks and ZEMAX to design parts for in-house CAM on CNC machines and a 3D printer. All motors are controlled by LabVIEW as is the SOAR TCS. The deployable IFU axes are controlled by Quicksilver Controls Inc. intelligent servos and $80 model robot (Firgelli Corp.) actuators driven by a PIC-microcontroller and a student designed custom PCB. Upgrades and students were supported by $200K from SOAR Corporation, Research Corporation, NSF, and UNC competitive funds, and NC NASA Space Grant, Sigma Xi, and NASA fellowships.

Austere, remote, and disaster medicine missions: an operational mnemonic can help organize a deployment.

PubMed

Macias, Darryl J; Williams, Jason

2013-01-01

Medical care in resource-limited environments (austere settings) can occur in the context of a disaster, wilderness, or a tactical field operation. Regardless of the type of environment, there are common organizational themes in most successful humanitarian missions that occur in harsh natural or manmade environmental conditions. These principles prioritize the initiation and execution of any given deployment in austere or remote settings, diverging from priorities that would occur in a situation in which change to the existing medical structure is intact and operating well. Attention to these priorities not only helps providers to deliver medical care to people in need during a period of resource limitations but it also can keep providers, teams, the public, and patients safe during and after a deployment.

Fast DNA sieving through submicrometer cylindrical glass capillary matrix.

PubMed

Cao, Zhen; Yobas, Levent

2014-01-07

Here, we report on DNA electrophoresis through a novel artificial sieving matrix based on the highly regular submicrometer cylindrical glass capillary segments alternatingly arranged with wells. Such round capillaries pose a higher-order confinement resulting in a lower partition coefficient and greater entropic energy barrier while limiting the driving field strength to a small fraction of the applied electric field. In return, the separation can be performed at high average field strengths (up to 1.6 kV/cm) without encountering the field-dependent loss of resolving power. This leads to fast DNA sieving as demonstrated here on the capillaries of 750 nm in diameter. The 600 bp to 21 kbp long chains are shown to resolve within 4 min after having undergone a fairly limited number of entropic barriers (128 in total). The capillary matrix also exhibits a critical field threshold below which DNA bands fail to launch, and this occurs at a considerably greater magnitude than in other matrixes. The submicrometer capillaries are batch-fabricated on silicon through a fabrication process that does not require high-resolution advanced lithography or well-controlled wafer bonding techniques to define their critical dimension.

Results from laboratory and field testing of nitrate measuring spectrophotometers

USGS Publications Warehouse

Snazelle, Teri T.

2015-01-01

In Phase II, the analyzers were deployed in field conditions at three diferent USGS sites. The measured nitrate concentrations were compared to discrete (reference) samples analyzed by the Direct UV method on a Shimadzu UV1800 bench top spectrophotometer, and by the National Environmental Methods Index (NEMI) method I-2548-11 at the USGS National Water Quality Laboratory. The first deployment at USGS site 0249620 on the East Pearl River in Hancock County, Mississippi, tested the ability of the TriOs ProPs (10-mm path length), Hach NITRATAX (5 mm), Satlantic SUNA (10 mm), and the S::CAN Spectro::lyser (5 mm) to accurately measure low-level (less than 2 mg-N/L) nitrate concentrations while observing the effect turbidity and colored dissolved organic matter (CDOM) would have on the analyzers' measurements. The second deployment at USGS site 01389005 Passaic River below Pompton River at Two Bridges, New Jersey, tested the analyzer's accuracy in mid-level (2-8 mg-N/L) nitrate concentrations. This site provided the means to test the analyzers' performance in two distinct matrices—the Passaic and the Pompton Rivers. In this deployment, three instruments tested in Phase I (TriOS, Hach, and SUNA) were deployed with the S::CAN Spectro::lyser (35 mm) already placed by the New Jersey Water Science Center (WSC). The third deployment at USGS site 05579610 Kickapoo Creek at 2100E Road near Bloomington, Illinois, tested the ability of the analyzers to measure high nitrate concentrations (greater than 8 mg-N/L) in turbid waters. For Kickapoo Creek, the HIF provided the TriOS (10 mm) and S::CAN (5 mm) from Phase I, and a SUNA V2 (5 mm) to be deployed adjacent to the Illinois WSC-owned Hach (2 mm). A total of 40 discrete samples were collected from the three deployment sites and analyzed. The nitrate concentration of the samples ranged from 0.3–22.2 mg-N/L. The average absolute difference between the TriOS measurements and discrete samples was 0.46 mg-N/L. For the combined data from the Hach 5-mm and 2-mm analyzers, the average absolute difference between the Hach samples and the discrete samples was 0.13 mg-N/L. For the SUNA and SUNA V2 combined data, the average absolute difference between the SUNA samples and the discrete samples was 0.66 mg-N/L. The average absolute difference between the S::CAN samples and the discrete samples was 0.63 mg-N/L.

Novel Tools in Determining the Physiological Demands and Nutritional Practices of Ontario FireRangers during Fire Deployments

PubMed Central

Robertson, A. H.; Larivière, C.; Leduc, C. R.; McGillis, Z.; Eger, T.; Godwin, A.; Larivière, M.; Dorman, S. C.

2017-01-01

Introduction The seasonal profession of wildland fire fighting in Canada requires individuals to work in harsh environmental conditions that are physically demanding. The purpose of this study was to use novel technologies to evaluate the physiological demands and nutritional practices of Canadian FireRangers during fire deployments. Methods Participants (n = 21) from a northern Ontario Fire Base volunteered for this study and data collection occurred during the 2014 fire season and included Initial Attack (IA), Project Fire (P), and Fire Base (B) deployments. Deployment-specific energy demands and physiological responses were measured using heart-rate variability (HRV) monitoring devices (Zephyr BioHarness3 units). Food consumption behaviour and nutrient quantity and quality were captured using audio-video food logs on iPod Touches and analyzed by NutriBase Pro 11 software. Results Insufficient kilocalories were consumed relative to expenditure for all deployment types. Average daily kilocalories consumed: IA: 3758 (80% consumption rate); P: 2945±888.8; B: 2433±570.8. Average daily kilocalorie expenditure: IA: 4538±106.3; P: 4012±1164.8; B: 2842±649.9. The Average Macronutrient Distribution Range (AMDR) for protein was acceptable: 22–25% (across deployment types). Whereas the AMDR for fat and carbohydrates were high: 40–50%; and low: 27–37% respectively, across deployment types. Conclusions This study is the first to use the described methodology to simultaneously evaluate energy expenditures and nutritional practices in an occupational setting. The results support the use of HRV monitoring and video-food capture, in occupational field settings, to assess job demands. FireRangers expended the most energy during IA, and the least during B deployments. These results indicate the need to develop strategies centered on maintaining physical fitness and improving food practices. PMID:28107380

An ARM Mobile Facility Designed for Marine Deployments

NASA Astrophysics Data System (ADS)

Wiscombe, W. J.

2007-05-01

The U.S. Dept. of Energy's ARM (Atmospheric Radiation Measurements) Program is designing a Mobile Facility exclusively for marine deployments. This marine facility is patterned after ARM's land Mobile Facility, which had its inaugural deployment at Point Reyes, California, in 2005, followed by deployments to Niger in 2006 and Germany in 2007 (ongoing), and a planned deployment to China in 2008. These facilities are primarily intended for the study of clouds, radiation, aerosols, and surface processes with a goal to include these processes accurately in climate models. They are preferably embedded within larger field campaigns which provide context. They carry extensive instrumentation (in several large containers) including: cloud radar, lidar, microwave radiometers, infrared spectrometers, broadband and narrowband radiometers, sonde-launching facilities, extensive surface aerosol measurements, sky imagers, and surface latent and sensible heat flux devices. ARM's Mobile Facilities are designed for 6-10 month deployments in order to capture climatically-relevant datasets. They are available to any scientist, U.S. or international, who wishes to submit a proposal during the annual Spring call. The marine facility will be adapted to, and ruggedized for, the harsh marine environment and will add a scanning two-frequency radar, a boundary-layer wind profiler, a shortwave spectrometer, and aerosol instrumentation adapted to typical marine aerosols like sea salt. Plans also include the use of roving small UAVs, automated small boats, and undersea autonomous vehicles in order to address the point-to-area-average problem which is so crucial for informing climate models. Initial deployments are planned for small islands in climatically- interesting cloud regimes, followed by deployments on oceanic platforms (like decommissioned oil rigs and the quasi-permanent platform of this session's title) and eventually on large ships like car carriers plying routine routes.

Novel Tools in Determining the Physiological Demands and Nutritional Practices of Ontario FireRangers during Fire Deployments.

PubMed

Robertson, A H; Larivière, C; Leduc, C R; McGillis, Z; Eger, T; Godwin, A; Larivière, M; Dorman, S C

2017-01-01

The seasonal profession of wildland fire fighting in Canada requires individuals to work in harsh environmental conditions that are physically demanding. The purpose of this study was to use novel technologies to evaluate the physiological demands and nutritional practices of Canadian FireRangers during fire deployments. Participants (n = 21) from a northern Ontario Fire Base volunteered for this study and data collection occurred during the 2014 fire season and included Initial Attack (IA), Project Fire (P), and Fire Base (B) deployments. Deployment-specific energy demands and physiological responses were measured using heart-rate variability (HRV) monitoring devices (Zephyr BioHarness3 units). Food consumption behaviour and nutrient quantity and quality were captured using audio-video food logs on iPod Touches and analyzed by NutriBase Pro 11 software. Insufficient kilocalories were consumed relative to expenditure for all deployment types. Average daily kilocalories consumed: IA: 3758 (80% consumption rate); P: 2945±888.8; B: 2433±570.8. Average daily kilocalorie expenditure: IA: 4538±106.3; P: 4012±1164.8; B: 2842±649.9. The Average Macronutrient Distribution Range (AMDR) for protein was acceptable: 22-25% (across deployment types). Whereas the AMDR for fat and carbohydrates were high: 40-50%; and low: 27-37% respectively, across deployment types. This study is the first to use the described methodology to simultaneously evaluate energy expenditures and nutritional practices in an occupational setting. The results support the use of HRV monitoring and video-food capture, in occupational field settings, to assess job demands. FireRangers expended the most energy during IA, and the least during B deployments. These results indicate the need to develop strategies centered on maintaining physical fitness and improving food practices.

First Results from UAS Deployed Ocean Sensor Systems during the 2013 MIZOPEX Campaign

NASA Astrophysics Data System (ADS)

Palo, S. E.; Weibel, D.; Lawrence, D.; LoDolce, G.; Bradley, A. C.; Adler, J.; Maslanik, J. A.; Walker, G.

2013-12-01

The Marginal Ice Zone Observations and Processes Experiment (MIZOPEX), is an Arctic field campaign which occurred during summer 2013. The goals of the project are to understand how warming of the marginal ice zone affects sea ice melt and if this warming has been over or underestimated by satellite measurements. To achieve these goals calibrated physical measurements, both remote and in-situ, of the marginal ice zone over scales of square kilometers with a resolution of square meters is required. This will be accomplished with a suite of unmanned aerial vehicles (UAVs) equipped with both remote sensing and in-situ instruments, air deployed microbuoys, and ship deployed buoys. In this talk we will present details about the air deployed microbouys (ADMB) and self-deployed surface sondes (SDSS) developed at the University of Colorado. Both the ADMB and SDSS share a common measurement suite with the capability to measure water temperature at three distinct depths and provide position information via GPS. The ADMB is 90 grams, 1.3 inches in diameter, 4.25 inches long and is designed for deployment from the InSitu ScanEagle platform. The designed and experimentally verified operational lifetime is 10 days, however this can be extended with additional batteries.. While the ADMB are deployed from the ScanEagle, the SDSS are vectorable and can be remotely and precisely positioned. Lab performance results, calibration results and initial results from the ADMB and SDSS that were deployed during the MIZOPEX mission will be presented. These results include day-in-the-life tests, antenna pattern analysis, range tests, temperature measurement accuracy and initial scientific results from the campaign.

Lessons Learned in the Development of Gamma-Rover (GRover) Inspection Device

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

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

2006-02-11

The Gamma-Rover (GRover) is an electrically powered crawler designed to visually inspect and characterize the radiological conditions within the B-Cell and D-Cell ventilation ducting in support of the Hanford Site’s 324 Building Stabilization/Deactivation Project. Due to the bid opening of the Department of Energy’s River Corridor Project prior to deployment, GRover has not yet been deployed. The delay in deployment has allowed the designers to develop lessons learned from the original development in order to propose improvements when the system is deployed in the future. Gamma field information is detected with a pair of Eberline DA1-8/RMS systems. One system ismore » mounted directly on the crawler, while the second is mounted on the deployment platform. Four web cameras on a pair of CAT-5e/USB channels provide video feedback from both the crawler and the deployment platform. The drive system was designed to overcome a potentially difficult path of the duct, which included three ninety-degree bends. Mockups of the duct bends yielded high friction on the tether, and a drive system to overcome this friction was especially difficult to design into such a small package. Deployment was to be performed during a routine air filter change-out. As such, a specialized deployment platform was designed to pass through the existing filter housing. GRover would be required to be staged within the hot cell prior to the filter change-out and could therefore be dosed in excess of 8 hours. Thus, the platform also had to protect the electronics from radiation damage for an extended period of time.« less

Ancient DNA studies: new perspectives on old samples

PubMed Central

2012-01-01

In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field. PMID:22697611

Separation/extraction, detection, and interpretation of DNA mixtures in forensic science (review).

PubMed

Tao, Ruiyang; Wang, Shouyu; Zhang, Jiashuo; Zhang, Jingyi; Yang, Zihao; Sheng, Xiang; Hou, Yiping; Zhang, Suhua; Li, Chengtao

2018-05-25

Interpreting mixed DNA samples containing material from multiple contributors has long been considered a major challenge in forensic casework, especially when encountering low-template DNA (LT-DNA) or high-order mixtures that may involve missing alleles (dropout) and unrelated alleles (drop-in), among others. In the last decades, extraordinary progress has been made in the analysis of mixed DNA samples, which has led to increasing attention to this research field. The advent of new methods for the separation and extraction of DNA from mixtures, novel or jointly applied genetic markers for detection and reliable interpretation approaches for estimating the weight of evidence, as well as the powerful massively parallel sequencing (MPS) technology, has greatly extended the range of mixed samples that can be correctly analyzed. Here, we summarized the investigative approaches and progress in the field of forensic DNA mixture analysis, hoping to provide some assistance to forensic practitioners and to promote further development involving this issue.

A reply to Iversen et al.'s comment “Monitoring of animal abundance by environmental DNA - An increasingly obscure perspective”

USGS Publications Warehouse

Klymus, Katy E.; Richter, Catherine A.; Chapman, Duane C.; Paukert, Craig P.

2015-01-01

We appreciate the conversation put forward by Iversen et al. (2015) in their response to our article “Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix” in the 2015 environmental DNA special issue of Biological Conservation.We agree with Iversen et al.'s concern about overly optimistic conclusions that could be drawn from the current eDNA literature. One hope for eDNA technology is that it can be used in estimating abundance or population density. Evidence suggests that eDNA measurements correlate with total biomass (Takahara et al., 2012) rather than abundance. We demonstrate a similar relationship between biomass and eDNA shedding rates. Nevertheless, without field testing of these methods and specific survey protocols, we cannot make strong conclusions regarding the technique's field applicability. In our manuscript, we attempted to point out areas in which more research is needed.

Preparedness Evaluation of French Military Orthopedic Surgeons Before Deployment.

PubMed

Choufani, Camille; Barbier, Olivier; Mayet, Aurélie; Rigal, Sylvain; Mathieu, Laurent

2018-06-13

A deployed military orthopedic surgeon is a trauma surgeon working in austere conditions. The first aim of this study was to analyze the current activity of French military orthopedic surgeons in the field and to identify the differences of the combat zone with their daily practice. The second aim was to assess the adequacy of the preparedness they received before their deployment and to identify additional needs that could be addressed in future training. An evaluation survey was sent to all French military orthopedic surgeons deployed in theaters of operations between 2004 and 2014. An analogic visual scale of 10 was used to evaluate their surgical activity abroad and prior training. A total of 55 surgeons, with a median deployment number of 7, were included in this study after they answered the survey. Debridement and external fixation were the most common orthopedic procedures. The practice of general surgery was mostly concerned with vascular and abdominal injuries as part of damage control procedures. Median scores were ranked at seven for surgical preparedness, five for physical readiness, and three for mental preparedness. There was a significant inverse relationship between the number of missions performed and the evaluation of surgical preparedness. The higher they perceived their mental preparedness, the better they estimated their surgical preparedness. In the French Army, deployed orthopedic surgeons perform general surgical activity. Their initial training must be adapted to this constraint and enhanced by continuing medical education.

