Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data

NASA Astrophysics Data System (ADS)

Trifonov, Vladimir; Pasqualucci, Laura; Dalla-Favera, Riccardo; Rabadan, Raul

2011-12-01

Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing (HTS), expression profiles, proteomics, and electronic health records (EHR) are some examples of such technologies. Extracting meaningful information from those technologies requires careful analysis of the large volumes of data they produce. In this note, we present a set of fractal-like distributions that commonly appear in the analysis of such data. The first set of examples are drawn from a HTS experiment. Here, the distributions appear as part of the evaluation of the error rate of the sequencing and the identification of tumorogenic genomic alterations. The other examples are obtained from risk factor evaluation and analysis of relative disease prevalence and co-mordbidity as these appear in EHR. The distributions are also relevant to identification of subclonal populations in tumors and the study of quasi-species and intrahost diversity of viral populations.

Characterization and complete genome sequence of a panicovirus from Bermuda grass by high-throughput sequencing.

PubMed

Tahir, Muhammad N; Lockhart, Ben; Grinstead, Samuel; Mollov, Dimitre

2017-04-01

Bermuda grass samples were examined by transmission electron microscopy and 28-30 nm spherical virus particles were observed. Total RNA from these plants was subjected to high-throughput sequencing (HTS). The nearly full genome sequence of a panicovirus was identified from one HTS scaffold. Sanger sequencing was used to confirm the HTS results and complete the genome sequence of 4404 nt. This virus was provisionally named Bermuda grass latent virus (BGLV). Its predicted open reading frames follow the typical arrangement of the genus Panicovirus. Based on sequence comparisons and phylogenetic analyses BGLV differs from other viruses and therefore taxonomically it is a new member of the genus Panicovirus, family Tombusviridae.

Advanced Virus Detection Technologies Interest Group (AVDTIG): Efforts on High Throughput Sequencing (HTS) for Virus Detection.

PubMed

Khan, Arifa S; Vacante, Dominick A; Cassart, Jean-Pol; Ng, Siemon H S; Lambert, Christophe; Charlebois, Robert L; King, Kathryn E

Several nucleic-acid based technologies have recently emerged with capabilities for broad virus detection. One of these, high throughput sequencing, has the potential for novel virus detection because this method does not depend upon prior viral sequence knowledge. However, the use of high throughput sequencing for testing biologicals poses greater challenges as compared to other newly introduced tests due to its technical complexities and big data bioinformatics. Thus, the Advanced Virus Detection Technologies Users Group was formed as a joint effort by regulatory and industry scientists to facilitate discussions and provide a forum for sharing data and experiences using advanced new virus detection technologies, with a focus on high throughput sequencing technologies. The group was initiated as a task force that was coordinated by the Parenteral Drug Association and subsequently became the Advanced Virus Detection Technologies Interest Group to continue efforts for using new technologies for detection of adventitious viruses with broader participation, including international government agencies, academia, and technology service providers. © PDA, Inc. 2016.

Comparison of Sanger and next generation sequencing performance for genotyping Cryptosporidium isolates at the 18S rRNA and actin loci.

PubMed

Paparini, Andrea; Gofton, Alexander; Yang, Rongchang; White, Nicole; Bunce, Michael; Ryan, Una M

2015-01-01

Cryptosporidium is an important enteric pathogen that infects a wide range of humans and animals. Rapid and reliable detection and characterisation methods are essential for understanding the transmission dynamics of the parasite. Sanger sequencing, and high-throughput sequencing (HTS) on an Ion Torrent platform, were compared with each other for their sensitivity and accuracy in detecting and characterising 25 Cryptosporidium-positive human and animal faecal samples. Ion Torrent reads (n = 123,857) were obtained at both 18S rRNA and actin loci for 21 of the 25 samples. Of these, one isolate at the actin locus (Cattle 05) and three at the 18S rRNA locus (HTS 10, HTS 11 and HTS 12), suffered PCR drop-out (i.e. PCR failures) when using fusion-tagged PCR. Sanger sequences were obtained for both loci for 23 of the 25 samples and showed good agreement with Ion Torrent-based genotyping. Two samples both from pythons (SK 02 and SK 05) produced mixed 18S and actin chromatograms by Sanger sequencing but were clearly identified by Ion Torrent sequencing as C. muris. One isolate (SK 03) was typed as C. muris by Sanger sequencing but was identified as a mixed C. muris and C. tyzzeri infection by HTS. 18S rRNA Type B sequences were identified in 4/6 C. parvum isolates when deep sequenced but were undetected in Sanger sequencing. Sanger was cheaper than Ion Torrent when sequencing a small numbers of samples, but when larger numbers of samples are considered (n = 60), the costs were comparative. Fusion-tagged amplicon based approaches are a powerful way of approaching mixtures, the only draw-back being the loss of PCR efficiency on low-template samples when using primers coupled to MID tags and adaptors. Taken together these data show that HTS has excellent potential for revealing the "true" composition of species/types in a Cryptosporidium infection, but that HTS workflows need to be carefully developed to ensure sensitivity, accuracy and contamination are controlled. Copyright © 2015 Elsevier Inc. All rights reserved.

A study on the required performance of a 2G HTS wire for HTS wind power generators

NASA Astrophysics Data System (ADS)

Sung, Hae-Jin; Park, Minwon; Go, Byeong-Soo; Yu, In-Keun

2016-05-01

YBCO or REBCO coated conductor (2G) materials are developed for their superior performance at high magnetic field and temperature. Power system applications based on high temperature superconducting (HTS) 2G wire technology are attracting attention, including large-scale wind power generators. In particular, to solve problems associated with the foundations and mechanical structure of offshore wind turbines, due to the large diameter and heavy weight of the generator, an HTS generator is suggested as one of the key technologies. Many researchers have tried to develop feasible large-scale HTS wind power generator technologies. In this paper, a study on the required performance of a 2G HTS wire for large-scale wind power generators is discussed. A 12 MW class large-scale wind turbine and an HTS generator are designed using 2G HTS wire. The total length of the 2G HTS wire for the 12 MW HTS generator is estimated, and the essential prerequisites of the 2G HTS wire based generator are described. The magnetic field distributions of a pole module are illustrated, and the mechanical stress and strain of the pole module are analysed. Finally, a reasonable price for 2G HTS wire for commercialization of the HTS generator is suggested, reflecting the results of electromagnetic and mechanical analyses of the generator.

Cross-species extrapolation of mammalian-based ToxCast Data using Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS)

EPA Science Inventory

In vitro high-throughput screening (HTS) and in silico technologies have emerged as 21st century tools for chemical hazard identification. In 2007 the U.S. Environmental Protection Agency (EPA) launched the ToxCast Program, which has screened thousands of chemicals in hundreds of...

Characterization of a new apple luteovirus identified by high-throughput sequencing.

PubMed

Liu, Huawei; Wu, Liping; Nikolaeva, Ekaterina; Peter, Kari; Liu, Zongrang; Mollov, Dimitre; Cao, Mengji; Li, Ruhui

2018-05-15

'Rapid Apple Decline' (RAD) is a newly emerging problem of young, dwarf apple trees in the Northeastern USA. The affected trees show trunk necrosis, cracking and canker before collapse in summer. In this study, we discovered and characterized a new luteovirus from apple trees in RAD-affected orchards using high-throughput sequencing (HTS) technology and subsequent Sanger sequencing. Illumina NextSeq sequencing was applied to total RNAs prepared from three diseased apple trees. Sequence reads were de novo assembled, and contigs were annotated by BLASTx. RT-PCR and 5'/3' RACE sequencing were used to obtain the complete genome of a new virus. RT-PCR was used to detect the virus. Three common apple viruses and a new luteovirus were identified from the diseased trees by HTS and RT-PCR. Sequence analyses of the complete genome of the new virus show that it is a new species of the genus Luteovirus in the family Luteoviridae. The virus is graft transmissible and detected by RT-PCR in apple trees in a couple of orchards. A new luteovirus and/or three known viruses were found to be associated with RAD. Molecular characterization of the new luteovirus provides important information for further investigation of its distribution and etiological role.

High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones.

PubMed

Salson, Mikaël; Giraud, Mathieu; Caillault, Aurélie; Grardel, Nathalie; Duployez, Nicolas; Ferret, Yann; Duez, Marc; Herbert, Ryan; Rocher, Tatiana; Sebda, Shéhérazade; Quief, Sabine; Villenet, Céline; Figeac, Martin; Preudhomme, Claude

2017-02-01

Minimal residual disease (MRD) is known to be an independent prognostic factor in patients with acute lymphoblastic leukemia (ALL). High-throughput sequencing (HTS) is currently used in routine practice for the diagnosis and follow-up of patients with hematological neoplasms. In this retrospective study, we examined the role of immunoglobulin/T-cell receptor-based MRD in patients with ALL by HTS analysis of immunoglobulin H and/or T-cell receptor gamma chain loci in bone marrow samples from 11 patients with ALL, at diagnosis and during follow-up. We assessed the clinical feasibility of using combined HTS and bioinformatics analysis with interactive visualization using Vidjil software. We discuss the advantages and drawbacks of HTS for monitoring MRD. HTS gives a more complete insight of the leukemic population than conventional real-time quantitative PCR (qPCR), and allows identification of new emerging clones at each time point of the monitoring. Thus, HTS monitoring of Ig/TR based MRD is expected to improve the management of patients with ALL. Copyright © 2016 Elsevier Ltd. All rights reserved.

Progress on applications of high temperature superconducting microwave filters

NASA Astrophysics Data System (ADS)

Chunguang, Li; Xu, Wang; Jia, Wang; Liang, Sun; Yusheng, He

2017-07-01

In the past two decades, various kinds of high performance high temperature superconducting (HTS) filters have been constructed and the HTS filters and their front-end subsystems have been successfully applied in many fields. The HTS filters with small insertion loss, narrow bandwidth, flat in-band group delay, deep out-of-band rejection, and steep skirt slope are reviewed. Novel HTS filter design technologies, including those in high power handling filters, multiband filters and frequency tunable filters, are reviewed, as well as the all-HTS integrated front-end receivers. The successful applications to various civilian fields, such as mobile communication, radar, deep space detection, and satellite technology, are also reviewed.

The autism sequencing consortium: large-scale, high-throughput sequencing in autism spectrum disorders.

PubMed

Buxbaum, Joseph D; Daly, Mark J; Devlin, Bernie; Lehner, Thomas; Roeder, Kathryn; State, Matthew W

2012-12-20

Research during the past decade has seen significant progress in the understanding of the genetic architecture of autism spectrum disorders (ASDs), with gene discovery accelerating as the characterization of genomic variation has become increasingly comprehensive. At the same time, this research has highlighted ongoing challenges. Here we address the enormous impact of high-throughput sequencing (HTS) on ASD gene discovery, outline a consensus view for leveraging this technology, and describe a large multisite collaboration developed to accomplish these goals. Similar approaches could prove effective for severe neurodevelopmental disorders more broadly. Copyright © 2012 Elsevier Inc. All rights reserved.

Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities

PubMed Central

Bokulich, Nicholas A.

2013-01-01

Ultra-high-throughput sequencing (HTS) of fungal communities has been restricted by short read lengths and primer amplification bias, slowing the adoption of newer sequencing technologies to fungal community profiling. To address these issues, we evaluated the performance of several common internal transcribed spacer (ITS) primers and designed a novel primer set and work flow for simultaneous quantification and species-level interrogation of fungal consortia. Primer comparison and validation were predicted in silico and by sequencing a “mock community” of mixed yeast species to explore the challenges of amplicon length and amplification bias for reconstructing defined yeast community structures. The amplicon size and distribution of this primer set are smaller than for all preexisting ITS primer sets, maximizing sequencing coverage of hypervariable ITS domains by very-short-amplicon, high-throughput sequencing platforms. This feature also enables the optional integration of quantitative PCR (qPCR) directly into the HTS preparatory work flow by substituting qPCR with these primers for standard PCR, yielding quantification of individual community members. The complete work flow described here, utilizing any of the qualified primer sets evaluated, can rapidly profile mixed fungal communities and capably reconstructed well-characterized beer and wine fermentation fungal communities. PMID:23377949

Experiences in implementing uHTS--cutting edge technology meets the real world.

PubMed

Gribbon, Philip; Schaertl, Sabine; Wickenden, Malcolm; Williams, Gareth; Grimley, Rachel; Stuhmeier, Frank; Preckel, Hartwig; Eggeling, Christian; Kraemer, Joachim; Everett, Jeremy; Keighley, Wilma W; Sewing, Andreas

2004-01-01

Driven by growing corporate compound files, the demands of target biology, and attempts to cut cost, the number of solutions to HTS has spiralled. In quick succession new assay technologies and screening platforms are appearing on the market, with the promise of screening faster than ever in low volume high density formats whilst providing high quality data. Within this world of rapid change, Pfizer has applied cutting edge technology to HTS by introducing screening in 1 microl formats utilising single molecule detection technology. Instead of resource intensive in-house development, Pfizer entered into a collaboration with Evotec OAI / Evotec Technologies and introduced their Mark-II EVOscreen platform. In this article we will outline the benefits of the approach taken at Pfizer, Sandwich, and introduce the Mark-II EVOscreen platform, illustrating the potential but also possible pitfalls of HTS miniaturisation.

Sequencing of the Cheese Microbiome and Its Relevance to Industry.

PubMed

Yeluri Jonnala, Bhagya R; McSweeney, Paul L H; Sheehan, Jeremiah J; Cotter, Paul D

2018-01-01

The microbiota of cheese plays a key role in determining its organoleptic and other physico-chemical properties. It is essential to understand the various contributions, positive or negative, of these microbial components in order to promote the growth of desirable taxa and, thus, characteristics. The recent application of high throughput DNA sequencing (HTS) facilitates an even more accurate identification of these microbes, and their functional properties, and has the potential to reveal those microbes, and associated pathways, responsible for favorable or unfavorable characteristics. This technology also facilitates a detailed analysis of the composition and functional potential of the microbiota of milk, curd, whey, mixed starters, processing environments, and how these contribute to the final cheese microbiota, and associated characteristics. Ultimately, this information can be harnessed by producers to optimize the quality, safety, and commercial value of their products. In this review we highlight a number of key studies in which HTS was employed to study the cheese microbiota, and pay particular attention to those of greatest relevance to industry.

The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain

PubMed Central

Oniciuc, Elena A.; Likotrafiti, Eleni; Alvarez-Molina, Adrián; Alvarez-Ordóñez, Avelino

2018-01-01

Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes. PMID:29789467

The University of Kansas High-Throughput Screening laboratory. Part I: meeting drug-discovery needs in the heartland of America with entrepreneurial flair.

PubMed

McDonald, Peter R; Roy, Anuradha; Chaguturu, Rathnam

2011-05-01

The University of Kansas High-Throughput Screening (KU HTS) core is a state-of-the-art drug-discovery facility with an entrepreneurial open-service policy, which provides centralized resources supporting public- and private-sector research initiatives. The KU HTS core applies pharmaceutical industry project-management principles in an academic setting by bringing together multidisciplinary teams to fill critical scientific and technology gaps, using an experienced team of industry-trained researchers and project managers. The KU HTS proactively engages in supporting grant applications for extramural funding, intellectual-property management and technology transfer. The KU HTS staff further provides educational opportunities for the KU faculty and students to learn cutting-edge technologies in drug-discovery platforms through seminars, workshops, internships and course teaching. This is the first instalment of a two-part contribution from the KU HTS laboratory.

Accurate Sample Assignment in a Multiplexed, Ultrasensitive, High-Throughput Sequencing Assay for Minimal Residual Disease.

PubMed

Bartram, Jack; Mountjoy, Edward; Brooks, Tony; Hancock, Jeremy; Williamson, Helen; Wright, Gary; Moppett, John; Goulden, Nick; Hubank, Mike

2016-07-01

High-throughput sequencing (HTS) (next-generation sequencing) of the rearranged Ig and T-cell receptor genes promises to be less expensive and more sensitive than current methods of monitoring minimal residual disease (MRD) in patients with acute lymphoblastic leukemia. However, the adoption of new approaches by clinical laboratories requires careful evaluation of all potential sources of error and the development of strategies to ensure the highest accuracy. Timely and efficient clinical use of HTS platforms will depend on combining multiple samples (multiplexing) in each sequencing run. Here we examine the Ig heavy-chain gene HTS on the Illumina MiSeq platform for MRD. We identify errors associated with multiplexing that could potentially impact the accuracy of MRD analysis. We optimize a strategy that combines high-purity, sequence-optimized oligonucleotides, dual indexing, and an error-aware demultiplexing approach to minimize errors and maximize sensitivity. We present a probability-based, demultiplexing pipeline Error-Aware Demultiplexer that is suitable for all MiSeq strategies and accurately assigns samples to the correct identifier without excessive loss of data. Finally, using controls quantified by digital PCR, we show that HTS-MRD can accurately detect as few as 1 in 10(6) copies of specific leukemic MRD. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)

PubMed Central

Tank, David C.

2016-01-01

Advances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses the Fluidigm Access Array System (Fluidigm, San Francisco, CA, USA) and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per Access Array). The final product is a pooled set of amplicons ready to be sequenced, and thus, there is no need to construct separate, costly genomic libraries for each sample. Further, we present a bioinformatics pipeline to process the raw HTS reads to either generate consensus sequences (with or without ambiguities) for every locus in every sample or—more importantly—recover the separate alleles from heterozygous target regions in each sample. This is important because it adds allelic information that is well suited for coalescent-based phylogenetic analyses that are becoming very common in conservation and evolutionary biology. To test our approach and bioinformatics pipeline, we sequenced 576 samples across 96 target regions belonging to the South American clade of the genus Bartsia L. in the plant family Orobanchaceae. After sequencing cleanup and alignment, the experiment resulted in ~25,300bp across 486 samples for a set of 48 primer pairs targeting the plastome, and ~13,500bp for 363 samples for a set of primers targeting regions in the nuclear genome. Finally, we constructed a combined concatenated matrix from all 96 primer combinations, resulting in a combined aligned length of ~40,500bp for 349 samples. PMID:26828929

Space applications for high temperature superconductivity - Brief review

NASA Technical Reports Server (NTRS)

Krishen, Kumar

1990-01-01

An overview is presented of materials and devices based on high-temperature superconductivity (HTS) that could have useful space-oriented applications. Of specific interest are applications of HTS technologies to mm and microwave systems, spaceborne and planet-surface sensors, and to magnetic subsystems for robotic, rescue, and docking maneuvers. HTS technologies can be used in optoelectronics, magnetic-field detectors, antennae, transmission/delay lines, and launch/payload coils.

Study on the effect of transition curve to the dynamic characteristics of high-temperature superconducting maglev

NASA Astrophysics Data System (ADS)

Qian, Nan; Zheng, Botian; Gou, Yanfeng; Chen, Ping; Zheng, Jun; Deng, Zigang

2015-12-01

High temperature superconducting (HTS) maglev technology is becoming more and more mature, and many key technologies have been deeply studied. However, the transition curve plays a key role in HTS maglev system, and related studies have not been carried out. In this paper series of simulations were conducted to test the lateral and vertical vibration of HTS maglev when passing through curves. Two magnetic guideways, of which one has transition curves but the other does not, are designed to test the vibration characteristics of a mini HTS maglev model running though curves. Results show that after adding transition curves between straight line and circular curve the vibration of HTS maglev model in lateral and vertical directions are all weakened in different degrees. It proves that adding transition curve into HTS maglev system is favorable and necessary.

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data.

PubMed

Massouras, Andreas; Decouttere, Frederik; Hens, Korneel; Deplancke, Bart

2010-07-01

High-throughput sequencing (HTS) is revolutionizing our ability to obtain cheap, fast and reliable sequence information. Many experimental approaches are expected to benefit from the incorporation of such sequencing features in their pipeline. Consequently, software tools that facilitate such an incorporation should be of great interest. In this context, we developed WebPrInSeS, a web server tool allowing automated full-length clone sequence identification and verification using HTS data. WebPrInSeS encompasses two separate software applications. The first is WebPrInSeS-C which performs automated sequence verification of user-defined open-reading frame (ORF) clone libraries. The second is WebPrInSeS-E, which identifies positive hits in cDNA or ORF-based library screening experiments such as yeast one- or two-hybrid assays. Both tools perform de novo assembly using HTS data from any of the three major sequencing platforms. Thus, WebPrInSeS provides a highly integrated, cost-effective and efficient way to sequence-verify or identify clones of interest. WebPrInSeS is available at http://webprinses.epfl.ch/ and is open to all users.

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data

PubMed Central

Massouras, Andreas; Decouttere, Frederik; Hens, Korneel; Deplancke, Bart

2010-01-01

High-throughput sequencing (HTS) is revolutionizing our ability to obtain cheap, fast and reliable sequence information. Many experimental approaches are expected to benefit from the incorporation of such sequencing features in their pipeline. Consequently, software tools that facilitate such an incorporation should be of great interest. In this context, we developed WebPrInSeS, a web server tool allowing automated full-length clone sequence identification and verification using HTS data. WebPrInSeS encompasses two separate software applications. The first is WebPrInSeS-C which performs automated sequence verification of user-defined open-reading frame (ORF) clone libraries. The second is WebPrInSeS-E, which identifies positive hits in cDNA or ORF-based library screening experiments such as yeast one- or two-hybrid assays. Both tools perform de novo assembly using HTS data from any of the three major sequencing platforms. Thus, WebPrInSeS provides a highly integrated, cost-effective and efficient way to sequence-verify or identify clones of interest. WebPrInSeS is available at http://webprinses.epfl.ch/ and is open to all users. PMID:20501601

Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens

PubMed Central

Loreille, Odile; Ratnayake, Shashikala; Stockwell, Timothy B.; Mallick, Swapan; Skoglund, Pontus; Onorato, Anthony J.; Bergman, Nicholas H.; Reich, David; Irwin, Jodi A.

2018-01-01

High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens. PMID:29494531

Savant Genome Browser 2: visualization and analysis for population-scale genomics.

PubMed

Fiume, Marc; Smith, Eric J M; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M; Robinson, Mark D; Wodak, Shoshana J; Brudno, Michael

2012-07-01

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com.

Savant Genome Browser 2: visualization and analysis for population-scale genomics

PubMed Central

Smith, Eric J. M.; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M.; Robinson, Mark D.; Wodak, Shoshana J.; Brudno, Michael

2012-01-01

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com. PMID:22638571

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.

PubMed

Althammer, Sonja; González-Vallinas, Juan; Ballaré, Cecilia; Beato, Miguel; Eyras, Eduardo

2011-12-15

High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein-DNA and protein-RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing. We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics. Open-source software, with tutorials and protocol files, is available at http://regulatorygenomics.upf.edu/pyicos or as a Galaxy server at http://regulatorygenomics.upf.edu/galaxy eduardo.eyras@upf.edu Supplementary data are available at Bioinformatics online.

Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding

PubMed Central

Best, Katharine; Oakes, Theres; Heather, James M.; Shawe-Taylor, John; Chain, Benny

2015-01-01

The polymerase chain reaction (PCR) is one of the most widely used techniques in molecular biology. In combination with High Throughput Sequencing (HTS), PCR is widely used to quantify transcript abundance for RNA-seq, and in the context of analysis of T and B cell receptor repertoires. In this study, we combine DNA barcoding with HTS to quantify PCR output from individual target molecules. We develop computational tools that simulate both the PCR branching process itself, and the subsequent subsampling which typically occurs during HTS sequencing. We explore the influence of different types of heterogeneity on sequencing output, and compare them to experimental results where the efficiency of amplification is measured by barcodes uniquely identifying each molecule of starting template. Our results demonstrate that the PCR process introduces substantial amplification heterogeneity, independent of primer sequence and bulk experimental conditions. This heterogeneity can be attributed both to inherited differences between different template DNA molecules, and the inherent stochasticity of the PCR process. The results demonstrate that PCR heterogeneity arises even when reaction and substrate conditions are kept as constant as possible, and therefore single molecule barcoding is essential in order to derive reproducible quantitative results from any protocol combining PCR with HTS. PMID:26459131

A magnetic levitation rotating plate model based on high-Tc superconducting technology

NASA Astrophysics Data System (ADS)

Zheng, Jun; Li, Jipeng; Sun, Ruixue; Qian, Nan; Deng, Zigang

2017-09-01

With the wide requirements of the training aids and display models of science, technology and even industrial products for the public like schools, museums and pleasure grounds, a simple-structure and long-term stable-levitation technology is needed for these exhibitions. Opportunely, high temperature superconducting (HTS) technology using bulk superconductors indeed has prominent advantages on magnetic levitation and suspension for its self-stable characteristic in an applied magnetic field without any external power or control. This paper explores the feasibility of designing a rotatable magnetic levitation (maglev) plate model with HTS bulks placed beneath a permanent magnet (PM) plate. The model is featured with HTS bulks together with their essential cryogenic equipment above and PMs below, therefore it eliminates the unclear visual effects by spray due to the low temperature coolant such as liquid nitrogen (LN2) and additional levitation weight of the cryogenic equipment. Besides that, a matched LN2 automation filling system is adopted to help achieving a long-term working state of the rotatable maglev plate. The key low-temperature working condition for HTS bulks is maintained by repeatedly opening a solenoid valve and automatically filling LN2 under the monitoring of a temperature sensor inside the cryostat. With the support of the cryogenic devices, the HTS maglev system can meet all requirements of the levitating display model for exhibitions, and may enlighten the research work on HTS maglev applications.

The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data.

PubMed

Lammers, Youri; Peelen, Tamara; Vos, Rutger A; Gravendeel, Barbara

2014-02-06

Mixtures of internationally traded organic substances can contain parts of species protected by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). These mixtures often raise the suspicion of border control and customs offices, which can lead to confiscation, for example in the case of Traditional Chinese medicines (TCMs). High-throughput sequencing of DNA barcoding markers obtained from such samples provides insight into species constituents of mixtures, but manual cross-referencing of results against the CITES appendices is labor intensive. Matching DNA barcodes against NCBI GenBank using BLAST may yield misleading results both as false positives, due to incorrectly annotated sequences, and false negatives, due to spurious taxonomic re-assignment. Incongruence between the taxonomies of CITES and NCBI GenBank can result in erroneous estimates of illegal trade. The HTS barcode checker pipeline is an application for automated processing of sets of 'next generation' barcode sequences to determine whether these contain DNA barcodes obtained from species listed on the CITES appendices. This analytical pipeline builds upon and extends existing open-source applications for BLAST matching against the NCBI GenBank reference database and for taxonomic name reconciliation. In a single operation, reads are converted into taxonomic identifications matched with names on the CITES appendices. By inclusion of a blacklist and additional names databases, the HTS barcode checker pipeline prevents false positives and resolves taxonomic heterogeneity. The HTS barcode checker pipeline can detect and correctly identify DNA barcodes of CITES-protected species from reads obtained from TCM samples in just a few minutes. The pipeline facilitates and improves molecular monitoring of trade in endangered species, and can aid in safeguarding these species from extinction in the wild. The HTS barcode checker pipeline is available at https://github.com/naturalis/HTS-barcode-checker.

The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data

PubMed Central

2014-01-01

Background Mixtures of internationally traded organic substances can contain parts of species protected by the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). These mixtures often raise the suspicion of border control and customs offices, which can lead to confiscation, for example in the case of Traditional Chinese medicines (TCMs). High-throughput sequencing of DNA barcoding markers obtained from such samples provides insight into species constituents of mixtures, but manual cross-referencing of results against the CITES appendices is labor intensive. Matching DNA barcodes against NCBI GenBank using BLAST may yield misleading results both as false positives, due to incorrectly annotated sequences, and false negatives, due to spurious taxonomic re-assignment. Incongruence between the taxonomies of CITES and NCBI GenBank can result in erroneous estimates of illegal trade. Results The HTS barcode checker pipeline is an application for automated processing of sets of 'next generation’ barcode sequences to determine whether these contain DNA barcodes obtained from species listed on the CITES appendices. This analytical pipeline builds upon and extends existing open-source applications for BLAST matching against the NCBI GenBank reference database and for taxonomic name reconciliation. In a single operation, reads are converted into taxonomic identifications matched with names on the CITES appendices. By inclusion of a blacklist and additional names databases, the HTS barcode checker pipeline prevents false positives and resolves taxonomic heterogeneity. Conclusions The HTS barcode checker pipeline can detect and correctly identify DNA barcodes of CITES-protected species from reads obtained from TCM samples in just a few minutes. The pipeline facilitates and improves molecular monitoring of trade in endangered species, and can aid in safeguarding these species from extinction in the wild. The HTS barcode checker pipeline is available at https://github.com/naturalis/HTS-barcode-checker. PMID:24502833

Integrated Cryogenic Satellite Communications Cross-Link Receiver Experiment

NASA Technical Reports Server (NTRS)

Romanofsky, R. R.; Bhasin, K. B.; Downey, A. N.; Jackson, C. J.; Silver, A. H.; Javadi, H. H. S.

1995-01-01

An experiment has been devised which will validate, in space, a miniature, high-performance receiver. The receiver blends three complementary technologies; high temperature superconductivity (HTS), pseudomorphic high electron mobility transistor (PHEMT) monolithic microwave integrated circuits (MMIC), and a miniature pulse tube cryogenic cooler. Specifically, an HTS band pass filter, InP MMIC low noise amplifier, HTS-sapphire resonator stabilized local oscillator (LO), and a miniature pulse tube cooler will be integrated into a complete 20 GHz receiver downconverter. This cooled downconverter will be interfaced with customized signal processing electronics and integrated onto the space shuttle's 'HitchHiker' carrier. A pseudorandom data sequence will be transmitted to the receiver, which is in low Earth orbit (LEO), via the Advanced Communication Technology Satellite (ACTS) on a 20 GHz carrier. The modulation format is QPSK and the data rate is 2.048 Mbps. The bit error rate (BER) will be measured in situ. The receiver is also equipped with a radiometer mode so that experiment success is not totally contingent upon the BER measurement. In this mode, the receiver uses the Earth and deep space as a hot and cold calibration source, respectively. The experiment closely simulates an actual cross-link scenario. Since the receiver performance depends on channel conditions, its true characteristics would be masked in a terrestrial measurement by atmospheric absorption and background radiation. Furthermore, the receiver's performance depends on its physical temperature, which is a sensitive function of platform environment, thermal design, and cryocooler performance. This empirical data is important for building confidence in the technology.

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

PubMed Central

Althammer, Sonja; González-Vallinas, Juan; Ballaré, Cecilia; Beato, Miguel; Eyras, Eduardo

2011-01-01

Motivation: High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein–DNA and protein–RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing. Results: We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics. Availability: Open-source software, with tutorials and protocol files, is available at http://regulatorygenomics.upf.edu/pyicos or as a Galaxy server at http://regulatorygenomics.upf.edu/galaxy Contact: eduardo.eyras@upf.edu Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:21994224

Research Techniques Made Simple: High-Throughput Sequencing of the T-Cell Receptor.

PubMed

Matos, Tiago R; de Rie, Menno A; Teunissen, Marcel B M

2017-06-01

High-throughput sequencing (HTS) of the T-cell receptor (TCR) is a rapidly advancing technique that allows sensitive and accurate identification and quantification of every distinct T-cell clone present within any biological sample. The relative frequency of each individual clone within the full T-cell repertoire can also be studied. HTS is essential to expand our knowledge on the diversity of the TCR repertoire in homeostasis or under pathologic conditions, as well as to understand the kinetics of antigen-specific T-cell responses that lead to protective immunity (i.e., vaccination) or immune-related disorders (i.e., autoimmunity and cancer). HTS can be tailored for personalized medicine, having the potential to monitor individual responses to therapeutic interventions and show prognostic and diagnostic biomarkers. In this article, we briefly review the methodology, advances, and limitations of HTS of the TCR and describe emerging applications of this technique in the field of investigative dermatology. We highlight studying the pathogenesis of T cells in allergic dermatitis and the application of HTS of the TCR in diagnosing, detecting recurrence early, and monitoring responses to therapy in cutaneous T-cell lymphoma. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data

PubMed Central

Dorff, Kevin C.; Chambwe, Nyasha; Zeno, Zachary; Simi, Manuele; Shaknovich, Rita; Campagne, Fabien

2013-01-01

We present GobyWeb, a web-based system that facilitates the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension mechanism. Analyses currently supported include quantification of gene expression for messenger and small RNA sequencing, estimation of DNA methylation (i.e., reduced bisulfite sequencing and whole genome methyl-seq), or the detection of pathogens in sequenced data. In contrast to previous analysis pipelines developed for analysis of HTS data, GobyWeb requires significantly less storage space, runs analyses efficiently on a parallel grid, scales gracefully to process tens or hundreds of multi-gigabyte samples, yet can be used effectively by researchers who are comfortable using a web browser. We conducted performance evaluations of the software and found it to either outperform or have similar performance to analysis programs developed for specialized analyses of HTS data. We found that most biologists who took a one-hour GobyWeb training session were readily able to analyze RNA-Seq data with state of the art analysis tools. GobyWeb can be obtained at http://gobyweb.campagnelab.org and is freely available for non-commercial use. GobyWeb plugins are distributed in source code and licensed under the open source LGPL3 license to facilitate code inspection, reuse and independent extensions http://github.com/CampagneLaboratory/gobyweb2-plugins. PMID:23936070

High-Power, High-Temperature Superconductor Technology Development

NASA Technical Reports Server (NTRS)

Bhasin, Kul B.

2005-01-01

Since the first discovery of high-temperature superconductors (HTS) 10 years ago, the most promising areas for their applications in microwave systems have been as passive components for communication systems. Soon after the discovery, experiments showed that passive microwave circuits made from HTS material exceeded the performance of conventional devices for low-power applications and could be 10 times as small or smaller. However, for superconducting microwave components, high-power microwave applications have remained elusive until now. In 1996, DuPont and Com Dev Ltd. developed high-power superconducting materials and components for communication applications under a NASA Lewis Research Center cooperative agreement, NCC3-344 "High Power High Temperature Superconductor (HTS) Technology Development." The agreement was cost shared between the Defense Advanced Research Projects Agency's (DARPA) Technology Reinvestment Program Office and the two industrial partners. It has the following objectives: 1) Material development and characterization for high-power HTS applications; 2) Development and validation of generic high-power microwave components; 3) Development of a proof-of-concept model for a high-power six-channel HTS output multiplexer.

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

PubMed Central

2013-01-01

Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described. PMID:23475615

GrigoraSNPs: Optimized Analysis of SNPs for DNA Forensics.

PubMed

Ricke, Darrell O; Shcherbina, Anna; Michaleas, Adam; Fremont-Smith, Philip

2018-04-16

High-throughput sequencing (HTS) of single nucleotide polymorphisms (SNPs) enables additional DNA forensic capabilities not attainable using traditional STR panels. However, the inclusion of sets of loci selected for mixture analysis, extended kinship, phenotype, biogeographic ancestry prediction, etc., can result in large panel sizes that are difficult to analyze in a rapid fashion. GrigoraSNP was developed to address the allele-calling bottleneck that was encountered when analyzing SNP panels with more than 5000 loci using HTS. GrigoraSNPs uses a MapReduce parallel data processing on multiple computational threads plus a novel locus-identification hashing strategy leveraging target sequence tags. This tool optimizes the SNP calling module of the DNA analysis pipeline with runtimes that scale linearly with the number of HTS reads. Results are compared with SNP analysis pipelines implemented with SAMtools and GATK. GrigoraSNPs removes a computational bottleneck for processing forensic samples with large HTS SNP panels. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

ViDiT-CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications.

PubMed

Verhoeven, Joost Theo Petra; Canuti, Marta; Munro, Hannah J; Dufour, Suzanne C; Lang, Andrew S

2018-04-19

High-throughput sequencing (HTS) technologies are becoming increasingly important within microbiology research, but aspects of library preparation, such as high cost per sample or strict input requirements, make HTS difficult to implement in some niche applications and for research groups on a budget. To answer these necessities, we developed ViDiT, a customizable, PCR-based, extremely low-cost (<5 US dollars per sample) and versatile library preparation method, and CACTUS, an analysis pipeline designed to rely on cloud computing power to generate high-quality data from ViDiT-based experiments without the need of expensive servers. We demonstrate here the versatility and utility of these methods within three fields of microbiology: virus discovery, amplicon-based viral genome sequencing and microbiome profiling. ViDiT-CACTUS allowed the identification of viral fragments from 25 different viral families from 36 oropharyngeal-cloacal swabs collected from wild birds, the sequencing of three almost complete genomes of avian influenza A viruses (>90% coverage), and the characterization and functional profiling of the complete microbial diversity (bacteria, archaea, viruses) within a deep-sea carnivorous sponge. ViDiT-CACTUS demonstrated its validity in a wide range of microbiology applications and its simplicity and modularity make it easily implementable in any molecular biology laboratory, towards various research goals.

Older Adults' Perceptions of Home Telehealth Services

PubMed Central

Brenčič, Maja Makovec; Trkman, Peter; de Leonni Stanonik, Mateja

2013-01-01

Abstract The success of home telemedicine depends on end-user adoption, which has been slow despite rapid advances in technological development. This study focuses on an examination of significant factors that may predict the successful adoption of home telemedicine services (HTS) among older adults. Based on previous studies in the fields of remote patient monitoring, assisted living technologies, and consumer health information technology acceptance, eight factors were identified as a framework for qualitative testing. Twelve focus groups were conducted with an older population living in both urban and rural environments. The results reveal seven predictors that play an important role in perceptions of HTS: perceived usefulness, effort expectancy, social influence, perceived security, computer anxiety, facilitating conditions, and physicians' opinion. The results provide important insights in the field of older adults' acceptance of HTS, with guidelines for the strategic planning, developing, and marketing of HTS for the graying market. PMID:23931702

Human Genomic Loci Important in Common Infectious Diseases: Role of High-Throughput Sequencing and Genome-Wide Association Studies

PubMed Central

Sserwadda, Ivan; Amujal, Marion; Namatovu, Norah

2018-01-01

HIV/AIDS, tuberculosis (TB), and malaria are 3 major global public health threats that undermine development in many resource-poor settings. Recently, the notion that positive selection during epidemics or longer periods of exposure to common infectious diseases may have had a major effect in modifying the constitution of the human genome is being interrogated at a large scale in many populations around the world. This positive selection from infectious diseases increases power to detect associations in genome-wide association studies (GWASs). High-throughput sequencing (HTS) has transformed both the management of infectious diseases and continues to enable large-scale functional characterization of host resistance/susceptibility alleles and loci; a paradigm shift from single candidate gene studies. Application of genome sequencing technologies and genomics has enabled us to interrogate the host-pathogen interface for improving human health. Human populations are constantly locked in evolutionary arms races with pathogens; therefore, identification of common infectious disease-associated genomic variants/markers is important in therapeutic, vaccine development, and screening susceptible individuals in a population. This review describes a range of host-pathogen genomic loci that have been associated with disease susceptibility and resistant patterns in the era of HTS. We further highlight potential opportunities for these genetic markers. PMID:29755620

Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation.

PubMed

Szatkiewicz, Jin P; Wang, WeiBo; Sullivan, Patrick F; Wang, Wei; Sun, Wei

2013-02-01

Structural variation is an important class of genetic variation in mammals. High-throughput sequencing (HTS) technologies promise to revolutionize copy-number variation (CNV) detection but present substantial analytic challenges. Converging evidence suggests that multiple types of CNV-informative data (e.g. read-depth, read-pair, split-read) need be considered, and that sophisticated methods are needed for more accurate CNV detection. We observed that various sources of experimental biases in HTS confound read-depth estimation, and note that bias correction has not been adequately addressed by existing methods. We present a novel read-depth-based method, GENSENG, which uses a hidden Markov model and negative binomial regression framework to identify regions of discrete copy-number changes while simultaneously accounting for the effects of multiple confounders. Based on extensive calibration using multiple HTS data sets, we conclude that our method outperforms existing read-depth-based CNV detection algorithms. The concept of simultaneous bias correction and CNV detection can serve as a basis for combining read-depth with other types of information such as read-pair or split-read in a single analysis. A user-friendly and computationally efficient implementation of our method is freely available.

Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure.

PubMed

Donaldson, Michael E; Rico, Yessica; Hueffer, Karsten; Rando, Halie M; Kukekova, Anna V; Kyle, Christopher J

2018-01-01

Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization-based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to "capture" specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300-kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on-target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer-read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune-related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.

Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches*

PubMed Central

He, Guo-qing; Liu, Tong-jie; Sadiq, Faizan A.; Gu, Jing-si; Zhang, Guo-hua

2017-01-01

Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with Chinese traditional fermented foods using culture-dependent as well as culture-independent methods, like different high-throughput sequencing (HTS) techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in Chinese traditional fermented foods revealed by HTS approaches. PMID:28378567

Probing the Rare Biosphere of the North-West Mediterranean Sea: An Experiment with High Sequencing Effort.

PubMed

Crespo, Bibiana G; Wallhead, Philip J; Logares, Ramiro; Pedrós-Alió, Carlos

2016-01-01

High-throughput sequencing (HTS) techniques have suggested the existence of a wealth of species with very low relative abundance: the rare biosphere. We attempted to exhaustively map this rare biosphere in two water samples by performing an exceptionally deep pyrosequencing analysis (~500,000 final reads per sample). Species data were derived by a 97% identity criterion and various parametric distributions were fitted to the observed counts. Using the best-fitting Sichel distribution we estimate a total species richness of 1,568-1,669 (95% Credible Interval) and 5,027-5,196 for surface and deep water samples respectively, implying that 84-89% of the total richness in those two samples was sequenced, and we predict that a quadrupling of the present sequencing effort would suffice to observe 90% of the total richness in both samples. Comparing the HTS results with a culturing approach we found that most of the cultured taxa were not obtained by HTS, despite the high sequencing effort. Culturing therefore remains a useful tool for uncovering marine bacterial diversity, in addition to its other uses for studying the ecology of marine bacteria.

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

PubMed Central

Goodacre, Norman; Aljanahi, Aisha; Nandakumar, Subhiksha; Mikailov, Mike

2018-01-01

ABSTRACT Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank. IMPORTANCE To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have developed a new reference viral database (RVDB) that provides a broad representation of different virus species from eukaryotes by including all viral, virus-like, and virus-related sequences (excluding bacteriophages), regardless of their size. In particular, RVDB contains endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Sequences were clustered to reduce redundancy while retaining high viral sequence diversity. A particularly useful feature of RVDB is the reduction of cellular sequences, which can enhance the run efficiency of large transcriptomic and genomic data analysis and increase the specificity of virus detection. PMID:29564396

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection.

PubMed

Goodacre, Norman; Aljanahi, Aisha; Nandakumar, Subhiksha; Mikailov, Mike; Khan, Arifa S

2018-01-01

Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank. IMPORTANCE To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have developed a new reference viral database (RVDB) that provides a broad representation of different virus species from eukaryotes by including all viral, virus-like, and virus-related sequences (excluding bacteriophages), regardless of their size. In particular, RVDB contains endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Sequences were clustered to reduce redundancy while retaining high viral sequence diversity. A particularly useful feature of RVDB is the reduction of cellular sequences, which can enhance the run efficiency of large transcriptomic and genomic data analysis and increase the specificity of virus detection.

Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles

PubMed Central

Zheng, Yun; Ji, Bo; Song, Renhua; Wang, Shengpeng; Li, Ting; Zhang, Xiaotuo; Chen, Kun; Li, Tianqing; Li, Jinyan

2016-01-01

Various types of mutation and editing (M/E) events in microRNAs (miRNAs) can change the stabilities of pre-miRNAs and/or complementarities between miRNAs and their targets. Small RNA (sRNA) high-throughput sequencing (HTS) profiles can contain many mutated and edited miRNAs. Systematic detection of miRNA mutation and editing sites from the huge volume of sRNA HTS profiles is computationally difficult, as high sensitivity and low false positive rate (FPR) are both required. We propose a novel method (named MiRME) for an accurate and fast detection of miRNA M/E sites using a progressive sequence alignment approach which refines sensitivity and improves FPR step-by-step. From 70 sRNA HTS profiles with over 1.3 billion reads, MiRME has detected thousands of statistically significant M/E sites, including 3′-editing sites, 57 A-to-I editing sites (of which 32 are novel), as well as some putative non-canonical editing sites. We demonstrated that a few non-canonical editing sites were not resulted from mutations in genome by integrating the analysis of genome HTS profiles of two human cell lines, suggesting the existence of new editing types to further diversify the functions of miRNAs. Compared with six existing studies or methods, MiRME has shown much superior performance for the identification and visualization of the M/E sites of miRNAs from the ever-increasing sRNA HTS profiles. PMID:27229138

A Robotic Platform for Quantitative High-Throughput Screening

PubMed Central

Michael, Sam; Auld, Douglas; Klumpp, Carleen; Jadhav, Ajit; Zheng, Wei; Thorne, Natasha; Austin, Christopher P.; Inglese, James

2008-01-01

Abstract High-throughput screening (HTS) is increasingly being adopted in academic institutions, where the decoupling of screening and drug development has led to unique challenges, as well as novel uses of instrumentation, assay formulations, and software tools. Advances in technology have made automated unattended screening in the 1,536-well plate format broadly accessible and have further facilitated the exploration of new technologies and approaches to screening. A case in point is our recently developed quantitative HTS (qHTS) paradigm, which tests each library compound at multiple concentrations to construct concentration-response curves (CRCs) generating a comprehensive data set for each assay. The practical implementation of qHTS for cell-based and biochemical assays across libraries of > 100,000 compounds (e.g., between 700,000 and 2,000,000 sample wells tested) requires maximal efficiency and miniaturization and the ability to easily accommodate many different assay formats and screening protocols. Here, we describe the design and utilization of a fully integrated and automated screening system for qHTS at the National Institutes of Health's Chemical Genomics Center. We report system productivity, reliability, and flexibility, as well as modifications made to increase throughput, add additional capabilities, and address limitations. The combination of this system and qHTS has led to the generation of over 6 million CRCs from > 120 assays in the last 3 years and is a technology that can be widely implemented to increase efficiency of screening and lead generation. PMID:19035846

An overview of rotating machine systems with high-temperature bulk superconductors

NASA Astrophysics Data System (ADS)

Zhou, Difan; Izumi, Mitsuru; Miki, Motohiro; Felder, Brice; Ida, Tetsuya; Kitano, Masahiro

2012-10-01

The paper contains a review of recent advancements in rotating machines with bulk high-temperature superconductors (HTS). The high critical current density of bulk HTS enables us to design rotating machines with a compact configuration in a practical scheme. The development of an axial-gap-type trapped flux synchronous rotating machine together with the systematic research works at the Tokyo University of Marine Science and Technology since 2001 are briefly introduced. Developments in bulk HTS rotating machines in other research groups are also summarized. The key issues of bulk HTS machines, including material progress of bulk HTS, in situ magnetization, and cooling together with AC loss at low-temperature operation are discussed.

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa.

PubMed

Geisen, S; Laros, I; Vizcaíno, A; Bonkowski, M; de Groot, G A

2015-09-01

Protists, the most diverse eukaryotes, are largely considered to be free-living bacterivores, but vast numbers of taxa are known to parasitize plants or animals. High-throughput sequencing (HTS) approaches now commonly replace cultivation-based approaches in studying soil protists, but insights into common biases associated with this method are limited to aquatic taxa and samples. We created a mock community of common free-living soil protists (amoebae, flagellates, ciliates), extracted DNA and amplified it in the presence of metazoan DNA using 454 HTS. We aimed at evaluating whether HTS quantitatively reveals true relative abundances of soil protists and at investigating whether the expected protist community structure is altered by the co-amplification of metazoan-associated protist taxa. Indeed, HTS revealed fundamentally different protist communities from those expected. Ciliate sequences were highly over-represented, while those of most amoebae and flagellates were under-represented or totally absent. These results underpin the biases introduced by HTS that prevent reliable quantitative estimations of free-living protist communities. Furthermore, we detected a wide range of nonadded protist taxa probably introduced along with metazoan DNA, which altered the protist community structure. Among those, 20 taxa most closely resembled parasitic, often pathogenic taxa. Therewith, we provide the first HTS data in support of classical observational studies that showed that potential protist parasites are hosted by soil metazoa. Taken together, profound differences in amplification success between protist taxa and an inevitable co-extraction of protist taxa parasitizing soil metazoa obscure the true diversity of free-living soil protist communities. © 2015 John Wiley & Sons Ltd.

High throughput screening technologies for ion channels

PubMed Central

Yu, Hai-bo; Li, Min; Wang, Wei-ping; Wang, Xiao-liang

2016-01-01

Ion channels are involved in a variety of fundamental physiological processes, and their malfunction causes numerous human diseases. Therefore, ion channels represent a class of attractive drug targets and a class of important off-targets for in vitro pharmacological profiling. In the past decades, the rapid progress in developing functional assays and instrumentation has enabled high throughput screening (HTS) campaigns on an expanding list of channel types. Chronologically, HTS methods for ion channels include the ligand binding assay, flux-based assay, fluorescence-based assay, and automated electrophysiological assay. In this review we summarize the current HTS technologies for different ion channel classes and their applications. PMID:26657056

Identification and Correction of Additive and Multiplicative Spatial Biases in Experimental High-Throughput Screening.

PubMed

Mazoure, Bogdan; Caraus, Iurie; Nadon, Robert; Makarenkov, Vladimir

2018-06-01

Data generated by high-throughput screening (HTS) technologies are prone to spatial bias. Traditionally, bias correction methods used in HTS assume either a simple additive or, more recently, a simple multiplicative spatial bias model. These models do not, however, always provide an accurate correction of measurements in wells located at the intersection of rows and columns affected by spatial bias. The measurements in these wells depend on the nature of interaction between the involved biases. Here, we propose two novel additive and two novel multiplicative spatial bias models accounting for different types of bias interactions. We describe a statistical procedure that allows for detecting and removing different types of additive and multiplicative spatial biases from multiwell plates. We show how this procedure can be applied by analyzing data generated by the four HTS technologies (homogeneous, microorganism, cell-based, and gene expression HTS), the three high-content screening (HCS) technologies (area, intensity, and cell-count HCS), and the only small-molecule microarray technology available in the ChemBank small-molecule screening database. The proposed methods are included in the AssayCorrector program, implemented in R, and available on CRAN.

Detecting and overcoming systematic bias in high-throughput screening technologies: a comprehensive review of practical issues and methodological solutions.

PubMed

Caraus, Iurie; Alsuwailem, Abdulaziz A; Nadon, Robert; Makarenkov, Vladimir

2015-11-01

Significant efforts have been made recently to improve data throughput and data quality in screening technologies related to drug design. The modern pharmaceutical industry relies heavily on high-throughput screening (HTS) and high-content screening (HCS) technologies, which include small molecule, complementary DNA (cDNA) and RNA interference (RNAi) types of screening. Data generated by these screening technologies are subject to several environmental and procedural systematic biases, which introduce errors into the hit identification process. We first review systematic biases typical of HTS and HCS screens. We highlight that study design issues and the way in which data are generated are crucial for providing unbiased screening results. Considering various data sets, including the publicly available ChemBank data, we assess the rates of systematic bias in experimental HTS by using plate-specific and assay-specific error detection tests. We describe main data normalization and correction techniques and introduce a general data preprocessing protocol. This protocol can be recommended for academic and industrial researchers involved in the analysis of current or next-generation HTS data. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Identification and characterization of EBV genomes in spontaneously immortalized human peripheral blood B lymphocytes by NGS technology.

PubMed

Lei, Haiyan; Li, Tianwei; Hung, Guo-Chiuan; Li, Bingjie; Tsai, Shien; Lo, Shyh-Ching

2013-11-19

We conducted genomic sequencing to identify Epstein Barr Virus (EBV) genomes in 2 human peripheral blood B lymphocytes that underwent spontaneous immortalization promoted by mycoplasma infections in culture, using the high-throughput sequencing (HTS) Illumina MiSeq platform. The purpose of this study was to examine if rapid detection and characterization of a viral agent could be effectively achieved by HTS using a platform that has become readily available in general biology laboratories. Raw read sequences, averaging 175 bps in length, were mapped with DNA databases of human, bacteria, fungi and virus genomes using the CLC Genomics Workbench bioinformatics tool. Overall 37,757 out of 49,520,834 total reads in one lymphocyte line (# K4413-Mi) and 28,178 out of 45,335,960 reads in the other lymphocyte line (# K4123-Mi) were identified as EBV sequences. The two EBV genomes with estimated 35.22-fold and 31.06-fold sequence coverage respectively, designated K4413-Mi EBV and K4123-Mi EBV (GenBank accession number KC440852 and KC440851 respectively), are characteristic of type-1 EBV. Sequence comparison and phylogenetic analysis among K4413-Mi EBV, K4123-Mi EBV and the EBV genomes previously reported to GenBank as well as the NA12878 EBV genome assembled from database of the 1000 Genome Project showed that these 2 EBVs are most closely related to B95-8, an EBV previously isolated from a patient with infectious mononucleosis and WT-EBV. They are less similar to EBVs associated with nasopharyngeal carcinoma (NPC) from Hong Kong and China as well as the Akata strain of a case of Burkitt's lymphoma from Japan. They are most different from type 2 EBV found in Western African Burkitt's lymphoma.

HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

PubMed

David, Fabrice P A; Delafontaine, Julien; Carat, Solenne; Ross, Frederick J; Lefebvre, Gregory; Jarosz, Yohan; Sinclair, Lucas; Noordermeer, Daan; Rougemont, Jacques; Leleu, Marion

2014-01-01

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch.

HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

PubMed Central

David, Fabrice P. A.; Delafontaine, Julien; Carat, Solenne; Ross, Frederick J.; Lefebvre, Gregory; Jarosz, Yohan; Sinclair, Lucas; Noordermeer, Daan; Rougemont, Jacques; Leleu, Marion

2014-01-01

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch. PMID:24475057

A perspective on 10-years HTS experience at the Walter and Eliza Hall Institute of Medical Research - eighteen million assays and counting.

PubMed

Lackovic, Kurt; Lessene, Guillaume; Falk, Hendrik; Leuchowius, Karl-Johan; Baell, Jonathan; Street, Ian

2014-03-01

The Walter and Eliza Hall Institute of Medical Research (WEHI) is Australia's longest serving medical research institute. WEHI's High Throughput Screening (HTS) Facility was established in 2003 with $5 million of infrastructure funds invested by WEHI, and the Victorian State Government's Strategic Technology Initiative through Bio21 Australia Ltd. The Facility was Australia's first truly academic HTS facility and was one of only a handful operating in publicly funded institutions worldwide at that time. The objectives were to provide access to enabling HTS technologies, such as assay design, liquid handling automation, compound libraries and expertise to promote translation of basic research in a national setting that has a relatively young biotech sector and does not have a big Pharma research presence. Ten years on and the WEHI HTS Facility has participated in over 92 collaborative projects, generated over 18 million data points, and most importantly, projects that began in the Facility have been commercialized successfully (due to strong ties with Business Development and emphasis on intellectual property management) and now have molecules progressing in clinical trials.

Development of non-destructive evaluation system using an HTS-SQUID gradiometer for magnetized materials

NASA Astrophysics Data System (ADS)

Kawano, J.; Tsukamoto, A.; Adachi, S.; Oshikubo, Y.; Hato, T.; Tanabe, K.; Okamura, T.

We have developed a new eddy-current non-destructive evaluation (NDE) system using an HTS SQUID gradiometer with the aim of applying it to practical materials with magnetization. The new NDE system employs a LN2-cooled external Cu pickup coil and an HTS SQUID chip placed in a magnetic shield made of HTS material. The HTS SQUID chip consists of an HTS planar gradiometer manufactured by using a ramp-edge junction technology and a multi-turn HTS thin film input coil coupled with the flip-chip configuration. The first-order coaxial gradiometric Cu pickup coil with a diameter of 16 mm and the baseline of 5.6 mm was used in the present NDE experiments. By using this NDE system, we could observe defect-induced magnetic signals without an appreciable influence of magnetization up to 10 mT. We also examined the ability of detecting deep-lying defects and compared with the results obtained using our previous NDE system.

Microbial ecology involved in the ripening of naturally fermented llama meat sausages. A focus on lactobacilli diversity.

PubMed

Fontana, Cecilia; Bassi, Daniela; López, Constanza; Pisacane, Vincenza; Otero, Maria Claudia; Puglisi, Edoardo; Rebecchi, Annalisa; Cocconcelli, Pier Sandro; Vignolo, Graciela

2016-11-07

Llama represents for the Andean regions a valid alternative to bovine and pork meat and thanks to the high proteins and low fat content; it can constitute a good product for the novel food market. In this study, culture-dependent and independent methods were applied to investigate the microbial ecology of naturally fermented llama sausages produced in Northwest Argentina. Two different production technologies of llama sausage were investigated: a pilot-plant scale (P) and an artisanal one (A). Results obtained by High-Throughput Sequencing (HTS) of 16S rRNA amplicons showed that the production technologies influenced the development of microbial communities with a different composition throughout the entire fermentation process. Both sequencing and microbiological counts demonstrated that Lactic Acid Bacteria (LAB) contributed largely to the dominant microbiota. When a total of 230 isolates were approached by RAPD-PCR, presumptive LAB strains from P production exhibited an initial variability in RAPD fingerprints switching to a single profile at the final of ripening, while A production revealed a more heterogeneous RAPD pattern during the whole fermentation process. The constant presence of Lactobacillus sakei along the fermentation in both productions was revealed by HTS and confirmed by species-specific PCR from isolated strains. The technological characterization of Lb. sakei isolates evidenced their ability to grow at 15°C, pH4.5 and 5% NaCl (95%). Most strains hydrolyzed myofibrillar and sarcoplasmic proteins. Bacteriocins encoding genes and antimicrobial resistance were found in 35% and 42.5% of the strains, respectively. An appropriate choice of a combination of autochthonous strains in a starter formulation is fundamental to improve and standardize llama sausages safety and quality. Copyright © 2016 Elsevier B.V. All rights reserved.

Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons.

PubMed

Połka, Justyna; Rebecchi, Annalisa; Pisacane, Vincenza; Morelli, Lorenzo; Puglisi, Edoardo

2015-04-01

The bacterial diversity involved in food fermentations is one of the most important factors shaping the final characteristics of traditional foods. Knowledge about this diversity can be greatly improved by the application of high-throughput sequencing technologies (HTS) coupled to the PCR amplification of the 16S rRNA subunit. Here we investigated the bacterial diversity in batches of Salame Piacentino PDO (Protected Designation of Origin), a dry fermented sausage that is typical of a regional area of Northern Italy. Salami samples from 6 different local factories were analysed at 0, 21, 49 and 63 days of ripening; raw meat at time 0 and casing samples at 21 days of ripening where also analysed, and the effect of starter addition was included in the experimental set-up. Culture-based microbiological analyses and PCR-DGGE were carried out in order to be compared with HTS results. A total of 722,196 high quality sequences were obtained after trimming, paired-reads assembly and quality screening of raw reads obtained by Illumina MiSeq sequencing of the two bacterial 16S hypervariable regions V3 and V4; manual curation of 16S database allowed a correct taxonomical classification at the species for 99.5% of these reads. Results confirmed the presence of main bacterial species involved in the fermentation of salami as assessed by PCR-DGGE, but with a greater extent of resolution and quantitative assessments that are not possible by the mere analyses of gel banding patterns. Thirty-two different Staphylococcus and 33 Lactobacillus species where identified in the salami from different producers, while the whole data set obtained accounted for 13 main families and 98 rare ones, 23 of which were present in at least 10% of the investigated samples, with casings being the major sources of the observed diversity. Multivariate analyses also showed that batches from 6 local producers tend to cluster altogether after 21 days of ripening, thus indicating that HTS has the potential for fine scale differentiation of local fermented foods. Copyright © 2014 Elsevier Ltd. All rights reserved.

Assessing the Diversity of Rodent-Borne Viruses: Exploring of High-Throughput Sequencing and Classical Amplification/Sequencing Approaches.

PubMed

Drewes, Stephan; Straková, Petra; Drexler, Jan F; Jacob, Jens; Ulrich, Rainer G

2017-01-01

Rodents are distributed throughout the world and interact with humans in many ways. They provide vital ecosystem services, some species are useful models in biomedical research and some are held as pet animals. However, many rodent species can have adverse effects such as damage to crops and stored produce, and they are of health concern because of the transmission of pathogens to humans and livestock. The first rodent viruses were discovered by isolation approaches and resulted in break-through knowledge in immunology, molecular and cell biology, and cancer research. In addition to rodent-specific viruses, rodent-borne viruses are causing a large number of zoonotic diseases. Most prominent examples are reemerging outbreaks of human hemorrhagic fever disease cases caused by arena- and hantaviruses. In addition, rodents are reservoirs for vector-borne pathogens, such as tick-borne encephalitis virus and Borrelia spp., and may carry human pathogenic agents, but likely are not involved in their transmission to human. In our days, next-generation sequencing or high-throughput sequencing (HTS) is revolutionizing the speed of the discovery of novel viruses, but other molecular approaches, such as generic RT-PCR/PCR and rolling circle amplification techniques, contribute significantly to the rapidly ongoing process. However, the current knowledge still represents only the tip of the iceberg, when comparing the known human viruses to those known for rodents, the mammalian taxon with the largest species number. The diagnostic potential of HTS-based metagenomic approaches is illustrated by their use in the discovery and complete genome determination of novel borna- and adenoviruses as causative disease agents in squirrels. In conclusion, HTS, in combination with conventional RT-PCR/PCR-based approaches, resulted in a drastically increased knowledge of the diversity of rodent viruses. Future improvements of the used workflows, including bioinformatics analysis, will further enhance our knowledge and preparedness in case of the emergence of novel viruses. Classical virological and additional molecular approaches are needed for genome annotation and functional characterization of novel viruses, discovered by these technologies, and evaluation of their zoonotic potential. © 2017 Elsevier Inc. All rights reserved.

Study on stabilization and quench protection of coils wound of HTS coated conductors considering quench origins - Proposal of criteria for stabilization and quench protection

NASA Astrophysics Data System (ADS)

Tsukamoto, Osami; Fujimoto, Yasutaka; Takao, Tomoaki

2014-09-01

It has been considered that HTS coils are hard to be quenched because of high quench energy due to high critical temperature and high specific heat of HTS wires. Therefore, attention to quench protection was not much paid. However, HTS coils still have possibility to be quenched during operation by mainly the following two origins, (a) presence of non-recoverable local defects in the conductors and (b) temperature rise of long part of the conductor. Actually, severe quench accidents, such as burning coils, are occurring in various places as scales of HTS increased. Purposes of this paper are to study on behaviors of normal zone and hot spot temperature of wires during quench detect/energy dump sequence and to find criteria for the stability and quench protection. In the paper, criteria are proposed for stability and quench protection of HTS coils. A criterion for the stability is that a coil can be operated stably without a quench against defects in coil windings and that for quench protection is that a coil can be safely protected from damages caused by a quench due to temperature rise of long part of coil wires. The criteria are used as design rules for HTS coils.

Measurable residual disease detection by high-throughput sequencing improves risk stratification for pediatric B-ALL

PubMed Central

Wood, Brent; Wu, David; Crossley, Beryl; Dai, Yunfeng; Williamson, David; Gawad, Charles; Borowitz, Michael J.; Devidas, Meenakshi; Maloney, Kelly W.; Larsen, Eric; Winick, Naomi; Raetz, Elizabeth; Carroll, William L.; Hunger, Stephen P.; Loh, Mignon L.; Robins, Harlan

2018-01-01

Early response to induction chemotherapy is an important prognostic factor in B-lymphoblastic leukemia (B-ALL). Here, we compare high-throughput sequencing (HTS) of IGH and TRG genes vs flow cytometry (FC) for measurable residual disease (MRD) detection at the end of induction chemotherapy in pediatric patients with newly diagnosed B-ALL. Six hundred nineteen paired pretreatment and end-of-induction bone marrow samples from Children’s Oncology Group studies AALL0331 (clinicaltrials.gov #NCT00103285) (standard risk [SR]; with MRD by FC at any level) and AALL0232 (clinicaltrials.gov #NCT00075725) (high risk; with day 29 MRD <0.1% by FC) were evaluated by HTS and FC for event-free (EFS) and overall survival (OS). HTS and FC showed similar 5-year EFS and OS for MRD-positive and -negative patients using an MRD threshold of 0.01%. However, there was a high discordant rate with HTS identifying 55 (38.7%) more patients MRD positive at this threshold. These discrepant patients have worse outcomes than FC MRD-negative patients. In addition, the increased analytic sensitivity of HTS permitted identification of 19.9% of SR patients without MRD at any detectable level who had excellent 5-year EFS (98.1%) and OS (100%). The higher analytic sensitivity and lower false-negative rate of HTS improves upon FC for MRD detection in pediatric B-ALL by identifying a novel subset of patients at end of induction who are essentially cured using current chemotherapy and identifying MRD at 0.01% in up to one-third of patients who are missed at the same threshold by FC. PMID:29284596

Issues with RNA-seq analysis in non-model organisms: A salmonid example.

PubMed

Sundaram, Arvind; Tengs, Torstein; Grimholt, Unni

2017-10-01

High throughput sequencing (HTS) is useful for many purposes as exemplified by the other topics included in this special issue. The purpose of this paper is to look into the unique challenges of using this technology in non-model organisms where resources such as genomes, functional genome annotations or genome complexity provide obstacles not met in model organisms. To describe these challenges, we narrow our scope to RNA sequencing used to study differential gene expression in response to pathogen challenge. As a demonstration species we chose Atlantic salmon, which has a sequenced genome with poor annotation and an added complexity due to many duplicated genes. We find that our RNA-seq analysis pipeline deciphers between duplicates despite high sequence identity. However, annotation issues provide problems in linking differentially expressed genes to pathways. Also, comparing results between approaches and species are complicated due to lack of standardized annotation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cheminformatic Analysis of the US EPA ToxCast Chemical Library

EPA Science Inventory

The ToxCast project is employing high throughput screening (HTS) technologies, along with chemical descriptors and computational models, to develop approaches for screening and prioritizing environmental chemicals for further toxicity testing. ToxCast Phase I generated HTS data f...

Identification of a novel vitivirus from grapevines in New Zealand.

PubMed

Blouin, Arnaud G; Keenan, Sandi; Napier, Kathryn R; Barrero, Roberto A; MacDiarmid, Robin M

2018-01-01

We report a sequence of a novel vitivirus from Vitis vinifera obtained using two high-throughput sequencing (HTS) strategies on RNA. The initial discovery from small-RNA sequencing was confirmed by HTS of the total RNA and Sanger sequencing. The new virus has a genome structure similar to the one reported for other vitiviruses, with five open reading frames (ORFs) coding for the conserved domains described for members of that genus. Phylogenetic analysis of the complete genome sequence confirmed its affiliation to the genus Vitivirus, with the closest described viruses being grapevine virus E (GVE) and Agave tequilana leaf virus (ATLV). However, the virus we report is distinct and shares only 51% amino acid sequence identity with GVE in the replicase polyprotein and 66.8% amino acid sequence identity with ATLV in the coat protein. This is well below the threshold determined by the ICTV for species demarcation, and we propose that this virus represents a new species. It is provisionally named "grapevine virus G".

16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

PubMed Central

Razzauti, Maria; Bard, Emilie; Bernard, Maria; Brouat, Carine; Charbonnel, Nathalie; Dehne-Garcia, Alexandre; Loiseau, Anne; Tatard, Caroline; Tamisier, Lucie; Vayssier-Taussat, Muriel; Vignes, Helene

2016-01-01

ABSTRACT The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculus domesticus, 189 Rattus rattus, 93 Mastomys natalensis, and 221 Mastomys erythroleucus, collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia. Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable to continuous pathogen surveillance in the context of disease-monitoring programs. IMPORTANCE Several recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as positivity, prevalence, and coinfection, using 16S rRNA amplicon sequencing on an Illumina MiSeq platform. This procedure, applied to 711 rodents collected in West Africa, detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses. PMID:27822541

Commercialization of Medium Voltage HTS Triax TM Cable Systems

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

Knoll, David

2012-12-31

The original project scope that was established in 2007 aimed to install a 1,700 meter (1.1 mile) medium voltage HTS Triax{TM} cable system into the utility grid in New Orleans, LA. In 2010, however, the utility partner withdrew from the project, so the 1,700 meter cable installation was cancelled and the scope of work was reduced. The work then concentrated on the specific barriers to commercialization of HTS cable technology. The modified scope included long-length HTS cable design and testing, high voltage factory test development, optimized cooling system development, and HTS cable life-cycle analysis. In 2012, Southwire again analyzed themore » market for HTS cables and deemed the near term market acceptance to be low. The scope of work was further reduced to the completion of tasks already started and to testing of the existing HTS cable system in Columbus, OH. The work completed under the project included: • Long-length cable modeling and analysis • HTS wire evaluation and testing • Cable testing for AC losses • Optimized cooling system design • Life cycle testing of the HTS cable in Columbus, OH • Project management. The 200 meter long HTS Triax{TM} cable in Columbus, OH was incorporated into the project under the initial scope changes as a test bed for life cycle testing as well as the site for an optimized HTS cable cooling system. The Columbus cable utilizes the HTS TriaxTM design, so it provided an economical tool for these of the project tasks.« less

Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples.

PubMed

Kresse, Stine H; Namløs, Heidi M; Lorenz, Susanne; Berner, Jeanne-Marie; Myklebost, Ola; Bjerkehagen, Bodil; Meza-Zepeda, Leonardo A

2018-01-01

Nucleic acid material of adequate quality is crucial for successful high-throughput sequencing (HTS) analysis. DNA and RNA isolated from archival FFPE material are frequently degraded and not readily amplifiable due to chemical damage introduced during fixation. To identify optimal nucleic acid extraction kits, DNA and RNA quantity, quality and performance in HTS applications were evaluated. DNA and RNA were isolated from five sarcoma archival FFPE blocks, using eight extraction protocols from seven kits from three different commercial vendors. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave higher yields and better amplifiable DNA, but all protocols gave comparable HTS library yields using Agilent SureSelect XT and performed well in downstream variant calling. For RNA extraction, all protocols gave comparable yields and amplifiable RNA. However, for fusion gene detection using the Archer FusionPlex Sarcoma Assay, the truXTRAC FFPE RNA kit from Covaris and Agencourt FormaPure kit from Beckman Coulter showed the highest percentage of unique read-pairs, providing higher complexity of HTS data and more frequent detection of recurrent fusion genes. truXTRAC simultaneous DNA and RNA extraction gave similar outputs as individual protocols. These findings show that although successful HTS libraries could be generated in most cases, the different protocols gave variable quantity and quality for FFPE nucleic acid extraction. Selecting the optimal procedure is highly valuable and may generate results in borderline quality specimens.

Study on AC loss measurements of HTS power cable for standardizing

NASA Astrophysics Data System (ADS)

Mukoyama, Shinichi; Amemiya, Naoyuki; Watanabe, Kazuo; Iijima, Yasuhiro; Mido, Nobuhiro; Masuda, Takao; Morimura, Toshiya; Oya, Masayoshi; Nakano, Tetsutaro; Yamamoto, Kiyoshi

2017-09-01

High-temperature superconducting power cables (HTS cables) have been developed for more than 20 years. In addition of the cable developments, the test methods of the HTS cables have been discussed and proposed in many laboratories and companies. Recently the test methods of the HTS cables is required to standardize and to common in the world. CIGRE made the working group (B1-31) for the discussion of the test methods of the HTS cables as a power cable, and published the recommendation of the test method. Additionally, IEC TC20 submitted the New Work Item Proposal (NP) based on the recommendation of CIGRE this year, IEC TC20 and IEC TC90 started the standardization work on Testing of HTS AC cables. However, the individual test method that used to measure a performance of HTS cables hasn’t been established as world’s common methods. The AC loss is one of the most important properties to disseminate low loss and economical efficient HTS cables in the world. We regard to establish the method of the AC loss measurements in rational and in high accuracy. Japan is at a leading position in the AC loss study, because Japanese researchers have studied on the AC loss technically and scientifically, and also developed the effective technologies for the AC loss reduction. The JP domestic commission of TC90 made a working team to discussion the methods of the AC loss measurements for aiming an international standard finally. This paper reports about the AC loss measurement of two type of the HTS conductors, such as a HTS conductor without a HTS shield and a HTS conductor with a HTS shield. The AC loss measurement method is suggested by the electrical method..

Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis.

PubMed

Ferret, Yann; Caillault, Aurélie; Sebda, Shéhérazade; Duez, Marc; Grardel, Nathalie; Duployez, Nicolas; Villenet, Céline; Figeac, Martin; Preudhomme, Claude; Salson, Mikaël; Giraud, Mathieu

2016-05-01

High-throughput sequencing (HTS) is considered a technical revolution that has improved our knowledge of lymphoid and autoimmune diseases, changing our approach to leukaemia both at diagnosis and during follow-up. As part of an immunoglobulin/T cell receptor-based minimal residual disease (MRD) assessment of acute lymphoblastic leukaemia patients, we assessed the performance and feasibility of the replacement of the first steps of the approach based on DNA isolation and Sanger sequencing, using a HTS protocol combined with bioinformatics analysis and visualization using the Vidjil software. We prospectively analysed the diagnostic and relapse samples of 34 paediatric patients, thus identifying 125 leukaemic clones with recombinations on multiple loci (TRG, TRD, IGH and IGK), including Dd2/Dd3 and Intron/KDE rearrangements. Sequencing failures were halved (14% vs. 34%, P = 0.0007), enabling more patients to be monitored. Furthermore, more markers per patient could be monitored, reducing the probability of false negative MRD results. The whole analysis, from sample receipt to clinical validation, was shorter than our current diagnostic protocol, with equal resources. V(D)J recombination was successfully assigned by the software, even for unusual recombinations. This study emphasizes the progress that HTS with adapted bioinformatics tools can bring to the diagnosis of leukaemia patients. © 2016 John Wiley & Sons Ltd.

Development of Ulta-Efficient Electric Motors

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

Shoykhet, B.; Schiferl, R.; Duckworth, R.

2008-05-01

Electric motors utilize a large amount of electrical energy in utility and industrial applications. Electric motors constructed with high temperature superconducting (HTS) materials have the potential to dramatically reduce electric motor size and losses. HTS motors are best suited for large motor applications at ratings above 1000 horsepower (hp), where the energy savings from the efficiency improvement can overcome the additional power required to keep the superconductors on the rotor cooled. Large HTS based motors are expected to be half the volume and have half the losses of conventional induction motors of the same rating. For a 5000 hp industrialmore » motor, this energy savings can result in $50,000 in operating cost savings over the course of a single year of operation. Since large horsepower motors utilize (or convert) about 30% of the electrical power generated in the United States and about 70% of large motors are candidates for replacement by HTS motors, the annual energy savings potential through the utilization of HTS motors can be up to $1 Billion in the United States alone. Research in the application of HTS materials to electric motors has lead to a number of HTS motor prototypes yet no industrial HTS motor product has yet been introduced. These motor demonstrations have been synchronous motors with HTS field windings, on the rotor. Figure 1-1 shows a solid model rendering of this type of motor. The rotor winding is made with HTS coils that are held at cryogenic temperature by introducing cooling fluid from the cryocooler to the rotor through a transfer coupling. The stator winding is made of copper wire. The HTS winding is thermally isolated from the warm armature and motor shafts by a vacuum insulation space and through the use of composite torque tubes. The stator in Figure 1-1 is an air core stator in that the stator teeth and a small part of the yoke is made up of nonmagnetic material so the magnetic fields distribute themselves as if in air. Between the HTS field winding and the physical air gap is a series of concentric cylinders that act as vacuum insulation space walls as well as conducting paths for induced currents to flow in order to shield the HTS winding and the rotor cold space from time dependent fields. These time dependent fields may be caused by rotor hunting, during a change in motor load, or by non-fundamental component voltages and currents applied by the inverter. These motors are variable speed controlled by the inverter. Common large motor utility and industrial applications are pump and fan drives that are best suited by a variable speed motor. Inverter control of the HTS motor eliminates the need to design the rotor for line starting, which would dump a large amount of heat into the rotor that would then heavily tax the cryogenic cooling system. The field winding is fed by a brushless exciter that provides DC current to the HTS rotor winding. The stator winding is air or water cooled. Technical and commercial hurdles to industrial HTS motor product introduction and customer acceptance include (1) the high cost of HTS wire and the cryogenic cooling system components, (2) customer concerns about reliability of HTS motors, and (3) the ability to attain the loss reduction potential of large HTS motors. Reliance Electric has demonstrated a number of HTS based electric motors up to a 1000 hp, variable speed synchronous motor with an HTS field winding in the year 2000. In 2001 this motor was tested to 1600 hp with a sinusoidal (constant frequency) supply. Figure 1-2 shows the HTS motor on the dynamometer test stand in the Reliance Electric test lab. The extensive test program of the 1000 hp motor successfully demonstrated the technical feasibility of large HTS motors and the basic technologies involved, however the test results did indicate the need for design refinements. In addition, test results served to identify other more fundamental critical technology issues, and revealed the need to continue research efforts in order to improve future HTS motor first cost, reliability, and performance. The lessons learned from the development and testing of the 1000 hp motor were the basis for the tasks proposed for the project that is being described in this final report. These eight tasks and the technology and commercial issues they address are listed in Table 1-1.« less

Evaluating imputation algorithms for low-depth genotyping-by-sequencing (GBS) data

USDA-ARS?s Scientific Manuscript database

Well-powered genomic studies require genome-wide marker coverage across many individuals. For non-model species with few genomic resources, high-throughput sequencing (HTS) methods, such as Genotyping-By-Sequencing (GBS), offer an inexpensive alternative to array-based genotyping. Although affordabl...

Power system applications of high temperature superconductors

NASA Astrophysics Data System (ADS)

Garlick, W. G.

This paper presents an overview of potential applications for high temperature superconductors (HTSs) in the field of power engineering. For almost 10 years material scientists, chemists and physicists have had the freedom to find, explore and characterize the properties of new HTS materials. 10 years is not a long time in the development of a revolutionary technology, but it seems like an age to the engineer who has recognized its potential and waits impatiently for the technology to stabilize in order to apply it. Largely due to Government and Industry partnerships, only a few years after the discovery of HTS, electrical power applications based on HTS are now being designed and tested. These applications offer many benefits to the resident electrical system: increased energy efficiency, smaller equipment, reduced emissions, increased stability and reliability, deferred expansion and flexible transmission and distribution. They have a common focus: lower electricity costs, improved environmental quality and more competitive products for a global market. For HTS to become a commercial success, the development of materials technologies is necessary but not sufficient on its own; the development of a capability to design and manufacture products that use the materials is also fundamental to a viable and successful industrial base.

Generation of cell lines for drug discovery through random activation of gene expression: application to the human histamine H3 receptor.

PubMed

Song, J; Doucette, C; Hanniford, D; Hunady, K; Wang, N; Sherf, B; Harrington, J J; Brunden, K R; Stricker-Krongrad, A

2005-06-01

Target-based high-throughput screening (HTS) plays an integral role in drug discovery. The implementation of HTS assays generally requires high expression levels of the target protein, and this is typically accomplished using recombinant cDNA methodologies. However, the isolated gene sequences to many drug targets have intellectual property claims that restrict the ability to implement drug discovery programs. The present study describes the pharmacological characterization of the human histamine H3 receptor that was expressed using random activation of gene expression (RAGE), a technology that over-expresses proteins by up-regulating endogenous genes rather than introducing cDNA expression vectors into the cell. Saturation binding analysis using [125I]iodoproxyfan and RAGE-H3 membranes revealed a single class of binding sites with a K(D) value of 0.77 nM and a B(max) equal to 756 fmol/mg of protein. Competition binding studies showed that the rank order of potency for H3 agonists was N(alpha)-methylhistamine approximately (R)-alpha- methylhistamine > histamine and that the rank order of potency for H3 antagonists was clobenpropit > iodophenpropit > thioperamide. The same rank order of potency for H3 agonists and antagonists was observed in the functional assays as in the binding assays. The Fluorometic Imaging Plate Reader assays in RAGE-H3 cells gave high Z' values for agonist and antagonist screening, respectively. These results reveal that the human H3 receptor expressed with the RAGE technology is pharmacologically comparable to that expressed through recombinant methods. Moreover, the level of expression of the H3 receptor in the RAGE-H3 cells is suitable for HTS and secondary assays.

Human papillomavirus detection using the Abbott RealTime high-risk HPV tests compared with conventional nested PCR coupled to high-throughput sequencing of amplification products in cervical smear specimens from a Gabonese female population.

PubMed

Moussavou-Boundzanga, Pamela; Koumakpayi, Ismaël Hervé; Labouba, Ingrid; Leroy, Eric M; Belembaogo, Ernest; Berthet, Nicolas

2017-12-21

Cervical cancer is the fourth most common malignancy in women worldwide. However, screening with human papillomavirus (HPV) molecular tests holds promise for reducing cervical cancer incidence and mortality in low- and middle-income countries. The performance of the Abbott RealTime High-Risk HPV test (AbRT) was evaluated in 83 cervical smear specimens and compared with a conventional nested PCR coupled to high-throughput sequencing (HTS) to identify the amplicons. The AbRT assay detected at least one HPV genotype in 44.57% of women regardless of the grade of cervical abnormalities. Except for one case, good concordance was observed for the genotypes detected with the AbRT assay in the high-risk HPV category determined with HTS of the amplicon generated by conventional nested PCR. The AbRT test is an easy and reliable molecular tool and was as sensitive as conventional nested PCR in cervical smear specimens for detection HPVs associated with high-grade lesions. Moreover, sequencing amplicons using an HTS approach effectively identified the genotype of the hrHPV identified with the AbRT test.

An accurate bacterial DNA quantification assay for HTS library preparation of human biological samples.

PubMed

Seashols-Williams, Sarah; Green, Raquel; Wohlfahrt, Denise; Brand, Angela; Tan-Torres, Antonio Limjuco; Nogales, Francy; Brooks, J Paul; Singh, Baneshwar

2018-05-17

Sequencing and classification of microbial taxa within forensically relevant biological fluids has the potential for applications in the forensic science and biomedical fields. The quantity of bacterial DNA from human samples is currently estimated based on quantity of total DNA isolated. This method can miscalculate bacterial DNA quantity due to the mixed nature of the sample, and consequently library preparation is often unreliable. We developed an assay that can accurately and specifically quantify bacterial DNA within a mixed sample for reliable 16S ribosomal DNA (16S rDNA) library preparation and high throughput sequencing (HTS). A qPCR method was optimized using universal 16S rDNA primers, and a commercially available bacterial community DNA standard was used to develop a precise standard curve. Following qPCR optimization, 16S rDNA libraries from saliva, vaginal and menstrual secretions, urine, and fecal matter were amplified and evaluated at various DNA concentrations; successful HTS data were generated with as low as 20 pg of bacterial DNA. Changes in bacterial DNA quantity did not impact observed relative abundances of major bacterial taxa, but relative abundance changes of minor taxa were observed. Accurate quantification of microbial DNA resulted in consistent, successful library preparations for HTS analysis. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization and complete genome sequence of a previously uncharacterized panicovirus from Bermuda grass detected by high throughput sequencing

USDA-ARS?s Scientific Manuscript database

Bermuda grass samples were examined by transmission electron microscopy and 28-30 nm spherical virus particles were observed. Total RNA from these plants was subjected to high throughput sequencing (HTS). The nearly full genome sequence of a previously uncharacterized Panicovirus was identified from...

AC Application of HTS Conductors in Highly Dynamic Electric Motors

NASA Astrophysics Data System (ADS)

Oswald, B.; Best, K.-J.; Setzer, M.; Duffner, E.; Soell, M.; Gawalek, W.; Kovalev, L. K.

2006-06-01

Based on recent investigations we design highly dynamic electric motors up to 400 kW and linear motors up to 120 kN linear force using HTS bulk material and HTS tapes. The introduction of HTS tapes into AC applications in electric motors needs fundamental studies on double pancake coils under transversal magnetic fields. First theoretical and experimental results on AC field distributions in double-pancake-coils and corresponding AC losses will be presented. Based on these results the simulation of the motor performance confirms extremely high power density and efficiency of both types of electric motors. Improved characteristics of rare earth permanent magnets used in our motors at low temperatures give an additional technological benefit.

The University of Kansas High-Throughput Screening Laboratory. Part II: enabling collaborative drug-discovery partnerships through cutting-edge screening technology.

PubMed

McDonald, Peter R; Roy, Anuradha; Chaguturu, Rathnam

2011-07-01

The University of Kansas High-Throughput Screening (KU HTS) core is a state-of-the-art drug-discovery facility with an entrepreneurial open-service policy, which provides centralized resources supporting public- and private-sector research initiatives. The KU HTS core was established in 2002 at the University of Kansas with support from an NIH grant and the state of Kansas. It collaborates with investigators from national and international academic, nonprofit and pharmaceutical organizations in executing HTS-ready assay development and screening of chemical libraries for target validation, probe selection, hit identification and lead optimization. This is part two of a contribution from the KU HTS laboratory.

Fundamental study on the magnetic field control method using multiple HTS coils for Magnetic Drug Delivery System

NASA Astrophysics Data System (ADS)

Hirano, R.; Kim, S. B.; Nakagawa, T.; Tomisaka, Y.; Ueda, H.

2017-07-01

The magnetic drug delivery system (MDDS) is a key technology to reduce the side effects in the medical applications, and the magnetic force control is very important issue in MDDS. In this application, the strength of magnetic field and gradient required to MDDS devices are 54 mT and 5.5 T/m, respectively. We proposed the new magnetic force control system that consists of the multiple racetrack HTS magnets. We can control the magnetic field gradient along the longitudinal direction by the arrangement of the multiple racetrack HTS magnets and operating current of each magnet. When the racetrack HTS magnets were used, the critical current was reduced by the self-magnetic field. Therefore, the shape design of HTS magnet to reduce the magnet field into the surface of HTS tapes was required. Therefore, the electromagnetic analysis based on finite element method (FEM) was carried out to design and optimize the shape of multiple racetrack HTS magnet. We were able to suppress the reduction of critical current by placing the magnetic substance at upper and lower side of the HTS magnets. It was confirmed that obtained maximum values of magnetic field strength and field gradient were 33 mT and 0.18 T/m, respectively.

Human telomere sequence DNA in water-free and high-viscosity solvents: G-quadruplex folding governed by Kramers rate theory.

PubMed

Lannan, Ford M; Mamajanov, Irena; Hud, Nicholas V

2012-09-19

Structures formed by human telomere sequence (HTS) DNA are of interest due to the implication of telomeres in the aging process and cancer. We present studies of HTS DNA folding in an anhydrous, high viscosity deep eutectic solvent (DES) comprised of choline choride and urea. In this solvent, the HTS DNA forms a G-quadruplex with the parallel-stranded ("propeller") fold, consistent with observations that reduced water activity favors the parallel fold, whereas alternative folds are favored at high water activity. Surprisingly, adoption of the parallel structure by HTS DNA in the DES, after thermal denaturation and quick cooling to room temperature, requires several months, as opposed to less than 2 min in an aqueous solution. This extended folding time in the DES is, in part, due to HTS DNA becoming kinetically trapped in a folded state that is apparently not accessed in lower viscosity solvents. A comparison of times required for the G-quadruplex to convert from its aqueous-preferred folded state to its parallel fold also reveals a dependence on solvent viscosity that is consistent with Kramers rate theory, which predicts that diffusion-controlled transitions will slow proportionally with solvent friction. These results provide an enhanced view of a G-quadruplex folding funnel and highlight the necessity to consider solvent viscosity in studies of G-quadruplex formation in vitro and in vivo. Additionally, the solvents and analyses presented here should prove valuable for understanding the folding of many other nucleic acids and potentially have applications in DNA-based nanotechnology where time-dependent structures are desired.

Streptococcus himalayensis sp. nov., isolated from the respiratory tract of Marmota himalayana.

PubMed

Niu, Lina; Lu, Shan; Lai, Xin-He; Hu, Shoukui; Chen, Cuixia; Zhang, Gui; Yang, Jing; Jin, Dong; Wang, Yi; Lan, Ruiting; Lu, Gang; Xie, Yingping; Ye, Changyun; Xu, Jianguo

2017-02-01

Five strains of Gram-positive-staining, catalase-negative, coccus-shaped, chain-forming organisms isolated separately from the respiratory tracts of five Marmota himalayana animals in the Qinghai-Tibet Plateau of China were subjected to phenotypic and molecular taxonomic analyses. Comparative analysis of the 16S rRNA gene indicated that these singular organisms represent a new member of the genus Streptococcus, being phylogenetically closest to Streptococcus marmotae DSM 101995T (98.4 % similarity). The groEL, sodA and rpoB sequence analysis showed interspecies similarity values between HTS2T and Streptococcus. marmotae DSM 101995T, its closest phylogenetic relative based on 16S rRNA gene sequences, of 98.2, 78.8 and 93.7 %, respectively. A whole-genome phylogenetic tree built from 82 core genes of genomes from 16 species of the genus Streptococcus validated that HTS2T forms a distinct subline and exhibits specific phylogenetic affinity with S. marmotae. In silico DNA-DNA hybridization of HTS2T showed an estimated DNA reassociation value of 40.5 % with Streptococcus. marmotae DSM 101995T. On the basis of their phenotypic characteristics and phylogenetic findings, it is proposed that the five isolates be classified as representatives of a novel species of the genus Streptococcus, Streptococcus himalayensis sp. nov. The type strain is HTS2T (=DSM 101997T=CGMCC 1.15533T). The genome of Streptococcus himalayensis sp. nov. strain HTS2T contains 2195 genes with a size of 2 275 471 bp and a mean DNA G+C content of 41.3 mol%.

PubChem BioAssay: A Decade's Development toward Open High-Throughput Screening Data Sharing.

PubMed

Wang, Yanli; Cheng, Tiejun; Bryant, Stephen H

2017-07-01

High-throughput screening (HTS) is now routinely conducted for drug discovery by both pharmaceutical companies and screening centers at academic institutions and universities. Rapid advance in assay development, robot automation, and computer technology has led to the generation of terabytes of data in screening laboratories. Despite the technology development toward HTS productivity, fewer efforts were devoted to HTS data integration and sharing. As a result, the huge amount of HTS data was rarely made available to the public. To fill this gap, the PubChem BioAssay database ( https://www.ncbi.nlm.nih.gov/pcassay/ ) was set up in 2004 to provide open access to the screening results tested on chemicals and RNAi reagents. With more than 10 years' development and contributions from the community, PubChem has now become the largest public repository for chemical structures and biological data, which provides an information platform to worldwide researchers supporting drug development, medicinal chemistry study, and chemical biology research. This work presents a review of the HTS data content in the PubChem BioAssay database and the progress of data deposition to stimulate knowledge discovery and data sharing. It also provides a description of the database's data standard and basic utilities facilitating information access and use for new users.

A novel approach to tracking antigen-experienced CD4 T cells into functional compartments via tandem deep and shallow TCR clonotyping.

PubMed

Estorninho, Megan; Gibson, Vivienne B; Kronenberg-Versteeg, Deborah; Liu, Yuk-Fun; Ni, Chester; Cerosaletti, Karen; Peakman, Mark

2013-12-01

Extensive diversity in the human repertoire of TCRs for Ag is both a cornerstone of effective adaptive immunity that enables host protection against a multiplicity of pathogens and a weakness that gives rise to potential pathological self-reactivity. The complexity arising from diversity makes detection and tracking of single Ag-specific CD4 T cells (ASTs) involved in these immune responses challenging. We report a tandem, multistep process to quantify rare TCRβ-chain variable sequences of ASTs in large polyclonal populations. The approach combines deep high-throughput sequencing (HTS) within functional CD4 T cell compartments, such as naive/memory cells, with shallow, multiple identifier-based HTS of ASTs identified by activation marker upregulation after short-term Ag stimulation in vitro. We find that clonotypes recognizing HLA class II-restricted epitopes of both pathogen-derived Ags and self-Ags are oligoclonal and typically private. Clonotype tracking within an individual reveals private AST clonotypes resident in the memory population, as would be expected, representing clonal expansions (identical nucleotide sequence; "ultraprivate"). Other AST clonotypes share CDR3β amino acid sequences through convergent recombination and are found in memory populations of multiple individuals. Tandem HTS-based clonotyping will facilitate studying AST dynamics, epitope spreading, and repertoire changes that arise postvaccination and following Ag-specific immunotherapies for cancer and autoimmune disease.

Placing and preserving priorities: projects, productivity, progress and people

PubMed Central

Babiak, John

1998-01-01

High throughput screening (HTS) involves using automated equipment to test a large number of samples against a defined molecular target to identify a reasonable number of active molecules in a timely fashion. Major factors which can influence priorities for the limited resources of the HTS group are projects, productivity, progress and people. The challenge to the HTS group is to provide excellent and timely screening services, but still devote efforts to new technologies and personnel development. This article explains why these factors are so important. PMID:18924829

The University of Kansas High-Throughput Screening Laboratory. Part II: enabling collaborative drug-discovery partnerships through cutting-edge screening technology

PubMed Central

McDonald, Peter R; Roy, Anuradha; Chaguturu, Rathnam

2011-01-01

The University of Kansas High-Throughput Screening (KU HTS) core is a state-of-the-art drug-discovery facility with an entrepreneurial open-service policy, which provides centralized resources supporting public- and private-sector research initiatives. The KU HTS core was established in 2002 at the University of Kansas with support from an NIH grant and the state of Kansas. It collaborates with investigators from national and international academic, nonprofit and pharmaceutical organizations in executing HTS-ready assay development and screening of chemical libraries for target validation, probe selection, hit identification and lead optimization. This is part two of a contribution from the KU HTS laboratory. PMID:21806374

Miniaturization Technologies for Efficient Single-Cell Library Preparation for Next-Generation Sequencing.

PubMed

Mora-Castilla, Sergio; To, Cuong; Vaezeslami, Soheila; Morey, Robert; Srinivasan, Srimeenakshi; Dumdie, Jennifer N; Cook-Andersen, Heidi; Jenkins, Joby; Laurent, Louise C

2016-08-01

As the cost of next-generation sequencing has decreased, library preparation costs have become a more significant proportion of the total cost, especially for high-throughput applications such as single-cell RNA profiling. Here, we have applied novel technologies to scale down reaction volumes for library preparation. Our system consisted of in vitro differentiated human embryonic stem cells representing two stages of pancreatic differentiation, for which we prepared multiple biological and technical replicates. We used the Fluidigm (San Francisco, CA) C1 single-cell Autoprep System for single-cell complementary DNA (cDNA) generation and an enzyme-based tagmentation system (Nextera XT; Illumina, San Diego, CA) with a nanoliter liquid handler (mosquito HTS; TTP Labtech, Royston, UK) for library preparation, reducing the reaction volume down to 2 µL and using as little as 20 pg of input cDNA. The resulting sequencing data were bioinformatically analyzed and correlated among the different library reaction volumes. Our results showed that decreasing the reaction volume did not interfere with the quality or the reproducibility of the sequencing data, and the transcriptional data from the scaled-down libraries allowed us to distinguish between single cells. Thus, we have developed a process to enable efficient and cost-effective high-throughput single-cell transcriptome sequencing. © 2016 Society for Laboratory Automation and Screening.

Towards a 20 kA high temperature superconductor current lead module using REBCO tapes

NASA Astrophysics Data System (ADS)

Heller, R.; Bagrets, N.; Fietz, W. H.; Gröner, F.; Kienzler, A.; Lange, C.; Wolf, M. J.

2018-01-01

Most of the large fusion devices presently under construction or in operation consisting of superconducting magnets like EAST, Wendelstein 7-X (W7-X), JT-60SA, and ITER, use high temperature superconductor (HTS) current leads (CL) to reduce the cryogenic load and operational cost. In all cases, the 1st generation HTS material Bi-2223 is used which is embedded in a low-conductivity matrix of AgAu. In the meantime, industry worldwide concentrates on the production of the 2nd generation HTS REBCO material because of the better field performance in particular at higher temperature. As the new material can only be produced in a multilayer thin-film structure rather than as a multi-filamentary tape, the technology developed for Bi-2223-based current leads cannot be transferred directly to REBCO. Therefore, several laboratories are presently investigating the design of high current HTS current leads made of REBCO. Karlsruhe Institute of Technology is developing a 20 kA HTS current lead using brass-stabilized REBCO tapes—as a further development to the Bi-2223 design used in the JT-60SA current leads. The same copper heat exchanger module as in the 20 kA JT-60SA current lead will be used for simplicity, which will allow a comparison of the newly developed REBCO CL with the earlier produced and investigated CL for JT-60SA. The present paper discusses the design and accompanying test of single tape and stack REBCO mock-ups. Finally, the fabrication of the HTS module using REBCO stacks is described.

HTS-DB: an online resource to publish and query data from functional genomics high-throughput siRNA screening projects.

PubMed

Saunders, Rebecca E; Instrell, Rachael; Rispoli, Rossella; Jiang, Ming; Howell, Michael

2013-01-01

High-throughput screening (HTS) uses technologies such as RNA interference to generate loss-of-function phenotypes on a genomic scale. As these technologies become more popular, many research institutes have established core facilities of expertise to deal with the challenges of large-scale HTS experiments. As the efforts of core facility screening projects come to fruition, focus has shifted towards managing the results of these experiments and making them available in a useful format that can be further mined for phenotypic discovery. The HTS-DB database provides a public view of data from screening projects undertaken by the HTS core facility at the CRUK London Research Institute. All projects and screens are described with comprehensive assay protocols, and datasets are provided with complete descriptions of analysis techniques. This format allows users to browse and search data from large-scale studies in an informative and intuitive way. It also provides a repository for additional measurements obtained from screens that were not the focus of the project, such as cell viability, and groups these data so that it can provide a gene-centric summary across several different cell lines and conditions. All datasets from our screens that can be made available can be viewed interactively and mined for further hit lists. We believe that in this format, the database provides researchers with rapid access to results of large-scale experiments that might facilitate their understanding of genes/compounds identified in their own research. DATABASE URL: http://hts.cancerresearchuk.org/db/public.

Modelling of the test of the JT-60SA HTS current leads

NASA Astrophysics Data System (ADS)

Zappatore, A.; Heller, R.; Savoldi, L.; Zanino, R.

2017-07-01

The CURLEAD code, which was developed at the Karlsruhe Institute of Technology (KIT), implements an integrated 1D transient model of a high temperature superconducting (HTS) current lead (CL) including the room termination (RT), the meander-flow type heat exchanger (HX), and the HTS module. CURLEAD was successfully used for the design of the 70 kA ITER demonstrator and of the W7-X and JT-60SA CLs. Recently the code was successfully applied to the prediction and analysis of steady state operation of the ITER correction coils (CC) HTS CL. Here the steady state and pulsed operation of the JT-60SA HTS CLs are analysed, which requires also the modelling of the HX shell and of the vacuum shell, which was not present in the ITER CC. The CURLEAD model extension is presented and the capability of the new version of CURLEAD to reproduce the transient experimental data of the JT-60SA HTS CL is shown. The results obtained provide a better understanding of key parameters of the CL, among which the temperature evolution at the HX-HTS interface, the GHe mass flow rate needed in the HX to achieve the target temperature at that location and the heat load at the cold end.

Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates.

PubMed

Dowle, Eddy J; Pochon, Xavier; C Banks, Jonathan; Shearer, Karen; Wood, Susanna A

2016-09-01

Recent studies have advocated biomonitoring using DNA techniques. In this study, two high-throughput sequencing (HTS)-based methods were evaluated: amplicon metabarcoding of the cytochrome C oxidase subunit I (COI) mitochondrial gene and gene enrichment using MYbaits (targeting nine different genes including COI). The gene-enrichment method does not require PCR amplification and thus avoids biases associated with universal primers. Macroinvertebrate samples were collected from 12 New Zealand rivers. Macroinvertebrates were morphologically identified and enumerated, and their biomass determined. DNA was extracted from all macroinvertebrate samples and HTS undertaken using the illumina miseq platform. Macroinvertebrate communities were characterized from sequence data using either six genes (three of the original nine were not used) or just the COI gene in isolation. The gene-enrichment method (all genes) detected the highest number of taxa and obtained the strongest Spearman rank correlations between the number of sequence reads, abundance and biomass in 67% of the samples. Median detection rates across rare (<1% of the total abundance or biomass), moderately abundant (1-5%) and highly abundant (>5%) taxa were highest using the gene-enrichment method (all genes). Our data indicated primer biases occurred during amplicon metabarcoding with greater than 80% of sequence reads originating from one taxon in several samples. The accuracy and sensitivity of both HTS methods would be improved with more comprehensive reference sequence databases. The data from this study illustrate the challenges of using PCR amplification-based methods for biomonitoring and highlight the potential benefits of using approaches, such as gene enrichment, which circumvent the need for an initial PCR step. © 2015 John Wiley & Sons Ltd.

Development and production of second generation high Tc superconducting tapes at SuperOx and first tests of model cables

NASA Astrophysics Data System (ADS)

Lee, S.; Petrykin, V.; Molodyk, A.; Samoilenkov, S.; Kaul, A.; Vavilov, A.; Vysotsky, V.; Fetisov, S.

2014-04-01

The SuperOx and SuperOx Japan LLC companies were founded with the goal of developing a cost-effective technology for second generation HTS (2G HTS) tapes by utilizing a combination of the most advanced chemical and physical deposition techniques, together with implementing original tape architectures. In this paper we present a brief overview of our production and experimental facilities and recent results of 2G HTS tape fabrication, and describe the first tests of the tapes in model cables for AC and DC power application.

HTSeq--a Python framework to work with high-throughput sequencing data.

PubMed

Anders, Simon; Pyl, Paul Theodor; Huber, Wolfgang

2015-01-15

A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq. © The Author 2014. Published by Oxford University Press.

Optimization of High-Throughput Sequencing Kinetics for determining enzymatic rate constants of thousands of RNA substrates

PubMed Central

Niland, Courtney N.; Jankowsky, Eckhard; Harris, Michael E.

2016-01-01

Quantification of the specificity of RNA binding proteins and RNA processing enzymes is essential to understanding their fundamental roles in biological processes. High Throughput Sequencing Kinetics (HTS-Kin) uses high throughput sequencing and internal competition kinetics to simultaneously monitor the processing rate constants of thousands of substrates by RNA processing enzymes. This technique has provided unprecedented insight into the substrate specificity of the tRNA processing endonuclease ribonuclease P. Here, we investigate the accuracy and robustness of measurements associated with each step of the HTS-Kin procedure. We examine the effect of substrate concentration on the observed rate constant, determine the optimal kinetic parameters, and provide guidelines for reducing error in amplification of the substrate population. Importantly, we find that high-throughput sequencing, and experimental reproducibility contribute their own sources of error, and these are the main sources of imprecision in the quantified results when otherwise optimized guidelines are followed. PMID:27296633

Viruses associated with Antarctic wildlife: From serology based detection to identification of genomes using high throughput sequencing.

PubMed

Smeele, Zoe E; Ainley, David G; Varsani, Arvind

2018-01-02

The Antarctic, sub-Antarctic islands and surrounding sea-ice provide a unique environment for the existence of organisms. Nonetheless, birds and seals of a variety of species inhabit them, particularly during their breeding seasons. Early research on Antarctic wildlife health, using serology-based assays, showed exposure to viruses in the families Birnaviridae, Flaviviridae, Herpesviridae, Orthomyxoviridae and Paramyxoviridae circulating in seals (Phocidae), penguins (Spheniscidae), petrels (Procellariidae) and skuas (Stercorariidae). It is only during the last decade or so that polymerase chain reaction-based assays have been used to characterize viruses associated with Antarctic animals. Furthermore, it is only during the last five years that full/whole genomes of viruses (adenoviruses, anelloviruses, orthomyxoviruses, a papillomavirus, paramyoviruses, polyomaviruses and a togavirus) have been sequenced using Sanger sequencing or high throughput sequencing (HTS) approaches. This review summaries the knowledge of animal Antarctic virology and discusses potential future directions with the advent of HTS in virus discovery and ecology. Copyright © 2017 Elsevier B.V. All rights reserved.

Accelerating the introduction of HTS products for a broad range of electric power and industrial applications

NASA Astrophysics Data System (ADS)

Eaton, Russell

2002-01-01

The Department of Energy (DOE), as part of its Superconductivity Program for Electric Systems, is successfully pursuing the development of electric power and industrial devices, incorporating significant high-temperature superconducting (HTS) components or subsystems, through its innovative Superconducting Partnership Initiative (SPI). The objective of the SPI is to accelerate the commercial introduction of the HTS products for a broad range of electric power and industrial applications. DOE's approach to accomplishing the SPI objective is to support cost shared projects carried out by industry led teams. DOE will fund projects to develop HTS devices that are either in (1) the research and development stage (Phase 1), (2) the pre-commercialization stage (Phase II), or (3) the commercial entry stage (Phase III). DOE's industry partners must contribute at least half a project's costs. These teams will include capabilities needed to develop the device as well as to develop the business plan for the commercial product introduction. DOE's partners consist of vertically integrated teams consisting of equipment manufacturers, HTS wire and coil suppliers, national laboratories, and end users, primarily utilities. These partners carry out the multi-year technology development efforts, consisting generally of design, construction, and testing of the HTS system. Finally, commercialization of HTS products will be discussed primarily in terms of benefits these products will have over competing products based upon conventional conductors and the critical need for affordable, practical HTS materials and conductors for these applications. .

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

PubMed

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

2012-01-01

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

EPA's ToxCast Project: Lessons learned and future directions for use of HTS in predicting in vivo toxicology -- A Chemical Perspective

EPA Science Inventory

U.S. EPA’s ToxCast and the related Tox21 projects are employing high-throughput screening (HTS) technologies to profile thousands of chemicals, which in turn serve as probes of a wide diversity of targets, pathways and mechanisms related to toxicity. Initial models relating ToxCa...

The Role of HTS in Drug Discovery at the University of Michigan

PubMed Central

Larsen, Martha J.; Larsen, Scott D.; Fribley, Andrew; Grembecka, Jolanta; Homan, Kristoff; Mapp, Anna; Haak, Andrew; Nikolovska-Coleska, Zaneta; Stuckey, Jeanne A.; Sun, Duxin

2014-01-01

High throughput screening (HTS) is an integral part of a highly collaborative approach to drug discovery at the University of Michigan. The HTS lab is one of four core centers that provide services to identify, produce, screen and follow-up on biomedical targets for faculty. Key features of this system are: protein cloning and purification, protein crystallography, small molecule and siRNA HTS, medicinal chemistry and pharmacokinetics. Therapeutic areas that have been targeted include anti-bacterial, metabolic, neurodegenerative, cardiovascular, anti-cancer and anti-viral. The centers work in a coordinated, interactive environment to affordably provide academic investigators with the technology, informatics and expertise necessary for successful drug discovery. This review provides an overview of these centers at the University of Michigan, along with case examples of successful collaborations with faculty. PMID:24409957

Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis.

PubMed

Parulekar, Niranjan Nitin; Kolekar, Pandurang; Jenkins, Andrew; Kleiven, Synne; Utkilen, Hans; Johansen, Anette; Sawant, Sangeeta; Kulkarni-Kale, Urmila; Kale, Mohan; Sæbø, Mona

2017-01-01

Interactions between different phytoplankton taxa and heterotrophic bacterial communities within aquatic environments can differentially support growth of various heterotrophic bacterial species. In this study, phytoplankton diversity was studied using traditional microscopic techniques and the bacterial communities associated with phytoplankton bloom were studied using High Throughput Sequencing (HTS) analysis of 16S rRNA gene amplicons from the V1-V3 and V3-V4 hypervariable regions. Samples were collected from Lake Akersvannet, a eutrophic lake in South Norway, during the growth season from June to August 2013. Microscopic examination revealed that the phytoplankton community was mostly represented by Cyanobacteria and the dinoflagellate Ceratium hirundinella. The HTS results revealed that Proteobacteria (Alpha, Beta, and Gamma), Bacteriodetes, Cyanobacteria, Actinobacteria and Verrucomicrobia dominated the bacterial community, with varying relative abundances throughout the sampling season. Species level identification of Cyanobacteria showed a mixed population of Aphanizomenon flos-aquae, Microcystis aeruginosa and Woronichinia naegeliana. A significant proportion of the microbial community was composed of unclassified taxa which might represent locally adapted freshwater bacterial groups. Comparison of cyanobacterial species composition from HTS and microscopy revealed quantitative discrepancies, indicating a need for cross validation of results. To our knowledge, this is the first study that uses HTS methods for studying the bacterial community associated with phytoplankton blooms in a Norwegian lake. The study demonstrates the value of considering results from multiple methods when studying bacterial communities.

Discovery of viruses and virus-like pathogens in pistachio using high-throughput sequencing

USDA-ARS?s Scientific Manuscript database

Pistachio (Pistacia vera L.) trees from the National Clonal Germplasm Repository (NCGR) and orchards in California were surveyed for viruses and virus-like agents by high-throughput sequencing (HTS). Analyses of 60 trees including clonal UCB-1 hybrid rootstock (P. atlantica × P. integerrima) identif...

Rapid Identification of Cell-Specific, Internalizing RNA Aptamers with Bioinformatics Analyses of a Cell-Based Aptamer Selection

PubMed Central

Thiel, William H.; Bair, Thomas; Peek, Andrew S.; Liu, Xiuying; Dassie, Justin; Stockdale, Katie R.; Behlke, Mark A.; Miller, Francis J.; Giangrande, Paloma H.

2012-01-01

Background The broad applicability of RNA aptamers as cell-specific delivery tools for therapeutic reagents depends on the ability to identify aptamer sequences that selectively access the cytoplasm of distinct cell types. Towards this end, we have developed a novel approach that combines a cell-based selection method (cell-internalization SELEX) with high-throughput sequencing (HTS) and bioinformatics analyses to rapidly identify cell-specific, internalization-competent RNA aptamers. Methodology/Principal Findings We demonstrate the utility of this approach by enriching for RNA aptamers capable of selective internalization into vascular smooth muscle cells (VSMCs). Several rounds of positive (VSMCs) and negative (endothelial cells; ECs) selection were performed to enrich for aptamer sequences that preferentially internalize into VSMCs. To identify candidate RNA aptamer sequences, HTS data from each round of selection were analyzed using bioinformatics methods: (1) metrics of selection enrichment; and (2) pairwise comparisons of sequence and structural similarity, termed edit and tree distance, respectively. Correlation analyses of experimentally validated aptamers or rounds revealed that the best cell-specific, internalizing aptamers are enriched as a result of the negative selection step performed against ECs. Conclusions and Significance We describe a novel approach that combines cell-internalization SELEX with HTS and bioinformatics analysis to identify cell-specific, cell-internalizing RNA aptamers. Our data highlight the importance of performing a pre-clear step against a non-target cell in order to select for cell-specific aptamers. We expect the extended use of this approach to enable the identification of aptamers to a multitude of different cell types, thereby facilitating the broad development of targeted cell therapies. PMID:22962591

Open Access High Throughput Drug Discovery in the Public Domain: A Mount Everest in the Making

PubMed Central

Roy, Anuradha; McDonald, Peter R.; Sittampalam, Sitta; Chaguturu, Rathnam

2013-01-01

High throughput screening (HTS) facilitates screening large numbers of compounds against a biochemical target of interest using validated biological or biophysical assays. In recent years, a significant number of drugs in clinical trails originated from HTS campaigns, validating HTS as a bona fide mechanism for hit finding. In the current drug discovery landscape, the pharmaceutical industry is embracing open innovation strategies with academia to maximize their research capabilities and to feed their drug discovery pipeline. The goals of academic research have therefore expanded from target identification and validation to probe discovery, chemical genomics, and compound library screening. This trend is reflected in the emergence of HTS centers in the public domain over the past decade, ranging in size from modestly equipped academic screening centers to well endowed Molecular Libraries Probe Centers Network (MLPCN) centers funded by the NIH Roadmap initiative. These centers facilitate a comprehensive approach to probe discovery in academia and utilize both classical and cutting-edge assay technologies for executing primary and secondary screening campaigns. The various facets of academic HTS centers as well as their implications on technology transfer and drug discovery are discussed, and a roadmap for successful drug discovery in the public domain is presented. New lead discovery against therapeutic targets, especially those involving the rare and neglected diseases, is indeed a Mount Everestonian size task, and requires diligent implementation of pharmaceutical industry’s best practices for a successful outcome. PMID:20809896

High-temperature superconductivity for avionic electronic warfare and radar systems

NASA Astrophysics Data System (ADS)

Ryan, Paul A.

1994-01-01

The electronic warfare (EW) and radar communities expect to be major beneficiaries of the performance advantages high-temperature superconductivity (HTS) has to offer over conventional technology. Near term upgrades to system hardware can be envisioned using extremely small, high Q, microwave filters and resonators; compact, wideband, low loss, microwave delay and transmission lines; as well as, wideband, low loss, monolithic microwave integrated circuit phase shifters. The most dramatic impact will be in the far term, using HTS to develop new, real time threat identification and response strategy receiver/processing systems designed to utilize the unique high frequency properties of microwave and ultimately digital HTS.

Use of high temperature superconductors in magnetoplasmadynamic systems

NASA Technical Reports Server (NTRS)

Reed, C. B.; Sovey, J. S.

1988-01-01

The use of Tesla-class high-temperature superconducting magnets may have an extremely large impact on critical development issues (erosion, heat transfer, and performance) related to magnetoplasmadynamic (MPD) thrusters and also may provide significant benefits in reducing the mass of magnetics used in the power processing system. These potential performance improvements, coupled with additional benefits of high-temperature superconductivity, provide a very strong motivation to develop high-temperature superconductivity (HTS) applied-field MPD thruster propulsion systems. The application of HTS to MPD thruster propulsion systems may produce an enabling technology for these electric propulsion systems. This paper summarizes the impact that HTS may have upon MPD propulsion systems.

Human Tissue Stimulator

NASA Technical Reports Server (NTRS)

1982-01-01

Neurodyne Corporation Human Tissue Stimulator (HTS) is a totally implantable system used for treatment of chronic pain and involuntary motion disorders by electrical stimulation. It was developed by Pacesetter Systems, Inc. in cooperation with the Applied Physics Laboratory. HTS incorporates a nickel cadmium battery, telemetry and command systems technologies of the same type as those used in NASA's Small Astronomy Satellite-3 in microminiature proportions so that the implantable element is the size of a deck of cards. The stimulator includes a rechargeable battery, an antenna and electronics to receive and process commands and to report on its own condition via telemetry, a wireless process wherein instrument data is converted to electrical signals and sent to a receiver where signals are presented as usable information. The HTS is targeted to nerve centers or to particular areas of the brain to provide relief from intractable pain or arrest involuntary motion. The nickel cadmium battery can be recharged through the skin. The first two HTS units were implanted last year and have been successful. Extensive testing is required before HTS can be made available for general use.

Hole-doped cuprate high temperature superconductors

NASA Astrophysics Data System (ADS)

Chu, C. W.; Deng, L. Z.; Lv, B.

2015-07-01

Hole-doped cuprate high temperature superconductors have ushered in the modern era of high temperature superconductivity (HTS) and have continued to be at center stage in the field. Extensive studies have been made, many compounds discovered, voluminous data compiled, numerous models proposed, many review articles written, and various prototype devices made and tested with better performance than their nonsuperconducting counterparts. The field is indeed vast. We have therefore decided to focus on the major cuprate materials systems that have laid the foundation of HTS science and technology and present several simple scaling laws that show the systematic and universal simplicity amid the complexity of these material systems, while referring readers interested in the HTS physics and devices to the review articles. Developments in the field are mostly presented in chronological order, sometimes with anecdotes, in an attempt to share some of the moments of excitement and despair in the history of HTS with readers, especially the younger ones.

Potential impact of high temperature superconductors on MAGLEV transportation

NASA Astrophysics Data System (ADS)

Hull, J. R.

1992-02-01

This report describes the potential impact that high-temperature superconductors (HTS's) may have on transportation by magnetically levitated vehicles. It is not intended as a planning document, but rather as an overview of potential HTS applications to magnetic-levitation (maglev) transportation. The present maglev program in the United States is summarized, and the present status of development of HTS's is described. Areas identified for possible impact on maglev technology are: (1) liquid-nitrogen-cooled levitation magnets; (2) magnetic-field shielding of the passenger compartment; (3) superconducting magnetic energy storage for wayside power; (4) superconducting bearings for flywheel energy storage for wayside power; (5) downleads to continuously powered liquid-helium-cooled levitation magnets; and (6) liquid-hydrogen-cooled levitation magnets and linear motor propulsion windings. Major technical issues that remain to be resolved for the use of HTS's in maglev applications include thermal magnetic stability, mechanical properties, and critical current density at liquid-nitrogen temperatures.

Evaluating Imputation Algorithms for Low-Depth Genotyping-By-Sequencing (GBS) Data

PubMed Central

2016-01-01

Well-powered genomic studies require genome-wide marker coverage across many individuals. For non-model species with few genomic resources, high-throughput sequencing (HTS) methods, such as Genotyping-By-Sequencing (GBS), offer an inexpensive alternative to array-based genotyping. Although affordable, datasets derived from HTS methods suffer from sequencing error, alignment errors, and missing data, all of which introduce noise and uncertainty to variant discovery and genotype calling. Under such circumstances, meaningful analysis of the data is difficult. Our primary interest lies in the issue of how one can accurately infer or impute missing genotypes in HTS-derived datasets. Many of the existing genotype imputation algorithms and software packages were primarily developed by and optimized for the human genetics community, a field where a complete and accurate reference genome has been constructed and SNP arrays have, in large part, been the common genotyping platform. We set out to answer two questions: 1) can we use existing imputation methods developed by the human genetics community to impute missing genotypes in datasets derived from non-human species and 2) are these methods, which were developed and optimized to impute ascertained variants, amenable for imputation of missing genotypes at HTS-derived variants? We selected Beagle v.4, a widely used algorithm within the human genetics community with reportedly high accuracy, to serve as our imputation contender. We performed a series of cross-validation experiments, using GBS data collected from the species Manihot esculenta by the Next Generation (NEXTGEN) Cassava Breeding Project. NEXTGEN currently imputes missing genotypes in their datasets using a LASSO-penalized, linear regression method (denoted ‘glmnet’). We selected glmnet to serve as a benchmark imputation method for this reason. We obtained estimates of imputation accuracy by masking a subset of observed genotypes, imputing, and calculating the sample Pearson correlation between observed and imputed genotype dosages at the site and individual level; computation time served as a second metric for comparison. We then set out to examine factors affecting imputation accuracy, such as levels of missing data, read depth, minor allele frequency (MAF), and reference panel composition. PMID:27537694

Evaluating Imputation Algorithms for Low-Depth Genotyping-By-Sequencing (GBS) Data.

PubMed

Chan, Ariel W; Hamblin, Martha T; Jannink, Jean-Luc

2016-01-01

Well-powered genomic studies require genome-wide marker coverage across many individuals. For non-model species with few genomic resources, high-throughput sequencing (HTS) methods, such as Genotyping-By-Sequencing (GBS), offer an inexpensive alternative to array-based genotyping. Although affordable, datasets derived from HTS methods suffer from sequencing error, alignment errors, and missing data, all of which introduce noise and uncertainty to variant discovery and genotype calling. Under such circumstances, meaningful analysis of the data is difficult. Our primary interest lies in the issue of how one can accurately infer or impute missing genotypes in HTS-derived datasets. Many of the existing genotype imputation algorithms and software packages were primarily developed by and optimized for the human genetics community, a field where a complete and accurate reference genome has been constructed and SNP arrays have, in large part, been the common genotyping platform. We set out to answer two questions: 1) can we use existing imputation methods developed by the human genetics community to impute missing genotypes in datasets derived from non-human species and 2) are these methods, which were developed and optimized to impute ascertained variants, amenable for imputation of missing genotypes at HTS-derived variants? We selected Beagle v.4, a widely used algorithm within the human genetics community with reportedly high accuracy, to serve as our imputation contender. We performed a series of cross-validation experiments, using GBS data collected from the species Manihot esculenta by the Next Generation (NEXTGEN) Cassava Breeding Project. NEXTGEN currently imputes missing genotypes in their datasets using a LASSO-penalized, linear regression method (denoted 'glmnet'). We selected glmnet to serve as a benchmark imputation method for this reason. We obtained estimates of imputation accuracy by masking a subset of observed genotypes, imputing, and calculating the sample Pearson correlation between observed and imputed genotype dosages at the site and individual level; computation time served as a second metric for comparison. We then set out to examine factors affecting imputation accuracy, such as levels of missing data, read depth, minor allele frequency (MAF), and reference panel composition.

Simultaneous identification and molecular characterization of viruses associated with an apple tree with mosaic symptom

USDA-ARS?s Scientific Manuscript database

We conducted genomic sequencing to identify viruses associated with mosaic disease of an apple tree using the high-throughput sequencing (HTS) Illumina RNA-seq platform. The objective was to examine if rapid identification and characterization of viruses could be effectively achieved by RNA-seq anal...

Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing.

PubMed

Giraud, Mathieu; Salson, Mikaël; Duez, Marc; Villenet, Céline; Quief, Sabine; Caillault, Aurélie; Grardel, Nathalie; Roumier, Christophe; Preudhomme, Claude; Figeac, Martin

2014-05-28

V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient follow-up. However, the full breadth of lymphocyte diversity is not fully understood. We propose new algorithms that process high-throughput sequencing (HTS) data to extract unnamed V(D)J junctions and gather them into clones for quantification. This analysis is based on a seed heuristic and is fast and scalable because in the first phase, no alignment is performed with germline database sequences. The algorithms were applied to TR γ HTS data from a patient with acute lymphoblastic leukemia, and also on data simulating hypermutations. Our methods identified the main clone, as well as additional clones that were not identified with standard protocols. The proposed algorithms provide new insight into the analysis of high-throughput sequencing data for leukemia, and also to the quantitative assessment of any immunological profile. The methods described here are implemented in a C++ open-source program called Vidjil.

Rotor compound concept for designing an industrial HTS synchronous motor

NASA Astrophysics Data System (ADS)

Kashani, M.; Hosseina, M.; Sarrafan, K.; Darabi, A.

2013-06-01

Recently, producing power with smaller amount of losses become as a goal in our daily life. Today, large amount of energy waste in power networks all around the world. The main reason is “resistive electric equipments” of power networks. Since early 1980s, simultaneous with the development of high temperature superconductive (HTS) technology, superconductors gently attracted the mankind attentions. Using superconductive equipments instead of conventional resistive ones are result in salient electric loss reduction in power systems. Especially to reduce losses in power networks superconductive industrial rotating machines can potentially perform a significant role. In early recent century, first generation of HTS rotating machines was born. But unfortunately they have long way to penetrate the commercial markets yet. In HTS rotating machines the conventional copper made windings are replaced with the HTS superconductors. In this paper an industrial HTS synchronous motor with YBCO coated conductor field windings was designed. As a new approach, model was equipped with a compound rotor that includes both magnetic and non-magnetic materials. So, large amount of heavy iron made part was replaced by light non-magnetic material such as G-10 fiberglass. Furthermore, in this structure iron loss in rotor could be reduced to its lowest value. Also less weight and more air gap energy density were the additional advantages. Regarding zero electric loss production in field windings and less iron loss in rotor construction, this model potentially is more effective than the other iron made HTS motors.

Advancements in Aptamer Discovery Technologies.

PubMed

Gotrik, Michael R; Feagin, Trevor A; Csordas, Andrew T; Nakamoto, Margaret A; Soh, H Tom

2016-09-20

Affinity reagents that specifically bind to their target molecules are invaluable tools in nearly every field of modern biomedicine. Nucleic acid-based aptamers offer many advantages in this domain, because they are chemically synthesized, stable, and economical. Despite these compelling features, aptamers are currently not widely used in comparison to antibodies. This is primarily because conventional aptamer-discovery techniques such as SELEX are time-consuming and labor-intensive and often fail to produce aptamers with comparable binding performance to antibodies. This Account describes a body of work from our laboratory in developing advanced methods for consistently producing high-performance aptamers with higher efficiency, fewer resources, and, most importantly, a greater probability of success. We describe our efforts in systematically transforming each major step of the aptamer discovery process: selection, analysis, and characterization. To improve selection, we have developed microfluidic devices (M-SELEX) that enable discovery of high-affinity aptamers after a minimal number of selection rounds by precisely controlling the target concentration and washing stringency. In terms of improving aptamer pool analysis, our group was the first to use high-throughput sequencing (HTS) for the discovery of new aptamers. We showed that tracking the enrichment trajectory of individual aptamer sequences enables the identification of high-performing aptamers without requiring full convergence of the selected aptamer pool. HTS is now widely used for aptamer discovery, and open-source software has become available to facilitate analysis. To improve binding characterization, we used HTS data to design custom aptamer arrays to measure the affinity and specificity of up to ∼10(4) DNA aptamers in parallel as a means to rapidly discover high-quality aptamers. Most recently, our efforts have culminated in the invention of the "particle display" (PD) screening system, which transforms solution-phase aptamers into "aptamer particles" that can be individually screened at high-throughput via fluorescence-activated cell sorting. Using PD, we have shown the feasibility of rapidly generating aptamers with exceptional affinities, even for proteins that have previously proven intractable to aptamer discovery. We are confident that these advanced aptamer-discovery methods will accelerate the discovery of aptamer reagents with excellent affinities and specificities, perhaps even exceeding those of the best monoclonal antibodies. Since aptamers are reproducible, renewable, stable, and can be distributed as sequence information, we anticipate that these affinity reagents will become even more valuable tools for both research and clinical applications.

Scale-up of 2G wire manufacturing at American Superconductor Corporation

NASA Astrophysics Data System (ADS)

Fleshler, S.; Buczek, D.; Carter, B.; Cedrone, P.; DeMoranville, K.; Gannon, J.; Inch, J.; Li, X.; Lynch, J.; Otto, A.; Podtburg, E.; Roy, D.; Rupich, M.; Sathyamurthy, S.; Schreiber, J.; Thieme, C.; Thompson, E.; Tucker, D.; Nagashima, K.; Ogata, M.

2009-10-01

American Superconductor Corporation (AMSC) has developed the base technology and a manufacturing line for initial volume production of low-cost second generation high temperature superconductor (2G HTS) wire for commercial and military applications. The manufacturing line is based on reel-to-reel processing of wide HTS strips using rolling assisted bi-axially textured substrate (RABiTS™) for the template and Metal Organic Deposition (MOD) for the HTS layer. AMSC’s wide strip process is a low cost manufacturing technology since multiple wires are produced in a single manufacturing pass by slitting the wide strip to narrower width in the last stage of the manufacturing process. Industry standard 4.4 mm wide wires are produced by laminating metallic foils, such as copper, stainless steel or any other material, to the HTS insert wire, and are chosen to tailor the electrical, thermal and mechanical properties of the wire for specific applications. The laminated, 4.4 mm wide wires are known as “344 superconductors.” In this paper, we summarize the status of AMSC’s manufacturing capability, the performance of the wire presently being produced, as well as the cost and technical advantages of AMSC’s manufacturing approach. In addition, future direction for research and development to improve electrical performance is presented.

Performance of new 400-MHz HTS power-driven magnet NMR technology on typical pharmaceutical API, cinacalcet HCl.

PubMed

Silva Elipe, Maria Victoria; Donovan, Neil; Krull, Robert; Pooke, Donald; Colson, Kimberly L

2018-04-17

After years towards higher field strength magnets, nuclear magnetic resonance (NMR) technology in commercial instruments in the past decade has expanded at low and high magnetic fields to take advantage of new opportunities. At lower field strengths, permanent magnets are well established, whereas for midrange and high field, developments utilize superconducting magnets cooled with cryogenic liquids. Recently, the desire to locate NMR spectrometers in nontypical NMR laboratories has created interest in the development of cryogen-free magnets. These magnets require no cryogenic maintenance, eliminating routine filling and large cryogen dewars in the facility. Risks of spontaneous quenches and safety concerns when working with cryogenic liquids are eliminated. The highest field commercially available cryogen-free NMR magnet previously reported was at 4.7 T in 2013. Here we tested a prototype cryogen-free 9.4-T power-driven high-temperature-superconducting (HTS) magnet mated to commercial NMR spectrometer electronics. We chose cinacalcet HCl, a typical active pharmaceutical ingredient, to evaluate its performance towards structure elucidation. Satisfactory standard 1D and 2D homonuclear and heteronuclear NMR results were obtained and compared with those from a standard 9.4-T cryogenically cooled superconducting NMR instrument. The results were similar between both systems with minor differences. Further comparison with different shims and probes in the HTS magnet system confirmed that the magnet homogeneity profile could be matched with commercially available NMR equipment for optimal results. We conclude that HTS magnet technology works well providing results comparable with those of standard instruments, leading us to investigate additional applications for this magnet technology outside a traditional NMR facility. Copyright © 2018 John Wiley & Sons, Ltd.

Small Layer-wound ReBCO Solenoids

NASA Astrophysics Data System (ADS)

Polyakov, A. V.; Shcherbakov, V. I.; Shevchenko, S. A.; Surin, M. I.

The development of the next generation of high field superconducting magnet systems demands studies of new technological approach for its internal sections. Several small HTS solenoids (21 mm inner diameter, 32 layers) were fabricated by layer-winding technique from SuperPower type SCS-4050 ReBCO wire insulated by polyimide wrapping. Different designs of external and internal joints also were also tested. The highest field generated by HTS coil was 2.4 T in a 10 T background field (total field was 12.4 T) at 4.2 K and achieved current density in the coil was 498 A/mm2. The results will be used in development of HTS inner sections for 25 T superconducting magnet.

A 100K well screen for a muscarinic receptor using the Epic label-free system--a reflection on the benefits of the label-free approach to screening seven-transmembrane receptors.

PubMed

Dodgson, K; Gedge, L; Murray, D C; Coldwell, M

2009-01-01

Seven-transmembrane receptors (7TMRs) are a family of proteins of great interest as therapeutic targets because of their abundance on the cell surface, diverse effects in modulating cell behavior and success as a key class of drugs. We have evaluated the Epic label-free system for the purpose of identifying antagonists of the muscarinic M3 receptor. We compared the data generated from the label-free technology with data for the same compounds in a calcium flux assay. We have shown that this technology can be used for high throughput screening (HTS) of 7TMRs and as an orthogonal approach to enable rapid evaluation of HTS outputs. A number of compounds have been identified which were not found in a functional HTS measuring the output from a single pathway, which may offer new approaches to inhibiting responses through this receptor.