Newberry Seismic Deployment Fieldwork Report

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

Wang, J; Templeton, D C

2012-03-21

This report summarizes the seismic deployment of Lawrence Livermore National Laboratory (LLNL) Geotech GS-13 short-period seismometers at the Newberry Enhanced Geothermal System (EGS) Demonstration site located in Central Oregon. This Department of Energy (DOE) demonstration project is managed by AltaRock Energy Inc. AltaRock Energy had previously deployed Geospace GS-11D geophones at the Newberry EGS Demonstration site, however the quality of the seismic data was somewhat low. The purpose of the LLNL deployment was to install more sensitive sensors which would record higher quality seismic data for use in future seismic studies, such as ambient noise correlation, matched field processing earthquakemore » detection studies, and general EGS microearthquake studies. For the LLNL deployment, seven three-component seismic stations were installed around the proposed AltaRock Energy stimulation well. The LLNL seismic sensors were connected to AltaRock Energy Gueralp CMG-DM24 digitizers, which are powered by AltaRock Energy solar panels and batteries. The deployment took four days in two phases. In phase I, the sites were identified, a cavity approximately 3 feet deep was dug and a flat concrete pad oriented to true North was made for each site. In phase II, we installed three single component GS-13 seismometers at each site, quality controlled the data to ensure that each station was recording data properly, and filled in each cavity with native soil.« less

Critical considerations for the application of environmental DNA methods to detect aquatic species

USGS Publications Warehouse

Goldberg, Caren S.; Turner, Cameron R.; Deiner, Kristy; Klymus, Katy E.; Thomsen, Philip Francis; Murphy, Melanie A.; Spear, Stephen F.; McKee, Anna; Oyler-McCance, Sara J.; Cornman, Robert S.; Laramie, Matthew B.; Mahon, Andrew R.; Lance, Richard F.; Pilliod, David S.; Strickler, Katherine M.; Waits, Lisette P.; Fremier, Alexander K.; Takahara, Teruhiko; Herder, Jelger E.; Taberlet, Pierre

2016-01-01

Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed.Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms.Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA.We present a synthesis of knowledge at this stage for application of this new and powerful detection method.

A magnetic shield/dual purpose mission

NASA Technical Reports Server (NTRS)

Watkins, Seth; Albertelli, Jamil; Copeland, R. Braden; Correll, Eric; Dales, Chris; Davis, Dana; Davis, Nechole; Duck, Rob; Feaster, Sandi; Grant, Patrick

1994-01-01

The objective of this work is to design, build, and fly a dual-purpose payload whose function is to produce a large volume, low intensity magnetic field and to test the concept of using such a magnetic field to protect manned spacecraft against particle radiation. An additional mission objective is to study the effect of this moving field on upper atmosphere plasmas. Both mission objectives appear to be capable of being tested using the same superconducting coil. The potential benefits of this magnetic shield concept apply directly to both earth-orbital and interplanetary missions. This payload would be a first step in assessing the true potential of large volume magnetic fields in the U.S. space program. Either converted launch systems or piggyback payload opportunities may be appropriate for this mission. The use of superconducting coils for magnetic shielding against solar flare radiation during manned interplanetary missions has long been contemplated and was considered in detail in the years preceding the Apollo mission. With the advent of new superconductors, it has now become realistic to reconsider this concept for a Mars mission. Even in near-earth orbits, large volume magnetic fields produced using conventional metallic superconductors allow novel plasma physics experiments to be contemplated. Both deployed field-coil and non-deployed field-coil shielding arrangements have been investigated, with the latter being most suitable for an initial test payload in a polar orbit.

The World through Glass: Developing Novel Methods with Wearable Computing for Urban Videographic Research

ERIC Educational Resources Information Center

Paterson, Mark; Glass, Michael R.

2015-01-01

Google Glass was deployed in an Urban Studies field course to gather videographic data for team-based student research projects. We evaluate the potential for wearable computing technology such as Glass, in combination with other mobile computing devices, to enhance reflexive research skills, and videography in particular, during field research.…

The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction.

PubMed

Renshaw, Mark A; Olds, Brett P; Jerde, Christopher L; McVeigh, Margaret M; Lodge, David M

2015-01-01

Current research targeting filtered macrobial environmental DNA (eDNA) often relies upon cold ambient temperatures at various stages, including the transport of water samples from the field to the laboratory and the storage of water and/or filtered samples in the laboratory. This poses practical limitations for field collections in locations where refrigeration and frozen storage is difficult or where samples must be transported long distances for further processing and screening. This study demonstrates the successful preservation of eDNA at room temperature (20 °C) in two lysis buffers, CTAB and Longmire's, over a 2-week period of time. Moreover, the preserved eDNA samples were seamlessly integrated into a phenol-chloroform-isoamyl alcohol (PCI) DNA extraction protocol. The successful application of the eDNA extraction to multiple filter membrane types suggests the methods evaluated here may be broadly applied in future eDNA research. Our results also suggest that for many kinds of studies recently reported on macrobial eDNA, detection probabilities could have been increased, and at a lower cost, by utilizing the Longmire's preservation buffer with a PCI DNA extraction. © 2014 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Development of Ecogenomic Sensors for Remote Detection of Marine Microbes, Their Genes and Gene Products

NASA Astrophysics Data System (ADS)

Scholin, C.; Preston, C.; Harris, A.; Birch, J.; Marin, R.; Jensen, S.; Roman, B.; Everlove, C.; Makarewicz, A.; Riot, V.; Hadley, D.; Benett, W.; Dzenitis, J.

2008-12-01

An internet search using the phrase "ecogenomic sensor" will return numerous references that speak broadly to the idea of detecting molecular markers indicative of specific organisms, genes or other biomarkers within an environmental context. However, a strict and unified definition of "ecogenomic sensor" is lacking and the phrase may be used for laboratory-based tools and techniques as well as semi or fully autonomous systems that can be deployed outside of laboratory. We are exploring development of an ecogenomic sensor from the perspective of a field-portable device applied towards oceanographic research and water quality monitoring. The device is known as the Environmental Sample Processor, or ESP. The ESP employs wet chemistry molecular analytical techniques to autonomously assess the presence and abundance of specific organisms, their genes and/or metabolites in near real-time. Current detection chemistries rely on low- density DNA probe and protein arrays. This presentation will emphasize results from 2007-8 field trials when the ESP was moored in Monterey Bay, CA, as well as current engineering activities for improving analytical capacity of the instrument. Changes in microbial community structure at the rRNA level were observed remotely in accordance with changing chemical and physical oceanographic conditions. Current developments include incorporation of a reusable solid phase extraction column for purifying nucleic acids and a 4-channel real-time PCR module. Users can configure this system to support a variety of PCR master mixes, primer/probe combinations and control templates. An update on progress towards fielding a PCR- enabled ESP will be given along with an outline of plans for its use in coastal and oligotrophic oceanic regimes.

Evaluation strategy for the I-95 CC electronic credentialing program

DOT National Transportation Integrated Search

1999-03-01

The electronic credentialing field operational test will undertake the model deployment of electronic credentialing for commercial vehicles. The project will involve the development of state-specific electronic credentialing systems.

Fast kinetic studies of plasmid DNA transfer in intact yeast cells mediated by electropulsation.

PubMed

Ganeva, V; Galutzov, B; Teissie, J

1995-09-25

Intact yeast cell Electrotransformation process was investigated. It is a two step process. The plasmid must be pre-mixed and present in contact with the cells during the pulse. During the millisecond field pulse, plasmid DNA is associated to the envelope. It therefore crosses the membrane by a process which lasts several seconds as shown by its sensitivity to a post pulse addition of DNase. Electrotransformation is not supported by an electrophoretic transfer due to the external field nor by a free diffusion across the electropermeabilized envelope. DNA is first bound during the field pulse and then is transferred by a still unknown active process due to cell metabolism.

Direct electrochemical stripping detection of cystic-fibrosis-related DNA linked through cadmium sulfide quantum dots

NASA Astrophysics Data System (ADS)

Marin, Sergio; Merkoçi, Arben

2009-02-01

Electrochemical detection of a cadmium sulfide quantum dots (CdS QDs)-DNA complex connected to paramagnetic microbeads (MB) was performed without the need for chemical dissolving. The method is based on dropping 20 µl of CdS QD-DNA-MB suspension on the surface of a screen-printed electrode. It is followed by magnetic collection on the surface of the working electrode and electrochemical detection using square-wave voltammetry (SWV), giving a well-shaped and sensitive analytical signal. A cystic-fibrosis-related DNA sequence was sandwiched between the two DNA probes. One DNA probe is linked via biotin-streptavidin bonding with MB and the other one via thiol groups with the CdS QD used as tags. Nonspecific signals of DNA were minimized using a blocking agent and the results obtained were successfully employed in a model DNA sensor with an interest in future applications in the clinical field. The developed nanoparticle biosensing system may offer numerous opportunities in other fields where fast, low cost and efficient detection of small volume samples is required.

Silicene nanoribbon as a new DNA sequencing device

NASA Astrophysics Data System (ADS)

Alesheikh, Sara; Shahtahmassebi, Nasser; Roknabadi, Mahmood Rezaee; Pilevar Shahri, Raheleh

2018-02-01

The importance of applying DNA sequencing in different fields, results in looking for fast and cheap methods. Nanotechnology helps this development by introducing nanostructures used for DNA sequencing. In this work we study the interaction between zigzag silicene nanoribbon and DNA nucleobases using DFT and non equilibrium Green's function approach, to investigate the possibility of using zigzag silicene nanoribbons as a biosensor for DNA sequencing.

Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches.

PubMed

Yahr, Rebecca; Schoch, Conrad L; Dentinger, Bryn T M

2016-09-05

The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity in appearance to distantly related taxa. This multiplicity of hurdles resulted in the early adoption of DNA-based comparisons to study fungal diversity, including linking curated DNA sequence data to expertly identified voucher specimens. DNA-barcoding approaches in fungi were first applied in specimen-based studies for identification and discovery of taxonomic diversity, but are now widely deployed for community characterization based on sequencing of environmental samples. Collectively, fungal barcoding approaches have yielded important advances across biological scales and research applications, from taxonomic, ecological, industrial and health perspectives. A major outstanding issue is the growing problem of 'sequences without names' that are somewhat uncoupled from the traditional framework of fungal classification based on morphology and preserved specimens. This review summarizes some of the most significant impacts of fungal barcoding, its limitations, and progress towards the challenge of effective utilization of the exponentially growing volume of data gathered from high-throughput sequencing technologies.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

Wave-Sediment Interaction in Muddy Environments: A Field Experiment

DTIC Science & Technology

2009-01-01

Geosciences project includes a field experiment on the Atchafalaya shelf, Louisiana, in Years 1 and 2 (2007-2008) and a data analysis and modeling effort in... analysis procedures. During the major field experiment effort in 2008 (Year 2), a total of 5 tripods were deployed at locations fronting the Atchafalaya...experiment effort. This final year of the project (2009, Year 3) has been focused upon data analysis and preparation of publications. APPROACH

Wave-Sediment Interaction in Muddy Environments: Subbottom Field Experiment

DTIC Science & Technology

2012-09-30

instrumentation deployed on nearby oil and gas platforms. WORK COMPLETED Field experiment and data analysis : The “Sub-bottom Field Experiment” project...Berkeley, Doctoral thesis, 149p. Chou, H.-T., M.A. Foda , and J.R. Hunt (1993). Rheological response of cohesive sediments to oscillatory forcing”, In...dissipation by muddy seafloors, Geophys. Res. Lett. 35/7, L07611. Foda , A.M., J.R. Hunt, and H.-T. Chou (1993). A nonlinear model for the

SensorKit: A Flexible and Extensible System for In-Situ Data Acquisition

NASA Astrophysics Data System (ADS)

Silva, F.; Deschon, A.; Chang, J.; Westrich, S.; Cho, Y. H.; Gullapalli, S.; Benzel, T.; Graham, E. A.

2009-12-01

Over the years, sensor networks technology has evolved tremendously and has great potential in environmental sensing applications. However, because sensor networks are usually designed and built by computer scientists and engineers with little input from the scientific community, the resulting technology is often complex and out of reach for most field scientists. A few sensor, and data logger vendors have released data acquisition systems that can be used with their products. Unfortunately, these are generally vendor-specific, requiring scientists with heterogeneous sensors to use multiple systems to acquire data from all their sensors. A few, more generic systems, are compatible with multiple brands. However, these often offer only limited functionality, little flexibility, and no extensibility. We built SensorKit to overcome these limitations and to accelerate the adoption of sensor networks by field scientists. Using a simplicity-through-sophistication approach, we provide scientists with a powerful tool for field data collection. SensorKit is hardware agnostic, and was built using commercial off-the-shelf components. By employing a Linux-based ultra low-power generic embedded processing platform with a variety of dataloggers (including Berkeley motes, National Instruments' Compact RIOs, as well as legacy and newer PakBus-based Campbell data loggers), we support requirements from a large number of scientists. The user interfaces are designed to be intuitive so that most scientists can deploy, configure, and operate the system without extensive training. Working in close collaboration with field scientists allowed us to better understand scientific requirements and ensure system relevancy. The requirements for data acquisition, data storage, and data communication vary significantly for each deployment. Data acquisition needs to include capabilities for different analog, digital, and other complex sensors (e.g. cameras, and robotic sensors). Moreover, the sensors may be geographically dispersed, requiring the use of a local sensor network for moving data at the site. Data storage has to accommodate varying sampling rates from several times a second, to once every hour (or longer), and handle situations where data is accumulated for several days or even weeks at a time. Additionally, different deployments require the use of varying communication technologies (e.g. satellite, cellular, long range radios, wi-fi, etc) and while some scientists need live access to their data, others are able to tolerate delays of hours, if not days. Finally, power and environmental conditions can have great influence in the type of data acquisition and communication technology that can be used at a certain site. During the past few years, we have used a spiral build, deploy, and revise approach in order to verify our design and incorporate what we have learned at each deployment. In this poster, we present our system architecture, how SensorKit has been used by scientists in a number of places around the world, and how it has evolved over time, adapting to a wide range of deployment requirements in order to accommodate different scientific applications.

The Development of a Mobile Health Platform and Naturalistic Game Applications for Health Assessment, Intervention, and Evaluation

DTIC Science & Technology

2015-12-01

in mild traumatic brain injuries (It is estimated that 20% of all combat troops will experience a concussion while deployed...combat   troops  will   experience  a   concussion  while   deployed)   increased  emphasis   has   rightly   been   placed   on   finding   ways...stemming  from  different  types   of   concussion .   Neither   testing   technique   is   as   readily   accessible   in   the   field   and

GEOS-20 m cable boom mechanism

NASA Technical Reports Server (NTRS)

Schmidt, B. K.; Suttner, K.

1977-01-01

The GEOS cable boom mechanism allows the controlled deployment of a 20 m long cable in a centrifugal force field. In launch configuration the flat cable is reeled on a 240 mm diameter drum. The electrical connection between the rotating drum and the stationary housing is accomplished via a flexlead positioned inside the drum. Active motion control of this drum is achieved by a self locking worm gear, driven by a stepper motor. The deployment length of the cable is monitored by an optical length indicator, sensing black bars engraved on the cable surface.

A deployable .015 inch diameter wire antenna

NASA Technical Reports Server (NTRS)

Dibiasi, L.

1979-01-01

This mechanism was developed to dispense a small diameter wire which serves as a receiving antenna for electric field measurements on an Earth orbiting satellite. The antenna is deployed radially from a spinning satellite. A brushless dc motor drives a storage spool to dispense the wire at a controlled rate. Centrifugal force, acting on a mass attached to the end of the wire, keeps the wire in the radial position. The mechanism design, testing, and performance characteristics are discussed. Finally, operational data of the mechanism while in orbit are presented.

Investigation on the diagnostic sensitivity of molecular tools used for detection of koi herpesvirus.

PubMed

Bergmann, Sven M; Riechardt, Meike; Fichtner, Dieter; Lee, Peiyu; Kempter, Jolanta

2010-02-01

Previous and new PCRs for KHV detection were compared by estimation of their sensitivity in recognizing KHV DNA in plasmids, cell culture extracted KHV DNA and total DNA obtained from field tissue samples. A modified real-time PCR (Gilad et al., 2004), combined with an internal control system (IC2, Hoffmann et al., 2006) in a duplex assay, was used as a "gold standard". The lowest reliably determined virus concentration between, 5 and 10 KHV DNA genomic equivalents, was found by real-time PCR (Gilad et al., 2004), nested PCR (Bergmann et al., 2006) and one-tube semi-nested PCR. All other published and unpublished PCRs, as well as the commercial Loopamp, recognized KHV DNA at higher concentrations only. Additionally, KHV variants, newly adapted to European conditions, which could not be detected by PCR according to Bercovier et al. (2005) were found in two field samples from carp and koi from different regions of Germany. A negative influence of sample pooling was shown with field samples tested by real-time PCR. 2009 Elsevier B.V. All rights reserved.