Design of Current Leads for the MICE Coupling Magnet

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

Wang, Li; Li, L.K.; Wu, Hong

2008-04-02

A pair of superconducting coupling magnets will be part of the Muon Ionization Cooling Experiment (MICE). They were designed and will be constructed by the Institute of Cryogenics and Superconductivity Technology, Harbin Institute of Technology, in collaboration with Lawrence Berkeley National Laboratory. The coupling magnet is to be cooled by using cryocoolers at 4.2K. In order to reduce the heat leak to the 4.2K cold mass from 300 K, a pair of current leads composed of conventional copper leads and high temperature superconductor (HTS) leads will be used to supply current to the magnet. This paper presents the optimization ofmore » the conventional conduction-cooled metal leads for the coupling magnet. Analyses on heat transfer down the leads using theoretical method and numerical simulation were carried out. The stray magnetic field around the HTS leads has been calculated and effects of the magnetic field on the performance of the HTS leads has also been analyzed.« less

From molecular engineering to process engineering: development of high-throughput screening methods in enzyme directed evolution.

PubMed

Ye, Lidan; Yang, Chengcheng; Yu, Hongwei

2018-01-01

With increasing concerns in sustainable development, biocatalysis has been recognized as a competitive alternative to traditional chemical routes in the past decades. As nature's biocatalysts, enzymes are able to catalyze a broad range of chemical transformations, not only with mild reaction conditions but also with high activity and selectivity. However, the insufficient activity or enantioselectivity of natural enzymes toward non-natural substrates limits their industrial application, while directed evolution provides a potent solution to this problem, thanks to its independence on detailed knowledge about the relationship between sequence, structure, and mechanism/function of the enzymes. A proper high-throughput screening (HTS) method is the key to successful and efficient directed evolution. In recent years, huge varieties of HTS methods have been developed for rapid evaluation of mutant libraries, ranging from in vitro screening to in vivo selection, from indicator addition to multi-enzyme system construction, and from plate screening to computation- or machine-assisted screening. Recently, there is a tendency to integrate directed evolution with metabolic engineering in biosynthesis, using metabolites as HTS indicators, which implies that directed evolution has transformed from molecular engineering to process engineering. This paper aims to provide an overview of HTS methods categorized based on the reaction principles or types by summarizing related studies published in recent years including the work from our group, to discuss assay design strategies and typical examples of HTS methods, and to share our understanding on HTS method development for directed evolution of enzymes involved in specific catalytic reactions or metabolic pathways.

The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations

PubMed Central

Oakley, Brian B.; Morales, Cesar A.; Line, J.; Berrang, Mark E.; Meinersmann, Richard J.; Tillman, Glenn E.; Wise, Mark G.; Siragusa, Gregory R.; Hiett, Kelli L.; Seal, Bruce S.

2013-01-01

Microbial communities associated with agricultural animals are important for animal health, food safety, and public health. Here we combine high-throughput sequencing (HTS), quantitative-PCR assays, and network analysis to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. Analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple sequence types most closely related to genera known to be pathogenic for animals and/or humans, including Campylobacter, Clostridium, and Shigella. After the final stage of commercial poultry processing, taxonomic richness was ca. 2–4 times lower than the richness of fecal samples from the same flocks and Campylobacter abundance was significantly reduced. Interestingly, however, carcasses sampled at 48 hr after processing harboured the greatest proportion of unique taxa (those not encountered in other samples), significantly more than expected by chance. Among these were anaerobes such as Prevotella, Veillonella, Leptrotrichia, and multiple Campylobacter sequence types. Retail products were dominated by Pseudomonas, but also contained 27 other genera, most of which were potentially metabolically active and encountered in on-farm samples. Network analysis was focused on the foodborne pathogen Campylobacter and revealed a majority of sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of Campylobacter. These data represent the first use of HTS to characterize the poultry microbiome across a series of farm-to-fork samples and demonstrate the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities. PMID:23468931

Miniature Heat Transport System for Nanosatellite Technology

NASA Technical Reports Server (NTRS)

Douglas, Donya M,

1999-01-01

The scientific understanding of key physical processes between the Sun and the Earth require simultaneous measurements from many vantage points in space. Nano-satellite technologies will enable a class of constellation missions for the NASA Space Science Sun-Earth Connections. This recent emphasis on the implementation of smaller satellites leads to a requirement for development of smaller subsystems in several areas. Key technologies under development include: advanced miniaturized chemical propulsion; miniaturized sensors; highly integrated, compact electronics; autonomous onboard and ground operations; miniatures low power tracking techniques for orbit determination; onboard RF communications capable of transmitting data to the ground from far distances; lightweight efficient solar array panels; lightweight, high output battery cells; lightweight yet strong composite materials for the nano-spacecraft and deployer-ship structures. These newer smaller systems may have higher power densities and higher thermal transport requirements than seen on previous small satellites. Furthermore, the small satellites may also have a requirement to maintain thermal control through extended earth shadows, possibly up to 8 hours long. Older thermal control technology, such as heaters, thermostats, and heat pipes, may not be sufficient to meet the requirements of these new systems. Conversely, a miniature two-phase heat transport system (Mini-HTS) such as a Capillary Pumped Loop (CPL) or Loop Heat Pipe (LBP) is a viable alternative. A Mini-HTS can provide fine temperature control, thermal diode action, and a highly efficient means of heat transfer. The Mini-HTS would have power capabilities in the range of tens of watts or less and provide thermal control over typical spacecraft ranges. The Mini-HTS would allow the internal portion of the spacecraft to be thermally isolated from the external radiator, thus protecting the internal components from extreme cold temperatures during an eclipse. The Mini-HTS would transport the beat from these components to a radiator during their operational modes, and it would be shutdown during non-operational or eclipse modes. Shutdown of the Mini-HTS would be accomplished with small heaters and has been successfully demonstrated on numerous occasions, both in the lab and on flight experiments. Efforts are now underway to miniaturize two-phase heat transport systems for the Nanosatellite project, with potential application to other small satellite programs. 'ne goal of this project is to design, build, and test miniature heat transport systems (MHTS) that would demonstrate the feasibility of a small Capillary Pumped Loop (CPL) or Loop Heat Pipe (LBP).

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

PubMed

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

2017-01-01

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

Applications of Superconductivity and Impact on U.S. Economy

NASA Astrophysics Data System (ADS)

Selvamanickam, Venkat

2014-03-01

In the past few decades, low temperature superconducting wires (niobium-titanium) have enabled multibillion dollar industries such as magnetic resonance imaging and nuclear magnetic resonance spectroscopy which otherwise would not have been possible. High temperature superconductors (HTS) hold the promise of impacting even a larger market in diverse applications such as energy, health, military, telecommunication, transportation and research. HTS tapes are now being manufactured in quantities of few hundred kilometers annually with current carrying capacity of about 300 times that of copper wire of the same cross section. Power transmission cables up to few kilometers in length made with HTS tapes have already been inserted in the power grid world-wide. In the past few of years, tremendous advancements have occurred in nanoscale defect engineering in these thin film superconducting tapes that has led to a doubling of critical current performance in high magnetic fields and operating temperatures of interest for various applications. Technologies developed in this area have been successfully inserted in production HTS tapes by industry. With the availability of such high performance HTS tapes, a number of coil-based applications are now being aggressively pursued by several institutions. HTS coils enable power devices with high power density with significant weight, size and power benefits. Energy storage, generation, use, transformation and transmission applications as well as magnetic applications such as magnetic shields, plasma confinement, and ultra-high field magnets are becoming possible with the availability of high-performance HTS tapes. An overview of the development and use of superconductors in electric power and magnetic applications will be provided in this presentation.

Soil DNA metabarcoding and high-throughput sequencing as a forensic tool: considerations, potential limitations and recommendations.

PubMed

Young, J M; Austin, J J; Weyrich, L S

2017-02-01

Analysis of physical evidence is typically a deciding factor in forensic casework by establishing what transpired at a scene or who was involved. Forensic geoscience is an emerging multi-disciplinary science that can offer significant benefits to forensic investigations. Soil is a powerful, nearly 'ideal' contact trace evidence, as it is highly individualistic, easy to characterise, has a high transfer and retention probability, and is often overlooked in attempts to conceal evidence. However, many real-life cases encounter close proximity soil samples or soils with low inorganic content, which cannot be easily discriminated based on current physical and chemical analysis techniques. The capability to improve forensic soil discrimination, and identify key indicator taxa from soil using the organic fraction is currently lacking. The development of new DNA sequencing technologies offers the ability to generate detailed genetic profiles from soils and enhance current forensic soil analyses. Here, we discuss the use of DNA metabarcoding combined with high-throughput sequencing (HTS) technology to distinguish between soils from different locations in a forensic context. Specifically, we provide recommendations for best practice, outline the potential limitations encountered in a forensic context and describe the future directions required to integrate soil DNA analysis into casework. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

ADVANCES IN DISCOVERING SMALL MOLECULES TO PROBE PROTEIN FUNCTION IN A SYSTEMS CONTEXT

PubMed Central

Doyle, Shelby K; Pop, Marius S; Evans, Helen L; Koehler, Angela N

2015-01-01

High throughput screening has historically been used for drug discovery almost exclusively by the pharmaceutical industry. Due to a significant decrease in costs associated with establishing a high throughput facility and an exponential interest in discovering probes of development and disease associated biomolecules, HTS core facilities have become an integral part of most academic and non-profit research institutions over the past decade. This major shift has led to the development of new HTS methodologies extending beyond the capabilities and target classes used in classical drug discovery approaches such as traditional enzymatic activity-based screens. In this brief review we describe some of the most interesting developments in HTS technologies and methods for chemical probe discovery. PMID:26615565

Experience of 12 kA / 16 V SMPS during the HTS Current Leads Test

NASA Astrophysics Data System (ADS)

Panchal, P.; Christian, D.; Panchal, R.; Sonara, D.; Purwar, G.; Garg, A.; Nimavat, H.; Singh, G.; Patel, J.; Tanna, V.; Pradhan, S.

2017-04-01

As a part of up gradation plans in SST-1 Tokamak, one pair of 3.3 kA rated prototype hybrid current leads were developed using Di-BSCCO as High Temperature Superconductors (HTS) and the copper heat exchanger. In order to validate the manufacturing procedure prior to go for series production of such current leads, it was recommended to test these current leads using dedicated and very reliable DC switch mode power supply (SMPS). As part of test facility, 12 kA, 16 VDC programmable SMPS was successfully installed, commissioned and tested. This power supply has special features such as modularity, N+1 redundancy, very low ripple voltage, precise current measurements with Direct Current Current Transformer, CC/CV modes with auto-crossover and auto-sequence programming. As a part of acceptance of this converter, A 5.8 mΩ water-cooled resistive dummy load and PLC based SCADA system is designed, developed for commissioning of power supply. The same power supply was used for the testing of the prototype HTS current leads. The paper describes the salient features and experience of state-of-art of power supply and results obtained from this converter during the HTS current leads test.

Yeast as a potential vehicle for neglected tropical disease drug discovery.

PubMed

Denny, P W; Steel, P G

2015-01-01

High-throughput screening (HTS) efforts for neglected tropical disease (NTD) drug discovery have recently received increased attention because several initiatives have begun to attempt to reduce the deficit in new and clinically acceptable therapies for this spectrum of infectious diseases. HTS primarily uses two basic approaches, cell-based and in vitro target-directed screening. Both of these approaches have problems; for example, cell-based screening does not reveal the target or targets that are hit, whereas in vitro methodologies lack a cellular context. Furthermore, both can be technically challenging, expensive, and difficult to miniaturize for ultra-HTS [(u)HTS]. The application of yeast-based systems may overcome some of these problems and offer a cost-effective platform for target-directed screening within a eukaryotic cell context. Here, we review the advantages and limitations of the technologies that may be used in yeast cell-based, target-directed screening protocols, and we discuss how these are beginning to be used in NTD drug discovery. © 2014 Society for Laboratory Automation and Screening.

Streptococcus halotolerans sp. nov. isolated from the respiratory tract of Marmota himalayana in Qinghai-Tibet Plateau of China.

PubMed

Niu, Lina; Lu, Shan; Hu, Shoukui; Jin, Dong; Lai, Xinhe; Yang, Jing; Chen, Cuixia; Wang, Yiting; Bai, Xiangning; Lan, Ruiting; Lv, Gang; Xie, Yingping; Ye, Changyun; Xu, Jianguo

2016-10-01

Two Gramstaining-positive, catalase-negative, α-hemolytic, coccus-shaped organisms were isolated separately from the respiratory tracts of two Marmota himalayana animals from the Qinghai-Tibet Plateau, PR China. Morphological, biological, biochemical, and molecular genetic studies were performed on these two isolates (HTS9T and HTS12). Their biochemical characteristics, such as acid production from different sugars and enzymatic activities, indicated that they represented a member of the genus Streptococcus. They are most closely related to Streptococcus thoraltensis CIP 105518T based on sequence analysis of their 16S rRNA, groEL, sodA and rpoB genes, with similarities of 97.6, 89.9, 92.6 and 91.1 % the four genes respectively. The whole genome phylogenetic tree reconstructed using 372 core genes from 65 genomes of members of the genus Streptococcus validates that HTS9T forms a distinct subline and exhibits specific phylogenetic affinity with S. thoraltensis. In silico DNA-DNA hybridization of HTS9T showed a DNA reassociation value of 32.1 %, closest to that of S. thoraltensis CIP 105518T. Based on their phenotypic characteristics and in particular the phylogenetic findings (DNA-DNA hybridization, three phylogenetic trees built from the partial 16S rRNA/housekeeping genes, and from 372 core genes of 65 genomes of members of the genus Streptococcus), we propose with confidence that strains HTS9T and HTS12 should be classified as representing a novel species of the genus Streptococcus, Streptococcus halotolerans sp. nov. The type strain is HTS9T (=DSM 101996T=CGMCC1.15532T). Genome analysis of Streptococcus halotolerans sp. nov. shows that its genome is 1 823 556 bp long with a DNA G+C content of 39.9 mol% and contains 2068 genes.

Emerging applications of high temperature superconductors for space communications

NASA Technical Reports Server (NTRS)

Heinen, Vernon O.; Bhasin, Kul B.; Long, Kenwyn J.

1990-01-01

Proposed space missions require longevity of communications system components, high input power levels, and high speed digital logic devices. The complexity of these missions calls for a high data bandwidth capacity. Incorporation of high temperature superconducting (HTS) thin films into some of these communications system components may provide a means of meeting these requirements. Space applications of superconducting technology has previously been limited by the requirement of cooling to near liquid helium temperatures. Development of HTS materials with transition temperatures above 77 K along with the natural cooling ability of space suggest that space applications may lead the way in the applications of high temperature superconductivity. In order for HTS materials to be incorporated into microwave and millimeter wave devices, the material properties such as electrical conductivity, current density, surface resistivity and others as a function of temperature and frequency must be well characterized and understood. The millimeter wave conductivity and surface resistivity were well characterized, and at 77 K are better than copper. Basic microwave circuits such as ring resonators were used to determine transmission line losses. Higher Q values than those of gold resonator circuits were observed below the transition temperature. Several key HTS circuits including filters, oscillators, phase shifters and phased array antenna feeds are feasible in the near future. For technology to improve further, good quality, large area films must be reproducibly grown on low dielectric constant, low loss microwave substrates.

SOPRA: Scaffolding algorithm for paired reads via statistical optimization.

PubMed

Dayarian, Adel; Michael, Todd P; Sengupta, Anirvan M

2010-06-24

High throughput sequencing (HTS) platforms produce gigabases of short read (<100 bp) data per run. While these short reads are adequate for resequencing applications, de novo assembly of moderate size genomes from such reads remains a significant challenge. These limitations could be partially overcome by utilizing mate pair technology, which provides pairs of short reads separated by a known distance along the genome. We have developed SOPRA, a tool designed to exploit the mate pair/paired-end information for assembly of short reads. The main focus of the algorithm is selecting a sufficiently large subset of simultaneously satisfiable mate pair constraints to achieve a balance between the size and the quality of the output scaffolds. Scaffold assembly is presented as an optimization problem for variables associated with vertices and with edges of the contig connectivity graph. Vertices of this graph are individual contigs with edges drawn between contigs connected by mate pairs. Similar graph problems have been invoked in the context of shotgun sequencing and scaffold building for previous generation of sequencing projects. However, given the error-prone nature of HTS data and the fundamental limitations from the shortness of the reads, the ad hoc greedy algorithms used in the earlier studies are likely to lead to poor quality results in the current context. SOPRA circumvents this problem by treating all the constraints on equal footing for solving the optimization problem, the solution itself indicating the problematic constraints (chimeric/repetitive contigs, etc.) to be removed. The process of solving and removing of constraints is iterated till one reaches a core set of consistent constraints. For SOLiD sequencer data, SOPRA uses a dynamic programming approach to robustly translate the color-space assembly to base-space. For assessing the quality of an assembly, we report the no-match/mismatch error rate as well as the rates of various rearrangement errors. Applying SOPRA to real data from bacterial genomes, we were able to assemble contigs into scaffolds of significant length (N50 up to 200 Kb) with very few errors introduced in the process. In general, the methodology presented here will allow better scaffold assemblies of any type of mate pair sequencing data.

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

PubMed Central

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

2012-01-01

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

The Hidden Diversity of Flagellated Protists in Soil.

PubMed

Venter, Paul Christiaan; Nitsche, Frank; Arndt, Hartmut

2018-07-01

Protists are among the most diverse and abundant eukaryotes in soil. However, gaps between described and sequenced protist morphospecies still present a pending problem when surveying environmental samples for known species using molecular methods. The number of sequences in the molecular PR 2 database (∼130,000) is limited compared to the species richness expected (>1 million protist species) - limiting the recovery rate. This is important, since high throughput sequencing (HTS) methods are used to find associative patterns between functional traits, taxa and environmental parameters. We performed HTS to survey soil flagellates in 150 grasslands of central Europe, and tested the recovery rate of ten previously isolated and cultivated cercomonad species, among locally found diversity. We recovered sequences for reference soil flagellate species, but also a great number of their phylogenetically evaluated genetic variants, among rare and dominant taxa with presumably own biogeography. This was recorded among dominant (cercozoans, Sandona), rare (apusozoans) and a large hidden diversity of predominantly aquatic protists in soil (choanoflagellates, bicosoecids) often forming novel clades associated with uncultured environmental sequences. Evaluating the reads, instead of the OTUs that individual reads are usually clustered into, we discovered that much of this hidden diversity may be lost due to clustering. Copyright © 2018 Elsevier GmbH. All rights reserved.

Capturing the Alternative Cleavage and Polyadenylation Sites of 14 NAC Genes in Populus Using a Combination of 3'-RACE and High-Throughput Sequencing.

PubMed

Wang, Haoran; Wang, Mingxiu; Cheng, Qiang

2018-03-08

Detection of complex splice sites (SSs) and polyadenylation sites (PASs) of eukaryotic genes is essential for the elucidation of gene regulatory mechanisms. Transcriptome-wide studies using high-throughput sequencing (HTS) have revealed prevalent alternative splicing (AS) and alternative polyadenylation (APA) in plants. However, small-scale and high-depth HTS aimed at detecting genes or gene families are very few and limited. We explored a convenient and flexible method for profiling SSs and PASs, which combines rapid amplification of 3'-cDNA ends (3'-RACE) and HTS. Fourteen NAC (NAM, ATAF1/2, CUC2) transcription factor genes of Populus trichocarpa were analyzed by 3'-RACE-seq. Based on experimental reproducibility, boundary sequence analysis and reverse transcription PCR (RT-PCR) verification, only canonical SSs were considered to be authentic. Based on stringent criteria, candidate PASs without any internal priming features were chosen as authentic PASs and assumed to be PAS-rich markers. Thirty-four novel canonical SSs, six intronic/internal exons and thirty 3'-UTR PAS-rich markers were revealed by 3'-RACE-seq. Using 3'-RACE and real-time PCR, we confirmed that three APA transcripts ending in/around PAS-rich markers were differentially regulated in response to plant hormones. Our results indicate that 3'-RACE-seq is a robust and cost-effective method to discover SSs and label active regions subjected to APA for genes or gene families. The method is suitable for small-scale AS and APA research in the initial stage.

Temperature Distribution and Critical Current of Long HTS Cables Cooled with Subcooled Liquid Nitrogen

NASA Astrophysics Data System (ADS)

Vyatkin, V. S.; Ivanov, Y. V.; Watanabe, H.; Chikumoto, N.; Yamaguchi, S.

2017-07-01

Cooling of the long HTS power transmission lines performs by pumping of subcooled liquid nitrogen (LN2) along the cable. The temperature of LN2 along the cable increases due to the heat losses of the cryostat and heat generation in the HTS cable. The experiment using test cable line in Ishikari shows that flow rate of 35 L/min retains increasing of LN2 temperature by 1 K per 1 km of length. The technology when the back flow of LN2 cools the radiation shield surrounding the cable pipe is also applied in Ishikari-2 project. In this case the ambient heat flow into cable pipe is 50 times less than that without radiation shield. Back flow of LN2 removes almost all heat coming from the environment. When transport current is close to the critical value the Joule heat of HTS cable is significant. This heat additionally increases the temperature of LN2 flowing along the HTS cable. Near the outlet the temperature of HTS cable is maximal and the local critical current is minimal. The current matching critical current criterion of average electrical field of E 0 = 10-4 V/m provides the voltage drop and significant Joule heat at the hot end of the cable. It can lead the damage of the cable. The present work contains analysis of temperature distribution along the cable and the way to achieve the fail-safe operation of long HTS cable cooled by subcooled LN2. We also performed extrapolation of obtained results for several times longer cable lines by decreasing the LN2 flow rate.

High-Throughput RNA Interference Screening: Tricks of the Trade

PubMed Central

Nebane, N. Miranda; Coric, Tatjana; Whig, Kanupriya; McKellip, Sara; Woods, LaKeisha; Sosa, Melinda; Sheppard, Russell; Rasmussen, Lynn; Bjornsti, Mary-Ann; White, E. Lucile

2016-01-01

The process of validating an assay for high-throughput screening (HTS) involves identifying sources of variability and developing procedures that minimize the variability at each step in the protocol. The goal is to produce a robust and reproducible assay with good metrics. In all good cell-based assays, this means coefficient of variation (CV) values of less than 10% and a signal window of fivefold or greater. HTS assays are usually evaluated using Z′ factor, which incorporates both standard deviation and signal window. A Z′ factor value of 0.5 or higher is acceptable for HTS. We used a standard HTS validation procedure in developing small interfering RNA (siRNA) screening technology at the HTS center at Southern Research. Initially, our assay performance was similar to published screens, with CV values greater than 10% and Z′ factor values of 0.51 ± 0.16 (average ± standard deviation). After optimizing the siRNA assay, we got CV values averaging 7.2% and a robust Z′ factor value of 0.78 ± 0.06 (average ± standard deviation). We present an overview of the problems encountered in developing this whole-genome siRNA screening program at Southern Research and how equipment optimization led to improved data quality. PMID:23616418

The effect of low temperature cryocoolers on the development of low temperature superconducting magnets

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

Green, Michael A.

2000-08-05

The commercial development of reliable 4 K cryocoolers improves the future prospects for magnets made from low temperature superconductors (LTS). The hope of the developers of high temperature superconductors (HTS) has been to replace liquid helium cooled LTS magnets with HTS magnets that operate at or near liquid nitrogen temperature. There has been limited success in this endeavor, but continued problems with HTS conductors have greatly slowed progress toward this goal. The development of cryocoolers that reliably operate below 4 K will allow magnets made from LTS conductor to remain very competitive for many years to come. A key enablingmore » technology for the use of low temperature cryocoolers on LTS magnets has been the development of HTS leads. This report describes the characteristics of LTS magnets that can be successfully melded to low-temperature cryocoolers. This report will also show when it is not appropriate to consider the use of low-temperature cryocoolers to cool magnets made with LTS conductor. A couple of specific examples of LTS magnets where cryocoolers can be used are given.« less

Creation of knock out and knock in mice by CRISPR/Cas9 to validate candidate genes for human male infertility, interest, difficulties and feasibility.

PubMed

Kherraf, Zine-Eddine; Conne, Beatrice; Amiri-Yekta, Amir; Kent, Marie Christou; Coutton, Charles; Escoffier, Jessica; Nef, Serge; Arnoult, Christophe; Ray, Pierre F

2018-06-15

High throughput sequencing (HTS) and CRISPR/Cas9 are two recent technologies that are currently revolutionizing biological and clinical research. Both techniques are complementary as HTS permits to identify new genetic variants and genes involved in various pathologies and CRISPR/Cas9 permits to create animals or cell models to validate the effect of the identified variants, to characterize the pathogeny of the identified variants and the function of the genes of interest and ultimately to provide ways of correcting the molecular defects. We analyzed a cohort of 78 infertile men presenting with multiple morphological anomalies of the sperm flagella (MMAF), a severe form of male infertility. Using whole exome sequencing (WES), homozygous mutations in autosomal candidate genes were identified in 63% of the tested subjects. We decided to produce by CRISPR/cas9 four knock-out (KO) and one knock-in (KI) mouse lines to confirm these results and to increase our understanding of the physiopathology associated with these genetic variations. Overall 31% of the live pups obtained presented a mutational event in one of the targeted regions. All identified events were insertions or deletions localized near the PAM sequence. Surprisingly we observed a high rate of germline mosaicism as 30% of the F1 displayed a different mutation than the parental event characterized on somatic tissue (tail), indicating that CRISPR/Cas9 mutational events kept happening several cell divisions after the injection. Overall, we created mouse models for 5 distinct loci and in each case homozygous animals could be obtained in approximately 6 months. These results demonstrate that the combined use of WES and CRISPR/Cas9 is an efficient and timely strategy to identify and validate mutations responsible for infertility phenotypes in human. Copyright © 2018 Elsevier B.V. All rights reserved.

Aptamers as tools for target prioritization and lead identification.

PubMed

Burgstaller, Petra; Girod, Anne; Blind, Michael

2002-12-15

The increasing number of potential drug target candidates has driven the development of novel technologies designed to identify functionally important targets and enhance the subsequent lead discovery process. Highly specific synthetic nucleic acid ligands--also known as aptamers--offer a new exciting route in the drug discovery process by linking target validation directly with HTS. Recently, aptamers have proven to be valuable tools for modulating the function of endogenous cellular proteins in their natural environment. A set of technologies has been developed to use these sophisticated ligands for the validation of potential drug targets in disease models. Moreover, aptamers that are specific antagonists of protein function can act as substitute interaction partners in HTS assays to facilitate the identification of small-molecule lead compounds.

SCALCE: boosting sequence compression algorithms using locally consistent encoding.

PubMed

Hach, Faraz; Numanagic, Ibrahim; Alkan, Can; Sahinalp, S Cenk

2012-12-01

The high throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for the computational infrastructure. Data management, storage and analysis have become major logistical obstacles for those adopting the new platforms. The requirement for large investment for this purpose almost signalled the end of the Sequence Read Archive hosted at the National Center for Biotechnology Information (NCBI), which holds most of the sequence data generated world wide. Currently, most HTS data are compressed through general purpose algorithms such as gzip. These algorithms are not designed for compressing data generated by the HTS platforms; for example, they do not take advantage of the specific nature of genomic sequence data, that is, limited alphabet size and high similarity among reads. Fast and efficient compression algorithms designed specifically for HTS data should be able to address some of the issues in data management, storage and communication. Such algorithms would also help with analysis provided they offer additional capabilities such as random access to any read and indexing for efficient sequence similarity search. Here we present SCALCE, a 'boosting' scheme based on Locally Consistent Parsing technique, which reorganizes the reads in a way that results in a higher compression speed and compression rate, independent of the compression algorithm in use and without using a reference genome. Our tests indicate that SCALCE can improve the compression rate achieved through gzip by a factor of 4.19-when the goal is to compress the reads alone. In fact, on SCALCE reordered reads, gzip running time can improve by a factor of 15.06 on a standard PC with a single core and 6 GB memory. Interestingly even the running time of SCALCE + gzip improves that of gzip alone by a factor of 2.09. When compared with the recently published BEETL, which aims to sort the (inverted) reads in lexicographic order for improving bzip2, SCALCE + gzip provides up to 2.01 times better compression while improving the running time by a factor of 5.17. SCALCE also provides the option to compress the quality scores as well as the read names, in addition to the reads themselves. This is achieved by compressing the quality scores through order-3 Arithmetic Coding (AC) and the read names through gzip through the reordering SCALCE provides on the reads. This way, in comparison with gzip compression of the unordered FASTQ files (including reads, read names and quality scores), SCALCE (together with gzip and arithmetic encoding) can provide up to 3.34 improvement in the compression rate and 1.26 improvement in running time. Our algorithm, SCALCE (Sequence Compression Algorithm using Locally Consistent Encoding), is implemented in C++ with both gzip and bzip2 compression options. It also supports multithreading when gzip option is selected, and the pigz binary is available. It is available at http://scalce.sourceforge.net. fhach@cs.sfu.ca or cenk@cs.sfu.ca Supplementary data are available at Bioinformatics online.

Correction of Microplate Data from High-Throughput Screening.

PubMed

Wang, Yuhong; Huang, Ruili

2016-01-01

High-throughput screening (HTS) makes it possible to collect cellular response data from a large number of cell lines and small molecules in a timely and cost-effective manner. The errors and noises in the microplate-formatted data from HTS have unique characteristics, and they can be generally grouped into three categories: run-wise (temporal, multiple plates), plate-wise (background pattern, single plate), and well-wise (single well). In this chapter, we describe a systematic solution for identifying and correcting such errors and noises, mainly basing on pattern recognition and digital signal processing technologies.

Towards liquid-helium-free, persistent-mode MgB2 MRI magnets: FBML experience

NASA Astrophysics Data System (ADS)

Iwasa, Yukikazu

2017-05-01

In this article I present our experience at the Magnet Technology Division of the MIT Francis Bitter Magnet Laboratory on liquid-helium (LHe)-free, persistent-mode MgB2 MRI magnets. Before reporting on our MgB2 magnets, I first summarize the basic work that we began in the late 1990s to develop LHe-free, high-temperature superconductor (HTS) magnets cooled in solid cryogen—I begin by discussing the enabling feature, particularly of solid nitrogen (SN2), for adiabatic HTS magnets. The next topic is our first LHe-free, SN2-HTS magnet, for which we chose Bi2223 because in the late 1990s Bi2223 was the only HTS available to build an HTS magnet. I then move on to two MgB2 magnets, I and II, developed after discovery of MgB2 in 2000. The SN2-MgB2 Magnet II—0.5 T/240 mm, SN2-cooled, and operated in persistent mode—was completed in January 2016. The final major topic in this article is a tabletop LHe-free, persistent-mode 1.5 T/70 mm SN2-MgB2 ‘finger’ MRI magnet for osteoporosis screening—we expect to begin this project in 2017. Before concluding this article, I present my current view on challenges and prospects for MgB2 MRI magnets.

Towards Liquid-Helium-Free, Persistent-Mode MgB2 MRI Magnets: FBML Experience.

PubMed

Iwasa, Yukikazu

2017-01-01

In this article I present our experience at the Magnet Technology Division of the MIT Francis Bitter Magnet Laboratory on liquid-helium (LHe)-free, persistent-mode MgB 2 MRI magnets. Before reporting on our MgB 2 magnets, I first summarize the basic work that we began in the late 1990s to develop LHe-free, high-temperature superconductor (HTS) magnets cooled in solid cryogen-I begin by discussing the enabling feature, particularly of solid nitrogen (SN2), for adiabatic HTS magnets. The next topic is our first LHe-free, SN2-HTS magnet, for which we chose Bi2223 because in the late 1990s Bi2223 was the only HTS available to build an HTS magnet. I then move on to two MgB 2 magnets, I and II, developed after discovery of MgB 2 in 2000. The SN2-MgB 2 Magnet II-0.5-T/240-mm, SN2-cooled, and operated in persistent mode-was completed in January 2016. The final major topic in this article is a tabletop LHe-free, persistent-mode 1.5-T/70-mm SN2-MgB 2 "finger" MRI magnet for osteoporosis screening-we expect to begin this project in 2017. Before concluding this article, I present my current view on challenges and prospects for MgB 2 MRI magnets.

Towards Liquid-Helium-Free, Persistent-Mode MgB2 MRI Magnets: FBML Experience

PubMed Central

Iwasa, Yukikazu

2017-01-01

In this article I present our experience at the Magnet Technology Division of the MIT Francis Bitter Magnet Laboratory on liquid-helium (LHe)-free, persistent-mode MgB2 MRI magnets. Before reporting on our MgB2 magnets, I first summarize the basic work that we began in the late 1990s to develop LHe-free, high-temperature superconductor (HTS) magnets cooled in solid cryogen—I begin by discussing the enabling feature, particularly of solid nitrogen (SN2), for adiabatic HTS magnets. The next topic is our first LHe-free, SN2-HTS magnet, for which we chose Bi2223 because in the late 1990s Bi2223 was the only HTS available to build an HTS magnet. I then move on to two MgB2 magnets, I and II, developed after discovery of MgB2 in 2000. The SN2-MgB2 Magnet II—0.5-T/240-mm, SN2-cooled, and operated in persistent mode—was completed in January 2016. The final major topic in this article is a tabletop LHe-free, persistent-mode 1.5-T/70-mm SN2-MgB2 “finger” MRI magnet for osteoporosis screening—we expect to begin this project in 2017. Before concluding this article, I present my current view on challenges and prospects for MgB2 MRI magnets. PMID:29568161

Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin.

PubMed

Denesvre, Caroline; Dumarest, Marine; Rémy, Sylvie; Gourichon, David; Eloit, Marc

2015-10-01

Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics.

Isolation and characterization of antigen-specific alpaca (Lama pacos) VHH antibodies by biopanning followed by high-throughput sequencing.

PubMed

Miyazaki, Nobuo; Kiyose, Norihiko; Akazawa, Yoko; Takashima, Mizuki; Hagihara, Yosihisa; Inoue, Naokazu; Matsuda, Tomonari; Ogawa, Ryu; Inoue, Seiya; Ito, Yuji

2015-09-01

The antigen-binding domain of camelid dimeric heavy chain antibodies, known as VHH or Nanobody, has much potential in pharmaceutical and industrial applications. To establish the isolation process of antigen-specific VHH, a VHH phage library was constructed with a diversity of 8.4 × 10(7) from cDNA of peripheral blood mononuclear cells of an alpaca (Lama pacos) immunized with a fragment of IZUMO1 (IZUMO1PFF) as a model antigen. By conventional biopanning, 13 antigen-specific VHHs were isolated. The amino acid sequences of these VHHs, designated as N-group VHHs, were very similar to each other (>93% identity). To find more diverse antibodies, we performed high-throughput sequencing (HTS) of VHH genes. By comparing the frequencies of each sequence between before and after biopanning, we found the sequences whose frequencies were increased by biopanning. The top 100 sequences of them were supplied for phylogenic tree analysis. In total 75% of them belonged to N-group VHHs, but the other were phylogenically apart from N-group VHHs (Non N-group). Two of three VHHs selected from non N-group VHHs showed sufficient antigen binding ability. These results suggested that biopanning followed by HTS provided a useful method for finding minor and diverse antigen-specific clones that could not be identified by conventional biopanning. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Transfer Efficiency and Cooling Cost by Thermal Loss based on Nitrogen Evaporation Method for Superconducting MAGLEV System

NASA Astrophysics Data System (ADS)

Chung, Y. D.; Kim, D. W.; Lee, C. Y.

2017-07-01

This paper presents the feasibility of technical fusion between wireless power transfer (WPT) and superconducting technology to improve the transfer efficiency and evaluate operating costs such as refrigerant consumption. Generally, in WPT technology, the various copper wires have been adopted. From this reason, the transfer efficiency is limited since the copper wires of Q value are intrinsically critical point. On the other hand, as superconducting wires keep larger current density and relatively higher Q value, the superconducting resonance coil can be expected as a reasonable option to deliver large transfer power as well as improve the transfer ratio since it exchanges energy at a much higher rate and keeps stronger magnetic fields out. However, since superconducting wires should be cooled indispensably, the cooling cost of consumed refrigerant for resonance HTS wires should be estimated. In this study, the transmission ratios using HTS resonance receiver (Rx) coil and various cooled and noncooled copper resonance Rx coils were presented under non cooled copper antenna within input power of 200 W of 370 kHz respectively. In addition, authors evaluated cooling cost of liquid nitrogen for HTS resonance coil and various cooled copper resonance coils based on nitrogen evaporation method.

Toxico-Cheminformatics: New and Expanding Public ...

EPA Pesticide Factsheets

High-throughput screening (HTS) technologies, along with efforts to improve public access to chemical toxicity information resources and to systematize older toxicity studies, have the potential to significantly improve information gathering efforts for chemical assessments and predictive capabilities in toxicology. Important developments include: 1) large and growing public resources that link chemical structures to biological activity and toxicity data in searchable format, and that offer more nuanced and varied representations of activity; 2) standardized relational data models that capture relevant details of chemical treatment and effects of published in vivo experiments; and 3) the generation of large amounts of new data from public efforts that are employing HTS technologies to probe a wide range of bioactivity and cellular processes across large swaths of chemical space. By annotating toxicity data with associated chemical structure information, these efforts link data across diverse study domains (e.g., ‘omics’, HTS, traditional toxicity studies), toxicity domains (carcinogenicity, developmental toxicity, neurotoxicity, immunotoxicity, etc) and database sources (EPA, FDA, NCI, DSSTox, PubChem, GEO, ArrayExpress, etc.). Public initiatives are developing systematized data models of toxicity study areas and introducing standardized templates, controlled vocabularies, hierarchical organization, and powerful relational searching capability across capt

Establishing MALDI-TOF as Versatile Drug Discovery Readout to Dissect the PTP1B Enzymatic Reaction.

PubMed

Winter, Martin; Bretschneider, Tom; Kleiner, Carola; Ries, Robert; Hehn, Jörg P; Redemann, Norbert; Luippold, Andreas H; Bischoff, Daniel; Büttner, Frank H

2018-07-01

Label-free, mass spectrometric (MS) detection is an emerging technology in the field of drug discovery. Unbiased deciphering of enzymatic reactions is a proficient advantage over conventional label-based readouts suffering from compound interference and intricate generation of tailored signal mediators. Significant evolvements of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, as well as associated liquid handling instrumentation, triggered extensive efforts in the drug discovery community to integrate the comprehensive MS readout into the high-throughput screening (HTS) portfolio. Providing speed, sensitivity, and accuracy comparable to those of conventional, label-based readouts, combined with merits of MS-based technologies, such as label-free parallelized measurement of multiple physiological components, emphasizes the advantages of MALDI-TOF for HTS approaches. Here we describe the assay development for the identification of protein tyrosine phosphatase 1B (PTP1B) inhibitors. In the context of this precious drug target, MALDI-TOF was integrated into the HTS environment and cross-compared with the well-established AlphaScreen technology. We demonstrate robust and accurate IC 50 determination with high accordance to data generated by AlphaScreen. Additionally, a tailored MALDI-TOF assay was developed to monitor compound-dependent, irreversible modification of the active cysteine of PTP1B. Overall, the presented data proves the promising perspective for the integration of MALDI-TOF into drug discovery campaigns.

UCLA's Molecular Screening Shared Resource: enhancing small molecule discovery with functional genomics and new technology.

PubMed

Damoiseaux, Robert

2014-05-01

The Molecular Screening Shared Resource (MSSR) offers a comprehensive range of leading-edge high throughput screening (HTS) services including drug discovery, chemical and functional genomics, and novel methods for nano and environmental toxicology. The MSSR is an open access environment with investigators from UCLA as well as from the entire globe. Industrial clients are equally welcome as are non-profit entities. The MSSR is a fee-for-service entity and does not retain intellectual property. In conjunction with the Center for Environmental Implications of Nanotechnology, the MSSR is unique in its dedicated and ongoing efforts towards high throughput toxicity testing of nanomaterials. In addition, the MSSR engages in technology development eliminating bottlenecks from the HTS workflow and enabling novel assays and readouts currently not available.

Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing.

PubMed

Morse, Alison M; Calabro, Kaitlyn R; Fear, Justin M; Bloom, David C; McIntyre, Lauren M

2017-08-16

High-throughput sequencing (HTS) has resulted in data for a number of herpes simplex virus (HSV) laboratory strains and clinical isolates. The knowledge of these sequences has been critical for investigating viral pathogenicity. However, the assembly of complete herpesviral genomes, including HSV, is complicated due to the existence of large repeat regions and arrays of smaller reiterated sequences that are commonly found in these genomes. In addition, the inherent genetic variation in populations of isolates for viruses and other microorganisms presents an additional challenge to many existing HTS sequence assembly pipelines. Here, we evaluate two approaches for the identification of genetic variants in HSV1 strains using Illumina short read sequencing data. The first, a reference-based approach, identifies variants from reads aligned to a reference sequence and the second, a de novo assembly approach, identifies variants from reads aligned to de novo assembled consensus sequences. Of critical importance for both approaches is the reduction in the number of low complexity regions through the construction of a non-redundant reference genome. We compared variants identified in the two methods. Our results indicate that approximately 85% of variants are identified regardless of the approach. The reference-based approach to variant discovery captures an additional 15% representing variants divergent from the HSV1 reference possibly due to viral passage. Reference-based approaches are significantly less labor-intensive and identify variants across the genome where de novo assembly-based approaches are limited to regions where contigs have been successfully assembled. In addition, regions of poor quality assembly can lead to false variant identification in de novo consensus sequences. For viruses with a well-assembled reference genome, a reference-based approach is recommended.

Acute effects of TiO2 nanomaterials on the viability and taxonomic composition of aquatic bacterial communities assessed via high-throughput screening and next generation sequencing.

PubMed

Binh, Chu Thi Thanh; Tong, Tiezheng; Gaillard, Jean-François; Gray, Kimberly A; Kelly, John J

2014-01-01

The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of complex microbial communities. In this study toxicity screening via a HTS platform was used in combination with next generation sequencing (NGS) to assess responses of bacterial communities from two aquatic habitats, Lake Michigan (LM) and the Chicago River (CR), to short-term exposure in their native waters to several commercial TiO2 nanomaterials under simulated solar irradiation. Results demonstrate that bacterial communities from LM and CR differed in their sensitivity to nano-TiO2, with the community from CR being more resistant. NGS analysis revealed that the composition of the bacterial communities from LM and CR were significantly altered by exposure to nano-TiO2, including decreases in overall bacterial diversity, decreases in the relative abundance of Actinomycetales, Sphingobacteriales, Limnohabitans, and Flavobacterium, and a significant increase in Limnobacter. These results suggest that the release of nano-TiO2 to the environment has the potential to alter the composition of aquatic bacterial communities, which could have implications for the stability and function of aquatic ecosystems. The novel combination of HTS and NGS described in this study represents a major advance over current methods for assessing ENM ecotoxicity because the relative toxicities of multiple ENMs to thousands of naturally occurring bacterial species can be assessed simultaneously under environmentally relevant conditions.

Acute Effects of TiO2 Nanomaterials on the Viability and Taxonomic Composition of Aquatic Bacterial Communities Assessed via High-Throughput Screening and Next Generation Sequencing

PubMed Central

Binh, Chu Thi Thanh; Tong, Tiezheng; Gaillard, Jean-François; Gray, Kimberly A.; Kelly, John J.

2014-01-01

The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of complex microbial communities. In this study toxicity screening via a HTS platform was used in combination with next generation sequencing (NGS) to assess responses of bacterial communities from two aquatic habitats, Lake Michigan (LM) and the Chicago River (CR), to short-term exposure in their native waters to several commercial TiO2 nanomaterials under simulated solar irradiation. Results demonstrate that bacterial communities from LM and CR differed in their sensitivity to nano-TiO2, with the community from CR being more resistant. NGS analysis revealed that the composition of the bacterial communities from LM and CR were significantly altered by exposure to nano-TiO2, including decreases in overall bacterial diversity, decreases in the relative abundance of Actinomycetales, Sphingobacteriales, Limnohabitans, and Flavobacterium, and a significant increase in Limnobacter. These results suggest that the release of nano-TiO2 to the environment has the potential to alter the composition of aquatic bacterial communities, which could have implications for the stability and function of aquatic ecosystems. The novel combination of HTS and NGS described in this study represents a major advance over current methods for assessing ENM ecotoxicity because the relative toxicities of multiple ENMs to thousands of naturally occurring bacterial species can be assessed simultaneously under environmentally relevant conditions. PMID:25162615

USDA Potato Small RNA Database

USDA-ARS?s Scientific Manuscript database

Small RNAs (sRNAs) are now understood to be involved in gene regulation, function and development. High throughput sequencing (HTS) of sRNAs generates large data sets for analyzing the abundance, source and roles for specific sRNAs. These sRNAs result from transcript degradation as well as specific ...

SeqAPASS: Sequence alignment to predict across-species susceptibility

EPA Science Inventory

Efforts to shift the toxicity testing paradigm from whole organism studies to those focused on the initiation of toxicity and relevant pathways have led to increased utilization of in vitro and in silico methods. Hence the emergence of high through-put screening (HTS) programs, s...

Development of remountable joints and heat removable techniques for high-temperature superconducting magnets

NASA Astrophysics Data System (ADS)

Hashizume, H.; Ito, S.; Yanagi, N.; Tamura, H.; Sagara, A.

2018-02-01

Segment fabrication is now a candidate for the design of superconducting helical magnets in the helical fusion reactor FFHR-d1, which adopts the joint winding of high-temperature superconducting (HTS) helical coils as a primary option and the ‘remountable’ HTS helical coil as an advanced option. This paper reports on recent progress in two key technologies: the mechanical joints (remountable joints) of the HTS conductors and the metal porous media inserted into the cooling channel for segment fabrication. Through our research activities it has been revealed that heat treatment during fabrication of the joint can reduce joint resistance and its dispersion, which can shorten the fabrication process and be applied to bent conductor joints. Also, heat transfer correlations of the cooling channel were established to evaluate heat transfer performance with various cryogenic coolants based on the correlations to analyze the thermal stability of the joint.

High voltage insulation of bushing for HTS power equipment

NASA Astrophysics Data System (ADS)

Kim, Woo-Jin; Choi, Jae-Hyeong; Kim, Sang-Hyun

2012-12-01

For the operation of high temperature superconducting (HTS) power equipments, it is necessary to develop insulating materials and high voltage (HV) insulation technology at cryogenic temperature of bushing. Liquid nitrogen (LN2) is an attractive dielectric liquid. Also, the polymer insulating materials are expected to be used as solid materials such as glass fiber reinforced plastic (GFRP), polytetra-fluoroethylene (PTFE, Teflon), Silicon (Si) rubber, aromatic polyamide (Nomex), EPDM/Silicon alloy compound (EPDM/Si). In this paper, the surface flashover characteristics of various insulating materials in LN2 are studied. These results are studied at both AC and impulse voltage under a non-uniform field. The use of GFRP and Teflon as insulation body for HTS bushing should be much desirable. Especially, GFRP is excellent material not only surface flashover characteristics but also mechanical characteristics at cryogenic temperature. The surface flashover is most serious problem for the shed design in LN2 and operation of superconducting equipments.

Effects of spaceflight on the immunoglobulin repertoire of unimmunized C57BL/6 mice

NASA Astrophysics Data System (ADS)

Ward, Claire; Rettig, Trisha A.; Hlavacek, Savannah; Bye, Bailey A.; Pecaut, Michael J.; Chapes, Stephen K.

2018-02-01

Spaceflight has been shown to suppress the adaptive immune response, altering the distribution and function of lymphocyte populations. B lymphocytes express highly specific and highly diversified receptors, known as immunoglobulins (Ig), that directly bind and neutralize pathogens. Ig diversity is achieved through the enzymatic splicing of gene segments within the genomic DNA of each B cell in a host. The collection of Ig specificities within a host, or Ig repertoire, has been increasingly characterized in both basic research and clinical settings using high-throughput sequencing technology (HTS). We utilized HTS to test the hypothesis that spaceflight affects the B-cell repertoire. To test this hypothesis, we characterized the impact of spaceflight on the unimmunized Ig repertoire of C57BL/6 mice that were flown aboard the International Space Station (ISS) during the Rodent Research One validation flight in comparison to ground controls. Individual gene segment usage was similar between ground control and flight animals, however, gene segment combinations and the junctions in which gene segments combine was varied among animals within and between treatment groups. We also found that spontaneous somatic mutations in the IgH and Igκ gene loci were not increased. These data suggest that space flight did not affect the B cell repertoire of mice flown and housed on the ISS over a short period of time.

On the use of high-throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats.

PubMed

Pessi, Igor Stelmach; Maalouf, Pedro De Carvalho; Laughinghouse, Haywood Dail; Baurain, Denis; Wilmotte, Annick

2016-06-01

The study of Antarctic cyanobacterial diversity has been mostly limited to morphological identification and traditional molecular techniques. High-throughput sequencing (HTS) allows a much better understanding of microbial distribution in the environment, but its application is hampered by several methodological and analytical challenges. In this work, we explored the use of HTS as a tool for the study of cyanobacterial diversity in Antarctic aquatic mats. Our results highlight the importance of using artificial communities to validate the parameters of the bioinformatics procedure used to analyze natural communities, since pipeline-dependent biases had a strong effect on the observed community structures. Analysis of microbial mats from five Antarctic lakes and an aquatic biofilm from the Sub-Antarctic showed that HTS is a valuable tool for the assessment of cyanobacterial diversity. The majority of the operational taxonomic units retrieved were related to filamentous taxa such as Leptolyngbya and Phormidium, which are common genera in Antarctic lacustrine microbial mats. However, other phylotypes related to different taxa such as Geitlerinema, Pseudanabaena, Synechococcus, Chamaesiphon, Calothrix, and Coleodesmium were also found. Results revealed a much higher diversity than what had been reported using traditional methods and also highlighted remarkable differences between the cyanobacterial communities of the studied lakes. The aquatic biofilm from the Sub-Antarctic had a distinct cyanobacterial community from the Antarctic lakes, which in turn displayed a salinity-dependent community structure at the phylotype level. © 2016 Phycological Society of America.

Minimal Residual Disease Detection and Evolved IGH Clones Analysis in Acute B Lymphoblastic Leukemia Using IGH Deep Sequencing.

PubMed

Wu, Jinghua; Jia, Shan; Wang, Changxi; Zhang, Wei; Liu, Sixi; Zeng, Xiaojing; Mai, Huirong; Yuan, Xiuli; Du, Yuanping; Wang, Xiaodong; Hong, Xueyu; Li, Xuemei; Wen, Feiqiu; Xu, Xun; Pan, Jianhua; Li, Changgang; Liu, Xiao

2016-01-01

Acute B lymphoblastic leukemia (B-ALL) is one of the most common types of childhood cancer worldwide and chemotherapy is the main treatment approach. Despite good response rates to chemotherapy regiments, many patients eventually relapse and minimal residual disease (MRD) is the leading risk factor for relapse. The evolution of leukemic clones during disease development and treatment may have clinical significance. In this study, we performed immunoglobulin heavy chain ( IGH ) repertoire high throughput sequencing (HTS) on the diagnostic and post-treatment samples of 51 pediatric B-ALL patients. We identified leukemic IGH clones in 92.2% of the diagnostic samples and nearly half of the patients were polyclonal. About one-third of the leukemic clones have correct open reading frame in the complementarity determining region 3 (CDR3) of IGH , which demonstrates that the leukemic B cells were in the early developmental stage. We also demonstrated the higher sensitivity of HTS in MRD detection and investigated the clinical value of using peripheral blood in MRD detection and monitoring the clonal IGH evolution. In addition, we found leukemic clones were extensively undergoing continuous clonal IGH evolution by variable gene replacement. Dynamic frequency change and newly emerged evolved IGH clones were identified upon the pressure of chemotherapy. In summary, we confirmed the high sensitivity and universal applicability of HTS in MRD detection. We also reported the ubiquitous evolved IGH clones in B-ALL samples and their response to chemotherapy during treatment.

New fluorescence techniques for high-throughput drug discovery.

PubMed

Jäger, S; Brand, L; Eggeling, C

2003-12-01

The rapid increase of compound libraries as well as new targets emerging from the Human Genome Project require constant progress in pharmaceutical research. An important tool is High-Throughput Screening (HTS), which has evolved as an indispensable instrument in the pre-clinical target-to-IND (Investigational New Drug) discovery process. HTS requires machinery, which is able to test more than 100,000 potential drug candidates per day with respect to a specific biological activity. This calls for certain experimental demands especially with respect to sensitivity, speed, and statistical accuracy, which are fulfilled by using fluorescence technology instrumentation. In particular the recently developed family of fluorescence techniques, FIDA (Fluorescence Intensity Distribution Analysis), which is based on confocal single-molecule detection, has opened up a new field of HTS applications. This report describes the application of these new techniques as well as of common fluorescence techniques--such as confocal fluorescence lifetime and anisotropy--to HTS. It gives experimental examples and presents advantages and disadvantages of each method. In addition the most common artifacts (auto-fluorescence or quenching by the drug candidates) emerging from the fluorescence detection techniques are highlighted and correction methods for confocal fluorescence read-outs are presented, which are able to circumvent this deficiency.

Contrasting responses of bacterial and fungal communities to aggregate-size fractions and long-term fertilizations in soils of northeastern China.

PubMed

Liao, Hao; Zhang, Yuchen; Zuo, Qinyan; Du, Binbin; Chen, Wenli; Wei, Dan; Huang, Qiaoyun

2018-04-20

Soils, with non-uniform distribution of nutrients across different aggregate-size fractions, provide spatially heterogeneous microhabitats for microorganisms. However, very limited information is available on microbial distributions and their response to fertilizations across aggregate-size fractions in agricultural soils. Here, we examined the structures of bacterial and fungal communities across different aggregate-size fractions (2000-250 μm, 250-53 μm and <53 μm) in response to 35-years organic and/or chemical fertilization regimes in the soil of northeastern China by phospholipid fatty acid (PLFA) and high throughput sequencing (HTS) technology. Our results show that larger fractions (>53 μm), especially 250-53 μm aggregates, which contain more soil C and N, are associated with greater microbial biomass and higher fungi/bacteria ratio. We firstly reported the fungal community composition in different aggregate-size fractions by HTS technology and found more Ascomycota but less Zygomycota in larger fractions with higher C content across all fertilization regimes. Fertilization and aggregate-size fractions significantly affect the compositions of bacterial and fungal communities although their effects are different. The bacterial community is mainly driven by fertilization, especially chemical fertilizers, and is closely related to the shifts of soil P (phosphorus). The fungal community is preferentially impacted by different aggregate-size fractions and is more associated with the changes of soil C and N. The distinct responses of microbial communities suggest different mechanisms controlling the assembly of soil bacterial and fungal communities at aggregate scale. The investigations of both bacterial and fungal communities could provide a better understanding on nutrient cycling across aggregate-size fractions. Copyright © 2018. Published by Elsevier B.V.

SeqAPASS to evaluate conservation of high-throughput screening targets across non-mammalian species

EPA Science Inventory

Cell-based high-throughput screening (HTS) and computational technologies are being applied as tools for toxicity testing in the 21st century. The U.S. Environmental Protection Agency (EPA) embraced these technologies and created the ToxCast Program in 2007, which has served as a...

High-Throughput Screening Enhances Kidney Organoid Differentiation from Human Pluripotent Stem Cells and Enables Automated Multidimensional Phenotyping.

PubMed

Czerniecki, Stefan M; Cruz, Nelly M; Harder, Jennifer L; Menon, Rajasree; Annis, James; Otto, Edgar A; Gulieva, Ramila E; Islas, Laura V; Kim, Yong Kyun; Tran, Linh M; Martins, Timothy J; Pippin, Jeffrey W; Fu, Hongxia; Kretzler, Matthias; Shankland, Stuart J; Himmelfarb, Jonathan; Moon, Randall T; Paragas, Neal; Freedman, Benjamin S

2018-05-15

Organoids derived from human pluripotent stem cells are a potentially powerful tool for high-throughput screening (HTS), but the complexity of organoid cultures poses a significant challenge for miniaturization and automation. Here, we present a fully automated, HTS-compatible platform for enhanced differentiation and phenotyping of human kidney organoids. The entire 21-day protocol, from plating to differentiation to analysis, can be performed automatically by liquid-handling robots, or alternatively by manual pipetting. High-content imaging analysis reveals both dose-dependent and threshold effects during organoid differentiation. Immunofluorescence and single-cell RNA sequencing identify previously undetected parietal, interstitial, and partially differentiated compartments within organoids and define conditions that greatly expand the vascular endothelium. Chemical modulation of toxicity and disease phenotypes can be quantified for safety and efficacy prediction. Screening in gene-edited organoids in this system reveals an unexpected role for myosin in polycystic kidney disease. Organoids in HTS formats thus establish an attractive platform for multidimensional phenotypic screening. Copyright © 2018 Elsevier Inc. All rights reserved.

EPA-Health Canada CompTox Collaboration

EPA Science Inventory

Research program of EPA’s National Center for Computational Toxicology addresses chemical screening and prioritization needs for pesticidal inerts, anti-microbials, CCLs, HPVs and MPVs, comprehensive use of HTS technologies to generate.

SCALCE: boosting sequence compression algorithms using locally consistent encoding

PubMed Central

Hach, Faraz; Numanagić, Ibrahim; Sahinalp, S Cenk

2012-01-01

Motivation: The high throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for the computational infrastructure. Data management, storage and analysis have become major logistical obstacles for those adopting the new platforms. The requirement for large investment for this purpose almost signalled the end of the Sequence Read Archive hosted at the National Center for Biotechnology Information (NCBI), which holds most of the sequence data generated world wide. Currently, most HTS data are compressed through general purpose algorithms such as gzip. These algorithms are not designed for compressing data generated by the HTS platforms; for example, they do not take advantage of the specific nature of genomic sequence data, that is, limited alphabet size and high similarity among reads. Fast and efficient compression algorithms designed specifically for HTS data should be able to address some of the issues in data management, storage and communication. Such algorithms would also help with analysis provided they offer additional capabilities such as random access to any read and indexing for efficient sequence similarity search. Here we present SCALCE, a ‘boosting’ scheme based on Locally Consistent Parsing technique, which reorganizes the reads in a way that results in a higher compression speed and compression rate, independent of the compression algorithm in use and without using a reference genome. Results: Our tests indicate that SCALCE can improve the compression rate achieved through gzip by a factor of 4.19—when the goal is to compress the reads alone. In fact, on SCALCE reordered reads, gzip running time can improve by a factor of 15.06 on a standard PC with a single core and 6 GB memory. Interestingly even the running time of SCALCE + gzip improves that of gzip alone by a factor of 2.09. When compared with the recently published BEETL, which aims to sort the (inverted) reads in lexicographic order for improving bzip2, SCALCE + gzip provides up to 2.01 times better compression while improving the running time by a factor of 5.17. SCALCE also provides the option to compress the quality scores as well as the read names, in addition to the reads themselves. This is achieved by compressing the quality scores through order-3 Arithmetic Coding (AC) and the read names through gzip through the reordering SCALCE provides on the reads. This way, in comparison with gzip compression of the unordered FASTQ files (including reads, read names and quality scores), SCALCE (together with gzip and arithmetic encoding) can provide up to 3.34 improvement in the compression rate and 1.26 improvement in running time. Availability: Our algorithm, SCALCE (Sequence Compression Algorithm using Locally Consistent Encoding), is implemented in C++ with both gzip and bzip2 compression options. It also supports multithreading when gzip option is selected, and the pigz binary is available. It is available at http://scalce.sourceforge.net. Contact: fhach@cs.sfu.ca or cenk@cs.sfu.ca Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23047557

Acoustic Droplet Ejection Technology and Its Application in High-Throughput RNA Interference Screening.

PubMed

Nebane, N Miranda; Coric, Tatjana; McKellip, Sara; Woods, LaKeisha; Sosa, Melinda; Rasmussen, Lynn; Bjornsti, Mary-Ann; White, E Lucile

2016-02-01

The development of acoustic droplet ejection (ADE) technology has resulted in many positive changes associated with the operations in a high-throughput screening (HTS) laboratory. Originally, this liquid transfer technology was used to simply transfer DMSO solutions of primarily compounds. With the introduction of Labcyte's Echo 555, which has aqueous dispense capability, the application of this technology has been expanded beyond its original use. This includes the transfer of many biological reagents solubilized in aqueous buffers, including siRNAs. The Echo 555 is ideal for siRNA dispensing because it is accurate at low volumes and a step-down dilution is not necessary. The potential for liquid carryover and cross-contamination is eliminated, as no tips are needed. Herein, we describe the siRNA screening platform at Southern Research's HTS Center using the ADE technology. With this technology, an siRNA library can be dispensed weeks or even months in advance of the assay itself. The protocol has been optimized to achieve assay parameters comparable to small-molecule screening parameters, and exceeding the norm reported for genomewide siRNA screens. © 2015 Society for Laboratory Automation and Screening.

SeqAPASS: Sequence alignment to predict across-species ...

EPA Pesticide Factsheets

Efforts to shift the toxicity testing paradigm from whole organism studies to those focused on the initiation of toxicity and relevant pathways have led to increased utilization of in vitro and in silico methods. Hence the emergence of high through-put screening (HTS) programs, such as U.S. EPA ToxCast, and application of the adverse outcome pathway (AOP) framework for identifying and defining biological key events triggered upon perturbation of molecular initiating events and leading to adverse outcomes occuring at a level of organization relevant for risk assessment [1]. With these recent initiatives to harness the power of “the pathway” in describing and evaluating toxicity comes the need to extrapolate data beyond the model species. Sequence alignment to predict across-species susceptibilty (SeqAPASS) is a web-based tool that allows the user to begin to understand how broadly HTS data or AOP constructs may plausibly be extrapolated across species, while describing the relative intrinsic susceptibiltiy of different taxa to chemicals with known modes of action (e.g., pharmaceuticals and pesticides). The tool rapidly and strategically assesses available molecular target information to describe protein sequence similarity at the primary amino acid sequence, conserved domain, and individual amino acid residue levels. This in silico approach to species extrapolation was designed to automate and streamline the relatively complex and time-consuming process of co

NEW PUBLIC DATA AND INTERNET RESOURCES ...

EPA Pesticide Factsheets

High-throughput screening (HTS) technologies, along with efforts to improve public access to chemical toxicity information resources and to systematize older toxicity studies, have the potential to significantly improve predictive capabilities in toxicology. Internet Resource

DEVELOPMENT OF EPA'S TOXCAST PROGRAM FOR PRIORITIZING THE TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS.

EPA Science Inventory

EPA is developing methods for utilizing computational chemistry, high-throughput screening (HTS)and genomic technologies to predict potential toxicity and prioritize the use of limited testing resources.

Separation of phospholipids in microfluidic chip device: application to high-throughput screening assays for lipid-modifying enzymes.

PubMed

Lin, Sansan; Fischl, Anthony S; Bi, Xiahui; Parce, Wally

2003-03-01

Phospholipid molecules such as ceramide and phosphoinositides play crucial roles in signal transduction pathways. Lipid-modifying enzymes including sphingomyelinase and phosphoinositide kinases regulate the generation and degradation of these lipid-signaling molecules and are important therapeutic targets in drug discovery. We now report a sensitive and convenient method to separate these lipids using microfluidic chip-based technology. The method takes advantage of the high-separation power of the microchips that separate lipids based on micellar electrokinetic capillary chromatography (MEKC) and the high sensitivity of fluorescence detection. We further exploited the method to develop a homogenous assay to monitor activities of lipid-modifying enzymes. The assay format consists of two steps: an on-plate enzymatic reaction using fluorescently labeled substrates followed by an on-chip MEKC separation of the reaction products from the substrates. The utility of the assay format for high-throughput screening (HTS) is demonstrated using phospholipase A(2) on the Caliper 250 HTS system: throughput of 80min per 384-well plate can be achieved with unattended running time of 5.4h. This enabling technology for assaying lipid-modifying enzymes is ideal for HTS because it avoids the use of radioactive substrates and complicated separation/washing steps and detects both substrate and product simultaneously.

Design, Test and Demonstration of Fault Current Limiting HTS Transformer

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

Hazelton, Drew

The project developed new technology that enables the creation of a high temperature superconductor-based FCL power transformer. SuperPower’s research and development created new methods to bond HTS conductor to a supporting substrate, test, and insulate the resulting bonded conductor, reduce winding ac losses, ensure FCL functionality during a transformer fault and build firm superconducting joints in the transformer harnesses and cabling. The bonded conductor in this program was shown to meet the critical operating parameters of providing the superconducting transformer operation while being able to meet the target normal state resistance required for FCL operation. The bonded conductor was alsomore » shown to be able to handle the fabrication stresses associated with the manufacture of the FCL transformer while also being able to handle the high hoop stresses and axial forces during a fault transient. Much of the technology developed here is applicable to the broader applied superconductivity community. The ability to tailor the clad conductors performance characteristics gives the designer of devices utilizing HTS a broader capability to address the particular needs of an given application. SuperPower worked with its sub-recipients Waukesha Electric Systems, ORNL, Southern California Edison and University of Houston to develop the design, fabrication, installation and operational aspects of a fault current limiting transformer on the electrical grid.« less

Assessing HTS Performance Using BioAssay Ontology: Screening and Analysis of a Bacterial Phospho-N-Acetylmuramoyl-Pentapeptide Translocase Campaign

PubMed Central

Moberg, Andreas; Hansson, Eva; Boyd, Helen

2014-01-01

Abstract With the public availability of biochemical assays and screening data constantly increasing, new applications for data mining and method analysis are evolving in parallel. One example is BioAssay Ontology (BAO) for systematic classification of assays based on screening setup and metadata annotations. In this article we report a high-throughput screening (HTS) against phospho-N-acetylmuramoyl-pentapeptide translocase (MraY), an attractive antibacterial drug target involved in peptidoglycan synthesis. The screen resulted in novel chemistry identification using a fluorescence resonance energy transfer assay. To address a subset of the false positive hits, a frequent hitter analysis was performed using an approach in which MraY hits were compared with hits from similar assays, previously used for HTS. The MraY assay was annotated according to BAO and three internal reference assays, using a similar assay design and detection technology, were identified. Analyzing the assays retrospectively, it was clear that both MraY and the three reference assays all showed a high false positive rate in the primary HTS assays. In the case of MraY, false positives were efficiently identified by applying a method to correct for compound interference at the hit-confirmation stage. Frequent hitter analysis based on the three reference assays with similar assay method identified additional false actives in the primary MraY assay as frequent hitters. This article demonstrates how assays annotated using BAO terms can be used to identify closely related reference assays, and that analysis based on these assays clearly can provide useful data to influence assay design, technology, and screening strategy. PMID:25415593

Evaluation of high temperature superconductive thermal bridges for space borne cryogenic detectors

NASA Technical Reports Server (NTRS)

Scott, Elaine P.

1996-01-01

Infrared sensor satellites are used to monitor the conditions in the earth's upper atmosphere. In these systems, the electronic links connecting the cryogenically cooled infrared detectors to the significantly warmer amplification electronics act as thermal bridges and, consequently, the mission lifetimes of the satellites are limited due to cryogenic evaporation. High-temperature superconductor (HTS) materials have been proposed by researchers at the National Aeronautics and Space Administration Langley's Research Center (NASA-LaRC) as an alternative to the currently used manganin wires for electrical connection. The potential for using HTS films as thermal bridges has provided the motivation for the design and the analysis of a spaceflight experiment to evaluate the performance of this superconductive technology in the space environment. The initial efforts were focused on the preliminary design of the experimental system which allows for the quantitative comparison of superconductive leads with manganin leads, and on the thermal conduction modeling of the proposed system. Most of the HTS materials were indicated to be potential replacements for the manganin wires. In the continuation of this multi-year research, the objectives of this study were to evaluate the sources of heat transfer on the thermal bridges that have been neglected in the preliminary conductive model and then to develop a methodology for the estimation of the thermal conductivities of the HTS thermal bridges in space. The Joule heating created by the electrical current through the manganin wires was incorporated as a volumetric heat source into the manganin conductive model. The radiative heat source on the HTS thermal bridges was determined by performing a separate radiant interchange analysis within a high-T(sub c) superconductor housing area. Both heat sources indicated no significant contribution on the cryogenic heat load, which validates the results obtained in the preliminary conduction model. A methodology was presented for the estimation of the thermal conductivities of the individual HTS thermal bridge materials and the effective thermal conductivities of the composite HTS thermal bridges as functions of temperature. This methodology included a sensitivity analysis and the demonstration of the estimation procedure using simulated data with added random errors. The thermal conductivities could not be estimated as functions of temperature; thus the effective thermal conductivities of the HTS thermal bridges were analyzed as constants.

NEW PUBLIC DATA AND INTERNET RESOURCES IMPACTING PREDICTIVE TOXICOLOGY.

EPA Science Inventory

High-throughput screening (HTS) technologies, along with efforts to improve public access to chemical toxicity information resources and to systematize older toxicity studies, have the potential to significantly improve predictive capabilities in toxicology.

Discovery and molecular characterization of a novel enamovirus, Grapevine enamovirus-1.

PubMed

Silva, João Marcos Fagundes; Al Rwahnih, Maher; Blawid, Rosana; Nagata, Tatsuya; Fajardo, Thor Vinícius Martins

2017-08-01

In this study, we describe a novel putative Enamovirus member, Grapevine enamovirus-1 (GEV-1), discovered by high-throughput sequencing (HTS). A limited survey using HTS of 17 grapevines (Vitis spp.) from the south, southeast, and northeast regions of Brazil led to the detection of GEV-1 exclusively on southern plants, infecting four grapevine cultivars (Cabernet Sauvignon, Semillon, CG 90450, and Cabernet franc) with a remarkable identity of around 99% at the nucleotide level. This novel virus was only detected in multiple-virus infected plants exhibiting viral-like symptoms. GEV-1 was also detected on a cv. Malvasia Longa by RT-PCR. We performed graft-transmissibility assays on GEV-1. The organization, products, and cis-acting regulatory elements of GEV-1 genome are also discussed here. The near complete genome sequence of GEV-1 was obtained during the course of this study, lacking only part of the 3' untranslated terminal region. This is the first report of a virus in the family Luteoviridae infecting grapevines. Based on its genomic properties and phylogenetic analyses, GEV-1 should be classified as a new member of the genus Enamovirus.

The Use of AlphaScreen Technology in HTS: Current Status

PubMed Central

Eglen, Richard M; Reisine, Terry; Roby, Philippe; Rouleau, Nathalie; Illy, Chantal; Bossé, Roger; Bielefeld, Martina

2008-01-01

AlphaScreen (Amplified Luminescent Proximity Homogeneous Assay Screen) is versatile assay technology developed to measuring analytes using a homogenous protocol. This technology is an example of a bead-based proximity assay and was developed from a diagnostic assay technology known as LOCI (Luminescent Oxygen Channeling Assay). Here, singlet oxygen molecules, generated by high energy irradiation of Donor beads, travel over a constrained distance (approx. 200 nm) to Acceptor beads. This results in excitation of a cascading series of chemical reactions, ultimately causing generation of a chemiluminescent signal. In the past decade, a wide variety of applications has been reported, ranging from detection of analytes involved in cell signaling, including protein:protein, protein:peptide, protein:small molecule or peptide:peptide interactions. Numerous homogeneous HTS-optimized assays have been reported using the approach, including generation of second messengers (such as accumulation of cyclic AMP, cyclic GMP, inositol [1, 4, 5] trisphosphate or phosphorylated ERK) from liganded GPCRs or tyrosine kinase receptors, post-translational modification of proteins (such as proteolytic cleavage, phosphorylation, ubiquination and sumoylation) as well as protein-protein and protein-nucleic acid interactions. Recently, the basic AlphaScreen technology was extended in that the chemistry of the Acceptor bead was modified such that emitted light is more intense and spectrally defined, thereby markedly reducing interference from biological fluid matrices (such as trace hemolysis in serum and plasma). In this format, referred to as AlphaLISA, it provides an alternative technology to classical ELISA assays and is suitable for high throughput automated fluid dispensing and detection systems. Collectively, AlphaScreen and AlphaLISA technologies provide a facile assay platform with which one can quantitate complex cellular processes using simple no-wash microtiter plate based assays. They provide the means by which large compound libraries can be screened in a high throughput fashion at a diverse range of therapeutically important targets, often not readily undertaken using other homogeneous assay technologies. This review assesses the current status of the technology in drug discovery, in general, and high throughput screening (HTS), in particular. PMID:20161822

Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils

PubMed Central

Song, Zewei; Schlatter, Dan; Kennedy, Peter; Kinkel, Linda L.; Kistler, H. Corby; Nguyen, Nhu; Bates, Scott T.

2015-01-01

Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS). The following treatments were considered: 1) the amount of soil used in DNA extraction, 2) the inclusion of additional steps (freeze/thaw cycles, sonication, or hot water bath incubation) in the extraction procedure, 3) the amount of DNA template used in PCR, and 4) the effect of sample pooling, either physically or computationally. Soils from two different ecosystems in Minnesota, USA, one prairie and one forest site, were used to assess the generality of our results. The first three treatments did not significantly influence observed fungal OTU richness or community structure at either site. Physical pooling captured more OTU richness compared to individual samples, but total OTU richness at each site was highest when individual samples were computationally combined. We conclude that standard extraction kit protocols are well optimized for fungal HTS surveys, but because sample pooling can significantly influence OTU richness estimates, it is important to carefully consider the study aims when planning sampling procedures. PMID:25974078

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities.

PubMed

Deiner, Kristy; Bik, Holly M; Mächler, Elvira; Seymour, Mathew; Lacoursière-Roussel, Anaïs; Altermatt, Florian; Creer, Simon; Bista, Iliana; Lodge, David M; de Vere, Natasha; Pfrender, Michael E; Bernatchez, Louis

2017-11-01

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Quantitative Analysis of Focused A-To-I RNA Editing Sites by Ultra-High-Throughput Sequencing in Psychiatric Disorders

PubMed Central

Zhu, Hu; Urban, Daniel J.; Blashka, Jared; McPheeters, Matthew T.; Kroeze, Wesley K.; Mieczkowski, Piotr; Overholser, James C.; Jurjus, George J.; Dieter, Lesa; Mahajan, Gouri J.; Rajkowska, Grazyna; Wang, Zefeng; Sullivan, Patrick F.; Stockmeier, Craig A.; Roth, Bryan L.

2012-01-01

A-to-I RNA editing is a post-transcriptional modification of single nucleotides in RNA by adenosine deamination, which thereby diversifies the gene products encoded in the genome. Thousands of potential RNA editing sites have been identified by recent studies (e.g. see Li et al, Science 2009); however, only a handful of these sites have been independently confirmed. Here, we systematically and quantitatively examined 109 putative coding region A-to-I RNA editing sites in three sets of normal human brain samples by ultra-high-throughput sequencing (uHTS). Forty of 109 putative sites, including 25 previously confirmed sites, were validated as truly edited in our brain samples, suggesting an overestimation of A-to-I RNA editing in these putative sites by Li et al (2009). To evaluate RNA editing in human disease, we analyzed 29 of the confirmed sites in subjects with major depressive disorder and schizophrenia using uHTS. In striking contrast to many prior studies, we did not find significant alterations in the frequency of RNA editing at any of the editing sites in samples from these patients, including within the 5HT2C serotonin receptor (HTR2C). Our results indicate that uHTS is a fast, quantitative and high-throughput method to assess RNA editing in human physiology and disease and that many prior studies of RNA editing may overestimate both the extent and disease-related variability of RNA editing at the sites we examined in the human brain. PMID:22912834

Ranking the selectivity of PubChem screening hits by activity-based protein profiling: MMP13 as a case study.

PubMed

Nakai, Ryuichiro; Salisbury, Cleo M; Rosen, Hugh; Cravatt, Benjamin F

2009-02-01

High-throughput screening (HTS) has become an integral part of academic and industrial efforts aimed at developing new chemical probes and drugs. These screens typically generate several 'hits', or lead active compounds, that must be prioritized for follow-up medicinal chemistry studies. Among primary considerations for ranking lead compounds is selectivity for the intended target, especially among mechanistically related proteins. Here, we show how the chemical proteomic technology activity-based protein profiling (ABPP) can serve as a universal assay to rank HTS hits based on their selectivity across many members of an enzyme superfamily. As a case study, four metalloproteinase-13 (MMP13) inhibitors of similar potency originating from a publically supported HTS and reported in PubChem were tested by ABPP for selectivity against a panel of 27 diverse metalloproteases. The inhibitors could be readily separated into two groups: (1) those that were active against several metalloproteases and (2) those that showed high selectivity for MMP13. The latter set of inhibitors was thereby designated as more suitable for future medicinal chemistry optimization. We anticipate that ABPP will find general utility as a platform to rank the selectivity of lead compounds emerging from HTS assays for a wide variety of enzymes.

Superconductor bearings, flywheels and transportation

NASA Astrophysics Data System (ADS)

Werfel, F. N.; Floegel-Delor, U.; Rothfeld, R.; Riedel, T.; Goebel, B.; Wippich, D.; Schirrmeister, P.

2012-01-01

This paper describes the present status of high temperature superconductors (HTS) and of bulk superconducting magnet devices, their use in bearings, in flywheel energy storage systems (FESS) and linear transport magnetic levitation (Maglev) systems. We report and review the concepts of multi-seeded REBCO bulk superconductor fabrication. The multi-grain bulks increase the averaged trapped magnetic flux density up to 40% compared to single-grain assembly in large-scale applications. HTS magnetic bearings with permanent magnet (PM) excitation were studied and scaled up to maximum forces of 10 kN axially and 4.5 kN radially. We examine the technology of the high-gradient magnetic bearing concept and verify it experimentally. A large HTS bearing is tested for stabilizing a 600 kg rotor of a 5 kWh/250 kW flywheel system. The flywheel rotor tests show the requirement for additional damping. Our compact flywheel system is compared with similar HTS-FESS projects. A small-scale compact YBCO bearing with in situ Stirling cryocooler is constructed and investigated for mobile applications. Next we show a successfully developed modular linear Maglev system for magnetic train operation. Each module levitates 0.25t at 10 mm distance during one-day operation without refilling LN2. More than 30 vacuum cryostats containing multi-seeded YBCO blocks are fabricated and are tested now in Germany, China and Brazil.

Reproducibility of HTS-SQUID magnetocardiography in an unshielded clinical environment.

PubMed

Leder, U; Schrey, F; Haueisen, J; Dörrer, L; Schreiber, J; Liehr, M; Schwarz, G; Solbrig, O; Figulla, H R; Seidel, P

2001-07-01

A new technology has been developed which measures the magnetic field of the human heart (magnetocardiogram, MCG) by using high temperature superconducting (HTS) sensors. These sensors can be operated at the temperature of liquid nitrogen without electromagnetic shielding. We tested the reproducibility of HTS-MCG measurements in healthy volunteers. Unshielded HTS-MCG measurements were performed in 18 healthy volunteers in left precordial position in two separate sessions in a clinical environment. The heart cycles of 10 min were averaged, smoothed, the baselines were adjusted, and the data were standardized to the respective areas under the curves (AUC) of the absolute values of the QRST amplitudes. The QRS complexes and the ST-T intervals were used to assess the reproducibility of the two measurements. Ratios (R(QRS), R(STT)) were calculated by dividing the AUC of the first measurement by the ones of the second measurement. The linear correlation coefficients (CORR(QRS), CORR(STT)) of the time intervals of the two measurements were calculated, too. The HTS-MCG signal was completely concealed by the high noise level in the raw data. The averaging and smoothing algorithms unmasked the QRS complex and the ST segment. A high reproducibility was found for the QRS complex (R(QRS)=1.2+/-0.3, CORR(QRS)=0.96+/-0.06). Similarly to the shape of the ECG it was characterized by three bends, the Q, R, and S waves. In the ST-T interval, the reproducibility was considerably lower (R(STT)=0.9+/-0.2, CORR(STT)=0.66+/-0.28). In contrast to the shape of the ECG, a baseline deflection after the T wave which may belong to U wave activity was found in a number of volunteers. HTS-MCG devices can be operated in a clinical environment without shielding. Whereas the reproducibility was found to be high for the depolarization interval, it was considerably lower for the ST segment and for the T wave. Therefore, before clinically applying HTS-MCG systems to the detection of repolarization abnormalities in acute coronary syndromes, further technical development of the systems is necessary to improve the signal-to-noise ratio.

Design and manufacture of a D-shape coil-based toroid-type HTS DC reactor using 2nd generation HTS wire

NASA Astrophysics Data System (ADS)

Kim, Kwangmin; Go, Byeong-Soo; Sung, Hae-Jin; Park, Hea-chul; Kim, Seokho; Lee, Sangjin; Jin, Yoon-Su; Oh, Yunsang; Park, Minwon; Yu, In-Keun

2014-09-01

This paper describes the design specifications and performance of a real toroid-type high temperature superconducting (HTS) DC reactor. The HTS DC reactor was designed using 2G HTS wires. The HTS coils of the toroid-type DC reactor magnet were made in the form of a D-shape. The target inductance of the HTS DC reactor was 400 mH. The expected operating temperature was under 20 K. The electromagnetic performance of the toroid-type HTS DC reactor magnet was analyzed using the finite element method program. A conduction cooling method was adopted for reactor magnet cooling. Performances of the toroid-type HTS DC reactor were analyzed through experiments conducted under the steady-state and charge conditions. The fundamental design specifications and the data obtained from this research will be applied to the design of a commercial-type HTS DC reactor.

EPA CHEMICAL PRIORITIZATION COMMUNITY OF PRACTICE.

EPA Science Inventory

IN 2005 THE NATIONAL CENTER FOR COMPUTATIONAL TOXICOLOGY (NCCT) ORGANIZED EPA CHEMICAL PRIORITIATION COMMUNITY OF PRACTICE (CPCP) TO PROVIDE A FORUM FOR DISCUSSING THE UTILITY OF COMPUTATIONAL CHEMISTRY, HIGH-THROUGHPUT SCREENIG (HTS) AND VARIOUS TOXICOGENOMIC TECHNOLOGIES FOR CH...

Computational Toxicology at the US EPA

EPA Science Inventory

Computational toxicology is the application of mathematical and computer models to help assess chemical hazards and risks to human health and the environment. Supported by advances in informatics, high-throughput screening (HTS) technologies, and systems biology, EPA is developin...

THE TOXCAST PROGRAM FOR PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS

EPA Science Inventory

The United States Environmental Protection Agency (EPA) is developing methods for utilizing computational chemistry, high-throughput screening (HTS) and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources towards chemicals...

A novel HTS magnetic levitation dining table

NASA Astrophysics Data System (ADS)

Lu, Yiyun; Huang, Huiying

2018-05-01

High temperature superconducting (HTS) bulk can levitate above or suspend below a permanent magnet stably. Many magnificent potential applications of HTS bulk are proposed by researchers. Until now, few reports have been found for real applications of HTS bulk. A complete set of small-scale HTS magnetic levitation table is proposed in the paper. The HTS magnetic levitation table includes an annular HTS magnetic levitation system which is composed of an annular HTS bulk array and an annular permanent magnet guideway (PMG). The annular PMG and the annular cryogenics vessel which used to maintain low temperature environment of the HTS bulk array are designed. 62 YBCO bulks are used to locate at the bottom of the annular vessel. A 3D-model finite element numerical method is used to design the HTS bulk magnetic levitation system. Equivalent magnetic levitation and guidance forces calculation rules are proposed aimed at the annular HTS magnetic levitation system stability. Based on the proposed method, levitation and guidance forces curves of the one YBCO bulk magnetic above PMG could be obtained. This method also can use to assist PMG design to check whether the designed PMG could reach the basic demand of the HTS magnetic levitation table.

Effects of spaceflight on the immunoglobulin repertoire of unimmunized C57BL/6 mice.

PubMed

Ward, Claire; Rettig, Trisha A; Hlavacek, Savannah; Bye, Bailey A; Pecaut, Michael J; Chapes, Stephen K

2018-02-01

Spaceflight has been shown to suppress the adaptive immune response, altering the distribution and function of lymphocyte populations. B lymphocytes express highly specific and highly diversified receptors, known as immunoglobulins (Ig), that directly bind and neutralize pathogens. Ig diversity is achieved through the enzymatic splicing of gene segments within the genomic DNA of each B cell in a host. The collection of Ig specificities within a host, or Ig repertoire, has been increasingly characterized in both basic research and clinical settings using high-throughput sequencing technology (HTS). We utilized HTS to test the hypothesis that spaceflight affects the B-cell repertoire. To test this hypothesis, we characterized the impact of spaceflight on the unimmunized Ig repertoire of C57BL/6 mice that were flown aboard the International Space Station (ISS) during the Rodent Research One validation flight in comparison to ground controls. Individual gene segment usage was similar between ground control and flight animals, however, gene segment combinations and the junctions in which gene segments combine was varied among animals within and between treatment groups. We also found that spontaneous somatic mutations in the IgH and Igκ gene loci were not increased. These data suggest that space flight did not affect the B cell repertoire of mice flown and housed on the ISS over a short period of time. Copyright © 2017 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

In vitro flow cytometry-based screening platform for cellulase engineering

PubMed Central

Körfer, Georgette; Pitzler, Christian; Vojcic, Ljubica; Martinez, Ronny; Schwaneberg, Ulrich

2016-01-01

Ultrahigh throughput screening (uHTS) plays an essential role in directed evolution for tailoring biocatalysts for industrial applications. Flow cytometry-based uHTS provides an efficient coverage of the generated protein sequence space by analysis of up to 107 events per hour. Cell-free enzyme production overcomes the challenge of diversity loss during the transformation of mutant libraries into expression hosts, enables directed evolution of toxic enzymes, and holds the promise to efficiently design enzymes of human or animal origin. The developed uHTS cell-free compartmentalization platform (InVitroFlow) is the first report in which a flow cytometry-based screened system has been combined with compartmentalized cell-free expression for directed cellulase enzyme evolution. InVitroFlow was validated by screening of a random cellulase mutant library employing a novel screening system (based on the substrate fluorescein-di-β-D-cellobioside), and yielded significantly improved cellulase variants (e.g. CelA2-H288F-M1 (N273D/H288F/N468S) with 13.3-fold increased specific activity (220.60 U/mg) compared to CelA2 wildtype: 16.57 U/mg). PMID:27184298

Synthesis and evaluation of 5-(arylthio)-9H-pyrimido[4,5-b]indole-2,4-diamines as receptor tyrosine kinase and thymidylate synthase inhibitors and as antitumor agents.