Protocol for quantitative tracing of surface water with synthetic DNA

NASA Astrophysics Data System (ADS)

Foppen, J. W.; Bogaard, T. A.

2012-04-01

Based on experiments we carried out in 2010 with various synthetic single stranded DNA markers with a size of 80 nucleotides (ssDNA; Foppen et al., 2011), we concluded that ssDNA can be used to carry out spatially distributed multi-tracer experiments in the environment. Main advantages are in principle unlimited amount of tracers, environmental friendly and tracer recovery at very high dilution rates (detection limit is very low). However, when ssDNA was injected in headwater streams, we found that at selected downstream locations, the total mass recovery was less than 100%. The exact reason for low mass recovery was unknown. In order to start identifying the cause of the loss of mass in these surface waters, and to increase our knowledge of the behaviour of synthetic ssDNA in the environment, we examined the effect of laboratory and field protocols working with artificial DNA by performing numerous batch experiments. Then, we carried out several field tests in different headwater streams in the Netherlands and in Luxembourg. The laboratory experiments consisted of a batch of water in a vessel with in the order of 10^10 ssDNA molecules injected into the batch. The total duration of each experiment was 10 hour, and, at regular time intervals, 100 µl samples were collected in a 1.5 ml Eppendorf vial for qPCR analyses. The waters we used ranged from milliQ water to river water with an Electrical Conductivity of around 400 μS/cm. The batch experiments were performed in different vessel types: polyethylene bottles, polypropylene copolymer bottles , and glass bottles. In addition, two filter types were tested: 1 µm pore size glass fibre filters and 0.2 µm pore size cellulose acetate filters. Lastly, stream bed sediment was added to the batch experiments to quantify interaction of the DNA with sediment. For each field experiment around 10^15 ssDNA molecules were injected, and water samples were collected 100 - 600 m downstream of the point of injection. Additionally, the field tests were performed with salt and deuterium as tracer. To study possible decay by sunlight and/or microbial activity for synthetic DNA, immediately in the field and for the duration of the entire experiment, we carried out batch experiments. All samples were stored in a 1.5 ml Eppendorf vial in a cool-box in dry ice (-80°C). Quantitative PCR on a Mini Opticon (Bio Rad, Hercules, CA, USA) was carried out to determine DNA concentrations in the samples. Results showed the importance of a strict protocol for working with ssDNA as a tracer for quantitative tracing, since ssDNA interacts with surface areas of glass and plastic, depending on water quality and ionic strength. Interaction with the sediment and decay due to sunlight and/or microbial activity was negligible in most cases. The ssDNA protocol was then tested in natural streams. Promising results were obtained using ssDNA as quantitative tracer. The breakthrough curves using ssDNA were similar to the ones of salt or deuterium. We will present the revised protocol to use ssDNA for multi-tracing experiments in natural streams and discuss the opportunities and limitations.

Analysis of NSWC Ocean EM Observatory Test Data

DTIC Science & Technology

2016-09-01

deployment locations. 1S. SUBJECT TERMS magnetic anomaly detection (MAD), oceanographic magnetic fields, coherence, magnetic noise reduction 16...analyses ......................................................................................... 11 3. Analysis of magnetic data...37 Appendix B: Feb 11 underwater magnetic data

The EarthScope USArray Observatories: Status and Results

NASA Astrophysics Data System (ADS)

Woodward, R.; Busby, R.; Alvarez, M.; Schultz, A.; Simpson, D.

2009-05-01

The EarthScope USArray program includes three seismic and two magnetotelluric components. The USArray seismic components consist of the Transportable Array (TA), the Flexible Array (FA), and the Reference Network. The TA component of USArray has now occupied over 700 sites in the western United States, from the Pacific coast through the Rocky Mountains. The three component broadband TA stations are deployed in a grid-like arrangement, with 70 km separation between stations. At any given time there are approximately 400 station sites, occupying a ~2000 km by 800 km "footprint." Each station is operated for two years. The FA component of USArray provides a pool of instruments, ranging from high frequency geophones to three- component broadband sensors, and these instruments are typically deployed for focused geological targets for time periods ranging from days to years. Finally, the Reference Network provides a fixed, permanent reference frame for the TA and FA, with approximately 100 broadband stations deployed across the contiguous US, at roughly 300 km spacing. The magnetotelluric (MT) component of USArray consists of both a fixed reference network as well as a transportable array of instruments that are deployed campaign style, using a 70 km by 70 km grid. The geographical extent of USArray allows unprecedented observation of geophysical targets. Instruments have been deployed across the west and mid-west of the US, with TA stations presently moving into the states spanning a north-south line from North Dakota to Texas. MT observations in Cascadia have been augmented by corresponding observations in Canada. Similarly, as the seismic TA moves east, plans are being developed to collaborate on TA seismic observations on both sides of the US-Canada border in the region of the Great Lakes. We will present the current status of USArray activities and progress to-date, with a special emphasis on standardized data products that are produced from USArray data, including phase picks, wave-field animations, observations of the ambient noise field, and MT transfer functions. We will also provide an overview of USArray deployment plans, to facilitate collaborative experiments and investigations, and discuss opportunities for the seismological education and research communities to participate in and leverage the FA and TA efforts.

An Evaluation of Oceanographic Optical Instruments and Deployment Methodologies

NASA Technical Reports Server (NTRS)

Hooker, Stanford B.; Maritorena, Stephane

1999-01-01

The primary objective of the Sea-viewing, Wide Field-of-view Sensor (SeaWiFS) Project is to produce water- leaving radiances with an uncertainty of 5% in clear-water regions and chlorophyll a concentrations within +/- 35% over the range of 0.05-50 mg/cu m. Any global mission, like SeaWiFS, requires validation data be submitted from a wide variety of investigators which places a significant challenge on quantifying the total uncertainty associated with the in situ measurements, because each investigator follows slightly different practices when it comes to implementing all of the steps associated with collecting field data, even those with a prescribed set of protocols. This study uses data from multiple cruises to quantify the uncertainties associated with implementing data collection procedures while utilizing differing in-water optical instruments and deployment methods. A comprehensive approach is undertaken and includes: (1) the use of a portable light source and in-water intercomparisons to monitor the stability of the field radiometers, (2) alternative methods for acquiring reference measurements, and (3) different techniques for making in-water profiles. The only system to meet the 5% radiometric objective of the SeaWiFS Project was a free-fall profiler using (relatively inexpensive) modular components, although a more sophisticated (and comparatively expensive) profiler using integral components was very close and only 1% higher. A relatively inexpensive system deployed with a winch and crane was also close, but the ship shadow contamination problem increased the total uncertainty to approximately 6.5%.

Optimization design combined with coupled structural-electrostatic analysis for the electrostatically controlled deployable membrane reflector

NASA Astrophysics Data System (ADS)

Liu, Chao; Yang, Guigeng; Zhang, Yiqun

2015-01-01

The electrostatically controlled deployable membrane reflector (ECDMR) is a promising scheme to construct large size and high precision space deployable reflector antennas. This paper presents a novel design method for the large size and small F/D ECDMR considering the coupled structure-electrostatic problem. First, the fully coupled structural-electrostatic system is described by a three field formulation, in which the structure and passive electrical field is modeled by finite element method, and the deformation of the electrostatic domain is predicted by a finite element formulation of a fictitious elastic structure. A residual formulation of the structural-electrostatic field finite element model is established and solved by Newton-Raphson method. The coupled structural-electrostatic analysis procedure is summarized. Then, with the aid of this coupled analysis procedure, an integrated optimization method of membrane shape accuracy and stress uniformity is proposed, which is divided into inner and outer iterative loops. The initial state of relatively high shape accuracy and uniform stress distribution is achieved by applying the uniform prestress on the membrane design shape and optimizing the voltages, in which the optimal voltage is computed by a sensitivity analysis. The shape accuracy is further improved by the iterative prestress modification using the reposition balance method. Finally, the results of the uncoupled and coupled methods are compared and the proposed optimization method is applied to design an ECDMR. The results validate the effectiveness of this proposed methods.

malERA: An updated research agenda for combination interventions and modelling in malaria elimination and eradication

PubMed Central

2017-01-01

This paper summarises key advances and priorities since the 2011 presentation of the Malaria Eradication Research Agenda (malERA), with a focus on the combinations of intervention tools and strategies for elimination and their evaluation using modelling approaches. With an increasing number of countries embarking on malaria elimination programmes, national and local decisions to select combinations of tools and deployment strategies directed at malaria elimination must address rapidly changing transmission patterns across diverse geographic areas. However, not all of these approaches can be systematically evaluated in the field. Thus, there is potential for modelling to investigate appropriate ‘packages’ of combined interventions that include various forms of vector control, case management, surveillance, and population-based approaches for different settings, particularly at lower transmission levels. Modelling can help prioritise which intervention packages should be tested in field studies, suggest which intervention package should be used at a particular level or stratum of transmission intensity, estimate the risk of resurgence when scaling down specific interventions after local transmission is interrupted, and evaluate the risk and impact of parasite drug resistance and vector insecticide resistance. However, modelling intervention package deployment against a heterogeneous transmission background is a challenge. Further validation of malaria models should be pursued through an iterative process, whereby field data collected with the deployment of intervention packages is used to refine models and make them progressively more relevant for assessing and predicting elimination outcomes. PMID:29190295

Multi-angle polarimeter inter-comparison: the PODEX and ACEPOL field campaigns

NASA Astrophysics Data System (ADS)

Knobelspiesse, K. D.; Tan, Q.; Redemann, J.; Cairns, B.; Diner, D. J.; Ferrare, R. A.; van Harten, G.; Hasekamp, O. P.; Kalashnikova, O. V.; Martins, J. V.; Yorks, J. E.; Seidel, F. C.

2017-12-01

A multi-angle polarimeter has been proposed for the NASA Aerosol-Cloud-Ecosystem (ACE) mission, recommended by the National Research Council's Decadal Survey. Such instruments are uncommon in orbit, and there is a great diversity of prototype instrument characteristics. For that reason, NASA funded two field campaigns where airborne polarimeter prototypes were deployed on the high altitude ER-2 aircraft. The first field campaign, POlarimeter DEfinition EXperiment (PODEX), was carried out in southern California in early 2013. Three polarimeters participated: the Airborne Multi-angle SpectroPolarimeter Imager (AirMSPI), the Passive Aerosol and Cloud Suite (PACS) and the Research Scanning Polarimeter (RSP). PACS, on its first deployment, suffered detector problems, while AirMSPI and RSP performed within expectations. Initial comparisons of AirMSPI and RSP observations found Degree of Linear Polarization (DoLP) biases. Following corrections to both instrument's calibration and/or geolocation techniques, these issues have improved. We will present the details of this comparison. The recent ACEPOL mission returned to southern California in October-November with a larger compliment of multi-angle polarimeters. This included AirMSPI and RSP, like in PODEX. Additional polarimetric instruments included AirHARP (Airborne HyperAngular Rainbow Polarimeter, a successor to PACS) and SPEX Airborne (SPectropolarimeter for Planetary Exploration). Two Lidars were also deployed: The High Spectral Resolution Lidar -2 (HSRL-2) and the Cloud Physics Lidar (CPL). While data processing is still underway, we will describe the objectives of this campaign and give a preview of what to expect in subsequent analysis.

Isotopic and Geochemical Investigation of Two Distinct Mars Analog Environments Using Evolved Gas Techniques in Svalbard, Norway

NASA Technical Reports Server (NTRS)

Stern, Jennifer Claire; Mcadam, Amy Catherine; Ten Kate, Inge L.; Bish, David L.; Blake, David F.; Morris, Richard V.; Bowden, Roxane; Fogel, Marilyn L.; Glamoclija, Mihaela; Mahaffy, Paul R.;

Field-Deployable Acoustic Digital Systems for Noise Measurement

NASA Technical Reports Server (NTRS)

Shams, Qamar A.; Wright, Kenneth D.; Lunsford, Charles B.; Smith, Charlie D.

2000-01-01

Langley Research Center (LaRC) has for years been a leader in field acoustic array measurement technique. Two field-deployable digital measurement systems have been developed to support acoustic research programs at LaRC. For several years, LaRC has used the Digital Acoustic Measurement System (DAMS) for measuring the acoustic noise levels from rotorcraft and tiltrotor aircraft. Recently, a second system called Remote Acquisition and Storage System (RASS) was developed and deployed for the first time in the field along with DAMS system for the Community Noise Flight Test using the NASA LaRC-757 aircraft during April, 2000. The test was performed at Airborne Airport in Wilmington, OH to validate predicted noise reduction benefits from alternative operational procedures. The test matrix was composed of various combinations of altitude, cutback power, and aircraft weight. The DAMS digitizes the acoustic inputs at the microphone site and can be located up to 2000 feet from the van which houses the acquisition, storage and analysis equipment. Digitized data from up to 10 microphones is recorded on a Jaz disk and is analyzed post-test by microcomputer system. The RASS digitizes and stores acoustic inputs at the microphone site that can be located up to three miles from the base station and can compose a 3 mile by 3 mile array of microphones. 16-bit digitized data from the microphones is stored on removable Jaz disk and is transferred through a high speed array to a very large high speed permanent storage device. Up to 30 microphones can be utilized in the array. System control and monitoring is accomplished via Radio Frequency (RF) link. This paper will present a detailed description of both systems, along with acoustic data analysis from both systems.

Evaluation of Two Lyophilized Molecular Assays to Rapidly Detect Foot-and-Mouth Disease Virus Directly from Clinical Samples in Field Settings.

PubMed

Howson, E L A; Armson, B; Madi, M; Kasanga, C J; Kandusi, S; Sallu, R; Chepkwony, E; Siddle, A; Martin, P; Wood, J; Mioulet, V; King, D P; Lembo, T; Cleaveland, S; Fowler, V L

2017-06-01

Accurate, timely diagnosis is essential for the control, monitoring and eradication of foot-and-mouth disease (FMD). Clinical samples from suspect cases are normally tested at reference laboratories. However, transport of samples to these centralized facilities can be a lengthy process that can impose delays on critical decision making. These concerns have motivated work to evaluate simple-to-use technologies, including molecular-based diagnostic platforms, that can be deployed closer to suspect cases of FMD. In this context, FMD virus (FMDV)-specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) and real-time RT-PCR (rRT-PCR) assays, compatible with simple sample preparation methods and in situ visualization, have been developed which share equivalent analytical sensitivity with laboratory-based rRT-PCR. However, the lack of robust 'ready-to-use kits' that utilize stabilized reagents limits the deployment of these tests into field settings. To address this gap, this study describes the performance of lyophilized rRT-PCR and RT-LAMP assays to detect FMDV. Both of these assays are compatible with the use of fluorescence to monitor amplification in real-time, and for the RT-LAMP assays end point detection could also be achieved using molecular lateral flow devices. Lyophilization of reagents did not adversely affect the performance of the assays. Importantly, when these assays were deployed into challenging laboratory and field settings within East Africa they proved to be reliable in their ability to detect FMDV in a range of clinical samples from acutely infected as well as convalescent cattle. These data support the use of highly sensitive molecular assays into field settings for simple and rapid detection of FMDV. © 2015 The Authors. Transboundary and Emerging Diseases Published by Blackwell Verlag GmbH.

Strong seasonality of Bonamia sp. infection and induced Crassostrea ariakensis mortality in Bogue and Masonboro Sounds, North Carolina, USA.

PubMed

Carnegie, Ryan B; Stokes, Nancy A; Audemard, Corinne; Bishop, Melanie J; Wilbur, Ami E; Alphin, Troy D; Posey, Martin H; Peterson, Charles H; Burreson, Eugene M

2008-07-01

Asian oyster Crassostrea ariakensis is being considered for introduction to Atlantic coastal waters of the USA. Successful aquaculture of this species will depend partly on mitigating impacts by Bonamia sp., a parasite that has caused high C. ariakensis mortality south of Virginia. To better understand the biology of this parasite and identify strategies for management, we evaluated its seasonal pattern of infection in C. ariakensis at two North Carolina, USA, locations in 2005. Small (<50 mm) triploid C. ariakensis were deployed to upwellers on Bogue Sound in late spring (May), summer (July), early fall (September), late fall (November), and early winter (December) 2005; and two field sites on Masonboro Sound in September 2005. Oyster growth and mortality were evaluated biweekly at Bogue Sound, and weekly at Masonboro, with Bonamia sp. prevalence evaluated using parasite-specific PCR. We used histology to confirm infections in PCR-positive oysters. Bonamia sp. appeared in the late spring Bogue Sound deployment when temperatures approached 25 degrees C, six weeks post-deployment. Summer- and early fall-deployed oysters displayed Bonamia sp. infections after 3-4 weeks. Bonamia sp. prevalences were 75% in Bogue Sound, and 60% in Masonboro. While oyster mortality reached 100% in late spring and summer deployments, early fall deployments showed reduced (17-82%) mortality. Late fall and early winter deployments, made at temperatures <20 degrees C, developed no Bonamia sp. infections at all. Seasonal Bonamia sp. cycling, therefore, is influenced greatly by temperature. Avoiding peak seasonal Bonamia sp. activity will be essential for culturing C. ariakensis in Bonamia sp.-enzootic waters.