PubMed

Zaware, Nilesh; Kisliuk, Roy; Bastian, Anja; Ihnat, Michael A; Gangjee, Aleem

2017-04-01

In an effort to optimize the structural requirements for combined cytostatic and cytotoxic effects in single agents, a series of 5-(arylthio)-9H-pyrimido[4,5-b]indole-2,4-diamines 3-7 were synthesized and evaluated as inhibitors of receptor tyrosine kinases (RTKs) as well as thymidylate synthase (TS). The synthesis of these compounds involved the nucleophilic displacement of the common intermediate 5-bromo/5-chloro-9H-pyrimido[4,5-b]indole-2,4-diamine with appropriate aryl thiols. A novel four step synthetic scheme to the common intermediate was developed which is more efficient relative to the previously reported six-step sequence. Biological evaluation of these compounds indicated dual activity in RTKs and human TS (hTS). In the VEGFR-2 assay, compound 5 was equipotent to the standard compound semaxanib and was better than standard TS inhibitor pemetrexed, in the hTS assay. Compounds 3, 6 and 7 were nanomolar inhibitors of hTS and were several fold better than pemetrexed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Seqenv: linking sequences to environments through text mining.

PubMed

Sinclair, Lucas; Ijaz, Umer Z; Jensen, Lars Juhl; Coolen, Marco J L; Gubry-Rangin, Cecile; Chroňáková, Alica; Oulas, Anastasis; Pavloudi, Christina; Schnetzer, Julia; Weimann, Aaron; Ijaz, Ali; Eiler, Alexander; Quince, Christopher; Pafilis, Evangelos

2016-01-01

Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the "nt" nucleotide database provided by NCBI and, out of every hit, extracts-if it is available-the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv.

High Temperature Superconductors: From Delivery to Applications (Presentation from 2011 Ernest Orlando Lawrence Award-winner, Dr. Amit Goyal, and including introduction by Energy Secretary, Dr. Steven Chu)

ScienceCinema

Goyal, Amit [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2018-04-27

Dr. Amit Goyal, a high temperature superconductivity (HTS) researcher at Oak Ridge National Laboratory, was named a 2011 winner of the Department of Energy's Ernest Orlando Lawrence Award honoring U.S. scientists and engineers for exceptional contributions in research and development supporting DOE and its mission. Winner of the award in the inaugural category of Energy Science and Innovation, Dr. Goyal was cited for his work in 'pioneering research and transformative contributions to the field of applied high temperature superconductivity, including fundamental materials science advances and technical innovations enabling large-scale applications of these novel materials.' Following his basic research in grain-to-grain supercurrent transport, Dr. Goyal focused his energy in transitioning this fundamental understanding into cutting-edge technologies. Under OE sponsorship, Dr. Goyal co-invented the Rolling Assisted Bi-Axially Textured Substrate technology (RABiTS) that is used as a substrate for second generation HTS wires. OE support also led to the invention of Structural Single Crystal Faceted Fiber Substrate (SSIFFS) and the 3-D Self Assembly of Nanodot Columns. These inventions and associated R&D resulted in 7 R&D 100 Awards including the 2010 R&D Magazine's Innovator of the Year Award, 3 Federal Laboratory Consortium Excellence in Technology Transfer National Awards, a DOE Energy 100 Award and many others. As a world authority on HTS materials, Dr. Goyal has presented OE-sponsored results in more than 150 invited talks, co-authored more than 350 papers and is a fellow of 7 professional societies.

Assessing cross species conservation of ToxCast Assay targets using Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS)

EPA Science Inventory

US EPA’s ToxCast program has screened thousands of chemicals in hundreds of mammalian-based HTS assays for biological activity suggestive of potential toxic effects. These data are being used to prioritize toxicity testing to focus on chemicals likely to lead to adverse health ef...

ToxCast HTS Assay Development and Retrofitting: Strategies ...

EPA Pesticide Factsheets

A presentation to EC JRC partners on new ToxCast HTS assay methods and strategies to address current limitations to HTS methods Slide presentation to EC JRC partners on new ToxCast HTS assay methods and strategies to address current limitations to HTS methods.

EPAS TOXCAST PROGRAM FOR PREDICTING HAZARD AND PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS(S).

EPA Science Inventory

EPAs National Center for Computational Toxicology is developing methods that apply computational chemistry, high-throughput screening (HTS) and genomic technologies to predict potential toxicity and prioritize the use of limited testing resources.

Library preparation and data analysis packages for rapid genome sequencing.

PubMed

Pomraning, Kyle R; Smith, Kristina M; Bredeweg, Erin L; Connolly, Lanelle R; Phatale, Pallavi A; Freitag, Michael

2012-01-01

High-throughput sequencing (HTS) has quickly become a valuable tool for comparative genetics and genomics and is now regularly carried out in laboratories that are not connected to large sequencing centers. Here we describe an updated version of our protocol for constructing single- and paired-end Illumina sequencing libraries, beginning with purified genomic DNA. The present protocol can also be used for "multiplexing," i.e. the analysis of several samples in a single flowcell lane by generating "barcoded" or "indexed" Illumina sequencing libraries in a way that is independent from Illumina-supported methods. To analyze sequencing results, we suggest several independent approaches but end users should be aware that this is a quickly evolving field and that currently many alignment (or "mapping") and counting algorithms are being developed and tested.

Novel strategy for protein exploration: high-throughput screening assisted with fuzzy neural network.

PubMed

Kato, Ryuji; Nakano, Hideo; Konishi, Hiroyuki; Kato, Katsuya; Koga, Yuchi; Yamane, Tsuneo; Kobayashi, Takeshi; Honda, Hiroyuki

2005-08-19

To engineer proteins with desirable characteristics from a naturally occurring protein, high-throughput screening (HTS) combined with directed evolutional approach is the essential technology. However, most HTS techniques are simple positive screenings. The information obtained from the positive candidates is used only as results but rarely as clues for understanding the structural rules, which may explain the protein activity. In here, we have attempted to establish a novel strategy for exploring functional proteins associated with computational analysis. As a model case, we explored lipases with inverted enantioselectivity for a substrate p-nitrophenyl 3-phenylbutyrate from the wild-type lipase of Burkhorderia cepacia KWI-56, which is originally selective for (S)-configuration of the substrate. Data from our previous work on (R)-enantioselective lipase screening were applied to fuzzy neural network (FNN), bioinformatic algorithm, to extract guidelines for screening and engineering processes to be followed. FNN has an advantageous feature of extracting hidden rules that lie between sequences of variants and their enzyme activity to gain high prediction accuracy. Without any prior knowledge, FNN predicted a rule indicating that "size at position L167," among four positions (L17, F119, L167, and L266) in the substrate binding core region, is the most influential factor for obtaining lipase with inverted (R)-enantioselectivity. Based on the guidelines obtained, newly engineered novel variants, which were not found in the actual screening, were experimentally proven to gain high (R)-enantioselectivity by engineering the size at position L167. We also designed and assayed two novel variants, namely FIGV (L17F, F119I, L167G, and L266V) and FFGI (L17F, L167G, and L266I), which were compatible with the guideline obtained from FNN analysis, and confirmed that these designed lipases could acquire high inverted enantioselectivity. The results have shown that with the aid of bioinformatic analysis, high-throughput screening can expand its potential for exploring vast combinatorial sequence spaces of proteins.

Detection of Local Temperature Change on HTS Cables via Time-Frequency Domain Reflectometry

NASA Astrophysics Data System (ADS)

Bang, Su Sik; Lee, Geon Seok; Kwon, Gu-Young; Lee, Yeong Ho; Ji, Gyeong Hwan; Sohn, Songho; Park, Kijun; Shin, Yong-June

2017-07-01

High temperature superconducting (HTS) cables are drawing attention as transmission and distribution cables in future grid, and related researches on HTS cables have been conducted actively. As HTS cables have come to the demonstration stage, failures of cooling systems inducing quench phenomenon of the HTS cables have become significant. Several diagnosis of the HTS cables have been developed but there are still some limitations of the experimental setup. In this paper, a non-destructive diagnostic technique for the detection of the local temperature change point is proposed. Also, a simulation model of HTS cables with a local temperature change point is suggested to verify the proposed diagnosis. The performance of the diagnosis is checked by comparative analysis between the proposed simulation results and experiment results of a real-world HTS cable. It is expected that the suggested simulation model and diagnosis will contribute to the commercialization of HTS cables in the power grid.

Development of toroid-type HTS DC reactor series for HVDC system

NASA Astrophysics Data System (ADS)

Kim, Kwangmin; Go, Byeong-Soo; Park, Hea-chul; Kim, Sung-kyu; Kim, Seokho; Lee, Sangjin; Oh, Yunsang; Park, Minwon; Yu, In-Keun

2015-11-01

This paper describes design specifications and performance of a toroid-type high-temperature superconducting (HTS) DC reactor. The first phase operation targets of the HTS DC reactor were 400 mH and 400 A. The authors have developed a real HTS DC reactor system during the last three years. The HTS DC reactor was designed using 2G GdBCO HTS wires. The HTS coils of the toroid-type DC reactor magnet were made in the form of a D-shape. The electromagnetic performance of the toroid-type HTS DC reactor magnet was analyzed using the finite element method program. A conduction cooling method was adopted for reactor magnet cooling. The total system has been successfully developed and tested in connection with LCC type HVDC system. Now, the authors are studying a 400 mH, kA class toroid-type HTS DC reactor for the next phase research. The 1500 A class DC reactor system was designed using layered 13 mm GdBCO 2G HTS wire. The expected operating temperature is under 30 K. These fundamental data obtained through both works will usefully be applied to design a real toroid-type HTS DC reactor for grid application.

Ultra Deep Sequencing of Listeria monocytogenes sRNA Transcriptome Revealed New Antisense RNAs

PubMed Central

Behrens, Sebastian; Widder, Stefanie; Mannala, Gopala Krishna; Qing, Xiaoxing; Madhugiri, Ramakanth; Kefer, Nathalie; Mraheil, Mobarak Abu; Rattei, Thomas; Hain, Torsten

2014-01-01

Listeria monocytogenes, a gram-positive pathogen, and causative agent of listeriosis, has become a widely used model organism for intracellular infections. Recent studies have identified small non-coding RNAs (sRNAs) as important factors for regulating gene expression and pathogenicity of L. monocytogenes. Increased speed and reduced costs of high throughput sequencing (HTS) techniques have made RNA sequencing (RNA-Seq) the state-of-the-art method to study bacterial transcriptomes. We created a large transcriptome dataset of L. monocytogenes containing a total of 21 million reads, using the SOLiD sequencing technology. The dataset contained cDNA sequences generated from L. monocytogenes RNA collected under intracellular and extracellular condition and additionally was size fractioned into three different size ranges from <40 nt, 40–150 nt and >150 nt. We report here, the identification of nine new sRNAs candidates of L. monocytogenes and a reevaluation of known sRNAs of L. monocytogenes EGD-e. Automatic comparison to known sRNAs revealed a high recovery rate of 55%, which was increased to 90% by manual revision of the data. Moreover, thorough classification of known sRNAs shed further light on their possible biological functions. Interestingly among the newly identified sRNA candidates are antisense RNAs (asRNAs) associated to the housekeeping genes purA, fumC and pgi and potentially their regulation, emphasizing the significance of sRNAs for metabolic adaptation in L. monocytogenes. PMID:24498259

Potential aerospace applications of high temperature superconductors

NASA Technical Reports Server (NTRS)

Selim, Raouf

1994-01-01

The recent discovery of High Temperature Superconductors (HTS) with superconducting transition temperature, T(sub c), above the boiling point of liquid nitrogen has opened the door for using these materials in new and practical applications. These materials have zero resistance to electric current, have the capability of carrying large currents and as such have the potential to be used in high magnetic field applications. One of the space applications that can use superconductors is electromagnetic launch of payloads to low-earth-orbit. An electromagnetic gun-type launcher can be used in small payload systems that are launched at very high velocity, while sled-type magnetically levitated launcher can be used to launch larger payloads at smaller velocities. Both types of launchers are being studied by NASA and the aerospace industry. The use of superconductors will be essential in any of these types of launchers in order to produce the large magnetic fields required to obtain large thrust forces. Low Temperature Superconductor (LTS) technology is mature enough and can be easily integrated in such systems. As for the HTS, many leading companies are currently producing HTS coils and magnets that potentially can be mass-produced for these launchers. It seems that designing and building a small-scale electromagnetic launcher is the next logical step toward seriously considering this method for launching payloads into low-earth-orbit. A second potential application is the use of HTS to build sensitive portable devices for the use in Non Destructive Evaluation (NDE). Superconducting Quantum Interference Devices (SQUID's) are the most sensitive instruments for measuring changes in magnetic flux. By using HTS in SQUID's, one will be able to design a portable unit that uses liquid nitrogen or a cryocooler pump to explore the use of gradiometers or magnetometers to detect deep cracks or corrosion in structures. A third use is the replacement of Infra-Red (IR) sensor leads on Earth Orbit Systems (EOS) with HTS leads. IR detectors on these EOS missions are cooled to a 4.2K to improve their signal to noise ratio. They are connected to data acquisitions systems using manganin wires (low thermal conductors) to reduce the heat load on the cryogen. Replacing these wires with HTS leads will increase the lifetime of these missions by about 50 percent. This is a promising application that is ready for actual implementation on such systems. The analysis also show that an the number of IR detectors increase in larger EOS systems, substantial increase in the lifetime of each mission will be realized by using HTS leads instead of the manganin ones.

A high-throughput screening system targeting the nuclear export pathway via the third nuclear export signal of influenza A virus nucleoprotein.

PubMed

Kakisaka, Michinori; Mano, Takafumi; Aida, Yoko

2016-06-02

Two classes of antiviral drugs, M2 channel inhibitors and neuraminidase (NA) inhibitors, are currently approved for the treatment of influenza; however, the development of resistance against these agents limits their efficacy. Therefore, the identification of new targets and the development of new antiviral drugs against influenza are urgently needed. The third nuclear export signal (NES3) of nucleoprotein (NP) is the most important for viral replication among seven NESs encoded by four viral proteins, NP, M1, NS1, and NS2. NP-NES3 is critical for the nuclear export of NP, and targeting NP-NES3 is therefore a promising strategy that may lead to the development of antiviral drugs. However, a high-throughput screening (HTS) system to identify inhibitors of NP nuclear export has not been established. Here, we developed a novel HTS system to evaluate the inhibitory effects of compounds on the nuclear export pathway mediated by NP-NES3 using a MDCK cell line stably expressing NP-NES3 fused to a green fluorescent protein from aequorea coerulescens (AcGFP-NP-NES3) and a cell imaging analyzer. This HTS system was used to screen a 9600-compound library, leading to the identification of several hit compounds with inhibitory activity against the nuclear export of AcGFP-NP-NES3. The present HTS system provides a useful strategy for the identification of inhibitors targeting the nuclear export of NP via its NES3 sequence. Copyright © 2016. Published by Elsevier B.V.

Current-carrying element based on second-generation high-temperature superconductor for the magnet system of a fusion neutron source

NASA Astrophysics Data System (ADS)

Novikov, M. S.; Ivanov, D. P.; Novikov, S. I.; Shuvaev, S. A.

2015-12-01

Application of current-carrying elements (CCEs) made of second-generation high-temperature superconductor (2G HTS) in magnet systems of a fusion neutron source (FNS) and other fusion devices will allow their magnetic field and thermodynamic stability to be increased substantially in comparison with those of low-temperature superconductor (LTS) magnets. For a toroidal magnet of the FNS, a design of a helical (partially transposed) CCE made of 2G HTS is under development with forced-flow cooling by helium gas, a current of 20-30 kA, an operating temperature of 10-20 K, and a magnetic field on the winding of 12-15 T (prospectively ~20 T). Short-sized samples of the helical flexible heavy-current CCE are being fabricated and investigated; a pilot-line unit for production of long-sized CCE pieces is under construction. The applied fabrication technique allows the CCE to be produced which combines a high operating current, thermal and mechanical stability, manufacturability, and low losses in the alternating modes. The possibility of fabricating the CCE with the outer dimensions and values of the operating parameter required for the FNS (and with a significant margin) using already available serial 2G HTS tapes is substantiated. The maximum field of toroidal magnets with CCEs made of 2G HTS will be limited only by mechanical properties of the magnet's casing and structure, while the thermal stability will be approximately two orders of magnitude higher than that of toroidal magnets with LTS-based CCEs. The helical CCE made of 2G HTS is very promising for fusion and hybrid electric power plants, and its design and technologies of production, as well as the prototype coils made of it for the FNS and other tokamaks, are worth developing now.

Formalization, Annotation and Analysis of Diverse Drug and Probe Screening Assay Datasets Using the BioAssay Ontology (BAO)

PubMed Central

Vempati, Uma D.; Przydzial, Magdalena J.; Chung, Caty; Abeyruwan, Saminda; Mir, Ahsan; Sakurai, Kunie; Visser, Ubbo; Lemmon, Vance P.; Schürer, Stephan C.

2012-01-01

Huge amounts of high-throughput screening (HTS) data for probe and drug development projects are being generated in the pharmaceutical industry and more recently in the public sector. The resulting experimental datasets are increasingly being disseminated via publically accessible repositories. However, existing repositories lack sufficient metadata to describe the experiments and are often difficult to navigate by non-experts. The lack of standardized descriptions and semantics of biological assays and screening results hinder targeted data retrieval, integration, aggregation, and analyses across different HTS datasets, for example to infer mechanisms of action of small molecule perturbagens. To address these limitations, we created the BioAssay Ontology (BAO). BAO has been developed with a focus on data integration and analysis enabling the classification of assays and screening results by concepts that relate to format, assay design, technology, target, and endpoint. Previously, we reported on the higher-level design of BAO and on the semantic querying capabilities offered by the ontology-indexed triple store of HTS data. Here, we report on our detailed design, annotation pipeline, substantially enlarged annotation knowledgebase, and analysis results. We used BAO to annotate assays from the largest public HTS data repository, PubChem, and demonstrate its utility to categorize and analyze diverse HTS results from numerous experiments. BAO is publically available from the NCBO BioPortal at http://bioportal.bioontology.org/ontologies/1533. BAO provides controlled terminology and uniform scope to report probe and drug discovery screening assays and results. BAO leverages description logic to formalize the domain knowledge and facilitate the semantic integration with diverse other resources. As a consequence, BAO offers the potential to infer new knowledge from a corpus of assay results, for example molecular mechanisms of action of perturbagens. PMID:23155465

EPA'S TOXCAST PROGRAM FOR PREDICTING HAZARD AND PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS

EPA Science Inventory

EPA is developing methods for utilizing computational chemistry, high-throughput screening (HTS) and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources towards chemicals that likely represent the greatest hazard to human ...

Toxico-Cheminformatics: New and Expanding Public Resources to Support Chemical Toxicity Assessments

EPA Science Inventory

High-throughput screening (HTS) technologies, along with efforts to improve public access to chemical toxicity information resources and to systematize older toxicity studies, have the potential to significantly improve information gathering efforts for chemical assessments and p...

Lattice parameters guide superconductivity in iron-arsenides

NASA Astrophysics Data System (ADS)

Konzen, Lance M. N.; Sefat, Athena S.

2017-03-01

The discovery of superconducting materials has led to their use in technological marvels such as magnetic-field sensors in MRI machines, powerful research magnets, short transmission cables, and high-speed trains. Despite such applications, the uses of superconductors are not widespread because they function much below room-temperature, hence the costly cooling. Since the discovery of Cu- and Fe-based high-temperature superconductors (HTS), much intense effort has tried to explain and understand the superconducting phenomenon. While no exact explanations are given, several trends are reported in relation to the materials basis in magnetism and spin excitations. In fact, most HTS have antiferromagnetic undoped ‘parent’ materials that undergo a superconducting transition upon small chemical substitutions in them. As it is currently unclear which ‘dopants’ can favor superconductivity, this manuscript investigates crystal structure changes upon chemical substitutions, to find clues in lattice parameters for the superconducting occurrence. We review the chemical substitution effects on the crystal lattice of iron-arsenide-based crystals (2008 to present). We note that (a) HTS compounds have nearly tetragonal structures with a-lattice parameter close to 4 Å, and (b) superconductivity can depend strongly on the c-lattice parameter changes with chemical substitution. For example, a decrease in c-lattice parameter is required to induce ‘in-plane’ superconductivity. The review of lattice parameter trends in iron-arsenides presented here should guide synthesis of new materials and provoke theoretical input, giving clues for HTS.

Lattice parameters guide superconductivity in iron-arsenides.

PubMed

Konzen, Lance M N; Sefat, Athena S

2017-03-01

The discovery of superconducting materials has led to their use in technological marvels such as magnetic-field sensors in MRI machines, powerful research magnets, short transmission cables, and high-speed trains. Despite such applications, the uses of superconductors are not widespread because they function much below room-temperature, hence the costly cooling. Since the discovery of Cu- and Fe-based high-temperature superconductors (HTS), much intense effort has tried to explain and understand the superconducting phenomenon. While no exact explanations are given, several trends are reported in relation to the materials basis in magnetism and spin excitations. In fact, most HTS have antiferromagnetic undoped 'parent' materials that undergo a superconducting transition upon small chemical substitutions in them. As it is currently unclear which 'dopants' can favor superconductivity, this manuscript investigates crystal structure changes upon chemical substitutions, to find clues in lattice parameters for the superconducting occurrence. We review the chemical substitution effects on the crystal lattice of iron-arsenide-based crystals (2008 to present). We note that (a) HTS compounds have nearly tetragonal structures with a-lattice parameter close to 4 Å, and (b) superconductivity can depend strongly on the c-lattice parameter changes with chemical substitution. For example, a decrease in c-lattice parameter is required to induce 'in-plane' superconductivity. The review of lattice parameter trends in iron-arsenides presented here should guide synthesis of new materials and provoke theoretical input, giving clues for HTS.

Developmental Challenges of SMES Technology for Applications

NASA Astrophysics Data System (ADS)

Rong, Charles C.; Barnes, Paul N.

2017-12-01

This paper reviews the current status of high temperature superconductor (HTS) based superconducting magnetic energy storage (SMES) technology as a developmental effort. Discussion centres on the major challenges in magnet optimization, loss reduction, cooling improvement, and new development of quench detection. The cryogenic operation for superconductivity in this technological application requires continued research and development, especially with a greater engineering effort that involves the end user. For the SMES-based technology to more fully mature, some suggestions are given for consideration and discussion.

History of HTS motor development at Reliance Electric

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

Schiferl, R.

1994-07-29

A review of the High Temperature Superconducting (HTS) motor development program at Reliance Electric is presented. The project was initiated in 1987 by EPRI to investigate the use of high temperature superconducting materials in electric motors. Liquid nitrogen was proposed as the HTS winding coolant. The ultimate goal, motivation, motor type and HTS wire requirements as well as the program milestones are outlined. It was concluded that the HTS motor development has paralleled wire development; progress continues toward the goal of large horsepower HTS motors for commercial applications; the team is well on the way toward completing the design ofmore » a 125 hp, 1800 rpm motor with HTS coils cooled to 20 to 40 K; and the program is a vital step in the development of HTS motors.« less

Electromagnetic Performance Calculation of HTS Linear Induction Motor for Rail Systems

NASA Astrophysics Data System (ADS)

Liu, Bin; Fang, Jin; Cao, Junci; Chen, Jie; Shu, Hang; Sheng, Long

2017-07-01

According to a high temperature superconducting (HTS) linear induction motor (LIM) designed for rail systems, the influence of electromagnetic parameters and mechanical structure parameters on the electromagnetic horizontal thrust, vertical force of HTS LIM and the maximum vertical magnetic field of HTS windings are analyzed. Through the research on the vertical field of HTS windings, the development regularity of the HTS LIM maximum input current with different stator frequency and different thickness value of the secondary conductive plate is obtained. The theoretical results are of great significance to analyze the stability of HTS LIM. Finally, based on theory analysis, HTS LIM test platform was built and the experiment was carried out with load. The experimental results show that the theoretical analysis is correct and reasonable.

Superconducting accelerator magnet technology in the 21st century: A new paradigm on the horizon?

NASA Astrophysics Data System (ADS)

Gourlay, S. A.

2018-06-01

Superconducting magnets for accelerators were first suggested in the mid-60's and have since become one of the major components of modern particle colliders. Technological progress has been slow but steady for the last half-century, based primarily on Nb-Ti superconductor. That technology has reached its peak with the Large Hadron Collider (LHC). Despite the superior electromagnetic properties of Nb3Sn and adoption by early magnet pioneers, it is just now coming into use in accelerators though it has not yet reliably achieved fields close to the theoretical limit. The discovery of the High Temperature Superconductors (HTS) in the late '80's created tremendous excitement, but these materials, with tantalizing performance at high fields and temperatures, have not yet been successfully developed into accelerator magnet configurations. Thanks to relatively recent developments in both Bi-2212 and REBCO, and a more focused international effort on magnet development, the situation has changed dramatically. Early optimism has been replaced with a reality that could create a new paradigm in superconducting magnet technology. Using selected examples of magnet technology from the previous century to define the context, this paper will describe the possible innovations using HTS materials as the basis for a new paradigm.

Nonlinear Behavior of a Shim Coil in an LTS/HTS NMR Magnet With an HTS Insert Comprising Double-Pancake HTS-Tape Coils

PubMed Central

Hahn, Seung-yong; Ahn, Min Cheol; Bascuñán, Juan; Yao, Weijun; Iwasa, Yukikazu

2010-01-01

This paper reports results, experimental and analytical, of the nonlinear behavior of a shim coil in the presence of an HTS coil assembled with double-pancake (DP) HTS-tape coils. The experimental results are from: 1) operation of a 700 MHz LTS/HTS NMR magnet (LH700) consisting of a 600 MHz LTS NMR magnet (L600) equipped with superconducting shim coils and a 100 MHz DP-assembled HTS insert (H100) and; 2) an experiment with a room-temperature (RT) Z1 shim coil coupled to a 50 MHz DP-as-sembled HTS insert (H50). A field mapping theory with a harmonic analysis is applied to interpret both results. Based on experimental results and analyses, we conclude that the screening-current-induced field (SCF) generated by a DP-assembled HTS insert is primarily responsible for the nonlinear behavior, including strength degradation, of a shim coil. PMID:20383282

Development of 66 kV class REBCO superconducting cable

NASA Astrophysics Data System (ADS)

Ohya, M.; Masuda, T.; Amemiya, N.; Ishiyama, A.; Ohkuma, T.

Sumitomo Electric Industries (SEI) has been involved in the development of 66 kV/5 kA-class HTS cables using REBCO wires. One of the technical targets was to reduce the AC loss to less than 2 W/m/phase at 5 kA. SEI developed a clad-type textured metal substrate with lower magnetization loss than NiW substrates. REBCO wires of 30 mm wide were slit into 4 mm-wide strips, and these strips were wound spirally on a former with small gaps. The measured AC loss of the manufactured cable was 1.8 W/m/phase at 5 kA, achieving the AC loss goal. Another important target was to manage fault current. The copper protection layers were designed based on simulation findings. Fault current tests (max. 31.5 kA, 2 sec) showed that the designed HTS cable has the required withstanding performance. The development of the elemental technologies was finished on schedule, and a 15 m-long HTS cable system will be constructed to demonstrate that it meets all the required specifications.

High-throughput screening technologies for botulinum neurotoxins.

PubMed

Bompiani, Kristin M; Dickerson, Tobin J

2014-01-01

Botulinum neurotoxins (BoNTs) are a class of bacterial neurotoxins that are the most potent toxic compounds reported to date. Exposure to relatively low concentrations of the toxin protein can result in major muscle paralysis, which may result in death in severe cases. In addition to their role in natural human disease, BoNTs are currently under close scrutiny because of their potential to be used as biowarfare agents. Clinical treatment options for botulism are currently limited, and finite stockpiles of antitoxin exist. In light of current bioterrorist threats, researchers have focused on identifying new molecules that can be applied to either sensitive toxin detection or improved clinical treatment. High-throughput screening (HTS) is a laboratory technique commonly employed to screen large libraries of diverse compounds based on specific compound binding capabilities or function. Here we review existing HTS platforms that have been applied to identify novel BoNT diagnostic or therapeutic agents. HTS platforms for screening antibodies, peptides, small molecules, and aptamers are described, as well as the screening results and current progress of the identified compounds.

Operating experience with the southwire 30-meter high-temperature superconducting power cable

NASA Astrophysics Data System (ADS)

Stovall, J. P.; Lue, J. W.; Demko, J. A.; Fisher, P. W.; Gouge, M. J.; Hawsey, R. A.; Armstrong, J. W.; Hughey, R. L.; Lindsay, D. T.; Roden, M. L.; Sinha, U. K.; Tolbert, J. C.

2002-05-01

Southwire Company is operating a high-temperature superconducting (HTS) cable system at its corporate headquarters. The 30-m long, 3-phase cable system is powering three Southwire manufacturing plants and is rated at 12.4-kV, 1250-A, 60-Hz. Cooling is provided by a pressurized liquid nitrogen system operating at 70-80 K. The cables were energized on January 5, 2000 for on-line testing and operation and in April 2000 were placed into extended service. As of June 1, 2001, the HTS cables have provided 100% of the customer load for 8000 hours. The cryogenic system has been in continuous operation since November 1999. The HTS cable system has not been the cause of any power outages to the average 20 MW industrial load served by the cable. The cable has been exposed to short-circuit currents caused by load-side faults without damage. Based upon field measurements described herein, the cable critical current-a key performance parameter-remains the same and has not been affected by the hours of real-world operation, further proving the viability of this promising technology.

Development of a single-phase 30 m HTS power cable

NASA Astrophysics Data System (ADS)

Cho, Jeonwook; Bae, Joon-Han; Kim, Hae-Jong; Sim, Ki-Deok; Kim, Seokho; Jang, Hyun-Man; Lee, Chang-Young; Kim, Dong-Wook

2006-05-01

HTS power transmission cables appear to be the replacement and retrofitting of underground cables in urban areas and HTS power transmission cable offers a number of technical and economic merits compared to the normal conductor cable system. A 30 m long, single-phase 22.9 kV class HTS power transmission cable system has been developed by Korea Electrotechnology Research Institute (KERI), LS Cable Ltd., and Korea Institute of Machinery and Materials (KIMM), which is one of the 21st century frontier project in Korea since 2001. The HTS power cable has been developed, cooled down and tested to obtain realistic thermal and electrical data on HTS power cable system. The evaluation results clarified such good performance of HTS cable that DC critical current of the HTS cable was 3.6 kA and AC loss was 0.98 W/m at 1260 Arms and shield current was 1000 Arms. These results proved the basic properties for 22.9 kV HTS power cable. As a next step, we have been developing a 30 m, three-phase 22.9 kV, 50 MV A HTS power cable system and long term evaluation is in progress now.

Technology Disruptions in Future Communication Payloads (Technologies de rupture pour futures charges utiles de telecommunications)

DTIC Science & Technology

2005-07-13

du froid: l’électronique refroidie, la supraconductivité et la cryogénie. Les supraconducteurs à haute température (HTS) permettent la conception de...récepteurs à très faible bruit, des filtres compacts et sans pertes. Les supraconducteurs à basse température (LTS) qui sont utilisés dans les circuits

High Temperature Superconductors: From Delivery to Applications (Presentation from 2011 Ernest Orlando Lawrence Award-winner, Dr. Amit Goyal, and including introduction by Energy Secretary, Dr. Steven Chu)

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

Goyal, Amit

Dr. Amit Goyal, a high temperature superconductivity (HTS) researcher at Oak Ridge National Laboratory, was named a 2011 winner of the Department of Energy's Ernest Orlando Lawrence Award honoring U.S. scientists and engineers for exceptional contributions in research and development supporting DOE and its mission. Winner of the award in the inaugural category of Energy Science and Innovation, Dr. Goyal was cited for his work in 'pioneering research and transformative contributions to the field of applied high temperature superconductivity, including fundamental materials science advances and technical innovations enabling large-scale applications of these novel materials.' Following his basic research in grain-to-grainmore » supercurrent transport, Dr. Goyal focused his energy in transitioning this fundamental understanding into cutting-edge technologies. Under OE sponsorship, Dr. Goyal co-invented the Rolling Assisted Bi-Axially Textured Substrate technology (RABiTS) that is used as a substrate for second generation HTS wires. OE support also led to the invention of Structural Single Crystal Faceted Fiber Substrate (SSIFFS) and the 3-D Self Assembly of Nanodot Columns. These inventions and associated R&D resulted in 7 R&D 100 Awards including the 2010 R&D Magazine's Innovator of the Year Award, 3 Federal Laboratory Consortium Excellence in Technology Transfer National Awards, a DOE Energy 100 Award and many others. As a world authority on HTS materials, Dr. Goyal has presented OE-sponsored results in more than 150 invited talks, co-authored more than 350 papers and is a fellow of 7 professional societies.« less

Thin Film Multilayer Conductor/Ferroelectric Tunable Microwave Components for Communication Applications

NASA Technical Reports Server (NTRS)

Miranda, Felix A.; Romanofsky, Robert R.; VanKeuls, Frederick W.; Mueller, Carl H.; Treece, Randolph E.; Rivkin, Tania V.

1997-01-01

High Temperature Superconductor/Ferroelectric (HTS/FE ) thin film multilayered structures deposited onto dielectric substrates are currently being investigated for use in low loss, tunable microwave components for satellite and ground based communications. The main goal for this technology is to achieve maximum tunability while keeping the microwave losses as low as possible, so as to avoid performance degradation when replacing conventional technology (e.g., filters and oscillators) with HTS/FE components. Therefore, for HTS/FE components to be successfully integrated into current working systems, full optimization of the material and electrical properties of the ferroelectric films, without degrading those of the HTS film; is required. Hence, aspects such as the appropriate type of ferroelectric and optimization of the deposition conditions (e.g., deposition temperature) should be carefully considered. The tunability range as well as the microwave losses of the desired varactor (i.e., tunable component) are also dependent on the geometry chosen (e.g., parallel plate capacitor, interdigital capacitor, coplanar waveguide, etc.). In addition, the performance of the circuit is dependent on the location of the varactor in the circuit and the biasing circuitry. In this paper, we will present our results on the study of the SrTiO3/YBa2Cu3O(7-delta)/LaAl03 (STO/YBCO/LAO) and the Ba(x)Sr(1-x)TiO3/YBa2Cu3O(7-delta)/LaAl03(BSTO/YBCO/ILAO) HTS/FE multilayered structures. We have observed that the amount of variation of the dielectric constant upon the application of a dc electric field is closely related to the microstructure of the film. The largest tuning of the STO/YBCO/LAO structure corresponded to single-phased, epitaxial STO films deposited at 800 C and with a thickness of 500 nm. Higher temperatures resulted in interfacial degradation and poor film quality, while lower deposition temperatures resulted in films with lower dielectric constants, lower tunabilities, and higher losses. For STO/LAO multilayer structures having STO film of similar quality we have observed that interdigital capacitor configurations allow for higher tunabilities and lower losses than parallel plate configurations, but required higher dc voltage. Results on the use of these geometries in working microwave components such as filters and stabilizing resonators for local oscillators (LO) will be discussed.

The Incidence and Genetic Diversity of Apple Mosaic Virus (ApMV) and Prune Dwarf Virus (PDV) in Prunus Species in Australia

PubMed Central

Constable, Fiona E.; Nancarrow, Narelle; Rodoni, Brendan

2018-01-01

Apple mosaic virus (ApMV) and prune dwarf virus (PDV) are amongst the most common viruses infecting Prunus species worldwide but their incidence and genetic diversity in Australia is not known. In a survey of 127 Prunus tree samples collected from five states in Australia, ApMV and PDV occurred in 4 (3%) and 13 (10%) of the trees respectively. High-throughput sequencing (HTS) of amplicons from partial conserved regions of RNA1, RNA2, and RNA3, encoding the methyltransferase (MT), RNA-dependent RNA polymerase (RdRp), and the coat protein (CP) genes respectively, of ApMV and PDV was used to determine the genetic diversity of the Australian isolates of each virus. Phylogenetic comparison of Australian ApMV and PDV amplicon HTS variants and full length genomes of both viruses with isolates occurring in other countries identified genetic strains of each virus occurring in Australia. A single Australian Prunus infecting ApMV genetic strain was identified as all ApMV isolates sequence variants formed a single phylogenetic group in each of RNA1, RNA2, and RNA3. Two Australian PDV genetic strains were identified based on the combination of observed phylogenetic groups in each of RNA1, RNA2, and RNA3 and one Prunus tree had both strains. The accuracy of amplicon sequence variants phylogenetic analysis based on segments of each virus RNA were confirmed by phylogenetic analysis of full length genome sequences of Australian ApMV and PDV isolates and all published ApMV and PDV genomes from other countries. PMID:29562672

Longitudinal, 3D Imaging of Collagen Remodeling in Murine Hypertrophic Scars In Vivo using Polarization-sensitive Optical Frequency Domain Imaging

PubMed Central

Lo, William C. Y.; Villiger, Martin; Golberg, Alexander; Broelsch, G. Felix; Khan, Saiqa; Lian, Christine G.; Austen, William G.; Yarmush, Martin; Bouma, Brett E.

2016-01-01

Hypertrophic scars (HTS), frequently seen after traumatic injuries and surgery, remain a major clinical challenge due to the limited success of existing therapies. A significant obstacle to understanding HTS etiology is the lack of tools to monitor scar remodeling longitudinally and non-invasively. We present an in vivo, label-free technique using polarization-sensitive optical frequency domain imaging (PS-OFDI) for the 3D, longitudinal assessment of collagen remodeling in murine HTS. In this study, HTS was induced with a mechanical tension device for 4 to 10 days on incisional wounds and imaged up to one month after device removal; an excisional HTS model was also imaged at 6 months after injury to investigate deeper and more mature scars. We showed that local retardation (LR) and degree of polarization (DOP) provide a robust signature for HTS. Compared to normal skin with heterogeneous LR and low DOP, HTS was characterized by an initially low LR, which increased as collagen fibers remodeled, and a persistently high DOP. This study demonstrates that PS-OFDI offers a powerful tool to gain significant biological insights into HTS remodeling by enabling longitudinal assessment of collagen in vivo, which is critical to elucidating HTS etiology and developing more effective HTS therapies. PMID:26763427

High resolution NMR measurements using a 400MHz NMR with an (RE)Ba2Cu3O7-x high-temperature superconducting inner coil: Towards a compact super-high-field NMR.

PubMed

Piao, R; Iguchi, S; Hamada, M; Matsumoto, S; Suematsu, H; Saito, A T; Li, J; Nakagome, H; Takao, T; Takahashi, M; Maeda, H; Yanagisawa, Y

2016-02-01

Use of high-temperature superconducting (HTS) inner coils in combination with conventional low-temperature superconducting (LTS) outer coils for an NMR magnet, i.e. a LTS/HTS NMR magnet, is a suitable option to realize a high-resolution NMR spectrometer with operating frequency >1GHz. From the standpoint of creating a compact magnet, (RE: Rare earth) Ba2Cu3O7-x (REBCO) HTS inner coils which can tolerate a strong hoop stress caused by a Lorentz force are preferred. However, in our previous work on a first-generation 400MHz LTS/REBCO NMR magnet, the NMR resolution and sensitivity were about ten times worse than that of a conventional LTS NMR magnet. The result was caused by a large field inhomogeneity in the REBCO coil itself and the shielding effect of a screening current induced in that coil. In the present paper, we describe the operation of a modified 400MHz LTS/REBCO NMR magnet with an advanced field compensation technology using a combination of novel ferromagnetic shimming and an appropriate procedure for NMR spectrum line shape optimization. We succeeded in obtaining a good NMR line shape and 2D NOESY spectrum for a lysozyme aqueous sample. We believe that this technology is indispensable for the realization of a compact super-high-field high-resolution NMR. Copyright © 2016 Elsevier Inc. All rights reserved.

380 kW synchronous machine with HTS rotor windings--development at Siemens and first test results

NASA Astrophysics Data System (ADS)

Nick, W.; Nerowski, G.; Neumüller, H.-W.; Frank, M.; van Hasselt, P.; Frauenhofer, J.; Steinmeyer, F.

2002-08-01

Applying HTS conductors in the rotor of synchronous machines allows the design of future motors or generators that are lighter, more compact and feature an improved coefficient of performance. To address these goals a project collaboration was installed within Siemens, including Automation & Drives, Large Drives as a leading supplier of electrical machines, Corporate Technology as a competence center for superconducting technology, and other partners. The main task of the project was to demonstrate the feasibility of basic concepts. The rotor was built from racetrack coils of Bi-2223 HTS tape conductor, these were assembled on a core and fixed by a bandage of glass-fibre composite. Rotor coil cooling is performed by thermal conduction, one end of the motor shaft is hollow to give access for the cooling system. Two cooling systems were designed and operated successfully: firstly an open circuit using cold gaseous helium from a storage vessel, but also a closed circuit system based on a cryogenerator. To take advantage of the increased rotor induction levels the stator winding was designed as an air gap winding. This was manufactured and fitted in a standard motor housing. After assembling of the whole system in a test facility with a DC machine load experiments have been started to prove the validity of our design, including operation with both cooling systems and driving the stator from the grid as well as by a power inverter.

Simulation of Field Dependence of Critical Current Densities of Bulk High Tc Superconducting Materials regarding Thermally Activated Flux Motion

NASA Astrophysics Data System (ADS)

Santosh, M.; Naik, S. Pavan Kumar; Koblischka, M. R.

2017-07-01

In the upcoming generation, bulk high temperature superconductors (HTS) will play a crucial and a promising role in numerous industrial applications ranging from Maglev trains to magnetic resonance imaging, etc. Especially, the bulk HTS as permanent magnets are suitable due to the fact that they can trap magnetic fields being several orders of magnitude higher than those of the best hard ferromagnets. The bulk HTS LREBa2Cu3O7-δ (LREBCO or LRE-123, LRE: Y, Gd, etc.,) materials could obtain very powerful compact superconducting super-magnets, which can be operated at the cheaper liquid nitrogen temperature or below due to higher critical temperatures (i.e., ∼90 K). As a result, the new advanced technology can be utilized in a more attractive manner for a variety of technological and medical applications which have the capacity to revolutionize the field. An understanding of the magnetic field dependence of the critical current density (J c(H)) is important to develop better adapted materials. To achieve this goal, a variety of Jc (H) behaviours of bulk LREBCO samples were modelled regarding thermally activated flux motion. In essence, the Jc (H) curves follows a certain criterion where an exponential model is applied. However, to fit the complete Jc (H) curve of the LRE-123 samples an unique model is necessary to explain the behavior at low and high fields. The modelling of the various superconducting materials could be understood in terms of the pinning mechanisms.

Superconducting technology for overcurrent limiting in a 25 kA current injection system

NASA Astrophysics Data System (ADS)

Heydari, Hossein; Faghihi, Faramarz; Sharifi, Reza; Poursoltanmohammadi, Amir Hossein

2008-09-01

Current injection transformer (CIT) systems are within the major group of the standard type test of high current equipment in the electrical industry, so their performance becomes very important. When designing high current systems, there are many factors to be considered from which their overcurrent protection must be ensured. The output of a CIT is wholly dependent on the impedance of the equipment under test (EUT). Therefore current flow beyond the allowable limit can occur. The present state of the art provides an important guide to developing current limiters not only for the grid application but also in industrial equipment. This paper reports the state of the art in the technology available that could be developed into an application of superconductivity for high current equipment (CIT) protection with no test disruption. This will result in a greater market choice and lower costs for equipment protection solutions, reduced costs and improved system reliability. The paper will also push the state of the art by using two distinctive circuits, closed-core and open-core, for overcurrent protection of a 25 kA CIT system, based on a flux-lock-type superconducting fault current limiter (SFCL) and magnetic properties of high temperature superconducting (HTS) elements. An appropriate location of the HTS element will enhance the rate of limitation with the help of the magnetic field generated by the CIT output busbars. The calculation of the HTS parameters for overcurrent limiting is also performed to suit the required current levels of the CIT.