Safe and Effective Deployment of Personnel to Support the Ebola Response - West Africa.

PubMed

Rouse, Edward N; Zarecki, Shauna Mettee; Flowers, Donald; Robinson, Shawn T; Sheridan, Reed J; Goolsby, Gary D; Nemhauser, Jeffrey; Kuwabara, Sachiko

2016-07-08

From the initial task of getting "50 deployers within 30 days" into the field to support the 2014-2016 Ebola virus disease (Ebola) epidemic response in West Africa to maintaining well over 200 staff per day in the most affected countries (Guinea, Liberia, and Sierra Leone) during the peak of the response, ensuring the safe and effective deployment of international responders was an unprecedented accomplishment by CDC. Response experiences shared by CDC deployed staff returning from West Africa were quickly incorporated into lessons learned and resulted in new activities to better protect the health, safety, security, and resiliency of responding personnel. Enhanced screening of personnel to better match skill sets and experience with deployment needs was developed as a staffing strategy. The mandatory predeployment briefings were periodically updated with these lessons to ensure that staff were aware of what to expect before, during, and after their deployments. Medical clearance, security awareness, and resiliency programs became a standard part of both predeployment and postdeployment activities. Response experience also led to the identification and provision of more appropriate equipment for the environment. Supporting the social and emotional needs of deployed staff and their families also became an agency focus for care and communication. These enhancements set a precedent as a new standard for future CDC responses, regardless of size or complexity.The activities summarized in this report would not have been possible without collaboration with many U.S and international partners (http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/partners.html).

Extremely low-frequency electromagnetic fields cause DNA strand breaks in normal cells

PubMed Central

2014-01-01

Background Extremely low frequency electromagnetic fields aren’t considered as a real carcinogenic agent despite the fact that some studies have showed impairment of the DNA integrity in different cells lines. The aim of this study was evaluation of the late effects of a 100 Hz and 5.6 mT electromagnetic field, applied continuously or discontinuously, on the DNA integrity of Vero cells assessed by alkaline Comet assay and by cell cycle analysis. Normal Vero cells were exposed to extremely low frequency electromagnetic fields (100 Hz, 5.6 mT) for 45 minutes. The Comet assay and cell cycle analysis were performed 48 hours after the treatment. Results Exposed samples presented an increase of the number of cells with high damaged DNA as compared with non-exposed cells. Quantitative evaluation of the comet assay showed a significantly (<0.001) increase of the tail lengths, of the quantity of DNA in tail and of Olive tail moments, respectively. Cell cycle analysis showed an increase of the frequency of the cells in S phase, proving the occurrence of single strand breaks. The most probable mechanism of induction of the registered effects is the production of different types of reactive oxygen species. Conclusions The analysis of the registered comet indices and of cell cycle showed that extremely low frequency electromagnetic field of 100 Hz and 5.6 mT had a genotoxic impact on Vero cells. PMID:24401758

Geokinetic environment investigations

NASA Astrophysics Data System (ADS)

Hartnett, E. B.; Carleen, E. D.; Blaney, J. I.

1981-03-01

This report covers the development and implementation of special concepts, techniques and instrumentation for the collection, analysis and application of geokinetic data. The Geokinetic Data Acquisition System (GDAS) was modified, maintained and operationally deployed to various sites designated by AFGL. Tests were conducted at the Defense Nuclear Agency (DNA) CASINO Facility in Maryland; Central Inertial Guidance Test Facility (CIGTF), Holloman AFB, N.M.; Space Transportation System (STS) Launch Complex, Vandenberg AFB, Ca. and the SAC Wing V Minuteman Complex at Cheyenne, Wy. The CASINO data contributed to SAMSO's MX/TGG Advanced Development Bridge II Program for radiation hardening of third generation hardware. The CIGTF investigation supported USAF requirements for highly precise azimuth reference. The Hill AFB the performance of a minuteman III missile guidance system in an engineering silo. The STS program at Vandenberg AFB was to assist in determining the nature of a Titan III-D pressure load. The SAC Wing V deployment was to investigate plateau/valley basin geologic characteristics in respect to motion response.

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline

PubMed Central

2014-01-01

Background Massively parallel DNA sequencing generates staggering amounts of data. Decreasing cost, increasing throughput, and improved annotation have expanded the diversity of genomics applications in research and clinical practice. This expanding scale creates analytical challenges: accommodating peak compute demand, coordinating secure access for multiple analysts, and sharing validated tools and results. Results To address these challenges, we have developed the Mercury analysis pipeline and deployed it in local hardware and the Amazon Web Services cloud via the DNAnexus platform. Mercury is an automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. Conclusions By taking advantage of cloud computing and with Mercury implemented on the DNAnexus platform, we have demonstrated a powerful combination of a robust and fully validated software pipeline and a scalable computational resource that, to date, we have applied to more than 10,000 whole genome and whole exome samples. PMID:24475911

Millstone: software for multiplex microbial genome analysis and engineering

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

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering.

PubMed

Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering

DOE PAGES

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.; ...

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

ADX: a high field, high power density, Advanced Divertor test eXperiment

NASA Astrophysics Data System (ADS)

Vieira, R.; Labombard, B.; Marmar, E.; Irby, J.; Shiraiwa, S.; Terry, J.; Wallace, G.; Whyte, D. G.; Wolfe, S.; Wukitch, S.; ADX Team

2014-10-01

The MIT PSFC and collaborators are proposing an advanced divertor experiment (ADX) - a tokamak specifically designed to address critical gaps in the world fusion research program on the pathway to FNSF/DEMO. This high field (6.5 tesla, 1.5 MA), high power density (P/S ~ 1.5 MW/m2) facility would utilize Alcator magnet technology to test innovative divertor concepts for next-step DT fusion devices (FNSF, DEMO) at reactor-level boundary plasma pressures and parallel heat flux densities while producing high performance core plasma conditions. The experimental platform would also test advanced lower hybrid current drive (LHCD) and ion-cyclotron range of frequency (ICRF) actuators and wave physics at the plasma densities and magnetic field strengths of a DEMO, with the unique ability to deploy launcher structures both on the low-magnetic-field side and the high-field side - a location where energetic plasma-material interactions can be controlled and wave physics is most favorable for efficient current drive, heating and flow drive. This innovative experiment would perform plasma science and technology R&D necessary to inform the conceptual development and accelerate the readiness-for-deployment of FNSF/DEMO - in a timely manner, on a cost-effective research platform. Supported by DE-FC02-99ER54512.

The BioSentinel Bioanalytical Microsystem: Characterizing DNA Radiation Damage in Living Organisms Beyond Earth Orbit

NASA Technical Reports Server (NTRS)

Ricco, A. J.; Hanel, R.; Bhattacharya, S.; Boone, T.; Tan, M.; Mousavi, A.; Rademacher, A.; Schooley, A.; Klamm, B.; Benton, J.;

Field-Based Approach for Assessing the Impact of Treated Pulp and Paper Mill Effluent on Endogenous Metabolites of Fathead Minnows (Pimephales promelas)

EPA Science Inventory

A field-based metabolomic study was conducted during a shutdown of a pulp and paper mill (PPM) to assess the impacts of treated PPM effluent on endogenous polar metabolites in fathead minnow (FHM; Pimephales promelas) livers. Caged male and female FHMs were deployed at a Great La...

Brady's Geothermal Field Nodal Seismometer Earthquake Data

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

Kurt Feigl

90-second records of data from 238 three-component nodal seismometer deployed at Bradys geothermal field. The time window catches an earthquake arrival. Earthquake data from USGS online catalog: Magnitude: 4.3 ml +/- 0.4 Location: 38.479 deg N 118.366 deg W +/- 0.7 km Depth: 9.9 km +/- 0.7 Date and Time: 2016-03-21 07:37:10.535 UTC

Overview of NASA FINESSE (Field Investigations to Enable Solar System Science and Exploration) Science and Exploration Results

NASA Technical Reports Server (NTRS)

Heldmann, Jennifer L.; Lim, Darlene S. S.; Hughes, S.; Kobs, S.; Garry, B.; Osinski, G. R.; Hodges, K.; Kobayashi, L.; Colaprete, A.

2015-01-01

NASA's FINESSE (Field Investigations to Enable Solar System Science and Exploration) project is focused on a science and exploration field-based research program to generate strategic knowledge in preparation for human and robotic exploration of other planetary bodies including our moon, Mars' moons Phobos and Deimos, and near-Earth asteroids. Scientific study focuses on planetary volcanism (e.g., the formation of volcanoes, evolution of magma chambers and the formation of multiple lava flow types, as well as the evolution and entrapment of volatile chemicals) and impact cratering (impact rock modification, cratering mechanics, and the chronologic record). FINESSE conducts multiple terrestrial field campaigns (Craters of the Moon National Monument and Preserve in Idaho for volcanics, and West Clearwater Impact Structure in Canada for impact studies) to study such features as analogs relevant to our moon, Phobos, Deimos, and asteroids. Here we present the science and exploration results from two deployments to Idaho (2014, 2015) and our first deployment to Canada (2014). FINESSE was selected as a research team by NASA's Solar System Exploration Research Virtual Institute (SSERVI). SSERVI is a joint effort by NASA's Science Mission Directorate (SMD) and Human Exploration and Operations Mission Directorate (HEOMD).

GENERAL EARTHQUAKE-OBSERVATION SYSTEM (GEOS).

USGS Publications Warehouse

Borcherdt, R.D.; Fletcher, Joe B.; Jensen, E.G.; Maxwell, G.L.; VanSchaack, J.R.; Warrick, R.E.; Cranswick, E.; Johnston, M.J.S.; McClearn, R.

1985-01-01

Microprocessor technology has permitted the development of a General Earthquake-Observation System (GEOS) useful for most seismic applications. Central-processing-unit control via robust software of system functions that are isolated on hardware modules permits field adaptability of the system to a wide variety of active and passive seismic experiments and straightforward modification for incorporation of improvements in technology. Various laboratory tests and numerous deployments of a set of the systems in the field have confirmed design goals, including: wide linear dynamic range (16 bit/96 dB); broad bandwidth (36 hr to 600 Hz; greater than 36 hr available); selectable sensor-type (accelerometer, seismometer, dilatometer); selectable channels (1 to 6); selectable record mode (continuous, preset, trigger); large data capacity (1. 4 to 60 Mbytes); selectable time standard (WWVB, master, manual); automatic self-calibration; simple field operation; full capability to adapt system in the field to a wide variety of experiments; low power; portability; and modest costs. System design goals for a microcomputer-controlled system with modular software and hardware components as implemented on the GEOS are presented. The systems have been deployed for 15 experiments, including: studies of near-source strong motion; high-frequency microearthquakes; crustal structure; down-hole wave propagation; teleseismicity; and earth-tidal strains.

Field calibration of polyurethane foam (PUF) disk passive air samplers for PCBs and OC pesticides.

PubMed

Chaemfa, Chakra; Barber, Jonathan L; Gocht, Tilman; Harner, Tom; Holoubek, Ivan; Klanova, Jana; Jones, Kevin C

2008-12-01

Different passive air sampler (PAS) strategies have been developed for sampling in remote areas and for cost-effective simultaneous spatial mapping of POPs (persistent organic pollutants) over differing geographical scales. The polyurethane foam (PUF) disk-based PAS is probably the most widely used. In a PUF-based PAS, the PUF disk is generally mounted inside two stainless steel bowls to buffer the air flow to the disk and to shield it from precipitation and light. The field study described in this manuscript was conducted to: compare performance of 3 different designs of sampler; to further calibrate the sampler against the conventional active sampler; to derive more information on field-based uptake rates and equilibrium times of the samplers. Samplers were also deployed at different locations across the field site, and at different heights up a meteorological tower, to investigate the possible influence of sampler location. Samplers deployed <5m above ground, and not directly sheltered from the wind gave similar uptake rates. Small differences in dimensions between the 3 designs of passive sampler chamber had no discernable effect on accumulation rates, allowing comparison with previously published data.

Relative Localization in Wireless Sensor Networks for Measurement of Electric Fields under HVDC Transmission Lines

PubMed Central

Cui, Yong; Wang, Qiusheng; Yuan, Haiwen; Song, Xiao; Hu, Xuemin; Zhao, Luxing

2015-01-01

In the wireless sensor networks (WSNs) for electric field measurement system under the High-Voltage Direct Current (HVDC) transmission lines, it is necessary to obtain the electric field distribution with multiple sensors. The location information of each sensor is essential to the correct analysis of measurement results. Compared with the existing approach which gathers the location information by manually labelling sensors during deployment, the automatic localization can reduce the workload and improve the measurement efficiency. A novel and practical range-free localization algorithm for the localization of one-dimensional linear topology wireless networks in the electric field measurement system is presented. The algorithm utilizes unknown nodes' neighbor lists based on the Received Signal Strength Indicator (RSSI) values to determine the relative locations of nodes. The algorithm is able to handle the exceptional situation of the output permutation which can effectively improve the accuracy of localization. The performance of this algorithm under real circumstances has been evaluated through several experiments with different numbers of nodes and different node deployments in the China State Grid HVDC test base. Results show that the proposed algorithm achieves an accuracy of over 96% under different conditions. PMID:25658390

Relative localization in wireless sensor networks for measurement of electric fields under HVDC transmission lines.

PubMed

Cui, Yong; Wang, Qiusheng; Yuan, Haiwen; Song, Xiao; Hu, Xuemin; Zhao, Luxing

2015-02-04

In the wireless sensor networks (WSNs) for electric field measurement system under the High-Voltage Direct Current (HVDC) transmission lines, it is necessary to obtain the electric field distribution with multiple sensors. The location information of each sensor is essential to the correct analysis of measurement results. Compared with the existing approach which gathers the location information by manually labelling sensors during deployment, the automatic localization can reduce the workload and improve the measurement efficiency. A novel and practical range-free localization algorithm for the localization of one-dimensional linear topology wireless networks in the electric field measurement system is presented. The algorithm utilizes unknown nodes' neighbor lists based on the Received Signal Strength Indicator (RSSI) values to determine the relative locations of nodes. The algorithm is able to handle the exceptional situation of the output permutation which can effectively improve the accuracy of localization. The performance of this algorithm under real circumstances has been evaluated through several experiments with different numbers of nodes and different node deployments in the China State Grid HVDC test base. Results show that the proposed algorithm achieves an accuracy of over 96% under different conditions.

Feasibility Study of Implementing a Mobile Collaborative Information Platform for International Safeguards Inspections

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

Gastelum, Zoe N.; Gitau, Ernest T. N.; Doehle, Joel R.

2014-09-01

In response to the growing pervasiveness of mobile technologies such as tablets and smartphones, the International Atomic Energy Agency and the U.S. Department of Energy National Laboratories have been exploring the potential use of these platforms for international safeguards activities. Specifically of interest are information systems (software, and accompanying servers and architecture) deployed on mobile devices to increase the situational awareness and productivity of an IAEA safeguards inspector in the field, while simultaneously reducing paperwork and pack weight of safeguards equipment. Exploratory development in this area has been met with skepticism regarding the ability to overcome technology deployment challenges formore » IAEA safeguards equipment. This report documents research conducted to identify potential challenges for the deployment of a mobile collaborative information system to the IAEA, and proposes strategies to mitigate those challenges.« less

Localization Framework for Real-Time UAV Autonomous Landing: An On-Ground Deployed Visual Approach

PubMed Central

Kong, Weiwei; Hu, Tianjiang; Zhang, Daibing; Shen, Lincheng; Zhang, Jianwei

2017-01-01

One of the greatest challenges for fixed-wing unmanned aircraft vehicles (UAVs) is safe landing. Hereafter, an on-ground deployed visual approach is developed in this paper. This approach is definitely suitable for landing within the global navigation satellite system (GNSS)-denied environments. As for applications, the deployed guidance system makes full use of the ground computing resource and feedbacks the aircraft’s real-time localization to its on-board autopilot. Under such circumstances, a separate long baseline stereo architecture is proposed to possess an extendable baseline and wide-angle field of view (FOV) against the traditional fixed baseline schemes. Furthermore, accuracy evaluation of the new type of architecture is conducted by theoretical modeling and computational analysis. Dataset-driven experimental results demonstrate the feasibility and effectiveness of the developed approach. PMID:28629189

Localization Framework for Real-Time UAV Autonomous Landing: An On-Ground Deployed Visual Approach.