MAGNET ENGINEERING AND TEST RESULTS OF THE HIGH FIELD MAGNET R AND D PROGRAM AT BNL.

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

COZZOLINO,J.; ANERELLA,M.; ESCALLIER,J.

2002-08-04

The Superconducting Magnet Division at Brookhaven National Laboratory (BNL) has been carrying out design, engineering, and technology development of high performance magnets for future accelerators. High Temperature Superconductors (HTS) play a major role in the BNL vision of a few high performance interaction region (IR) magnets that would be placed in a machine about ten years from now. This paper presents the engineering design of a ''react and wind'' Nb{sub 3}Sn magnet that will provide a 12 Tesla background field on HTS coils. In addition, the coil production tooling as well as the most recent 10-turn R&D coil test resultsmore » will be discussed.« less

An Analytical Technique to Elucidate Field Impurities From Manufacturing Uncertainties of an Double Pancake Type HTS Insert for High Field LTS/HTS NMR Magnets

PubMed Central

Hahn, Seung-yong; Ahn, Min Cheol; Bobrov, Emanuel Saul; Bascuñán, Juan; Iwasa, Yukikazu

2010-01-01

This paper addresses adverse effects of dimensional uncertainties of an HTS insert assembled with double-pancake coils on spatial field homogeneity. Each DP coil was wound with Bi2223 tapes having dimensional tolerances larger than one order of magnitude of those accepted for LTS wires used in conventional NMR magnets. The paper presents: 1) dimensional variations measured in two LTS/HTS NMR magnets, 350 MHz (LH350) and 700 MHz (LH700), both built and operated at the Francis Bitter Magnet Laboratory; and 2) an analytical technique and its application to elucidate the field impurities measured with the two LTS/HTS magnets. Field impurities computed with the analytical model and those measured with the two LTS/HTS magnets agree quite well, demonstrating that this analytical technique is applicable to design a DP-assembled HTS insert with an improved field homogeneity for a high-field LTS/HTS NMR magnet. PMID:20407595

Defining the taxonomic domain of applicability for mammalian-based high-throughput screening assays

EPA Science Inventory

Cell-based high throughput screening (HTS) technologies are becoming mainstream in chemical safety evaluations. The US Environmental Protection Agency (EPA) Toxicity Forecaster (ToxCastTM) and the multi-agency Tox21 Programs have been at the forefront in advancing this science, m...

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

Impact of physics and technology innovations on compact tokamak fusion pilot plants

NASA Astrophysics Data System (ADS)

Menard, Jonathan

2016-10-01

For magnetic fusion to be economically attractive and have near-term impact on the world energy scene it is important to focus on key physics and technology innovations that could enable net electricity production at reduced size and cost. The tokamak is presently closest to achieving the fusion conditions necessary for net electricity at acceptable device size, although sustaining high-performance scenarios free of disruptions remains a significant challenge for the tokamak approach. Previous pilot plant studies have shown that electricity gain is proportional to the product of the fusion gain, blanket thermal conversion efficiency, and auxiliary heating wall-plug efficiency. In this work, the impact of several innovations is assessed with respect to maximizing fusion gain. At fixed bootstrap current fraction, fusion gain varies approximately as the square of the confinement multiplier, normalized beta, and major radius, and varies as the toroidal field and elongation both to the third power. For example, REBCO high-temperature superconductors (HTS) offer the potential to operate at much higher toroidal field than present fusion magnets, but HTS cables are also beginning to access winding pack current densities up to an order of magnitude higher than present technology, and smaller HTS TF magnet sizes make low-aspect-ratio HTS tokamaks potentially attractive by leveraging naturally higher normalized beta and elongation. Further, advances in kinetic stabilization and feedback control of resistive wall modes could also enable significant increases in normalized beta and fusion gain. Significant reductions in pilot plant size will also likely require increased plasma energy confinement, and control of turbulence and/or low edge recycling (for example using lithium walls) would have major impact on fusion gain. Reduced device size could also exacerbate divertor heat loads, and the impact of novel divertor solutions on pilot plant configurations is addressed. For missions including tritium breeding, high-thermal-efficiency liquid metal breeding blankets are attractive, and novel immersion blankets offer the potential for simplified fabrication and maintenance and reduced cost. Lastly, the optimal aspect ratio for a tokamak pilot plant is likely a function of the device mission and associated cost, with low aspect ratio favored for minimizing TF magnet mass and higher aspect ratio favored for minimizing blanket mass. The interplay between a range of physics and technology innovations for enabling compact pilot plants will be described. This work was supported by U.S. DOE Contract Number DE-AC02-09CH11466.

High Tc Superconducting Magnet Excited by a Semiconductor Thermoelectric Element

NASA Astrophysics Data System (ADS)

Kuriyama, T.; Ono, M.; Tabe, S.; Oguchi, A.; Okamura, T.

2006-04-01

A high Tc superconducting (HTS) magnet excited by a thermal electromotive force of a thermoelectric element is studied. This HTS magnet has the advantages of compactness, lightweight and continuous excitation in comparison with conventional HTS magnets, because this HTS magnet does not need a large external power source. In this system, a heat input into the cryogenic environment is necessary to excite the thermoelectric element for constant operation. This heat generation, however, causes a rise in temperature of an HTS coil and reduces the system performance. In this paper, a newly designed magnet system which adopted a two-stage GM cryocooler was investigated. It enabled us to control the temperature of a thermoelectric element and that of an HTS coil independently. The temperature of the HTS coil could be kept at 10-20 K at the second stage of the GM cryocooler, while the thermoelectric element could be excited at higher temperature in the range of 50-70 K at the first stage, where the performance of the thermoelectric element was higher. The experimental results on this HTS magnet are shown and the possibility of the thermoelectric element as a main power source of the HTS magnets is discussed.

Operating characteristic analysis of a 400 mH class HTS DC reactor in connection with a laboratory scale LCC type HVDC system

NASA Astrophysics Data System (ADS)

Kim, Sung-Kyu; Kim, Kwangmin; Park, Minwon; Yu, In-Keun; Lee, Sangjin

2015-11-01

High temperature superconducting (HTS) devices are being developed due to their advantages. Most line commutated converter based high voltage direct current (HVDC) transmission systems for long-distance transmission require large inductance of DC reactor; however, generally, copper-based reactors cause a lot of electrical losses during the system operation. This is driving researchers to develop a new type of DC reactor using HTS wire. The authors have developed a 400 mH class HTS DC reactor and a laboratory scale test-bed for line-commutated converter type HVDC system and applied the HTS DC reactor to the HVDC system to investigate their operating characteristics. The 400 mH class HTS DC reactor is designed using a toroid type magnet. The HVDC system is designed in the form of a mono-pole system with thyristor-based 12-pulse power converters. In this paper, the investigation results of the HTS DC reactor in connection with the HVDC system are described. The operating characteristics of the HTS DC reactor are analyzed under various operating conditions of the system. Through the results, applicability of an HTS DC reactor in an HVDC system is discussed in detail.

Electrically Stimulated Antagonist Muscle Contraction Increased Muscle Mass and Bone Mineral Density of One Astronaut - Initial Verification on the International Space Station.

PubMed

Shiba, Naoto; Matsuse, Hiroo; Takano, Yoshio; Yoshimitsu, Kazuhiro; Omoto, Masayuki; Hashida, Ryuki; Tagawa, Yoshihiko; Inada, Tomohisa; Yamada, Shin; Ohshima, Hiroshi

2015-01-01

Musculoskeletal atrophy is one of the major problems of extended periods of exposure to weightlessness such as on the International Space Station (ISS). We developed the Hybrid Training System (HTS) to maintain an astronaut's musculoskeletal system using an electrically stimulated antagonist to resist the volitional contraction of the agonist instead of gravity. The present study assessed the system's orbital operation capability and utility, as well as its preventative effect on an astronaut's musculoskeletal atrophy. HTS was attached to the non-dominant arm of an astronaut staying on the ISS, and his dominant arm without HTS was established as the control (CTR). 10 sets of 10 reciprocal elbow curls were one training session, and 12 total sessions of training (3 times per week for 4 weeks) were performed. Pre and post flight ground based evaluations were performed by Biodex (muscle performance), MRI (muscle volume), and DXA (BMD, lean [muscle] mass, fat mass). Pre and post training inflight evaluations were performed by a hand held dynamometer (muscle force) and a measuring tape (upper arm circumference). The experiment was completed on schedule, and HTS functioned well without problems. Isokinetic elbow extension torque (Nm) changed -19.4% in HTS, and -21.7% in CTR. Isokinetic elbow flexion torque changed -23.7% in HTS, and there was no change in CTR. Total Work (Joule) of elbow extension changed -8.3% in HTS, and +0.3% in CTR. For elbow flexion it changed -23.3% in HTS and -32.6% in CTR. Average Power (Watts) of elbow extension changed +22.1% in HTS and -8.0% in CTR. For elbow flexion it changed -6.5% in HTS and -4.8% in CTR. Triceps muscle volume according to MRI changed +11.7% and that of biceps was +2.1% using HTS, however -0.1% and -0.4% respectively for CTR. BMD changed +4.6% in the HTS arm and -1.2% for CTR. Lean (muscle) mass of the arm changed only +10.6% in HTS. Fat mass changed -12.6% in HTS and -6.4% in CTR. These results showed the orbital operation capability and utility, and the preventive effect of HTS for an astronaut's musculoskeletal atrophy. The initial flight data together with the ground data obtained so far will be utilized in the future planning of human space exploration.

The Effect of Magnetic Field on HTS Leads What Happens when thePower Fails at RAL?

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

Green, Michael A.

2007-02-14

The key to being able to operate the MICE superconducting solenoids on small coolers is the use of high temperature superconducting (HTS) leads between the first stage of the cooler and the magnet, which operates at around 4.2 K. Because MICE magnets are not shielded, all of the MICE magnets have a stray magnetic field in the region where the coolers and the HTS leads are located. The behavior of the HTS leads in a magnetic field depends strongly on the HTS material used for the leads and the temperature of the cooler first stage temperature. The HTS leads canmore » be specified to operate at the maximum current for the magnet. This report shows how the HTS leads can be specified for use the MICE magnets. MICE magnets take from 1.3 hours (the tracker solenoids) to 3.7 hours (the coupling magnet) to charge to the highest projected operating currents. If the power fails, the cooler and the upper ends of the HTS leads warm up. The question is how one can discharge the magnet to protect the HTS leads without quenching the MICE magnets. This report describes a method that one can use to protect the HTS leads in the event of a power failure at the Rutherford Appleton Laboratory (RAL).« less

Toxicokinetic and Dosimetry Modeling Tools for Exposure Reconstruction: US EPA's Rapid Exposure and Dosimetry (RED) Project

EPA Science Inventory

New technologies and in vitro testing approaches have been valuable additions to risk assessments that have historically relied solely on in vivo test results. Compared to in vivo methods, in vitro high throughput screening (HTS) assays are less expensive, faster and can provide ...

China’s Approach to Technology Acquisition: Part 3. Summary Observations

DTIC Science & Technology

1975-02-01

examples, and the Hasselblad 500 C/M camera one of the most recent. Copying need not, of course, take the form of completely reproducing an item...of Westinghouse Electric) Allgemeine Elek- trizitHts- Gesel - schaften AEG- Telefunken August Thyssen- HUtte AG-Rassel- stein AG Brown, Boverie

Extrapolating toxicity data across species using U.S. EPA SeqAPASS tool

EPA Science Inventory

In vitro high-throughput screening (HTS) and in silico technologies have emerged as 21st century tools for chemical hazard identification. In 2007 the U.S. Environmental Protection Agency (EPA) launched the ToxCast Program, which has screened thousands of chemicals in hundreds of...

The present status of the high temperature superconducting Maglev vehicle in China

NASA Astrophysics Data System (ADS)

Wang, J. S.; Wang, S. Y.; Zeng, Y. W.; Deng, C. Y.; Ren, Z. Y.; Wang, X. R.; Song, H. H.; Wang, X. Z.; Zheng, J.; Zhao, Y.

2005-02-01

Since the first successful running of the people-carrying high temperature superconducting (HTS) Maglev test vehicle on 31 December 2000, about 27 000 people have taken it, and the accumulated running distance is about 400 km. The levitation force of the onboard HTS equipment is measured periodically, and new experimental results measured on 5 March 2003 show that the performance of the onboard HTS Maglev equipment is almost the same as that of two years ago. Experimental results indicate that the long-term stability of the HTS Maglev vehicle is good. This further proves the feasibility of the HTS Maglev vehicle for practical transportation. It is worth mentioning that all the results are measured at a low speed; however, investigations of the dynamic performance of the HTS Maglev vehicle at high speed are necessary for practical application. Research on the dynamic performance of the HTS Maglev vehicle is ongoing.

US Navy superconductivity program

NASA Technical Reports Server (NTRS)

Gubser, Donald U.

1991-01-01

Both the new high temperature superconductors (HTS) and the low temperature superconductors (LTS) are important components of the Navy's total plan to integrate superconductivity into field operational systems. Fundamental research is an important component of the total Navy program and focuses on the HTS materials. Power applications (ship propulsion) use LTS materials while space applications (millimeter wave electronics) use HTS materials. The Space Experiment to be conducted at NRL will involve space flight testing of HTS devices built by industry and will demonstrate the ability to engineer and space qualify these devices for systems use. Another important component of the Navy's effort is the development of Superconducting Quantum Interference Device (SQUID) magnetometers. This program will use LTS materials initially, but plans to implement HTS materials as soon as possible. Hybrid HTS/LTS systems are probable in many applications. A review of the status of the Navy's HTS materials research is given as well as an update on the Navy's development efforts in superconductivity.

Therapeutic potential of fibroblast growth factor-2 for hypertrophic scars: upregulation of MMP-1 and HGF expression.

PubMed

Eto, Hitomi; Suga, Hirotaka; Aoi, Noriyuki; Kato, Harunosuke; Doi, Kentaro; Kuno, Shinichiro; Tabata, Yasuhiko; Yoshimura, Kotaro

2012-02-01

Although hypertrophic scars (HTSs) and keloids are challenging problems, their pathogenesis is not well understood, making therapy difficult. We showed that matrix metalloproteinase (MMP)-1 expression was downregulated in HTS compared with normal skin from the same patients, whereas type 1 and 3 collagen and transforming growth factor-β (TGF-β) were upregulated. These differences, however, were not seen in cultured fibroblasts, suggesting the involvement of microenvironmental factors in the pathogenesis of HTS. Fibroblast growth factor-2 (FGF-2) highly upregulated the expression of MMP-1 and hepatocyte growth factor (HGF) in both HTS-derived and control fibroblasts; the upregulation was reversed by extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK) inhibitors. An animal study using human HTS tissue implanted into nude mice indicated that controlled-release FGF-2 resulted in significantly less weight and decreased hydroxyproline content in HTS. Degradation of collagen fibers in FGF-2-treated HTS was also confirmed histologically. Western blotting showed that FGF-2-treated HTS expressed significantly higher MMP-1 protein than control. Decreased MMP-1 expression may be an important transcriptional change in HTS, and its reversal as well as upregulation of HGF by FGF-2 could be a new therapeutic approach for HTS.

A Cryogenic Magnetostrictive Actuator using a Persistent High Temperature Superconducting Magnet, Part 1: Concept and Design. Part 1; Concept and Design

NASA Technical Reports Server (NTRS)

Horner, Garnett C.; Bromberg, Leslie; Teter, J. P.

2001-01-01

Cryogenic magnetostrictive materials, such as rare earth zinc crystals, offer high strains and high forces with minimally applied magnetic fields, making the material ideally suited for deformable optics applications. For cryogenic temperature applications, such as Next Generation Space Telescope (NGST), the use of superconducting magnets offer the possibility of a persistent mode of operation, i.e., the magnetostrictive material will maintain a strain field without power. High temperature superconductors (HTS) are attractive options if the temperature of operation is higher than 10 degrees Kelvin (K) and below 77 K. However, HTS wires have constraints that limit the minimum radius of winding, and even if good wires can be produced, the technology for joining superconducting wires does not exist. In this paper, the design and capabilities of a rare earth zinc magnetostrictive actuator using bulk HTS is described. Bulk superconductors can be fabricated in the sizes required with excellent superconducting properties. Equivalent permanent magnets, made with this inexpensive material, are persistent, do not require a persistent switch as in HTS wires, and can be made very small. These devices are charged using a technique which is similar to the one used for charging permanent magnets, e.g., by driving them into saturation. A small normal conducting coil can be used for charging or discharging. Very fast charging and discharging of HTS tubes, as short as 100 microseconds, has been demonstrated. Because of the magnetic field capability of the superconductor material, a very small amount of superconducting magnet material is needed to actuate the rare earth zinc. In this paper, several designs of actuators using YBCO and BSCCO 2212 superconducting materials are presented. Designs that include magnetic shielding to prevent interaction between adjacent actuators will also be described. Preliminary experimental results and comparison with theory for BSSCO 2212 with a magnetostrictive element will be discussed.

Cryostatless high temperature supercurrent bearings for rocket engine turbopumps

NASA Technical Reports Server (NTRS)

Rao, Dantam K.; Dill, James F.

1989-01-01

The rocket engine systems examined include SSME, ALS, and CTV systems. The liquid hydrogen turbopumps in the SSME and ALS vehicle systems are identified as potentially attractive candidates for development of Supercurrent Bearings since the temperatures around the bearings is about 30 K, which is considerably lower than the 95 K transition temperatures of HTS materials. At these temperatures, the current HTS materials are shown to be capable of developing significantly higher current densities. This higher current density capability makes the development of supercurrent bearings for rocket engines an attractive proposition. These supercurrent bearings are also shown to offer significant advantages over conventional bearings used in rocket engines. They can increase the life and reliability over rolling element bearings because of noncontact operation. They offer lower power loss over conventional fluid film bearings. Compared to conventional magnetic bearings, they can reduce the weight of controllers significantly, and require lower power because of the use of persistent currents. In addition, four technology areas that require further attention have been identified. These are: Supercurrent Bearing Conceptual Design Verification; HTS Magnet Fabrication and Testing; Cryosensors and Controller Development; and Rocket Engine Environmental Compatibility Testing.

Electrically Stimulated Antagonist Muscle Contraction Increased Muscle Mass and Bone Mineral Density of One Astronaut - Initial Verification on the International Space Station

PubMed Central

Takano, Yoshio; Yoshimitsu, Kazuhiro; Omoto, Masayuki; Hashida, Ryuki; Tagawa, Yoshihiko; Inada, Tomohisa; Yamada, Shin; Ohshima, Hiroshi

2015-01-01

Background Musculoskeletal atrophy is one of the major problems of extended periods of exposure to weightlessness such as on the International Space Station (ISS). We developed the Hybrid Training System (HTS) to maintain an astronaut’s musculoskeletal system using an electrically stimulated antagonist to resist the volitional contraction of the agonist instead of gravity. The present study assessed the system’s orbital operation capability and utility, as well as its preventative effect on an astronaut’s musculoskeletal atrophy. Methods HTS was attached to the non-dominant arm of an astronaut staying on the ISS, and his dominant arm without HTS was established as the control (CTR). 10 sets of 10 reciprocal elbow curls were one training session, and 12 total sessions of training (3 times per week for 4 weeks) were performed. Pre and post flight ground based evaluations were performed by Biodex (muscle performance), MRI (muscle volume), and DXA (BMD, lean [muscle] mass, fat mass). Pre and post training inflight evaluations were performed by a hand held dynamometer (muscle force) and a measuring tape (upper arm circumference). Results The experiment was completed on schedule, and HTS functioned well without problems. Isokinetic elbow extension torque (Nm) changed -19.4% in HTS, and -21.7% in CTR. Isokinetic elbow flexion torque changed -23.7% in HTS, and there was no change in CTR. Total Work (Joule) of elbow extension changed -8.3% in HTS, and +0.3% in CTR. For elbow flexion it changed -23.3% in HTS and -32.6% in CTR. Average Power (Watts) of elbow extension changed +22.1% in HTS and -8.0% in CTR. For elbow flexion it changed -6.5% in HTS and -4.8% in CTR. Triceps muscle volume according to MRI changed +11.7% and that of biceps was +2.1% using HTS, however -0.1% and -0.4% respectively for CTR. BMD changed +4.6% in the HTS arm and -1.2% for CTR. Lean (muscle) mass of the arm changed only +10.6% in HTS. Fat mass changed -12.6% in HTS and -6.4% in CTR. Conclusions These results showed the orbital operation capability and utility, and the preventive effect of HTS for an astronaut’s musculoskeletal atrophy. The initial flight data together with the ground data obtained so far will be utilized in the future planning of human space exploration. PMID:26296204

Development of High Temperature Superconducting Josephson Junction Device Technology

DTIC Science & Technology

1998-07-09

neodymium gallate , cerium oxide-buffered sapphire, and lanthanum aluminate, are not ideal for an in situ thallium cuprate junction technology. Moreover...determined that the standard HTS substrates, neodymium gallate , cerium oxide-buffered sapphire, and lanthanum aluminate, are not ideal for an in situ...2.2.1. Deposition Uniformity 10 2.2.2. Radiative Element 12 2.3. SUBSTRATES 13 2.3.1. Neodymium gallate 14 2.3.2. Cerium Oxide-Buffered Sapphire 16

Experimental Investigation of a Broadband High-Temperature Superconducting Terahertz Mixer Operating at Temperatures Between 40 and 77 K

NASA Astrophysics Data System (ADS)

Gao, Xiang; Du, Jia; Zhang, Ting; Jay Guo, Y.; Foley, Cathy P.

2017-11-01

This paper presents a systematic investigation of a broadband thin-film antenna-coupled high-temperature superconducting (HTS) terahertz (THz) harmonic mixer at relatively high operating temperature from 40 to 77 K. The mixer device chip was fabricated using the CSIRO established step-edge YBa2Cu3O7-x (YBCO) Josephson junction technology, packaged in a well-designed module and cooled in a temperature adjustable cryocooler. Detailed experimental characterizations were carried out for the broadband HTS mixer at both the 200 and 600 GHz bands in harmonic mixing mode. The DC current-voltage characteristics (IVCs), bias current condition, local oscillator (LO) power requirement, frequency response, as well as conversion efficiency under different bath temperatures were thoroughly investigated for demonstrating the frequency down-conversion performance.

Superconducting Electric Machine with Permanent Magnets and Bulk HTS Elements

NASA Astrophysics Data System (ADS)

Levin, A. V.; Vasich, P. S.; Dezhin, D. S.; Kovalev, L. K.; Kovalev, K. L.; Poltavets, V. N.; Penkin, V. T.

Theoretical methods of calculating of two-dimensional magnetic fields, inductive parameters and output characteristics of the new type of high-temperature superconducting (HTS) synchronous motors with a composite rotor are presented. The composite rotor has the structure containing HTS flat elements, permanent magnets and ferromagnetic materials. The developed calculation model takes into account the concentrations and physical properties of these rotor elements. The simulation results of experimental HTS motor with a composite rotor are presented. The application of new type of HTS motor in different constructions of industrial high dynamic drivers is discussed.

Testing of a 1.25-m HTS Cable Made from YBCO Tapes

NASA Astrophysics Data System (ADS)

Gouge, M. J.; Lue, J. W.; Demko, J. A.; Duckworth, R. C.; Fisher, P. W.; Daumling, M.; Lindsay, D. T.; Roden, M. L.; Tolbert, J. C.

2004-06-01

Ultera and Oak Ridge National Laboratory (ORNL) have jointly designed, built, and tested a 1.25-m-long, prototype high-temperature superconducting (HTS) power cable made from 1-cm-wide, second-generation YBa2Cu3Ox (YBCO)-coated conductor tapes. Electrical tests of this cable were performed in boiling liquid nitrogen at 77 K. DC testing of the 1.25-m cable included determination of the V-I curve, with a critical current of 4200 A. This was consistent with the properties of the 24 individual YBCO tapes. AC testing of the cable was conducted at currents up to 2500 Arms. The ac losses were measured calorimetrically by measuring the response of a calibrated temperature sensor placed on the former and electrically by use of a Rogowski coil with a lock-in amplifier. AC losses of about 2 W/m were measured at a cable ac current of 2000 Arms. Overcurrent testing was conducted at peak current values up to 12 kA for pulse lengths of 0.1-0.2 s. The cable temperature increased to 105 K for a 12 kA, 0.2 s overcurrent pulse, and the cable showed no degradation after the sequence of overcurrent testing. This commercial-grade HTS cable demonstrated the feasibility of second-generation YBCO tapes in an ac cable application.

A new approach for AC loss reduction in HTS transformer using auxiliary windings, case study: 25 kA HTS current injection transformer

NASA Astrophysics Data System (ADS)

Heydari, Hossein; Faghihi, Faramarz; Aligholizadeh, Reza

2008-01-01

AC loss is one of the important parameters in HTS (high temperature superconducting) AC devices. Among the HTS AC power devices, the transformer is an essential part in the electrical power system. The AC losses in an HTS tape depend on the magnetic field. One of the techniques usually adopted to mitigate the unwanted magnetic field is using a system of coils that produce a magnetic field opposite to the incident one, reducing the total magnetic field. In this paper adding two auxiliary windings to the HTS transformer to produce this opposite magnetic field is proposed. The proper use of these auxiliary windings could reduce the leakage flux and, therefore, the AC loss. A mathematical model is used to describe the behaviour of a transformer operating with auxiliary windings, based on the theory of electromagnetic coupled circuits. The influence of the auxiliary windings on the leakage field is studied by the finite element method (FEM) and the AC loss of an HTS transformer was calculated. Also, the simulation results show that employing auxiliary windings will improve the HTS transformer efficiency.

Spatial and Temporal Variations of a Screening Current Induced Magnetic Field in a Double-Pancake HTS Insert of an LTS/HTS NMR Magnet

PubMed Central

Ahn, Min Cheol; Yagai, Tsuyoshi; Hahn, Seungyong; Ando, Ryuya; Bascuñán, Juan; Iwasa, Yukikazu

2010-01-01

This paper presents experimental and simulation results of a screening current induced magnetic field (SCF) in a high temperature superconductor (HTS) insert that constitutes a low-/high-temperature superconductor (LTS/HTS) NMR magnet. In this experiment, the HTS insert, a stack of 50 double-pancake coils, each wound with Bi2223 tape, was operated at 77 K. A screening current was induced in the HTS insert by three magnetic field sources: 1) a self field from the HTS insert; 2) an external field from a 5-T background magnet; and 3) combinations of 1) and 2). For each field excitation, which induced an SCF, its axial field distribution and temporal variations were measured and compared with simulation results based on the critical state model. Agreement on field profile between experiment and simulation is satisfactory but more work is needed to make the simulation useful for designing shim coils that will cancel the SCF. PMID:20401187

(ENVIRONMENTAL SCIENCE and TECHNOLOGY) An Intuitive Approach for Predicting Human Risk with the Tox21 10k Library

EPA Science Inventory

In vitro to in vivo extrapolation (IVIVE) analyses translating high-throughput screening (HTS) data to human relevance have been limited. This is the first time IVIVE approaches and exposure comparisons have explored the entire Tox21 federal collaboration’s 10,000 chemi...

Potentialities of HTS Superconductor Technology in Telecommunication Satellites

DTIC Science & Technology

2005-07-13

satellites de télécommunications, utilisant des composants supraconducteurs à haute température critique et de l’électronique refroidie sont présentés... supraconducteur ) is the focal array of a receiving antenna (FAFR). The target application is a receive multi-beam satellite antenna in Ka-band. Small

Extrapolation of mammalian-based ToxCast assay results to non-mammalian species to evaluate endocrine disruption

EPA Science Inventory

In vitro high-throughput screening (HTS) and in silico technologies have emerged as 21st century tools for chemical hazard identification. In 2007 the U.S. Environmental Protection Agency (EPA) launched the ToxCast Program, which has screened thousands of chemicals in hundreds of...

Design of a Very Large Pulse Tube Cryocooler for HTS Cable Application

NASA Astrophysics Data System (ADS)

Tanchon, J.; Ercolani, E.; Trollier, T.; Ravex, A.; Poncet, J. M.

2006-04-01

The needs for large cooling powers are more and more increasing together with the increase of superconductor capabilities. Within the framework of an High Voltage HTS cable project (LIPA project funded by the DOE with American Superconductor AMSC, Nexans, LIPA and Air Liquide as consortium partners), the Technologies & Innovation Department of Air Liquide with the partnership of the CEA/SBT are currently developing a prototype of a Very Large Pulse Tube Cooler (VLPTC). This prototype is traditionally based on an In-Line pulse tube configuration, making use of an inertance and a buffer volume as phase shifter. The expected performances are 280W heat lift at 65K with a 300K rejection temperature. The cold head prototype has been manufactured and preliminary tests have been carried out with a 8 kW flexure bearing Stirling Technology Corporation STC linear compressor. One of the objectives of this prototype is to compete the Gifford-MacMahon coolers in term of cooling capacity while offering the advantage of the high frequency Pulse Tube in term of high lifetime, reliability and reduced exported vibrations.

Conductor requirements for high-temperature superconducting utility power transformers

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

Pleva, E. F.; Mehrotra, V.; Schwenterly, S W

High-temperature superconducting (HTS) coated conductors in utility power transformers must satisfy a set of operating requirements that are driven by two major considerations-HTS transformers must be economically competitive with conventional units, and the conductor must be robust enough to be used in a commercial manufacturing environment. The transformer design and manufacturing process will be described in order to highlight the various requirements that it imposes on the HTS conductor. Spreadsheet estimates of HTS transformer costs allow estimates of the conductor cost required for an HTS transformer to be competitive with a similarly performing conventional unit.

Novel Multiplexed Assay for Identifying SH2 Domain Antagonists of STAT Family Proteins

PubMed Central

Takakuma, Kazuyuki; Ogo, Naohisa; Uehara, Yutaka; Takahashi, Susumu; Miyoshi, Nao; Asai, Akira

2013-01-01

Some of the signal transducer and activator of transcription (STAT) family members are constitutively activated in a wide variety of human tumors. The activity of STAT depends on their Src homology 2 (SH2) domain-mediated binding to sequences containing phosphorylated tyrosine. Thus, antagonizing this binding is a feasible approach to inhibiting STAT activation. We have developed a novel multiplexed assay for STAT3- and STAT5b-SH2 binding, based on amplified luminescent proximity homogeneous assay (Alpha) technology. AlphaLISA and AlphaScreen beads were combined in a single-well assay, which allowed the binding of STAT3- and STAT5b-SH2 to phosphotyrosine peptides to be simultaneously monitored. Biotin-labeled recombinant human STAT proteins were obtained as N- and C-terminal deletion mutants. The spacer length of the DIG-labeled peptide, the reaction time, and the concentration of sodium chloride were optimized to establish a HTS system with Z’ values of greater than 0.6 for both STAT3- and STAT5b-SH2 binding. We performed a HTS campaign for chemical libraries using this multiplexed assay and identified hit compounds. A 2-chloro-1,4-naphthalenedione derivative, Compound 1, preferentially inhibited STAT3-SH2 binding in vitro, and the nuclear translocation of STAT3 in HeLa cells. Initial structure activity relationship (SAR) studies using the multiplexed assay showed the 3-substituent effect on both the activity and selectivity of STAT3 and STAT5b inhibition. Therefore, this multiplexed assay is useful for not only searching for potential lead compounds but also obtaining SAR data for developing new STAT3/STAT5b inhibitors. PMID:23977103

Novel multiplexed assay for identifying SH2 domain antagonists of STAT family proteins.

PubMed

Takakuma, Kazuyuki; Ogo, Naohisa; Uehara, Yutaka; Takahashi, Susumu; Miyoshi, Nao; Asai, Akira

2013-01-01

Some of the signal transducer and activator of transcription (STAT) family members are constitutively activated in a wide variety of human tumors. The activity of STAT depends on their Src homology 2 (SH2) domain-mediated binding to sequences containing phosphorylated tyrosine. Thus, antagonizing this binding is a feasible approach to inhibiting STAT activation. We have developed a novel multiplexed assay for STAT3- and STAT5b-SH2 binding, based on amplified luminescent proximity homogeneous assay (Alpha) technology. AlphaLISA and AlphaScreen beads were combined in a single-well assay, which allowed the binding of STAT3- and STAT5b-SH2 to phosphotyrosine peptides to be simultaneously monitored. Biotin-labeled recombinant human STAT proteins were obtained as N- and C-terminal deletion mutants. The spacer length of the DIG-labeled peptide, the reaction time, and the concentration of sodium chloride were optimized to establish a HTS system with Z' values of greater than 0.6 for both STAT3- and STAT5b-SH2 binding. We performed a HTS campaign for chemical libraries using this multiplexed assay and identified hit compounds. A 2-chloro-1,4-naphthalenedione derivative, Compound 1, preferentially inhibited STAT3-SH2 binding in vitro, and the nuclear translocation of STAT3 in HeLa cells. Initial structure activity relationship (SAR) studies using the multiplexed assay showed the 3-substituent effect on both the activity and selectivity of STAT3 and STAT5b inhibition. Therefore, this multiplexed assay is useful for not only searching for potential lead compounds but also obtaining SAR data for developing new STAT3/STAT5b inhibitors.

Progress of applied superconductivity research at Materials Research Laboratories, ITRI (Taiwan)

NASA Technical Reports Server (NTRS)

Liu, R. S.; Wang, C. M.

1995-01-01

A status report based on the applied high temperature superconductivity (HTS) research at Materials Research Laboratories (MRL), Industrial Technology Research Institute (ITRI) is given. The aim is to develop fabrication technologies for the high-TC materials appropriate to the industrial application requirements. To date, the majorities of works have been undertaken in the areas of new materials, wires/tapes with long length, prototypes of magnets, large-area thin films, SQUID's and microwave applications.

Should trained lay providers perform HIV testing? A systematic review to inform World Health Organization guidelines.

PubMed

Kennedy, C E; Yeh, P T; Johnson, C; Baggaley, R

2017-12-01

New strategies for HIV testing services (HTS) are needed to achieve UN 90-90-90 targets, including diagnosis of 90% of people living with HIV. Task-sharing HTS to trained lay providers may alleviate health worker shortages and better reach target groups. We conducted a systematic review of studies evaluating HTS by lay providers using rapid diagnostic tests (RDTs). Peer-reviewed articles were included if they compared HTS using RDTs performed by trained lay providers to HTS by health professionals, or to no intervention. We also reviewed data on end-users' values and preferences around lay providers preforming HTS. Searching was conducted through 10 online databases, reviewing reference lists, and contacting experts. Screening and data abstraction were conducted in duplicate using systematic methods. Of 6113 unique citations identified, 5 studies were included in the effectiveness review and 6 in the values and preferences review. One US-based randomized trial found patients' uptake of HTS doubled with lay providers (57% vs. 27%, percent difference: 30, 95% confidence interval: 27-32, p < 0.001). In Malawi, a pre/post study showed increases in HTS sites and tests after delegation to lay providers. Studies from Cambodia, Malawi, and South Africa comparing testing quality between lay providers and laboratory staff found little discordance and high sensitivity and specificity (≥98%). Values and preferences studies generally found support for lay providers conducting HTS, particularly in non-hypothetical scenarios. Based on evidence supporting using trained lay providers, a WHO expert panel recommended lay providers be allowed to conduct HTS using HIV RDTs. Uptake of this recommendation could expand HIV testing to more people globally.

PREFACE: Special section featuring selected papers from the 3rd International Workshop on Numerical Modelling of High Temperature Superconductors Special section featuring selected papers from the 3rd International Workshop on Numerical Modelling of High Temperature Superconductors

NASA Astrophysics Data System (ADS)

Granados, Xavier; Sánchez, Àlvar; López-López, Josep

2012-10-01

The development of superconducting applications and superconducting engineering requires the support of consistent tools which can provide models for obtaining a good understanding of the behaviour of the systems and predict novel features. These models aim to compute the behaviour of the superconducting systems, design superconducting devices and systems, and understand and test the behavior of the superconducting parts. 50 years ago, in 1962, Charles Bean provided the superconducting community with a model efficient enough to allow the computation of the response of a superconductor to external magnetic fields and currents flowing through in an understandable way: the so called critical-state model. Since then, in addition to the pioneering critical-state approach, other tools have been devised for designing operative superconducting systems, allowing integration of the superconducting design in nearly standard electromagnetic computer-aided design systems by modelling the superconducting parts with consideration of time-dependent processes. In April 2012, Barcelona hosted the 3rd International Workshop on Numerical Modelling of High Temperature Superconductors (HTS), the third in a series of workshops started in Lausanne in 2010 and followed by Cambridge in 2011. The workshop reflected the state-of-the-art and the new initiatives of HTS modelling, considering mathematical, physical and technological aspects within a wide and interdisciplinary scope. Superconductor Science and Technology is now publishing a selection of papers from the workshop which have been selected for their high quality. The selection comprises seven papers covering mathematical, physical and technological topics which contribute to an improvement in the development of procedures, understanding of phenomena and development of applications. We hope that they provide a perspective on the relevance and growth that the modelling of HTS superconductors has achieved in the past 25 years.

Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity.

PubMed

Terekhov, Stanislav S; Smirnov, Ivan V; Stepanova, Anastasiya V; Bobik, Tatyana V; Mokrushina, Yuliana A; Ponomarenko, Natalia A; Belogurov, Alexey A; Rubtsova, Maria P; Kartseva, Olga V; Gomzikova, Marina O; Moskovtsev, Alexey A; Bukatin, Anton S; Dubina, Michael V; Kostryukova, Elena S; Babenko, Vladislav V; Vakhitova, Maria T; Manolov, Alexander I; Malakhova, Maja V; Kornienko, Maria A; Tyakht, Alexander V; Vanyushkina, Anna A; Ilina, Elena N; Masson, Patrick; Gabibov, Alexander G; Altman, Sidney

2017-03-07

Ultrahigh-throughput screening (uHTS) techniques can identify unique functionality from millions of variants. To mimic the natural selection mechanisms that occur by compartmentalization in vivo, we developed a technique based on single-cell encapsulation in droplets of a monodisperse microfluidic double water-in-oil-in-water emulsion (MDE). Biocompatible MDE enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography-mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions. This platform was probed with uHTS for biocatalysts anchored to yeast with enrichment close to the theoretically calculated limit and cell-to-cell interactions. MDE-FACS allowed the identification of human butyrylcholinesterase mutants that undergo self-reactivation after inhibition by the organophosphorus agent paraoxon. The versatility of the platform allowed the identification of bacteria, including slow-growing oral microbiota species that suppress the growth of a common pathogen, Staphylococcus aureus , and predicted which genera were associated with inhibitory activity.

Structural analyses of human thymidylate synthase reveal a site that may control conformational switching between active and inactive states.

PubMed

Chen, Dan; Jansson, Anna; Sim, Daniel; Larsson, Andreas; Nordlund, Pär

2017-08-11

Thymidylate synthase (TS) is the sole enzyme responsible for de novo biosynthesis of thymidylate (TMP) and is essential for cell proliferation and survival. Inhibition of human TS (hTS) has been extensively investigated for cancer chemotherapy, but several aspects of its activity and regulation are still uncertain. In this study, we performed comprehensive structural and biophysical studies of hTS using crystallography and thermal shift assay and provided the first detailed structural information on the conformational changes induced by ligand binding to the hTS active site. We found that upon binding of the antifolate agents raltitrexed and nolatrexed, the two insert regions in hTS, the functions of which are unclear, undergo positional shifts toward the catalytic center. We investigated the inactive conformation of hTS and found that the two insert regions are also involved in the conformational transition between the active and inactive state of hTS. Moreover, we identified a ligand-binding site in the dimer interface, suggesting that the cavity in the dimer interface could serve as an allosteric site of hTS to regulate the conformational switching between the active and inactive states. On the basis of these findings, we propose a regulatory mechanism of hTS activity that involves allosteric regulation of interactions of hTS with its own mRNA depending on cellular demands for TMP. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

A new ring-shape high-temperature superconducting trapped-field magnet

NASA Astrophysics Data System (ADS)

Sheng, Jie; Zhang, Min; Wang, Yawei; Li, Xiaojian; Patel, Jay; Yuan, Weijia

2017-09-01

This paper presents a new trapped-field magnet made of second-generation high-temperature superconducting (2G HTS) rings. This so-called ring-shape 2G HTS magnet has the potential to provide much stronger magnetic fields relative to existing permanent magnets. Compared to existing 2G HTS trapped- field magnets, e.g. 2G HTS bulks and stacks, this new ring-shape 2G HTS magnet is more flexible in size and can be made into magnets with large dimensions for industrial applications. Effective magnetization is the key to being able to use trapped-field magnets. Therefore, this paper focuses on the magnetization mechanism of this new magnet using both experimental and numerical methods. Unique features have been identified and quantified for this new type of HTS magnet in the field cooling and zero field cooling process. The magnetization mechanism can be understood by the interaction between shielding currents and the penetration of external magnetic fields. An accumulation in the trapped field was observed by using multiple pulse field cooling. Three types of demagnetization were studied to measure the trapped-field decay for practical applications. Our results show that this new ring-shape HTS magnet is very promising in the trapping of a high magnetic field. As a super-permanent magnet, it will have a significant impact on large-scale industrial applications, e.g. the development of HTS machines with a very high power density and HTS magnetic resonance imaging devices.

Deep Sequencing of Plant and Animal DNA Contained within Traditional Chinese Medicines Reveals Legality Issues and Health Safety Concerns

PubMed Central

Coghlan, Megan L.; Haile, James; Houston, Jayne; Murray, Dáithí C.; White, Nicole E.; Moolhuijzen, Paula; Bellgard, Matthew I.; Bunce, Michael

2012-01-01

Traditional Chinese medicine (TCM) has been practiced for thousands of years, but only within the last few decades has its use become more widespread outside of Asia. Concerns continue to be raised about the efficacy, legality, and safety of many popular complementary alternative medicines, including TCMs. Ingredients of some TCMs are known to include derivatives of endangered, trade-restricted species of plants and animals, and therefore contravene the Convention on International Trade in Endangered Species (CITES) legislation. Chromatographic studies have detected the presence of heavy metals and plant toxins within some TCMs, and there are numerous cases of adverse reactions. It is in the interests of both biodiversity conservation and public safety that techniques are developed to screen medicinals like TCMs. Targeting both the p-loop region of the plastid trnL gene and the mitochondrial 16S ribosomal RNA gene, over 49,000 amplicon sequence reads were generated from 15 TCM samples presented in the form of powders, tablets, capsules, bile flakes, and herbal teas. Here we show that second-generation, high-throughput sequencing (HTS) of DNA represents an effective means to genetically audit organic ingredients within complex TCMs. Comparison of DNA sequence data to reference databases revealed the presence of 68 different plant families and included genera, such as Ephedra and Asarum, that are potentially toxic. Similarly, animal families were identified that include genera that are classified as vulnerable, endangered, or critically endangered, including Asiatic black bear (Ursus thibetanus) and Saiga antelope (Saiga tatarica). Bovidae, Cervidae, and Bufonidae DNA were also detected in many of the TCM samples and were rarely declared on the product packaging. This study demonstrates that deep sequencing via HTS is an efficient and cost-effective way to audit highly processed TCM products and will assist in monitoring their legality and safety especially when plant reference databases become better established. PMID:22511890

A novel no-insulation winding technique of high temperature-superconducting racetrack coil for rotating applications: A progress report in Korea university.