PubMed

Kong, Weiwei; Hu, Tianjiang; Zhang, Daibing; Shen, Lincheng; Zhang, Jianwei

2017-06-19

[-5]One of the greatest challenges for fixed-wing unmanned aircraft vehicles (UAVs) is safe landing. Hereafter, an on-ground deployed visual approach is developed in this paper. This approach is definitely suitable for landing within the global navigation satellite system (GNSS)-denied environments. As for applications, the deployed guidance system makes full use of the ground computing resource and feedbacks the aircraft's real-time localization to its on-board autopilot. Under such circumstances, a separate long baseline stereo architecture is proposed to possess an extendable baseline and wide-angle field of view (FOV) against the traditional fixed baseline schemes. Furthermore, accuracy evaluation of the new type of architecture is conducted by theoretical modeling and computational analysis. Dataset-driven experimental results demonstrate the feasibility and effectiveness of the developed approach.

Application of travel time information for traffic management.

DOT National Transportation Integrated Search

2012-03-01

This report summarizes findings and implementations of probe vehicle data collection based on Bluetooth MAC address matching : technology. Probe vehicle travel time data are studied in the following field deployment case studies: analysis of traffic ...

Parachute Testing for Mars Science Laboratory

NASA Image and Video Library

2007-12-20

The team developing the landing system for NASA Mars Science Laboratory tested the deployment of an early parachute design in mid-October 2007 inside the world largest wind tunnel, at NASA Ames Research Center, Moffett Field, California.

Transcardiac conducted electrical weapon (TASER) probe deployments: incidence and outcomes.

PubMed

Bozeman, William P; Teacher, Eric; Winslow, James E

2012-12-01

TASER (TASER International, Scottsdale, AZ) conducted electrical weapons (CEWs) are commonly used by law enforcement officers. Although animal studies have suggested that transcardiac CEW discharges may produce direct cardiac effects, this has not been demonstrated in human studies. This study sought to determine the incidence and outcomes of transcardiac CEW probe impact locations in a large series of actual CEW deployments. A multi-center database of consecutive CEW uses by law enforcement officers was retrospectively reviewed. Case report forms were independently reviewed by three investigators to identify cases with paired probe configurations potentially producing a transcardiac discharge vector. Descriptive analysis was performed and inter-rater reliability was assessed. Among 1201 total CEW uses, 813 included probe deployments and 178 cases had paired anterior probe impacts potentially capable of producing a transcardiac discharge vector. This represents 14.8% of all CEW uses (95% confidence interval [CI] 12.9-16.9%) and 21.9% of CEW uses in probe mode (95% CI 19.1-24.9%). Inter-rater agreement was very good, with kappa = 0.82. There were no immediate deaths in any cases (97.5% CI 0.0-0.3%) to suggest a cardiac dysrhythmia, including those with transcardiac discharge vector. CEW deployments with probe impact configurations capable of producing a transcardiac discharge occur in a minority of cases in field use conditions. None of these cases, transcardiac or otherwise, produced immediately fatal dysrhythmias. These data support the overall safety of CEWs and provide a benchmark estimate of the likelihood of transcardiac discharge vectors occurring in field use of CEWs. Copyright © 2012 Elsevier Inc. All rights reserved.

Deployment of field hospitals to disaster regions: Insights from ten medical relief operations spanning three decades.

PubMed

Naor, Michael; Heyman, Samuel N; Bader, Tarif; Merin, Ofer

2017-01-01

The Israeli Defense Force (IDF) Medical Corps developed a model of airborne field hospital. This model was structured to deal with disaster settings, requiring self-sufficiency, innovation and flexible operative mode in the setup of large margins of uncertainty regarding the disaster environment. The current study is aimed to critically analyze the experience, gathered in ten such missions worldwide. Interviews with physicians who actively participated in the missions from 1988 until 2015 as chief medical officers combined with literature review of principal medical and auxiliary publications in order to assess and integrate information about the assembly of these missions. A body of knowledge was accumulated over the years by the IDF Medical Corps from deploying numerous relief missions to both natural (earthquake, typhoon, and tsunami), and man-made disasters, occurring in nine countries (Armenia, Rwanda, Kosovo, Turkey, India, Haiti, Japan, Philippines, and Nepal). This study shows an evolutionary pattern with improvements implemented from one mission to the other, with special adaptations (creativity and improvisation) to accommodate logistics barriers. The principals and operative function for deploying medical relief system, proposed over 20 years ago, were challenged and validated in the subsequent missions of IDF outlined in the current study. These principals, with the advantage of the military infrastructure and the expertise of drafted civilian medical professionals enable the rapid assembly and allocation of highly competent medical facilities in disaster settings. This structure model is to large extent self-sufficient with a substantial operative flexibility that permits early deployment upon request while the disaster assessment and definition of needs are preliminary.

Development and Calibration of a Field-Deployable Microphone Phased Array for Propulsion and Airframe Noise Flyover Measurements

NASA Technical Reports Server (NTRS)

Humphreys, William M., Jr.; Lockard, David P.; Khorrami, Mehdi R.; Culliton, William G.; McSwain, Robert G.; Ravetta, Patricio A.; Johns, Zachary

2016-01-01

A new aeroacoustic measurement capability has been developed consisting of a large channelcount, field-deployable microphone phased array suitable for airframe noise flyover measurements for a range of aircraft types and scales. The array incorporates up to 185 hardened, weather-resistant sensors suitable for outdoor use. A custom 4-mA current loop receiver circuit with temperature compensation was developed to power the sensors over extended cable lengths with minimal degradation of the signal to noise ratio and frequency response. Extensive laboratory calibrations and environmental testing of the sensors were conducted to verify the design's performance specifications. A compact data system combining sensor power, signal conditioning, and digitization was assembled for use with the array. Complementing the data system is a robust analysis system capable of near real-time presentation of beamformed and deconvolved contour plots and integrated spectra obtained from array data acquired during flyover passes. Additional instrumentation systems needed to process the array data were also assembled. These include a commercial weather station and a video monitoring / recording system. A detailed mock-up of the instrumentation suite (phased array, weather station, and data processor) was performed in the NASA Langley Acoustic Development Laboratory to vet the system performance. The first deployment of the system occurred at Finnegan Airfield at Fort A.P. Hill where the array was utilized to measure the vehicle noise from a number of sUAS (small Unmanned Aerial System) aircraft. A unique in-situ calibration method for the array microphones using a hovering aerial sound source was attempted for the first time during the deployment.

Wave-Sediment Interaction in Muddy Environments: Subbottom Field Experiment

DTIC Science & Technology

2011-09-30

instrumentation deployed on nearby oil and gas platforms. WORK COMPLETED Field experiment and data analysis : The “Sub-bottom Field Experiment” project...Berkeley, Doctoral thesis, 149p. Chou, H.-T., M.A. Foda , and J.R. Hunt (1993). Rheological response of cohesive sediments to oscillatory forcing”, In...Wave dissipation by muddy seafloors, Geophys. Res. Lett. 35/7, L07611. Foda , A.M., J.R. Hunt, and H.-T. Chou (1993). A nonlinear model for the

Sampling the potential energy surface of a DNA duplex damaged by a food carcinogen: Force field parameterization by ab initio quantum calculations and conformational searching using molecular mechanics computations

NASA Astrophysics Data System (ADS)

Wu, Xiangyang

1999-07-01

The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B-DNA orientations, compromising its ability to act as a faithful template during DNA replication.

A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline.

PubMed

Niemeyer, Bastian; Epp, Laura S; Stoof-Leichsenring, Kathleen R; Pestryakova, Luidmila A; Herzschuh, Ulrike

2017-11-01

Reliable information on past and present vegetation is important to project future changes, especially for rapidly transitioning areas such as the boreal treeline. To study past vegetation, pollen analysis is common, while current vegetation is usually assessed by field surveys. Application of detailed sedimentary DNA (sedDNA) records has the potential to enhance our understanding of vegetation changes, but studies systematically investigating the power of this proxy are rare to date. This study compares sedDNA metabarcoding and pollen records from surface sediments of 31 lakes along a north-south gradient of increasing forest cover in northern Siberia (Taymyr peninsula) with data from field surveys in the surroundings of the lakes. sedDNA metabarcoding recorded 114 plant taxa, about half of them to species level, while pollen analyses identified 43 taxa, both exceeding the 31 taxa found by vegetation field surveys. Increasing Larix percentages from north to south were consistently recorded by all three methods and principal component analyses based on percentage data of vegetation surveys and DNA sequences separated tundra from forested sites. Comparisons of the ordinations using procrustes and protest analyses show a significant fit among all compared pairs of records. Despite similarities of sedDNA and pollen records, certain idiosyncrasies, such as high percentages of Alnus and Betula in all pollen and high percentages of Salix in all sedDNA spectra, are observable. Our results from the tundra to single-tree tundra transition zone show that sedDNA analyses perform better than pollen in recording site-specific richness (i.e., presence/absence of taxa in the vicinity of the lake) and perform as well as pollen in tracing vegetation composition. © 2017 John Wiley & Sons Ltd.

Automatic Detection of Previously-Unseen Application States for Deployment Environment Testing and Analysis

PubMed Central

Murphy, Christian; Vaughan, Moses; Ilahi, Waseem; Kaiser, Gail

2010-01-01

For large, complex software systems, it is typically impossible in terms of time and cost to reliably test the application in all possible execution states and configurations before releasing it into production. One proposed way of addressing this problem has been to continue testing and analysis of the application in the field, after it has been deployed. A practical limitation of many such automated approaches is the potentially high performance overhead incurred by the necessary instrumentation. However, it may be possible to reduce this overhead by selecting test cases and performing analysis only in previously-unseen application states, thus reducing the number of redundant tests and analyses that are run. Solutions for fault detection, model checking, security testing, and fault localization in deployed software may all benefit from a technique that ignores application states that have already been tested or explored. In this paper, we present a solution that ensures that deployment environment tests are only executed in states that the application has not previously encountered. In addition to discussing our implementation, we present the results of an empirical study that demonstrates its effectiveness, and explain how the new approach can be generalized to assist other automated testing and analysis techniques intended for the deployment environment. PMID:21197140

Calibration procedure for Slocum glider deployed optical instruments.

PubMed

Cetinić, Ivona; Toro-Farmer, Gerardo; Ragan, Matthew; Oberg, Carl; Jones, Burton H

2009-08-31

Recent developments in the field of the autonomous underwater vehicles allow the wide usage of these platforms as part of scientific experiments, monitoring campaigns and more. The vehicles are often equipped with sensors measuring temperature, conductivity, chlorophyll a fluorescence (Chl a), colored dissolved organic matter (CDOM) fluorescence, phycoerithrin (PE) fluorescence and spectral volume scattering function at 117 degrees, providing users with high resolution, real time data. However, calibration of these instruments can be problematic. Most in situ calibrations are performed by deploying complementary instrument packages or water samplers in the proximity of the glider. Laboratory calibrations of the mounted sensors are difficult due to the placement of the instruments within the body of the vehicle. For the laboratory calibrations of the Slocum glider instruments we developed a small calibration chamber where we can perform precise calibrations of the optical instruments aboard our glider, as well as sensors from other deployment platforms. These procedures enable us to obtain pre- and post-deployment calibrations for optical fluorescence instruments, which may differ due to the biofouling and other physical damage that can occur during long-term glider deployments. We found that biofouling caused significant changes in the calibration scaling factors of fluorescent sensors, suggesting the need for consistent and repetitive calibrations for gliders as proposed in this paper.

Field testing of Schistosoma japonicum DNA vaccines in cattle in China.

PubMed

Shi, Fuhui; Zhang, Yaobi; Lin, Jiaojiao; Zuo, Xin; Shen, Wei; Cai, Yiumin; Ye, Ping; Bickle, Quentin D; Taylor, Martin G

2002-11-01

Vaccines are needed to reduce the zoonotic reservoir of Schistosoma japonicum infection in bovines in China. We have developed two experimental DNA vaccines and have already shown these to be capable of inducing partial protection in water buffalo naturally exposed to the risk of S. japonicum infection in the field. We now report a similar field trial in cattle, the other major bovine reservoir host species in China. Groups of cattle were vaccinated with the VRSj28 vaccine or the VRSj23 vaccine, or, to test whether protection could be enhanced by combination vaccination, with both these DNA vaccines together. After vaccination, the cattle were exposed to natural infection in the field for a period of 54 days. Worm and egg counts carried out at the end of the experiment showed that each of the vaccine groups showed partial resistance, and that combined vaccination was not more effective than vaccination with the individual plasmids.

Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters.

PubMed

Jasiński, Maciej; Feig, Michael; Trylska, Joanna

2018-06-06

Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.

Coupling Spore Traps and Quantitative PCR Assays for Detection of the Downy Mildew Pathogens of Spinach (Peronospora effusa) and Beet (P. schachtii)

PubMed Central

Klosterman, Steven J.; Anchieta, Amy; McRoberts, Neil; Koike, Steven T.; Subbarao, Krishna V.; Voglmayr, Hermann; Choi, Young-Joon; Thines, Marco; Martin, Frank N.

2016-01-01

Downy mildew of spinach (Spinacia oleracea), caused by Peronospora effusa, is a production constraint on production worldwide, including in California, where the majority of U.S. spinach is grown. The aim of this study was to develop a real-time quantitative polymerase chain reaction (qPCR) assay for detection of airborne inoculum of P. effusa in California. Among oomycete ribosomal DNA (rDNA) sequences examined for assay development, the highest nucleotide sequence identity was observed between rDNA sequences of P. effusa and P. schachtii, the cause of downy mildew on sugar beet and Swiss chard in the leaf beet group (Beta vulgaris subsp. vulgaris). Single-nucleotide polymorphisms were detected between P. effusa and P. schachtii in the 18S rDNA regions for design of P. effusa- and P. schachtii-specific TaqMan probes and reverse primers. An allele-specific probe and primer amplification method was applied to determine the frequency of both P. effusa and P. schachtii rDNA target sequences in pooled DNA samples, enabling quantification of rDNA of P. effusa from impaction spore trap samples collected from spinach production fields. The rDNA copy numbers of P. effusa were, on average, ≈3,300-fold higher from trap samples collected near an infected field compared with those levels recorded at a site without a nearby spinach field. In combination with disease-conducive weather forecasting, application of the assays may be helpful to time fungicide applications for disease management. PMID:24964150

Time Series Analysis for Spatial Node Selection in Environment Monitoring Sensor Networks

PubMed Central

Bhandari, Siddhartha; Jurdak, Raja; Kusy, Branislav

2017-01-01

Wireless sensor networks are widely used in environmental monitoring. The number of sensor nodes to be deployed will vary depending on the desired spatio-temporal resolution. Selecting an optimal number, position and sampling rate for an array of sensor nodes in environmental monitoring is a challenging question. Most of the current solutions are either theoretical or simulation-based where the problems are tackled using random field theory, computational geometry or computer simulations, limiting their specificity to a given sensor deployment. Using an empirical dataset from a mine rehabilitation monitoring sensor network, this work proposes a data-driven approach where co-integrated time series analysis is used to select the number of sensors from a short-term deployment of a larger set of potential node positions. Analyses conducted on temperature time series show 75% of sensors are co-integrated. Using only 25% of the original nodes can generate a complete dataset within a 0.5 °C average error bound. Our data-driven approach to sensor position selection is applicable for spatiotemporal monitoring of spatially correlated environmental parameters to minimize deployment cost without compromising data resolution. PMID:29271880

Artificially designed pathogens - a diagnostic option for future military deployments.

PubMed

Zautner, Andreas E; Masanta, Wycliffe O; Hinz, Rebecca; Hagen, Ralf Matthias; Frickmann, Hagen

2015-01-01

Diagnostic microbial isolates of bio-safety levels 3 and 4 are difficult to handle in medical field camps under military deployment settings. International transport of such isolates is challenging due to restrictions by the International Air Transport Association. An alternative option might be inactivation and sequencing of the pathogen at the deployment site with subsequent sequence-based revitalization in well-equipped laboratories in the home country for further scientific assessment. A literature review was written based on a PubMed search. First described for poliovirus in 2002, de novo synthesis of pathogens based on their sequence information has become a well-established procedure in science. Successful syntheses have been demonstrated for both viruses and prokaryotes. However, the technology is not yet available for routine diagnostic purposes. Due to the potential utility of diagnostic sequencing and sequence-based de novo synthesis of pathogens, it seems worthwhile to establish the technology for diagnostic purposes over the intermediate term. This is particularly true for resource-restricted deployment settings, where safe handling of harmful pathogens cannot always be guaranteed.

Surveillance of a 2D Plane Area with 3D Deployed Cameras

PubMed Central

Fu, Yi-Ge; Zhou, Jie; Deng, Lei

2014-01-01

As the use of camera networks has expanded, camera placement to satisfy some quality assurance parameters (such as a good coverage ratio, an acceptable resolution constraints, an acceptable cost as low as possible, etc.) has become an important problem. The discrete camera deployment problem is NP-hard and many heuristic methods have been proposed to solve it, most of which make very simple assumptions. In this paper, we propose a probability inspired binary Particle Swarm Optimization (PI-BPSO) algorithm to solve a homogeneous camera network placement problem. We model the problem under some more realistic assumptions: (1) deploy the cameras in the 3D space while the surveillance area is restricted to a 2D ground plane; (2) deploy the minimal number of cameras to get a maximum visual coverage under more constraints, such as field of view (FOV) of the cameras and the minimum resolution constraints. We can simultaneously optimize the number and the configuration of the cameras through the introduction of a regulation item in the cost function. The simulation results showed the effectiveness of the proposed PI-BPSO algorithm. PMID:24469353

DNA-based construction at the nanoscale: emerging trends and applications

NASA Astrophysics Data System (ADS)

Lourdu Xavier, P.; Chandrasekaran, Arun Richard

2018-02-01

The field of structural DNA nanotechnology has evolved remarkably—from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes—in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.

Ancient genomics

PubMed Central

Der Sarkissian, Clio; Allentoft, Morten E.; Ávila-Arcos, María C.; Barnett, Ross; Campos, Paula F.; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J.; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D.; Moreno-Mayar, J. Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M. Thomas P.; Willerslev, Eske; Orlando, Ludovic

2015-01-01

The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. PMID:25487338

DNA-based construction at the nanoscale: emerging trends and applications.

PubMed

Xavier, P Lourdu; Chandrasekaran, Arun Richard

2018-02-09

The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.

DNA barcoding of the vegetable leafminer Liriomyza sativae Blanchard (Diptera: Agromyzidae) in Bangladesh

USDA-ARS?s Scientific Manuscript database

DNA barcoding revealed the presence of the polyphagous leafminer pest Liriomyza sativae Blanchard in Bangladesh. DNA barcode sequences for mitochondrial COI were generated for Agromyzidae larvae, pupae and adults collected from field populations across Bangladesh. BLAST sequence similarity searches ...

Imaging and sizing of single DNA molecules on a mobile phone.

PubMed

Wei, Qingshan; Luo, Wei; Chiang, Samuel; Kappel, Tara; Mejia, Crystal; Tseng, Derek; Chan, Raymond Yan Lok; Yan, Eddie; Qi, Hangfei; Shabbir, Faizan; Ozkan, Haydar; Feng, Steve; Ozcan, Aydogan

2014-12-23

DNA imaging techniques using optical microscopy have found numerous applications in biology, chemistry and physics and are based on relatively expensive, bulky and complicated set-ups that limit their use to advanced laboratory settings. Here we demonstrate imaging and length quantification of single molecule DNA strands using a compact, lightweight and cost-effective fluorescence microscope installed on a mobile phone. In addition to an optomechanical attachment that creates a high contrast dark-field imaging setup using an external lens, thin-film interference filters, a miniature dovetail stage and a laser-diode for oblique-angle excitation, we also created a computational framework and a mobile phone application connected to a server back-end for measurement of the lengths of individual DNA molecules that are labeled and stretched using disposable chips. Using this mobile phone platform, we imaged single DNA molecules of various lengths to demonstrate a sizing accuracy of <1 kilobase-pairs (kbp) for 10 kbp and longer DNA samples imaged over a field-of-view of ∼2 mm2.

Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer

PubMed Central

Bennett, Catherine W.; Berchem, Guy; Kim, Yeoun Jin; El-Khoury, Victoria

2016-01-01

Personalized medicine has emerged as the future of cancer care to ensure that patients receive individualized treatment specific to their needs. In order to provide such care, molecular techniques that enable oncologists to diagnose, treat, and monitor tumors are necessary. In the field of lung cancer, cell free DNA (cfDNA) shows great potential as a less invasive liquid biopsy technique, and next-generation sequencing (NGS) is a promising tool for analysis of tumor mutations. In this review, we outline the evolution of cfDNA and NGS and discuss the progress of using them in a clinical setting for patients with lung cancer. We also present an analysis of the role of cfDNA as a liquid biopsy technique and NGS as an analytical tool in studying EGFR and MET, two frequently mutated genes in lung cancer. Ultimately, we hope that using cfDNA and NGS for cancer diagnosis and treatment will become standard for patients with lung cancer and across the field of oncology. PMID:27589834

Moessbauer/XRF MIMOS Instrumentation and Operation During the 2012 Analog Field Test on Mauna Kea Volcano, Hawaii

NASA Technical Reports Server (NTRS)

Graff, Trevor G.; Morris, R. V.; Klingelhofer, G.; Blumers, M.

2013-01-01

Field testing and scientific investigations were conducted on the Mauna Kea Volcano, Hawaii, as part of the 2012 Moon and Mars Analog Mission Activities (MMAMA). Measurements were conducted using both stand-alone and rover-mounted instruments to determine the geophysical and geochemical properties of the field site, as well as provide operational constraints and science considerations for future robotic and human missions [1]. Reported here are the results from the two MIMOS instruments deployed as part of this planetary analog field test.

EarthScope's Transportable Array: Status of the Alaska Deployment and Guide to Resources for Lower48 Deployment

NASA Astrophysics Data System (ADS)

Busby, R. W.; Woodward, R.; Aderhold, K.; Frassetto, A.

2017-12-01

The Alaska Transportable Array deployment is completely installed, totaling 280 stations, with 194 new stations and 86 existing stations, 28 of those upgraded with new sensor emplacement. We briefly summarize the deployment of this seismic network, describe the added meteorological instruments and soil temperature gauges, and review our expectations for operation and demobilization. Curation of data from the contiguous Lower-48 States deployment of Transportable Array (>1800 stations, 2004-2015) has continued with the few gaps in real-time data replaced by locally archived files as well as minor adjustments in metadata. We highlight station digests that provide more detail on the components and settings of individual stations, documentation of standard procedures used throughout the deployment and other resources available online. In cooperation with IRIS DMC, a copy of the complete TA archive for the Lower-48 period has been transferred to a local disk to experiment with data access and software workflows that utilize most or all of the seismic timeseries, in contrast to event segments. Assembling such large datasets reliably - from field stations to a well managed data archive to a user's workspace - is complex. Sharing a curated and defined data volume with researchers is a potentially straightforward way to make data intensive analyses less difficult. We note that data collection within the Lower-48 continues with 160 stations of the N4 network operating at increased sample rates (100 sps) as part of the CEUSN, as operational support transitions from NSF to USGS.

Multi-Gene Detection and Identification of Mosquito-Borne RNA Viruses Using an Oligonucleotide Microarray

PubMed Central

Grubaugh, Nathan D.; McMenamy, Scott S.; Turell, Michael J.; Lee, John S.

2013-01-01

Background Arthropod-borne viruses are important emerging pathogens world-wide. Viruses transmitted by mosquitoes, such as dengue, yellow fever, and Japanese encephalitis viruses, infect hundreds of millions of people and animals each year. Global surveillance of these viruses in mosquito vectors using molecular based assays is critical for prevention and control of the associated diseases. Here, we report an oligonucleotide DNA microarray design, termed ArboChip5.1, for multi-gene detection and identification of mosquito-borne RNA viruses from the genera Flavivirus (family Flaviviridae), Alphavirus (Togaviridae), Orthobunyavirus (Bunyaviridae), and Phlebovirus (Bunyaviridae). Methodology/Principal Findings The assay utilizes targeted PCR amplification of three genes from each virus genus for electrochemical detection on a portable, field-tested microarray platform. Fifty-two viruses propagated in cell-culture were used to evaluate the specificity of the PCR primer sets and the ArboChip5.1 microarray capture probes. The microarray detected all of the tested viruses and differentiated between many closely related viruses such as members of the dengue, Japanese encephalitis, and Semliki Forest virus clades. Laboratory infected mosquitoes were used to simulate field samples and to determine the limits of detection. Additionally, we identified dengue virus type 3, Japanese encephalitis virus, Tembusu virus, Culex flavivirus, and a Quang Binh-like virus from mosquitoes collected in Thailand in 2011 and 2012. Conclusions/Significance We demonstrated that the described assay can be utilized in a comprehensive field surveillance program by the broad-range amplification and specific identification of arboviruses from infected mosquitoes. Furthermore, the microarray platform can be deployed in the field and viral RNA extraction to data analysis can occur in as little as 12 h. The information derived from the ArboChip5.1 microarray can help to establish public health priorities, detect disease outbreaks, and evaluate control programs. PMID:23967358

Identification of Rays through DNA Barcoding: An Application for Ecologists

PubMed Central

Cerutti-Pereyra, Florencia; Meekan, Mark G.; Wei, Nu-Wei V.; O'Shea, Owen; Bradshaw, Corey J. A.; Austin, Chris M.

2012-01-01

DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the ‘uarnak’ complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data. PMID:22701556

DNA-DNA interaction beyond the ground state

NASA Astrophysics Data System (ADS)

Lee, D. J.; Wynveen, A.; Kornyshev, A. A.

2004-11-01

The electrostatic interaction potential between DNA duplexes in solution is a basis for the statistical mechanics of columnar DNA assemblies. It may also play an important role in recombination of homologous genes. We develop a theory of this interaction that includes thermal torsional fluctuations of DNA using field-theoretical methods and Monte Carlo simulations. The theory extends and rationalizes the earlier suggested variational approach which was developed in the context of a ground state theory of interaction of nonhomologous duplexes. It shows that the heuristic variational theory is equivalent to the Hartree self-consistent field approximation. By comparison of the Hartree approximation with an exact solution based on the QM analogy of path integrals, as well as Monte Carlo simulations, we show that this easily analytically-tractable approximation works very well in most cases. Thermal fluctuations do not remove the ability of DNA molecules to attract each other at favorable azimuthal conformations, neither do they wash out the possibility of electrostatic “snap-shot” recognition of homologous sequences, considered earlier on the basis of ground state calculations. At short distances DNA molecules undergo a “torsional alignment transition,” which is first order for nonhomologous DNA and weaker order for homologous sequences.

Environmental DNA (eDNA): A tool for quantifying the abundant but elusive round goby (Neogobius melanostomus)

USGS Publications Warehouse

Nevers, Meredith; Byappanahalli, Muruleedhara; Morris, Charles C.; Shively, Dawn; Przybyla-Kelly, Katarzyna; Spoljaric, Ashley M.; Dickey, Joshua; Roseman, Edward

2018-01-01

Environmental DNA (eDNA) is revolutionizing biodiversity monitoring, occupancy estimates, and real-time detections of invasive species. In the Great Lakes, the round goby (Neogobius melanostomus), an invasive benthic fish from the Black Sea, has spread to encompass all five lakes and many tributaries, outcompeting or consuming native species; however, estimates of round goby abundance are confounded by behavior and habitat preference, which impact reliable methods for estimating their population. By integrating eDNA into round goby monitoring, improved estimates of biomass may be obtainable. We conducted mesocosm experiments to estimate rates of goby DNA shedding and decay. Further, we compared eDNA with several methods of traditional field sampling to compare its use as an alternative/complementary monitoring method. Environmental DNA decay was comparable to other fish species, and first-order decay was lower at 12°C (k = 0.043) than at 19°C (k = 0.058). Round goby eDNA was routinely detected in known invaded sites of Lake Michigan and its tributaries (range log10 4.8–6.2 CN/L), but not upstream of an artificial fish barrier. Traditional techniques (mark-recapture, seining, trapping) in Lakes Michigan and Huron resulted in fewer, more variable detections than eDNA, but trapping and eDNA were correlated (Pearson R = 0.87). Additional field testing will help correlate round goby abundance with eDNA, providing insight on its role as a prey fish and its impact on food webs.

Environmental DNA (eDNA): A tool for quantifying the abundant but elusive round goby (Neogobius melanostomus)

PubMed Central

Byappanahalli, Murulee N.; Morris, Charles C.; Shively, Dawn; Przybyla-Kelly, Kasia; Spoljaric, Ashley M.; Dickey, Joshua; Roseman, Edward F.

2018-01-01

Environmental DNA (eDNA) is revolutionizing biodiversity monitoring, occupancy estimates, and real-time detections of invasive species. In the Great Lakes, the round goby (Neogobius melanostomus), an invasive benthic fish from the Black Sea, has spread to encompass all five lakes and many tributaries, outcompeting or consuming native species; however, estimates of round goby abundance are confounded by behavior and habitat preference, which impact reliable methods for estimating their population. By integrating eDNA into round goby monitoring, improved estimates of biomass may be obtainable. We conducted mesocosm experiments to estimate rates of goby DNA shedding and decay. Further, we compared eDNA with several methods of traditional field sampling to compare its use as an alternative/complementary monitoring method. Environmental DNA decay was comparable to other fish species, and first-order decay was lower at 12°C (k = 0.043) than at 19°C (k = 0.058). Round goby eDNA was routinely detected in known invaded sites of Lake Michigan and its tributaries (range log10 4.8–6.2 CN/L), but not upstream of an artificial fish barrier. Traditional techniques (mark-recapture, seining, trapping) in Lakes Michigan and Huron resulted in fewer, more variable detections than eDNA, but trapping and eDNA were correlated (Pearson R = 0.87). Additional field testing will help correlate round goby abundance with eDNA, providing insight on its role as a prey fish and its impact on food webs. PMID:29357382

Environmental DNA (eDNA): A tool for quantifying the abundant but elusive round goby (Neogobius melanostomus).

PubMed

Nevers, Meredith B; Byappanahalli, Murulee N; Morris, Charles C; Shively, Dawn; Przybyla-Kelly, Kasia; Spoljaric, Ashley M; Dickey, Joshua; Roseman, Edward F

2018-01-01

Environmental DNA (eDNA) is revolutionizing biodiversity monitoring, occupancy estimates, and real-time detections of invasive species. In the Great Lakes, the round goby (Neogobius melanostomus), an invasive benthic fish from the Black Sea, has spread to encompass all five lakes and many tributaries, outcompeting or consuming native species; however, estimates of round goby abundance are confounded by behavior and habitat preference, which impact reliable methods for estimating their population. By integrating eDNA into round goby monitoring, improved estimates of biomass may be obtainable. We conducted mesocosm experiments to estimate rates of goby DNA shedding and decay. Further, we compared eDNA with several methods of traditional field sampling to compare its use as an alternative/complementary monitoring method. Environmental DNA decay was comparable to other fish species, and first-order decay was lower at 12°C (k = 0.043) than at 19°C (k = 0.058). Round goby eDNA was routinely detected in known invaded sites of Lake Michigan and its tributaries (range log10 4.8-6.2 CN/L), but not upstream of an artificial fish barrier. Traditional techniques (mark-recapture, seining, trapping) in Lakes Michigan and Huron resulted in fewer, more variable detections than eDNA, but trapping and eDNA were correlated (Pearson R = 0.87). Additional field testing will help correlate round goby abundance with eDNA, providing insight on its role as a prey fish and its impact on food webs.

DNA nanomaterials for preclinical imaging and drug delivery.

PubMed

Jiang, Dawei; England, Christopher G; Cai, Weibo

2016-10-10

Besides being the carrier of genetic information, DNA is also an excellent biological organizer to establish well-designed nanostructures in the fields of material engineering, nanotechnology, and biomedicine. DNA-based materials represent a diverse nanoscale system primarily due to their predictable base pairing and highly regulated conformations, which greatly facilitate the construction of DNA nanostructures with distinct shapes and sizes. Integrating the emerging advancements in bioconjugation techniques, DNA nanostructures can be readily functionalized with high precision for many purposes ranging from biosensors to imaging to drug delivery. Recent progress in the field of DNA nanotechnology has exhibited collective efforts to employ DNA nanostructures as smart imaging agents or delivery platforms within living organisms. Despite significant improvements in the development of DNA nanostructures, there is limited knowledge regarding the in vivo biological fate of these intriguing nanomaterials. In this review, we summarize the current strategies for designing and purifying highly-versatile DNA nanostructures for biological applications, including molecular imaging and drug delivery. Since DNA nanostructures may elicit an immune response in vivo, we also present a short discussion of their potential toxicities in biomedical applications. Lastly, we discuss future perspectives and potential challenges that may limit the effective preclinical and clinical employment of DNA nanostructures. Due to their unique properties, we predict that DNA nanomaterials will make excellent agents for effective diagnostic imaging and drug delivery, improving patient outcome in cancer and other related diseases in the near future. Copyright © 2016 Elsevier B.V. All rights reserved.

Genotypic analysis of strains of mutans streptococci by pulsed-field gel electrophoresis.

PubMed

Mineyama, R; Yoshino, S; Fukushima, K

2004-01-01

The species and serotypes of various strains of S. mutans and S. sobrinus were characterized by pulsed-field gel electrophoresis after the genomic DNA from the various strains had been digested with five restriction enzymes (EcoR I, Xba I, Hind III, Sfi I and BssH II) separately. Among these restriction enzymes, BssH II was very useful for the characterization of species and serotypes and, in particular, digestion discriminated between serotypes d and g. The restriction patterns obtained from the genomic DNA of isolates isolated from children's saliva were essentially identical to those from the genomic DNA of the standard laboratory strains. Patterns of BssH II digests of the genomic DNA of 10 isolates identified as S. sobrinus were characteristic of serotype g of the standard laboratory strains. Our results indicate that digestion with BssH II and subsequence analysis by pulsed-field gel electrophoresis should be useful for the characterization of species and serotypes and for epidemiological studies of mutans streptococci.

Design and end-to-end modelling of a deployable telescope

NASA Astrophysics Data System (ADS)

Dolkens, Dennis; Kuiper, Hans

2017-09-01

Deployable optics have the potential of revolutionizing the field of high resolution Earth Observation. By offering the same resolutions as a conventional telescope, while using a much smaller launch volume and mass, the costs of high resolution image data can be brought down drastically. In addition, the technology will ultimately enable resolutions that are currently unattainable due to limitations imposed by the size of launcher fairings. To explore the possibilities and system complexities of a deployable telescope, a concept study was done to design a competitive deployable imager. A deployable telescope was designed for a ground sampling distance of 25 cm from an orbital altitude of 550 km. It offers an angular field of view of 0.6° and has a panchromatic channel as well as four multispectral bands in the visible and near infrared spectrum. The optical design of the telescope is based on an off-axis Korsch Three Mirror Anastigmat. A freeform tertiary mirror is used to ensure a diffraction limited image quality for all channels, while maintaining a compact design. The segmented primary mirror consists of four tapered aperture segments, which can be folded down during launch, while the secondary mirror is mounted on a deployable boom. In its stowed configuration, the telescope fits within a quarter of the volume of a conventional telescope reaching the same resolution. To reach a diffraction limited performance while operating in orbit, the relative position of each individual mirror segment must be controlled to a fraction of a wavelength. Reaching such tolerances with deployable telescope challenging, due to inherent uncertainties in the deployment mechanisms. Adding to the complexity is the fact that the telescope will be operating in a Low Earth Orbit (LEO) where it will be exposed to very dynamic thermal conditions. Therefore, the telescope will be equipped with a robust calibration system. Actuators underneath the primary mirror will be controlled using a closed-loop system based on measurements of the image sharpness as well as measurements obtained with edge sensors placed between the mirror segments. In addition, a phase diversity system will be used to recover residual wavefront aberrations. To aid the design of the deployable telescope, an end-to-end performance model was developed. The model is built around a dedicated ray-trace program written in Matlab. This program was built from the ground up for the purpose of modelling segmented telescope systems and allows for surface data computed with Finite Element Models (FEM) to be imported in the model. The program also contains modules which can simulate the closed-loop calibration of the telescope and it can use simulated images as an input for phase diversity and image processing algorithms. For a given thermo-mechanical state, the end-to-end model can predict the image quality that will be obtained after the calibration has been completed and the image has been processed. As such, the model is a powerful systems engineering tool, which can be used to optimize the in-orbit performance of a segmented, deployable telescope.

Study of a chimeric foot-and-mouth disease virus DNA vaccine containing structural genes of serotype O in a genome backbone of serotype Asia 1 in guinea pigs.

PubMed

Chockalingam, A K; Thiyagarajan, S; Govindasamy, N; Patnaikuni, R; Garlapati, S; Golla, R R; Joyappa, D H; Krishnamshetty, P; Veluvarti, V V S; Veluvati, V V S

2010-01-01

Since foot-and-mouth disease virus (FMDV) serotypes display a great genetic and antigenic diversity, there is a constant requirement to monitor the performance of FMDV vaccines in the field with respect to their antigenic coverage. To avoid possible antigenic changes in field FMDV isolates during their adaptation to BHK-21 cells, a standard step used in production of conventional FMDV vaccines, the custom-made chimeric conventional or DNA vaccines, in which antigenic determinants are replaced with those of appropriate field strains, should be constructed. Using this approach, we made a plasmid-based chimeric FMDV DNA vaccine containing structural genes of serotype O in the genome backbone of serotype Asia 1, all under the control of Human cytomegalovirus (HCMV) immediate early gene promoter. BHK-21 cells transfected with the chimeric DNA vaccine did not show cytopathic effect (CPE), but expressed virus-specific proteins as demonstrated by 35S-methionine labeling and immunoprecipitation. Guinea pigs immunized with the chimeric DNA vaccine produced virus-specific antibodies assayed by ELISA and virus neutralization test (VNT), respectively. The chimeric DNA vaccine showed a partial protection of guinea pigs challenged with the virulent FMDV. Although the chimeric DNA vaccine, in general, was not as effective as a conventional one, this study encourages further work towards the development of genetically engineered custom-made chimeric vaccines against FMDV.

A silicon carbide nanowire field effect transistor for DNA detection

NASA Astrophysics Data System (ADS)

Fradetal, L.; Bano, E.; Attolini, G.; Rossi, F.; Stambouli, V.

2016-06-01

This work reports on the label-free electrical detection of DNA molecules for the first time, using silicon carbide (SiC) as a novel material for the realization of nanowire field effect transistors (NWFETs). SiC is a promising semiconductor for this application due to its specific characteristics such as chemical inertness and biocompatibility. Non-intentionally n-doped SiC NWs are first grown using a bottom-up vapor-liquid-solid (VLS) mechanism, leading to the NWs exhibiting needle-shaped morphology, with a length of approximately 2 μm and a diameter ranging from 25 to 60 nm. Then, the SiC NWFETs are fabricated and functionalized with DNA molecule probes via covalent coupling using an amino-terminated organosilane. The drain current versus drain voltage (I d-V d) characteristics obtained after the DNA grafting and hybridization are reported from the comparative and simultaneous measurements carried out on the SiC NWFETs, used either as sensors or references. As a representative result, the current of the sensor is lowered by 22% after probe DNA grafting and by 7% after target DNA hybridization, while the current of the reference does not vary by more than ±0.6%. The current decrease confirms the field effect induced by the negative charges of the DNA molecules. Moreover, the selectivity, reproducibility, reversibility and stability of the studied devices are emphasized by de-hybridization, non-complementary hybridization and re-hybridization experiments. This first proof of concept opens the way for future developments using SiC-NW-based sensors.

Direct, Operational Field Test Evaluation, Institutional Issues

DOT National Transportation Integrated Search

1998-08-01

INSTITUTIONAL ISSUES HAVE BEEN DEFINED AS NON-TECHNICAL ISSUES OR CONCERNS THAT INFLUENCE THE COURSE AND OUTCOME OF AN OPERATIONAL TEST. OFTEN THEY ARE EVENTS AND/OR CIRCUMSTANCES THAT AFFECT ADMINISTRATION, DESIGN, DEPLOYMENT AND EVALUATION OF THE O...

Promising transit applications of fuel cells and alternative fuels

DOT National Transportation Integrated Search

2002-06-01

For over a decade, the Volpe Center has been providing technical support to the Federal Transit Administration (FTA) Office of Research, Demonstration and Innovation towards the development, deployment, field test and safety evaluation of advanced tr...

Database architecture and query structures for probe data processing.

DOT National Transportation Integrated Search

2012-03-01

This report summarizes findings and implementations of probe vehicle data collection based on Bluetooth MAC address matching technology. Probe vehicle travel time data are studied in the following field deployment case studies: analysis of traffic ch...

Deployment of Autonomous GPS Stations in Marie Byrd Land, Antartica

NASA Technical Reports Server (NTRS)

Donnellan, A.; Luyendyk, B.; Smith, M.; Dace, G.

1999-01-01

During the 1998-1999 Antarctic field season, we installed three autonomous GPS stations in Marie Byrd Land, West Antarctica to measure glacio-isostatic rebound and rates of spreading across the West Antartic Rift System.

RivGen, Igiugig Deployment, Control System Specifications and Models

DOE Data Explorer

Forbush, Dominic; Cavagnaro, Robert J.; Guerra, Maricarmen; Donegan, James; McEntee, Jarlath; Thomson, Jim; Polagye, Brian; Fabien, Brian; Kilcher, Levi

2016-03-21

Control System simulation models, case studies, and processing codes for analyzing field data. Raw data files included from VFD and SCADA. MatLab and Simulink are required to open some data files and all model files.

In-Field Performance Testing of Stormwater Treatment Devices

EPA Science Inventory

The Environmental Technology Verification (ETV) Program was created by EPA’s Office of Research and Development to facilitate the deployment of innovative or improved environmental technologies through performance verification and dissemination of information. The program’s goal ...

Site 300 Bat Monitoring Final Report

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

Drennan, Joe; Tortosa, Justin

2016-07-18

From June 15 to 18, 2015, GANDA biologist Graham Neale assisted in programming and fieldtesting of the bat monitoring equipment. The equipment was deployed in the field on a meteorological (MET) tower within Site 300 on June 18, 2015.

Register to Download the Automotive Deployment Options Projection Tool |

Science.gov Websites

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Setting the stage - building and working in an ancient DNA laboratory.

PubMed

Knapp, Michael; Clarke, Andrew C; Horsburgh, K Ann; Matisoo-Smith, Elizabeth A

2012-01-20

With the introduction of next generation high throughput sequencing in 2005 and the resulting revolution in genetics, ancient DNA research has rapidly developed from an interesting but marginal field within evolutionary biology into one that can contribute significantly to our understanding of evolution in general and the development of our own species in particular. While the amount of sequence data available from ancient human, other animal and plant remains has increased dramatically over the past five years, some key limitations of ancient DNA research remain. Most notably, reduction of contamination and the authentication of results are of utmost importance. A number of studies have addressed different aspects of sampling, DNA extraction and DNA manipulation in order to establish protocols that most efficiently generate reproducible and authentic results. As increasing numbers of researchers from different backgrounds become interested in using ancient DNA technology to address key questions, the need for practical guidelines on how to construct and use an ancient DNA facility arises. The aim of this article is therefore to provide practical tips for building a state-of-the-art ancient DNA facility. It is intended to help researchers new to the field of ancient DNA research generally, and those considering the application of next generation sequencing, in their planning process. Copyright © 2011 Elsevier GmbH. All rights reserved.

Wireless Sensor Networks for Oceanographic Monitoring: A Systematic Review

PubMed Central

Albaladejo, Cristina; Sánchez, Pedro; Iborra, Andrés; Soto, Fulgencio; López, Juan A.; Torres, Roque

2010-01-01

Monitoring of the marine environment has come to be a field of scientific interest in the last ten years. The instruments used in this work have ranged from small-scale sensor networks to complex observation systems. Among small-scale networks, Wireless Sensor Networks (WSNs) are a highly attractive solution in that they are easy to deploy, operate and dismantle and are relatively inexpensive. The aim of this paper is to identify, appraise, select and synthesize all high quality research evidence relevant to the use of WSNs in oceanographic monitoring. The literature is systematically reviewed to offer an overview of the present state of this field of study and identify the principal resources that have been used to implement networks of this kind. Finally, this article details the challenges and difficulties that have to be overcome if these networks are to be successfully deployed. PMID:22163583

Active Time Domain Reflectometry for Tamper Indication in Unattended Safeguards Systems

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

Sheen, David M.; Smith, Leon E.; Tedeschi, Jonathan R.

2015-07-14

The International Atomic Energy Agency (IAEA) continues to expand its use of unattended measurement systems. An increasing number of systems and an expanding family of instruments create challenges in terms of deployment efficiency and the implementation of data authentication measures. In collaboration with the IAEA, tamper-indicating measures to address data-transmission authentication challenges with unattended safeguards systems are under investigation. Pacific Northwest National Laboratory is studying the viability of active time-domain reflectometry (TDR) along two parallel but interconnected paths: (1) swept-frequency TDR as the highly flexible, laboratory gold standard to which field-deployable options can be compared, and (2) a low-cost commerciallymore » available spread-spectrum TDR technology as one option for field implementation. This paper describes the TDR methods under investigation and the associated benchtop test-bed, tampering scenarios of interest,, and viability measurement results to date (e.g., comparison of relative sensitivity to tamper scenarios).« less

An exploratory study of apex fence flaps on a 74 deg delta wing

NASA Technical Reports Server (NTRS)

Wahls, R. A.; Vess, R. J.

1985-01-01

An exploratory wind tunnel investigation was performed to observe the flow field effects produced by vertically deployed apex fences on a planar 74 degree delta wing. The delta shaped fences, each comprising approximately 3.375 percent of the wing area, were affixed along the first 25 percent of the wing leading edge in symmetric as well as asymmetric (i.e., fence on one side only) arrangements. The vortex flow field was visualized at angles of attack from 0 to 20 degrees using helium bubble and oil flow techniques; upper surface pressures were also measured along spanwise rows. The results were used to construct a preliminary description of the vortex patterns and induced pressures associated with vertical apex fence deployment. The objective was to obtain an initial evaluation of the potential of apex fences as vortex devices for subsonic lift modulation as well as lateral directional control of delta wing aircraft.

Deployment of a Reverse Transcription Loop-Mediated Isothermal Amplification Test for Ebola Virus Surveillance in Remote Areas in Guinea.

PubMed

Kurosaki, Yohei; Magassouba, N'Faly; Bah, Hadja Aïssatou; Soropogui, Barré; Doré, Amadou; Kourouma, Fodé; Cherif, Mahamoud Sama; Keita, Sakoba; Yasuda, Jiro

2016-10-15

To strengthen the laboratory diagnostic capacity for Ebola virus disease (EVD) in the remote areas of Guinea, we deployed a mobile field laboratory and implemented reverse transcription loop-mediated isothermal amplification (RT-LAMP) for postmortem testing. We tested 896 oral swab specimens and 21 serum samples, using both RT-LAMP and reverse transcription-polymerase chain reaction (RT-PCR). Neither test yielded a positive result, and the results from RT-LAMP and RT-PCR were consistent. More than 95% of the samples were tested within 2 days of sample collection. These results highlight the usefulness of the RT-LAMP assay as an EVD diagnostic testing method in the field or remote areas. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Intelligent Rover Execution for Detecting Life in the Atacama Desert

NASA Technical Reports Server (NTRS)

Baskaran, Vijayakumar; Muscettola, Nicola; Rijsman, David; Plaunt, Chris; Fry, Chuck

2006-01-01

On-board supervisory execution is crucial for the deployment of more capable and autonomous remote explorers. Planetary science is considering robotic explorers operating for long periods of time without ground supervision while interacting with a changing and often hostile environment. Effective and robust operations require on-board supervisory control with a high level of awareness of the principles of functioning of the environment and of the numerous internal subsystems that need to be coordinated. We describe an on-board rover executive that was deployed on a rover as past of the "Limits of Life in the Atacama Desert (LITA)" field campaign sponsored by the NASA ASTEP program. The executive was built using the Intelligent Distributed Execution Architecture (IDEA), an execution framework that uses model-based and plan-based supervisory control of its fundamental computational paradigm. We present the results of the third field experiment conducted in the Atacama desert (Chile) in August - October 2005.

A multiscale and multidisciplinary investigation of ecosystem-atmosphere CO2 exchange over the rocky mountains of colorado

USGS Publications Warehouse

Sun, Jielun; Oncley, S.P.; Burns, Sean P.; Stephens, B.B.; Lenschow, D.H.; Campos, T.; Monson, Russell K.; Schimel, D.S.; Sacks, W.J.; De Wekker, S. F. J.; Lai, C.-T.; Lamb, B.; Ojima, D.; Ellsworth, P.Z.; Sternberg, L.S.L.; Zhong, S.; Clements, C.; Moore, D.J.P.; Anderson, D.E.; Watt, A.S.; Hu, Jiawen; Tschudi, M.; Aulenbach, S.; Allwine, E.; Coons, T.

2010-01-01

A field study combined with modeling investigation demonstrated that the organization of CO2 transport by mountain terrain strongly affects the regional CO2 budget. Atmospheric dynamics can lead to complicated flows generated by inhomogeneous landscapes, topography or synoptic weather systems. The field campaign conducted of a ground deployment, the Carbon in the Mountain Experiment (CME04), and an aircraft deployment of the national Center for Atmospheric Research (NCAR) C-130, the Airborne Carbon in the Mountains Experiment (ACME04) over the period of spring to fall of 2004 to cover the seasonal variation of ecosystem-atmosphere carbon exchange. The role of the mountain circulation in CO2 transport can be played over seemingly flat terrain by mesoscale flows generated by various physical processes. The three dimensional observation strategy considered can also be applied over flat terrain.

Aerosol Optical Properties at the Ground Sites during the 2010 CARES Field Campaign

NASA Astrophysics Data System (ADS)

Atkinson, D. B.; Radney, J. G.; Harworth, J. W.

2010-12-01

Preliminary results from the ground sites at the 2010 CARES field campaign (T0 near Sacramento, CA and T1 near Cool, CA) will be presented. A number of aerosol optical properties were measured at high time resolution for the four week study period using custom instruments. The aerosol extinction coefficient was measured at T0 using a cavity ring-down transmissometer (CRDT) at two wavelengths (532 and 1064 nm) and the aerosol scattering coefficient was measured at 532 nm using a Radiance Research M903 nephelometer. At T1, a new CRDT instrument was deployed that measured the extinction coefficient at three wavelengths (355, 532, and 1064 nm) for sub-10 μm (nominal) and sub-2.5 μm aerosols at ambient, elevated, and reduced relative humidity. A new type of custom nephelometer that measures the aerosol scattering coefficient at 532 nm using an array detector was also deployed at T1.

Aircraft Wake Vortex Spacing System (AVOSS) Performance Update and Validation Study

NASA Technical Reports Server (NTRS)

Rutishauser, David K.; OConnor, Cornelius J.

2001-01-01

An analysis has been performed on data generated from the two most recent field deployments of the Aircraft Wake VOrtex Spacing System (AVOSS). The AVOSS provides reduced aircraft spacing criteria for wake vortex avoidance as compared to the FAA spacing applied under Instrument Flight Rules (IFR). Several field deployments culminating in a system demonstration at Dallas Fort Worth (DFW) International Airport in the summer of 2000 were successful in showing a sound operational concept and the system's potential to provide a significant benefit to airport operations. For DFW, a predicted average throughput increase of 6% was observed. This increase implies 6 or 7 more aircraft on the ground in a one-hour period for DFW operations. Several studies of performance correlations to system configuration options, design options, and system inputs are also reported. The studies focus on the validation performance of the system.

Accidental Turbulent Discharge Rate Estimation from Videos

NASA Astrophysics Data System (ADS)

Ibarra, Eric; Shaffer, Franklin; Savaş, Ömer

2015-11-01

A technique to estimate the volumetric discharge rate in accidental oil releases using high speed video streams is described. The essence of the method is similar to PIV processing, however the cross correlation is carried out on the visible features of the efflux, which are usually turbulent, opaque and immiscible. The key step in the process is to perform a pixelwise time filtering on the video stream, in which the parameters are commensurate with the scales of the large eddies. The velocity field extracted from the shell of visible features is then used to construct an approximate velocity profile within the discharge. The technique has been tested on laboratory experiments using both water and oil jets at Re ~105 . The technique is accurate to 20%, which is sufficient for initial responders to deploy adequate resources for containment. The software package requires minimal user input and is intended for deployment on an ROV in the field. Supported by DOI via NETL.

Pathfinder

NASA Image and Video Library

2001-07-01

This photograph shows two Marshall Space Flight Center (MSFC) engineers, Mark Vaccaro (left) and Ken Welzyn, testing electrodynamic tethers in the MSFC Tether Winding and Spark Testing Facility. For 4 years, MSFC and industry partners have been developing the Propulsive Small Expendable Deployer System experiment, called ProSEDS. ProSEDS will test electrodynamic tether propulsion technology. Electrodynamic tethers are long, thin wires that collect electrical current when passing through a magnetic field. The tether works as a thruster as a magnetic field exerts a force on a current-carrying wire. Since electrodynamic tethers require no propellant, they could substantially reduce the weight of the spacecraft and provide a cost-effective method of reboosting spacecraft. The initial flight of ProSEDS is scheduled to fly aboard an Air Force Delta II rocket in the summer of 2002. In orbit, ProSEDS will deploy from a Delta II second stage. It will be a 3.1-mile (5 kilometer) long, ultrathin base-wire tether cornected with a 6.2-mile (10 kilometer) long non-conducting tether. This photograph shows Less Johnson, a scientist at MSFC, inspecting the nonconducting part of a tether as it exits a deployer similar to the one to be used in the ProSEDS experiment. The ProSEDS experiment is managed by the Space Transportation Directorate at MSFC.

UAV Deployment Exercise for Mapping Purposes: Evaluation of Emergency Response Applications

PubMed Central

Boccardo, Piero; Chiabrando, Filiberto; Dutto, Furio; Giulio Tonolo, Fabio; Lingua, Andrea

2015-01-01

Exploiting the decrease of costs related to UAV technology, the humanitarian community started piloting the use of similar systems in humanitarian crises several years ago in different application fields, i.e., disaster mapping and information gathering, community capacity building, logistics and even transportation of goods. Part of the author’s group, composed of researchers in the field of applied geomatics, has been piloting the use of UAVs since 2006, with a specific focus on disaster management application. In the framework of such activities, a UAV deployment exercise was jointly organized with the Regional Civil Protection authority, mainly aimed at assessing the operational procedures to deploy UAVs for mapping purposes and the usability of the acquired data in an emergency response context. In the paper the technical features of the UAV platforms will be described, comparing the main advantages/disadvantages of fixed-wing versus rotor platforms. The main phases of the adopted operational procedure will be discussed and assessed especially in terms of time required to carry out each step, highlighting potential bottlenecks and in view of the national regulation framework, which is rapidly evolving. Different methodologies for the processing of the acquired data will be described and discussed, evaluating the fitness for emergency response applications. PMID:26147728

Marine Animal Alert System -- Task 2.1.5.3: Development of Monitoring Technologies -- FY 2011 Progress Report

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

Carlson, Thomas J.; Deng, Zhiqun; Myers, Joshua R.

2011-09-30

The Marine Animal Alert System (MAAS) in development by the Pacific Northwest National Laboratory is focused on providing elements of compliance monitoring to support deployment of marine hydrokinetic energy devices. An initial focus is prototype tidal turbines to be deployed in Puget Sound in Washington State. The MAAS will help manage the risk of injury or mortality to marine animals from blade strike or contact with tidal turbines. In particular, development has focused on detection, classification, and localization of listed Southern Resident killer whales within 200 m of prototype turbines using both active and passive acoustic approaches. At the closemore » of FY 2011, a passive acoustic system consisting of a pair of four-element star arrays and parallel processing of eight channels of acoustic receptions has been designed and built. Field tests of the prototype system are scheduled for the fourth quarter of calendar year 2011. Field deployment and testing of the passive acoustic prototype is scheduled for the first quarter of FY 2012. The design of an active acoustic system that could be built using commercially available off-the-shelf components from active acoustic system vendors is also in the final stages of design and specification.« less

Detection of Sub-fM DNA with Target Recycling and Self-Assembly Amplification on Graphene Field-Effect Biosensors

PubMed Central

2018-01-01

All-electronic DNA biosensors based on graphene field-effect transistors (GFETs) offer the prospect of simple and cost-effective diagnostics. For GFET sensors based on complementary probe DNA, the sensitivity is limited by the binding affinity of the target oligonucleotide, in the nM range for 20 mer targets. We report a ∼20 000× improvement in sensitivity through the use of engineered hairpin probe DNA that allows for target recycling and hybridization chain reaction. This enables detection of 21 mer target DNA at sub-fM concentration and provides superior specificity against single-base mismatched oligomers. The work is based on a scalable fabrication process for biosensor arrays that is suitable for multiplexed detection. This approach overcomes the binding-affinity-dependent sensitivity of nucleic acid biosensors and offers a pathway toward multiplexed and label-free nucleic acid testing with high accuracy and selectivity. PMID:29768011

Detection of Sub-fM DNA with Target Recycling and Self-Assembly Amplification on Graphene Field-Effect Biosensors.

PubMed

Gao, Zhaoli; Xia, Han; Zauberman, Jonathan; Tomaiuolo, Maurizio; Ping, Jinglei; Zhang, Qicheng; Ducos, Pedro; Ye, Huacheng; Wang, Sheng; Yang, Xinping; Lubna, Fahmida; Luo, Zhengtang; Ren, Li; Johnson, Alan T Charlie

2018-06-13

All-electronic DNA biosensors based on graphene field-effect transistors (GFETs) offer the prospect of simple and cost-effective diagnostics. For GFET sensors based on complementary probe DNA, the sensitivity is limited by the binding affinity of the target oligonucleotide, in the nM range for 20 mer targets. We report a ∼20 000× improvement in sensitivity through the use of engineered hairpin probe DNA that allows for target recycling and hybridization chain reaction. This enables detection of 21 mer target DNA at sub-fM concentration and provides superior specificity against single-base mismatched oligomers. The work is based on a scalable fabrication process for biosensor arrays that is suitable for multiplexed detection. This approach overcomes the binding-affinity-dependent sensitivity of nucleic acid biosensors and offers a pathway toward multiplexed and label-free nucleic acid testing with high accuracy and selectivity.

Quantitative Single-Molecule Surface-Enhanced Raman Scattering by Optothermal Tuning of DNA Origami-Assembled Plasmonic Nanoantennas.

PubMed

Simoncelli, Sabrina; Roller, Eva-Maria; Urban, Patrick; Schreiber, Robert; Turberfield, Andrew J; Liedl, Tim; Lohmüller, Theobald

2016-11-22

DNA origami is a powerful approach for assembling plasmonic nanoparticle dimers and Raman dyes with high yields and excellent positioning control. Here we show how optothermal-induced shrinking of a DNA origami template can be employed to control the gap sizes between two 40 nm gold nanoparticles in a range from 1 to 2 nm. The high field confinement achieved with this optothermal approach was demonstrated by detection of surface-enhanced Raman spectroscopy (SERS) signals from single molecules that are precisely placed within the DNA origami template that spans the nanoparticle gap. By comparing the SERS intensity with respect to the field enhancement in the plasmonic hot-spot region, we found good agreement between measurement and theory. Our straightforward approach for the fabrication of addressable plasmonic nanosensors by DNA origami demonstrates a path toward future sensing applications with single-molecule resolution.

DETECTION OF LOW DOSE RADIATION-AND CHEMICALLY-INDUCED DNA DAMAGE USING TEMPERATURE DIFFERENTIAL FLUORESCENCE ASSAYS

EPA Science Inventory

Rapid, sensitive and simple assays for radiation- and chemically-induced DNA damage can be of significant benefit to a number of fields including radiation biology, clinical research, and environmental monitoring. Although temperature-induced DNA strand separation has been use...

Methods of DNA methylation analysis.

USDA-ARS?s Scientific Manuscript database

The purpose of this review was to provide guidance for investigators who are new to the field of DNA methylation analysis. Epigenetics is the study of mitotically heritable alterations in gene expression potential that are not mediated by changes in DNA sequence. Recently, it has become clear that n...

Detection of the Odor Signature of Ovarian Cancer using DNA-Decorated Carbon Nanotube Field Effect Transistor Arrays

NASA Astrophysics Data System (ADS)

Kehayias, Christopher; Kybert, Nicholas; Yodh, Jeremy; Johnson, A. T. Charlie

Carbon nanotubes are low-dimensional materials that exhibit remarkable chemical and bio-sensing properties and have excellent compatibility with electronic systems. Here, we present a study that uses an electronic olfaction system based on a large array of DNA-carbon nanotube field effect transistors vapor sensors to analyze the VOCs of blood plasma samples collected from patients with malignant ovarian cancer, patients with benign ovarian lesions, and age-matched healthy subjects. Initial investigations involved coating each CNT sensor with single-stranded DNA of a particular base sequence. 10 distinct DNA oligomers were used to functionalize the carbon nanotube field effect transistors, providing a 10-dimensional sensor array output response. Upon performing a statistical analysis of the 10-dimensional sensor array responses, we showed that blood samples from patients with malignant cancer can be reliably differentiated from those of healthy control subjects with a p-value of 3 x 10-5. The results provide preliminary evidence that the blood of ovarian cancer patients contains a discernable volatile chemical signature that can be detected using DNA-CNT nanoelectronic vapor sensors, a first step towards a minimally invasive electronic diagnostic technology for ovarian cancer.

One-step analysis of DNA/chitosan complexes by field-flow fractionation reveals particle size and free chitosan content.

PubMed

Ma, Pei Lian; Buschmann, Michael D; Winnik, Françoise M

2010-03-08

The composition of samples obtained upon complexation of DNA with chitosan was analyzed by asymmetrical flow field flow fractionation (AF4) with online UV-visible, multiangle light scattering (MALS), and dynamic light scattering (DLS) detectors. A chitosan labeled with rhodamine B to facilitate UV-vis detection of the polycation was complexed with DNA under conditions commonly used for transfection (chitosan glucosamine to DNA phosphate molar ratio of 5). AF4 analysis revealed that 73% of the chitosan-rhodamine remained free in the dispersion and that the DNA/chitosan complexes had a broad size distribution ranging from 20 to 160 nm in hydrodynamic radius. The accuracy of the data was assessed by comparison with data from batch-mode DLS and scanning electron microscopy. The AF4 combined with DLS allowed the characterization of small particles that were not detected by conventional batch-mode DLS. The AF4 analysis will prove to be an important tool in the field of gene therapy because it readily provides, in a single measurement, three important physicochemical parameters of the complexes: the amount of unbound polycation, the hydrodynamic size of the complexes, and their size distribution.

The First Interlaced Continuum Robot, Devised to Intrinsically Follow the Leader

PubMed Central

Kang, Byungjeon; Kojcev, Risto; Sinibaldi, Edoardo

2016-01-01

Flexible probes that are safely deployed to hard-to-reach targets while avoiding critical structures are strategic in several high-impact application fields, including the biomedical sector and the sector of inspections at large. A critical problem for these tools is the best approach for deploying an entire tool body, not only its tip, on a sought trajectory. A probe that achieves this deployment is considered to follow the leader (or to achieve follow-the-leader deployment) because its body sections follow the track traced by its tip. Follow-the-leader deployment through cavities is complicated due to a lack of external supports. Currently, no definitive implementation for a probe that is intrinsically able to follow the leader, i.e., without relying on external supports, has been achieved. In this paper, we present a completely new device, namely the first interlaced continuum robot, devised to intrinsically follow the leader. We developed the interlaced configuration by pursuing a conceptual approach irrespective of application-specific constraints and assuming two flexible tools with controllable stiffness. We questioned the possibility of solving the previously mentioned deployment problem by harnessing probe symmetry during the design process. This study examines the entire development of the novel interlaced probe: model-based conceptual design, detailed design and prototyping, and preliminary experimental assessment. Our probe can build a track with a radius of curvature that is as small as twice the probe diameter, which enables it to outperform state-of-the-art tools that are aimed at follow-the-leader deployment. Despite the limitations that are inherently associated with its original character, this study provides a prototypical approach to the design of interlaced continuum systems and demonstrates the first interlaced continuum probe, which is intrinsically able to follow the leader. PMID:26914328

The First Interlaced Continuum Robot, Devised to Intrinsically Follow the Leader.

PubMed

Kang, Byungjeon; Kojcev, Risto; Sinibaldi, Edoardo

2016-01-01

Flexible probes that are safely deployed to hard-to-reach targets while avoiding critical structures are strategic in several high-impact application fields, including the biomedical sector and the sector of inspections at large. A critical problem for these tools is the best approach for deploying an entire tool body, not only its tip, on a sought trajectory. A probe that achieves this deployment is considered to follow the leader (or to achieve follow-the-leader deployment) because its body sections follow the track traced by its tip. Follow-the-leader deployment through cavities is complicated due to a lack of external supports. Currently, no definitive implementation for a probe that is intrinsically able to follow the leader, i.e., without relying on external supports, has been achieved. In this paper, we present a completely new device, namely the first interlaced continuum robot, devised to intrinsically follow the leader. We developed the interlaced configuration by pursuing a conceptual approach irrespective of application-specific constraints and assuming two flexible tools with controllable stiffness. We questioned the possibility of solving the previously mentioned deployment problem by harnessing probe symmetry during the design process. This study examines the entire development of the novel interlaced probe: model-based conceptual design, detailed design and prototyping, and preliminary experimental assessment. Our probe can build a track with a radius of curvature that is as small as twice the probe diameter, which enables it to outperform state-of-the-art tools that are aimed at follow-the-leader deployment. Despite the limitations that are inherently associated with its original character, this study provides a prototypical approach to the design of interlaced continuum systems and demonstrates the first interlaced continuum probe, which is intrinsically able to follow the leader.

Propulsive Small Expendable Deployer System (ProSEDS)

NASA Technical Reports Server (NTRS)

1999-01-01

This Quick Time movie is of NASA's Propulsive Small Expendable Deployer System experiment (ProSEDS). ProSEDS will demonstrate the use of an electrodynamic tether, basically a long, thin wire, for propulsion. An electrodynamic tether uses the same principles as electric motors in toys, appliances and computer disk drives, and generators in automobiles and power plants. When electrical current is flowing through the tether, a magnetic field is produced that pushes against the magnetic field of the Earth. For ProSEDS, the current in the tether results by virtue of the voltage generated when the tether moves through the Earth's magnetic field at more than 17,000 mph. This approach can produce drag thrust generating useable power. Since electrodynamic tethers require no propellant, they could substantially reduce the weight of the spacecraft and provide a cost-effective method of reboosting spacecraft. The tether would be a 3.1-mile (5 kilometer) long, ultrathin base-wire tether connected with a 6.2-mile (10 kilometer) long nonconducting tether. The ProSEDS experiment is managed by the Space Transportation Directorate at the Marshall Space Flight Center.