PubMed

Choi, Y H; Song, J B; Yang, D G; Kim, Y G; Hahn, S; Lee, H G

2016-10-01

This paper presents our recent progress on core technology development for a megawatt-class superconducting wind turbine generator supported by the international collaborative R&D program of the Korea Institute of Energy Technology Evaluation and Planning. To outperform the current high-temperature-superconducting (HTS) magnet technology in the wind turbine industry, a novel no-insulation winding technique was first proposed to develop the second-generation HTS racetrack coil for rotating applications. Here, we briefly report our recent studies on no-insulation (NI) winding technique for GdBCO coated conductor racetrack coils in the following areas: (1) Charging-discharging characteristics of no-insulation GdBCO racetrack coils with respect to external pressures applied to straight sections; (2) thermal and electrical stabilities of no-insulation GdBCO racetrack coils encapsulated with various impregnating materials; (3) quench behaviors of no-insulation racetrack coils wound with GdBCO conductor possessing various lamination layers; (4) electromagnetic characteristics of no-insulation GdBCO racetrack coils under time-varying field conditions. Test results confirmed that this novel NI winding technique was highly promising. It could provide development of a compact, mechanically dense, and self-protecting GdBCO magnet for use in real-world superconducting wind turbine generators.

A novel no-insulation winding technique of high temperature-superconducting racetrack coil for rotating applications: A progress report in Korea university

NASA Astrophysics Data System (ADS)

Choi, Y. H.; Song, J. B.; Yang, D. G.; Kim, Y. G.; Hahn, S.; Lee, H. G.

2016-10-01

This paper presents our recent progress on core technology development for a megawatt-class superconducting wind turbine generator supported by the international collaborative R&D program of the Korea Institute of Energy Technology Evaluation and Planning. To outperform the current high-temperature-superconducting (HTS) magnet technology in the wind turbine industry, a novel no-insulation winding technique was first proposed to develop the second-generation HTS racetrack coil for rotating applications. Here, we briefly report our recent studies on no-insulation (NI) winding technique for GdBCO coated conductor racetrack coils in the following areas: (1) Charging-discharging characteristics of no-insulation GdBCO racetrack coils with respect to external pressures applied to straight sections; (2) thermal and electrical stabilities of no-insulation GdBCO racetrack coils encapsulated with various impregnating materials; (3) quench behaviors of no-insulation racetrack coils wound with GdBCO conductor possessing various lamination layers; (4) electromagnetic characteristics of no-insulation GdBCO racetrack coils under time-varying field conditions. Test results confirmed that this novel NI winding technique was highly promising. It could provide development of a compact, mechanically dense, and self-protecting GdBCO magnet for use in real-world superconducting wind turbine generators.

Second-Generation High-Temperature Superconductor Wires for the Electric Power Grid

NASA Astrophysics Data System (ADS)

Malozemoff, A. P.

2012-08-01

Superconductors offer major advantages for the electric power grid, including high current and power capacity, high efficiency arising from the lossless current flow, and a unique current-limiting functionality arising from a superconductor-to-resistive transition. These advantages can be brought to bear on equipment such as underground power cables, fault current limiters, rotating machinery, transformers, and energy storage. The first round of significant commercial-scale superconductor power-equipment demonstrations, carried out during the past decade, relied on a first-generation high-temperature superconductor (HTS) wire. However, during the past few years, with the recent commercial availability of high-performance second-generation HTS wires, power-equipment demonstrations have increasingly been carried out with these new wires, which bring important advantages. The foundation is being laid for commercial expansion of this important technology into the power grid.

Effect of Discontinuities and Penetrations on the Shielding Efficacy of High Temperature Superconducting Magnetic Shields

NASA Astrophysics Data System (ADS)

Hatwar, R.; Kvitkovic, J.; Herman, C.; Pamidi, S.

2015-12-01

High Temperature Superconducting (HTS) materials have been demonstrated to be suitable for applications in shielding of both DC and AC magnetic fields. Magnetic shielding is required for protecting sensitive instrumentation from external magnetic fields and for preventing the stray magnetic fields produced by high power density equipment from affecting neighbouring devices. HTS shields have high current densities at relatively high operating temperatures (40-77 K) and can be easily fabricated using commercial HTS conductor. High current densities in HTS materials allow design and fabrication of magnetic shields that are lighter and can be incorporated into the body and skin of high power density devices. HTS shields are particularly attractive for HTS devices because a single cryogenic system can be used for cooling the device and the associated shield. Typical power devices need penetrations for power and signal cabling and the penetrations create discontinuities in HTS shields. Hence it is important to assess the effect of the necessary discontinuities on the efficacy of the shields and the design modifications necessary to accommodate the penetrations.

Recent Progress in Electrical Insulation Techniques for HTS Power Apparatus

NASA Astrophysics Data System (ADS)

Hayakawa, Naoki; Kojima, Hiroki; Hanai, Masahiro; Okubo, Hitoshi

This paper describes the electrical insulation techniques at cryogenic temperatures, i.e. Cryodielectrics, for HTS power apparatus, e.g. HTS power transmission cables, transformers, fault current limiters and SMES. Breakdown and partial discharge characteristics are discussed for different electrical insulation configurations of LN2, sub-cooled LN2, solid, vacuum and their composite insulation systems. Dynamic and static insulation performances with and without taking account of quench in HTS materials are also introduced.

High temperature superconducting synchronous motor design and test

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

Schiferl, R.; Zhang, B.; Shoykhet, B.

1996-10-01

High horsepower synchronous motors with high temperature superconducting (HTS) field windings offer the potential to cut motor operating losses in half compared to conventional energy efficient induction motors available today. The design, construction and test of a prototype, air core, synchronous motor with helium gas cooled HTS field coils will be described in this paper. The work described is part of a US Department of Energy, Superconductivity Partnership Initiative award. The motor uses a modified conventional motor armature combined with a vacuum insulated rotor that contains the four racetrack-shaped HTS field coils. The rotor is cooled by helium gas somore » that the HTS coils operate at a temperature of 30 K. This paper provides a status report on HTS motor research and development at Reliance Lab., Rockwell Automation that will lead to commercial HTS motors for utility and industrial applications.« less

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

PubMed

Liao, Wei; Jordaan, Gwen; Nham, Phillipp; Phan, Ryan T; Pelegrini, Matteo; Sharma, Sanjai

2015-10-16

To determine differentially expressed and spliced RNA transcripts in chronic lymphocytic leukemia specimens a high throughput RNA-sequencing (HTS RNA-seq) analysis was performed. Ten CLL specimens and five normal peripheral blood CD19+ B cells were analyzed by HTS RNA-seq. The library preparation was performed with Illumina TrueSeq RNA kit and analyzed by Illumina HiSeq 2000 sequencing system. An average of 48.5 million reads for B cells, and 50.6 million reads for CLL specimens were obtained with 10396 and 10448 assembled transcripts for normal B cells and primary CLL specimens respectively. With the Cuffdiff analysis, 2091 differentially expressed genes (DEG) between B cells and CLL specimens based on FPKM (fragments per kilobase of transcript per million reads and false discovery rate, FDR q < 0.05, fold change >2) were identified. Expression of selected DEGs (n = 32) with up regulated and down regulated expression in CLL from RNA-seq data were also analyzed by qRT-PCR in a test cohort of CLL specimens. Even though there was a variation in fold expression of DEG genes between RNA-seq and qRT-PCR; more than 90 % of analyzed genes were validated by qRT-PCR analysis. Analysis of RNA-seq data for splicing alterations in CLL and B cells was performed by Multivariate Analysis of Transcript Splicing (MATS analysis). Skipped exon was the most frequent splicing alteration in CLL specimens with 128 significant events (P-value <0.05, minimum inclusion level difference >0.1). The RNA-seq analysis of CLL specimens identifies novel DEG and alternatively spliced genes that are potential prognostic markers and therapeutic targets. High level of validation by qRT-PCR for a number of DEG genes supports the accuracy of this analysis. Global comparison of transcriptomes of B cells, IGVH non-mutated CLL (U-CLL) and mutated CLL specimens (M-CLL) with multidimensional scaling analysis was able to segregate CLL and B cell transcriptomes but the M-CLL and U-CLL transcriptomes were indistinguishable. The analysis of HTS RNA-seq data to identify alternative splicing events and other genetic abnormalities specific to CLL is an added advantage of RNA-seq that is not feasible with other genome wide analysis.

Fluorescence imaging technology (FI) for high-throughput screening of selenide-modified nano-TiO2 catalysts.

PubMed

Wang, Liping; Lee, Jianchao; Zhang, Meijuan; Duan, Qiannan; Zhang, Jiarui; Qi, Hailang

2016-02-18

A high-throughput screening (HTS) method based on fluorescence imaging (FI) was implemented to evaluate the catalytic performance of selenide-modified nano-TiO2. Chemical ink-jet printing (IJP) technology was reformed to fabricate a catalyst library comprising 1405 (Ni(a)Cu(b)Cd(c)Ce(d)In(e)Y(f))Se(x)/TiO2 (M6Se/Ti) composite photocatalysts. Nineteen M6Se/Tis were screened out from the 1405 candidates efficiently.

Computational Toxicology as Implemented by the U.S. EPA: Providing High Throughput Decision Support Tools for Screening and Assessing Chemical Exposure, Hazard and Risk

EPA Science Inventory

Computational toxicology is the application of mathematical and computer models to help assess chemical hazards and risks to human health and the environment. Supported by advances in informatics, high-throughput screening (HTS) technologies, and systems biology, the U.S. Environ...

Application of extrinsic fluorescence spectroscopy for the high throughput formulation screening of aluminum-adjuvanted vaccines.

PubMed

Ausar, Salvador F; Chan, Judy; Hoque, Warda; James, Olive; Jayasundara, Kavisha; Harper, Kevin

2011-02-01

High throughput screening (HTS) of excipients for proteins in solution can be achieved by several analytical techniques. The screening of stabilizers for proteins adsorbed onto adjuvants, however, may be difficult due to the limited amount of techniques that can measure stability of adsorbed protein in high throughput mode. Here, we demonstrate that extrinsic fluorescence spectroscopy can be successfully applied to study the physical stability of adsorbed antigens at low concentrations in 96-well plates, using a real-time polymerase chain reaction (RT-PCR) instrument. HTS was performed on three adjuvanted pneumococcal proteins as model antigens in the presence of a standard library of stabilizers. Aluminum hydroxide appeared to decrease the stability of all three proteins at relatively high and low pH values, showing a bell-shaped curve as the pH was increased from 5 to 9 with a maximum stability at near neutral pH. Nonspecific stabilizers such as mono- and disaccharides could increase the conformational stability of the antigens. In addition, those excipients that increased the melting temperature of adsorbed antigens could improve antigenicity and chemical stability. To the best of our knowledge, this is the first report describing an HTS technology amenable for low concentration of antigens adsorbed onto aluminum-containing adjuvants. Copyright © 2010 Wiley-Liss, Inc.

Cloud computing approaches to accelerate drug discovery value chain.

PubMed

Garg, Vibhav; Arora, Suchir; Gupta, Chitra

2011-12-01

Continued advancements in the area of technology have helped high throughput screening (HTS) evolve from a linear to parallel approach by performing system level screening. Advanced experimental methods used for HTS at various steps of drug discovery (i.e. target identification, target validation, lead identification and lead validation) can generate data of the order of terabytes. As a consequence, there is pressing need to store, manage, mine and analyze this data to identify informational tags. This need is again posing challenges to computer scientists to offer the matching hardware and software infrastructure, while managing the varying degree of desired computational power. Therefore, the potential of "On-Demand Hardware" and "Software as a Service (SAAS)" delivery mechanisms cannot be denied. This on-demand computing, largely referred to as Cloud Computing, is now transforming the drug discovery research. Also, integration of Cloud computing with parallel computing is certainly expanding its footprint in the life sciences community. The speed, efficiency and cost effectiveness have made cloud computing a 'good to have tool' for researchers, providing them significant flexibility, allowing them to focus on the 'what' of science and not the 'how'. Once reached to its maturity, Discovery-Cloud would fit best to manage drug discovery and clinical development data, generated using advanced HTS techniques, hence supporting the vision of personalized medicine.

Gender differences in the prevalence and impact factors of hysterical tendencies in adolescents from three eastern Chinese provinces.

PubMed

Cheng, Qinglin; Xie, Li; Hu, Yunkai; Hu, Jinfeng; Gao, Wei; Lv, Yongxiang; Xu, Yong

2018-02-07

Few studies have attempted to compare the differences in the prevalence and impact factors of hysterical tendencies (HTs) in adolescents. Thus, the aim of this study was to examine gender differences in the prevalence and impact factors of adolescents' HTs across three eastern Chinese provinces (Anhui, Jiangsu, and Zhejiang). A multicenter, school-based, cross-sectional study was conducted in three provinces (Anhui, Jiangsu, and Zhejiang) in China in 2014. The sample included 10,131 middle-school students aged 13-18 years who were randomly selected using a multiphase, stratified, cluster sampling technique. A two-stage appraisal procedure was used to determine the adolescents' HTs. We also designed a multicenter, school-based, case control (1329 cases with 2661 control individuals) study to collect data on the common factors affecting this population using a common protocol and questionnaire. An overall positive rate of HTs among adolescents across the three eastern Chinese provinces studied was found at 13.1% (95% confidence interval (CI) 12.5-13.8%), at 14.5% (95% CI 13.3-15.7%) for females, and at 12.2% (95% CI 11.1-13.4%) for males. Gender-stratified, multiple conditional regression analyses revealed that superstitious beliefs pertaining to life, somatotype, teacher-student satisfaction, and family achievement orientation were significantly linked to HTs only in males, while left-behind adolescents, emotional and social adaptation, teacher-student support, family cohesion, and the Hospital Anxiety and Depression Scale - depression scores were significantly associated with female HTs only. The models indicated that of all the independent variables studied, family medical history was the strongest impact factor for both male HTs (adjusted matched odds ratio (amOR) = 2.92, 95% CI = 1.84-4.86) and female HTs (amOR = 2.74, 95% CI = 1.59-4.98). HTs are prevalent among adolescents in the three eastern Chinese provinces studied. Gender differences in the prevalence and impact factors of HTs are significant in adolescents, and HTs seem to affect more females than males. Therefore, sex-specific intervention programs against HTs in adolescents should be considered to reduce HT prevalence in adolescents by modifying influential social, school, and family factors.

Man versus machine: the preferred modality.

PubMed

Sanko, Jill; Shekhter, Ilya; Rosen, Lisa; Arheart, Kristopher; Birnbach, David

2012-12-01

When learning objectives do not specifically dictate the use of one simulation modality over another, we sought to answer the question of which modality is preferred. We also assessed the impact of debriefing, and the frequency of participants asserting their leadership, as well as self-reported comfort and competence, and the ability to generate differential diagnoses when either a standardised patient (SP) or high-technology simulator (HTS) was used. One hundred and forty medical students participated in a simulation-based activity focusing on teamwork, task delegation, role clarity and effective communication. Two similar clinical scenarios were presented, and either an HTS or an SP was used. Following each scenario, participants were surveyed on the realism of the simulation and the patient, and also on their self-assessed comfort and competence. They were also asked to indicate which role they played, to list possible differential diagnoses for the case and, following the second scenario, which modality they preferred. The surveys indicated that 91 per cent (127) of students preferred the SP. The perceived realism of the simulation was higher for the second scenario than for the first. Scenarios with an SP were found to be significantly more realistic than the scenarios where the HTS was used. Comfort and competence scores were higher following the second scenario. No differences in the ability of participants to generate a list of differentials were found, and nearly twice as many participants reported taking the leadership role during their second simulation. We have found low and high technology to have similar effectiveness for achieving learning objectives and for the demonstration of skills; however, students clearly preferred the SPs. © Blackwell Publishing Ltd 2012.

A Possible Path from BCS through HTS to VHTS

NASA Astrophysics Data System (ADS)

Chu, C. W.

2010-03-01

Three years after celebrating the 50th anniversary of the BCS theory and the 20th anniversary of the discovery of high temperature superconductivity (HTS), it appears to be most fitting for us to contemplate the possibility of very high temperature superconductivity (VHTS). VHTS, preferably at room temperature, if achieved, could change the world both scientifically and technologically. Unfortunately, it has long been considered by some to belong to the domain of science fiction and to occur only ``at an astronomical distance and under an astronomical pressure.'' With the advent of liquid nitrogen superconductivity in 1987, the outlook has become much brighter. Currently, there appears to be no reason, either theoretical or experimental, why VHTS would be impossible, in spite of the 2006 prediction of the death of HTS by 2010-2015 through the so-called scientometric analysis of the publication record of the previous 20 years. The recent discovery of the new class of Fe-pnictide HTSs fuels more cautious optimism. Since its inception, BCS theory has provided the basic framework for the occurrence and understanding of superconductivity, but it has failed to show where and how to find superconductivity at a higher temperature. This may be attributed to the small energy scale of superconductivity in comparison with those of other excitations in the solids. After examining existing data, we believe that a holistic multidisciplinary enlightened empirical approach appears to be the most effective way to discover novel superconductors with higher transition temperatures. In this talk, I shall present several possible approaches toward VHTS that we are currently pursuing, after briefly summarizing what has happened in the long search for HTS and VHTS.

A Cryogenic Magnetostrictive Actuator Using a Persistent High Temperature Superconducting Magnet. Part 1; Concept and Design

NASA Technical Reports Server (NTRS)

Horner, Garnett; Bromberg, Leslie; Teter, J. P.

2000-01-01

Cryogenic magnetostrictive materials, such as rare earth zinc crystals, offer high strains and high forces with minimally applied magnetic fields, making the material ideally suited for deformable optics applications. For cryogenic temperature applications the use of superconducting magnets offer the possibility of a persistent mode of operation, i.e., the magnetostrictive material will maintain a strain field without power. High temperature superconductors (HTS) are attractive options if the temperature of operation is higher than 10 degrees Kelvin (K) and below 77 K. However, HTS wires have constraints that limit the minimum radius of winding, and even if good wires can be produced, the technology for joining superconducting wires does not exist. In this paper, the design and capabilities of a rare earth zinc magnetostrictive actuator using bulk HTS is described. Bulk superconductors can be fabricated in the sizes required with excellent superconducting properties. Equivalent permanent magnets, made with this inexpensive material, are persistent, do not require a persistent switch as in HTS wires, and can be made very small. These devices are charged using a technique which is similar to the one used for charging permanent magnets, e.g., by driving them into saturation. A small normal conducting coil can be used for charging or discharging. Because of the magnetic field capability of the superconductor material, a very small amount of superconducting magnet material is needed to actuate the rare earth zinc. In this paper, several designs of actuators using YBCO and BSCCO 2212 superconducting materials are presented. Designs that include magnetic shielding to prevent interaction between adjacent actuators will also be described. Preliminary experimental results and comparison with theory for BSCCO 2212 with a magnetostrictive element will be discussed.

Roebel cables from REBCO coated conductors: a one-century-old concept for the superconductivity of the future

NASA Astrophysics Data System (ADS)

Goldacker, Wilfried; Grilli, Francesco; Pardo, Enric; Kario, Anna; Schlachter, Sonja I.; Vojenčiak, Michal

2014-09-01

Energy applications employing high-temperature superconductors (HTS), such as motors/generators, transformers, transmission lines and fault current limiters, are usually operated in the alternate current (ac) regime. In order to be efficient, the HTS devices need to have a sufficiently low value of ac loss, in addition to the necessary current-carrying capacity. Most applications are operated with currents beyond the current capacity of single conductors and consequently require cabled conductor solutions with much higher current carrying capacity, from a few kA up to 20-30 kA for large hydro-generators. A century ago, in 1914, Ludwig Roebel invented a low-loss cable design for copper cables, which was successively named after him. The main idea behind Roebel cables is to separate the current in different strands and to provide a full transposition of the strands along the cable direction. Nowadays, these cables are commonly used in the stator of large generators. Based on the same design concept of their conventional material counterparts, HTS Roebel cables from REBCO coated conductors were first manufactured at the Karlsruhe Institute of Technology and have been successively developed in a number of varieties that provide all the required technical features such as fully transposed strands, high transport currents and low ac losses, yet retaining enough flexibility for a specific cable design. In the past few years a large number of scientific papers have been published on the concept, manufacturing and characterization of such cables. Therefore it is timely for a review of those results. The goal is to provide an overview and a succinct and easy-to-consult guide for users, developers, and manufacturers of this kind of HTS cable.

Time-Resolved Fluorescence Resonance Energy Transfer Assay for Discovery of Small-Molecule Inhibitors of Methyl-CpG Binding Domain Protein 2.

PubMed

Wyhs, Nicolas; Walker, David; Giovinazzo, Hugh; Yegnasubramanian, Srinivasan; Nelson, William G

2014-08-01

Methylated DNA binding proteins such as Methyl-CpG Binding Domain Protein 2 (MBD2) can transduce DNA methylation alterations into a repressive signal by recruiting transcriptional co-repressor complexes. Interfering with MBD2 could lead to reactivation of tumor suppressor genes and therefore represents an attractive strategy for epigenetic therapy. We developed and compared fluorescence polarization (FP) and time-resolved fluorescence resonance energy transfer (TR-FRET)-based high-throughput screening (HTS) assays to identify small-molecule inhibitors of the interaction between the methyl binding domain of MBD2 (MBD2-MBD) and methylated DNA. Although both assays performed well in 96-well format, the TR-FRET assay (Z' factor = 0.58) emerged as a superior screening strategy compared with FP (Z' factor = 0.08) when evaluated in an HTS 384-well plate format. Using TR-FRET, we screened the Sigma LOPAC library for MBD2-MBD inhibitors and identified four compounds that also validated in a dose-response series. This included two known DNA intercalators (mitoxantrone and idarubicin) among two other inhibitory compounds (NF449 and aurintricarboxylic acid). All four compounds also inhibited the binding of SP-1, a transcription factor with a GC-rich binding sequence, to a methylated oligonucleotide, demonstrating that the activity was nonspecific. Our results provide proof of principle for using TR-FRET-based HTS to identify small-molecule inhibitors of MBD2 and other DNA-protein interactions. © 2014 Society for Laboratory Automation and Screening.

Daily thanatomicrobiome changes in soil as an approach of postmortem interval estimation: An ecological perspective.

PubMed

Adserias-Garriga, Joe; Hernández, Marta; Quijada, Narciso M; Rodríguez Lázaro, David; Steadman, Dawnie; Garcia-Gil, Jesús

2017-09-01

Understanding human decomposition is critical for its use in postmortem interval (PMI) estimation, having a significant impact on forensic investigations. In recognition of the need to establish the scientific basis for PMI estimation, several studies on decomposition have been carried out in the last years. The aims of the present study were: (i) to identify soil microbiota communities involved in human decomposition through high-throughput sequencing (HTS) of DNA sequences from the different bacteria, (ii) to monitor quantitatively and qualitatively the decay of such signature species, and (iii) to describe succesional changes in bacterial populations from the early putrefaction state until skeletonization. Three donated individuals to the University of Tennessee FAC were studied. Soil samples around the body were taken from the placement of the donor until advanced decay/dry remains stage. Bacterial DNA extracts were obtained from the samples, HTS techniques were applied and bioinformatic data analysis was performed. The three cadavers showed similar overall successional changes. At the beginning of the decomposition process the soil microbiome consisted of diverse indigenous soil bacterial communities. As decomposition advanced, Firmicutes community abundance increased in the soil during the bloat stage. The growth curve of Firmicutes from human remains can be used to estimate time since death during Tennessee summer conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Diversity and dynamics of lactic acid bacteria in Atole agrio, a traditional maize-based fermented beverage from South-Eastern Mexico, analysed by high throughput sequencing and culturing.

PubMed

Pérez-Cataluña, Alba; Elizaquível, Patricia; Carrasco, Purificación; Espinosa, Judith; Reyes, Dolores; Wacher, Carmen; Aznar, Rosa

2018-03-01

The purpose of this work was to analyse the diversity and dynamics of lactic acid bacteria (LAB) throughout the fermentation process in Atole agrio, a traditional maize based food of Mexican origin. Samples of different fermentation times were analysed using culture-dependent and -independent approaches. Identification of LAB isolates revealed the presence of members of the genera Pediococcus, Weissella, Lactobacillus, Leuconostoc and Lactococcus, and the predominance of Pediococcus pentosaceus and Weissella confusa in liquid and solid batches, respectively. High-throughput sequencing (HTS) of the 16S rRNA gene confirmed the predominance of Lactobacillaceae and Leuconostocaceae at the beginning of the process. In liquid fermentation Acetobacteraceae dominate after 4 h as pH decreased. In contrast, Leuconostocaceae dominated the solid fermentation except at 12 h that were overgrown by Acetobacteraceae. Regarding LAB genera, Lactobacillus dominated the liquid fermentation except at 12 h when Weissella, Lactococcus and Streptococcus were the most abundant. In solid fermentation Weissella predominated all through the process. HTS determined that Lactobacillus plantarum and W. confusa dominated in the liquid and solid batches, respectively. Two oligotypes have been identified for L. plantarum and W. confusa populations, differing in a single nucleotide position each. Only one of the oligotypes was detected among the isolates obtained from each species, the biological significance of which remains unclear.

A Temperature-Stable Cryo-System for High-Temperature Superconducting MR In-Vivo Imaging

PubMed Central

Lin, In-Tsang; Yang, Hong-Chang; Chen, Jyh-Horng

2013-01-01

To perform a rat experiment using a high-temperature superconducting (HTS) surface resonator, a cryostat is essential to maintain the rat's temperature. In this work, a compact temperature-stable HTS cryo-system, keeping animal rectal temperature at 37.4°C for more than 3 hours, was successfully developed. With this HTS cryo-system, a 40-mm-diameter Bi2Sr2Ca2Cu3Ox (Bi-2223) surface resonator at 77 K was demonstrated in a 3-Tesla MRI system. The proton resonant frequency (PRF) method was employed to monitor the rat's temperature. Moreover, the capacity of MR thermometry in the HTS experiments was evaluated by correlating with data from independent fiber-optic sensor temperature measurements. The PRF thermal coefficient was derived as 0.03 rad/°C and the temperature-monitoring architecture can be implemented to upgrade the quality and safety in HTS experiments. The signal-to-noise ratio (SNR) of the HTS surface resonator at 77 K was higher than that of a professionally made copper surface resonator at 300 K, which has the same geometry, by a 3.79-fold SNR gain. Furthermore, the temperature-stable HTS cryo-system we developed can obtain stable SNR gain in every scan. A temperature-stable HTS cryo-system with an external air-blowing circulation system is demonstrated. PMID:23637936

Adapting High-Throughput Screening Methods and Assays for Biocontainment Laboratories

PubMed Central

Tigabu, Bersabeh; White, E. Lucile; Bostwick, Robert; Tower, Nichole; Bukreyev, Alexander; Rockx, Barry; LeDuc, James W.; Noah, James W.

2015-01-01

Abstract High-throughput screening (HTS) has been integrated into the drug discovery process, and multiple assay formats have been widely used in many different disease areas but with limited focus on infectious agents. In recent years, there has been an increase in the number of HTS campaigns using infectious wild-type pathogens rather than surrogates or biochemical pathogen-derived targets. Concurrently, enhanced emerging pathogen surveillance and increased human mobility have resulted in an increase in the emergence and dissemination of infectious human pathogens with serious public health, economic, and social implications at global levels. Adapting the HTS drug discovery process to biocontainment laboratories to develop new drugs for these previously uncharacterized and highly pathogenic agents is now feasible, but HTS at higher biosafety levels (BSL) presents a number of unique challenges. HTS has been conducted with multiple bacterial and viral pathogens at both BSL-2 and BSL-3, and pilot screens have recently been extended to BSL-4 environments for both Nipah and Ebola viruses. These recent successful efforts demonstrate that HTS can be safely conducted at the highest levels of biological containment. This review outlines the specific issues that must be considered in the execution of an HTS drug discovery program for high-containment pathogens. We present an overview of the requirements for HTS in high-level biocontainment laboratories. PMID:25710545

In vitro effects of 3% hypertonic saline and 20% mannitol on canine whole blood coagulation and platelet function.

PubMed

Adamik, Katja-Nicole; Butty, Emmanuelle; Howard, Judith

2015-09-24

Hyperosmolar therapy, using either mannitol or hypertonic saline (HTS), is considered the treatment of choice for intracranial hypertension. However, hyperosmolar agents may impair coagulation and platelet function, limiting their use in patients at risk for hemorrhage. Despite this, studies evaluating the effects of mannitol compared to other hyperosmolar agents in dogs are largely lacking. The aim of this study was to compare the in vitro effects on global hemostasis and platelet function of 20% mannitol and 3% HTS on canine blood. Citrated whole blood from 15 healthy dogs was diluted with 0.9% saline, 20% mannitol and 3% HTS in ratios of 1:16 and 1:8. Rotational thromboelastometry (ROTEM) was used to assess clotting time (CT), clot formation time (CFT) and maximal clot firmness (MCF) following extrinsic activation (Ex-tem) and after platelet inhibition (Fib-tem). A platelet function analyzer (PFA-100) was used to assess closure time (Ct(PFA)). No significant differences were observed between untreated whole blood and samples diluted with saline. Samples diluted with both mannitol and HTS were hypocoagulable compared to untreated whole blood samples. At a dilution of 1:16, no significant differences were found between any measured parameter in samples diluted with saline compared to mannitol or HTS. At a 1:8 dilution, Ct(PFA) was prolonged in samples diluted with mannitol and HTS compared to saline, and Ct(PFA) was prolonged more with mannitol than HTS. Ex-tem CT was increased at a 1:8 dilution with mannitol compared to HTS. Ex-tem CFT was prolonged at a 1:8 dilution with both agents compared to saline, and was prolonged more with mannitol than HTS. Ex-tem MCF was reduced at a 1:8 dilution with both agents compared to saline. Data in this study indicate that both mannitol and HTS affect canine platelet function and whole blood coagulation in vitro in a dose-dependent fashion. The most pronounced effects were observed after high dilutions with mannitol, which impaired platelet aggregation, clot formation time, clot strength, and fibrin formation significantly more than HTS. Further in vivo studies are necessary before recommendations can be made.

HTS thin films: Passive microwave components and systems integration issues

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

Miranda, F.A.; Chorey, C.M.; Bhasin, K.B.

1994-12-31

The excellent microwave properties of the High-Temperature-Superconductors (HTS) have been amply demonstrated in the laboratory by techniques such as resonant cavity, power transmission and microstrip resonator measurements. The low loss and high Q passive structures made possible with HTS, present attractive options for applications in commercial, military and space-based systems. However, to readily insert HTS into these systems improvement is needed in such areas as repeatability in the deposition and processing of the HTS films, metal-contact formation, wire bonding, and overall film endurance to fabrication and assembly procedures. In this paper we present data compiled in our lab which illustratemore » many of the problems associated with these issues. Much of this data were obtained in the production of a space qualified hybrid receiver-downconverter module for the Naval Research Laboratory`s High Temperature Superconductivity Space Experiment II (HTSSE-II). Examples of variations observed in starting films and finished circuits will be presented. It is shown that under identical processing the properties of the HTS films can degrade to varying extents. Finally, we present data on ohmic contacts and factors affecting their adhesion to HTS films, strength of wire bonds made to such contacts, and aging effects.« less

HTS thin films: Passive microwave components and systems integration issues

NASA Technical Reports Server (NTRS)

Miranda, F. A.; Chorey, C. M.; Bhasin, K. B.

1995-01-01

The excellent microwave properties of the High-Temperature-Superconductors (HTS) have been amply demonstrated in the laboratory by techniques such as resonant cavity, power transmission and microstrip resonator measurements. The low loss and high Q passive structures made possible with HTS, present attractive options for applications in commercial, military and spacebased systems. However, to readily insert HTS into these systems improvement is needed in such areas as repeatability in the deposition and processing of the HTS films, metal-contact formation, wire bonding, and overall film endurance to fabrication and assembly procedures. In this paper we present data compiled in our lab which illustrate many of the problems associated with these issues. Much of this data were obtained in the production of a space qualified hybrid receiver-downconverter module for the Naval Research Laboratory's High Temperature Superconductivity Space Experiment 2 (HTSSE-2). Examples of variations observed in starting films and finished circuits will be presented. It is shown that under identical processing the properties of the HTS films can degrade to varying extents. Finally, we present data on ohmic contacts and factors affecting their adhesion to HTS films, strength of wire bonds made to such contacts, and aging effects.

Simulation of chain of quenches on toroidal HTS-SMES taking account of thermal and electromagnetic characteristics

NASA Astrophysics Data System (ADS)

Oga, Y.; Noguchi, S.; Igarashi, H.

When a temperature rise occurs at a local area inside a coil of toroidal HTS-SMES by any reason, a temperature hotspot which results in a thermal runaway appears at the local area. Subsequently, after appearing the local normal zone in the HTS coil, the transport current of the HTS coil decrease since the resistance of HTS coil appears and the current partially flows into a parallel-connecting shunt resistance. However, if the transport current of the normal-transitioned HTS coil is hardly changed, the temperature on the hotspot would rise more and then the normal zone would spread rapidly. It may cause a serious accident due to high stored energy. Therefore, using the numerical simulation, we have investigated the behaviors of the coil current, the critical current, and the temperature in the superconducting element coils of HTS-SMES. Consequently, the temperature of the superconducting element coils rises up extremely when a large heat is generated at a certain area of one of them by any reason. Moreover, there is a possibility that the shunt resister hardly functions for protection since the coil is burned out due to high inductances and low resistance of the superconducting element coil.

Effect of a superconducting coil as a fault current limiter on current density distribution in BSCCO tape after an over-current pulse

NASA Astrophysics Data System (ADS)

Tallouli, M.; Shyshkin, O.; Yamaguchi, S.

2017-07-01

The development of power transmission lines based on long-length high temperature superconducting (HTS) tapes is complicated and technically challenging task. A serious problem for transmission line operation could become HTS power cable damage due to over-current pulse conditions. To avoid the cable damage in any urgent case the superconducting coil technology, i.e. superconductor fault current limiter (SFCL) is required. Comprehensive understanding of the current density characteristics of HTS tapes in both cases, either after pure over-current pulse or after over-current pulse limited by SFCL, is needed to restart or to continue the operation of the power transmission line. Moreover, current density distribution along and across the HTS tape provides us with the sufficient information about the quality of the tape performance in different current feeding regimes. In present paper we examine BSCCO HTS tape under two current feeding regimes. The first one is 100A feeding preceded by 900A over-current pulse. In this case none of tape protection was used. The second scenario is similar to the fist one but SFCL is used to limit an over-current value. For both scenarios after the pulse is gone and the current feeding is set up at 100A we scan magnetic field above the tape by means of Hall probe sensor. Then the feeding is turned of and the magnetic field scanning is repeated. Using the inverse problem numerical solver we calculate the corresponding direct and permanent current density distributions during the feeding and after switch off. It is demonstrated that in the absence of SFCL the current distribution is highly peaked at the tape center. At the same time the current distribution in the experiment with SFCL is similar to that observed under normal current feeding condition. The current peaking in the first case is explained by the effect of an opposite electric field induced at the tape edges during the overcurrent pulse decay, and by degradation of superconductivity at the edges due to penetration of magnetic field in superconducting core during the pulse.

Development of a HTS transceiver sub-system for 3G mobile communication TD-SCDMA base station

NASA Astrophysics Data System (ADS)

Zhang, Xueqiang; He, Xiaofeng; Wang, Yuehui; Duan, Tao; Wang, Guizhen; Zhang, Yan; Li, Chunguang; Zhang, Qiang; Li, Hong; He, Yusheng

2010-02-01

A prototype of a high temperature superconducting (HTS) transceiver sub-system for applications in a TD-SCDMA, one of the third generation (3G) communication standards, base station has been developed. Both the HTS sub-system and the conventional counterpart have been implemented into a TD-SCDMA commercial communication network and comparison test studies were carried out. The measured results showed that the HTS sub-system could remarkably improve the RF performance of both transmitting and receiving chains.

Magnolol attenuates the lung injury in hypertonic saline treatment from mesenteric ischemia reperfusion through diminishing iNOS.

PubMed

Shih, Hsin-Chin; Huang, Mu-Shun; Lee, Chen-Hsen

2012-06-15

Hypertonic saline (HTS) administration can decrease the inflammation following ischemia reperfusion. Magnolol is a potent antioxidant. The present study investigated whether combined treatment of magnolol and HTS could provide further protection in mesenteric ischemia reperfusion injury. Male C3H/HeOuJ mice were randomly segregated into the following groups: sham-operated (sham), vehicle treatment and mesenteric ischemia reperfusion (MSIR) (vehicle-treated), magnolol treatment and MSIR (magnolol-treated), HTS treatment and MSIR (HTS-treated), as well as co-administration of magnolol plus HTS and MSIR (combined-treated). In MSIR, mice were subjected to mesenteric ischemia for 60 min followed by reperfusion for 30 min. Lung injury was evaluated by lung edema (water ratio) and myeloperoxide (MPO) activity; RNA expression of inducible nitric oxide synthetase (iNOS), TNF-α, and IL-6 were assayed by real time RT-PCR. The formation of peroxynitrite in plasma was assayed by the peroxynitrite-dependent oxidation of dihydrorhodamine 123 (DHR 123) to rhodamine. Compared with those in the sham-treated group, lung edema and MPO activity, expressions of iNOS, TNF-α and IL-6, and plasma peroxynitrite were significantly increased in the vehicle-treated group. Significant attenuations of these parameters were found in the magnolol-treated or HTS-treated animals. Combined treatment of magnolol and HTS further suppressed the lung edema, iNOS, and TNF-α expressions, and plasma peroxynitrite, compared with the results of a single treatment of magnolol or HTS. Compared with single-agent use, co-administration of magnolol and HTS further decreases iNOS expression and plasma peroxynitrite as well as the degree of lung injury from MISR. These results may provide another treatment measure for post-injury immunomodulation. Copyright © 2012 Elsevier Inc. All rights reserved.

Complication Rates of 3% Hypertonic Saline Infusion Through Peripheral Intravenous Access.

PubMed

Perez, Claudia Andira; Figueroa, Stephen A

2017-06-01

Hyperosmolar therapy with hypertonic saline (HTS) is a cornerstone in the management of intracranial hypertension and hyponatremia in the neurological intensive care unit. Theoretical safety concerns remain for infiltration, thrombophlebitis, tissue ischemia, and venous thrombosis associated with continuous 3% HTS administered via peripheral intravenous (pIV) catheters. It is common practice at many institutions to allow only central venous catheter infusion of 3% HTS. Hospital policy was changed to allow the administration of 3% HTS via 16- to 20-gauge pIVs to a maximum infusion rate of 50 mL/h in patients without central venous access. We prospectively monitored patients who received peripheral 3% HTS as part of a quality improvement project. We documented gauge, location, maximum infusion rate, and total hours of administration. Patients were assessed for infiltration, erythema, swelling, phlebitis, thrombosis, and line infection. There were 28 subjects across 34 peripheral lines monitored. Overall, subjects received 3% HTS for a duration between 1 and 124 hours with infusion rates of 30 to 50 mL/h. The rate of complications observed was 10.7% among all subjects. Documented complications included infiltration (n = 2), with an incidence of 6%, and thrombophlebitis (n = 1), with an incidence of 3%. There has been a long concern among healthcare providers, including nursing staff, in regard to pIV administration of prolonged 3% HTS infusion therapy. Our study indicates that peripheral administration of 3% HTS carries a low risk of minor, nonlimb, or life-threatening complications. Although central venous infusion may reduce the risk of these minor complications, it may increase the risk of more serious complications such as large vessel thrombosis, bloodstream infection, pneumothorax, and arterial injury. The concern regarding the risks of pIV administration of 3% HTS may be overstated and unfounded.

Magnetic fields end-face effect investigation of HTS bulk over PMG with 3D-modeling numerical method

NASA Astrophysics Data System (ADS)

Qin, Yujie; Lu, Yiyun

2015-09-01

In this paper, the magnetic fields end-face effect of high temperature superconducting (HTS) bulk over a permanent magnetic guideway (PMG) is researched with 3D-modeling numerical method. The electromagnetic behavior of the bulk is simulated using finite element method (FEM). The framework is formulated by the magnetic field vector method (H-method). A superconducting levitation system composed of one rectangular HTS bulk and one infinite long PMG is successfully investigated using the proposed method. The simulation results show that for finite geometrical HTS bulk, even the applied magnetic field is only distributed in x-y plane, the magnetic field component Hz which is along the z-axis can be observed interior the HTS bulk.

Critical current studies of a HTS rectangular coil

NASA Astrophysics Data System (ADS)

Zhong, Z.; Chudy, M.; Ruiz, H. S.; Zhang, X.; Coombs, T.

2017-05-01

Nowadays, superconducting high field magnets are used in numerous applications due to their superior properties. High temperature superconductors (HTS) are usually used for production of circular pancake or racetrack coils. However different geometries of HTS coils might be required for some specific applications. In this study, the HTS coil wound on a rectangular frame was fully characterized in homogeneous DC background field. The study contains measurements of critical current angular dependencies. The critical current of the entire coil and two selected strands under different magnitudes and orientations of external magnetic fields are measured. The critical regions of the coil in different angular regimes are determined. This study brings better understanding of the in- field performance of HTS coils wound on frames with right-angles.

High temperature superconducting Maglev equipment on vehicle

NASA Astrophysics Data System (ADS)

Wang, S. Y.; Wang, J. S.; Ren, Z. Y.; Zhu, M.; Jiang, H.; Wang, X. R.; Shen, X. M.; Song, H. H.

2003-04-01

Onboard high temperature superconducting (HTS) Maglev equipment is a heart part of a HTS Maglev vehicle, which is composed of YBaCuO bulks and rectangle-shape liquid nitrogen vessel and used successfully in the first manned HTS Maglev test vehicle. Arrangement of YBaCuO bulks in liquid nitrogen vessel, structure of the vessel, levitation forces of a single vessel and two vessels, and total levitation force are reported. The first manned HTS Maglev test vehicle in the world has operated well more than one year after it was born on Dec. 31, 2000, and more than 23,000 passengers have taken the vehicle till now. Well operation of more than one year proves the reliability of the onboard HTS Maglev equipment.

Dynamic response characteristics of the high-temperature superconducting maglev system under lateral eccentric distance

NASA Astrophysics Data System (ADS)

Wang, Bo; Zheng, Jun; Si, Shuaishuai; Qian, Nan; Li, Haitao; Li, Jipeng; Deng, Zigang

2016-07-01

Off-centre operation of high-temperature superconducting (HTS) maglev systems caused by inevitable conditions such as the misregistration of vehicle, crosswind and curve negotiation, may change the distribution of the trapped flux in the HTS bulks and the magnetic interaction between HTS bulks and the PMG. It impacts on the performance of HTS maglev, and more seriously makes the maglev vehicle overturned. Therefore, understanding the performance of the HTS maglev in off-center operation is very important. In this paper, the dynamic response characteristics of a cryostat with twenty-four onboard YBaCuO superconductor bulks were experimentally investigated at different eccentric distances under loads before the initial FC process. Parameters such as vibration accelerations, displacement, natural frequency and dynamic stiffness were acquired and analyzed via the B&K vibration analyzer and laser displacement sensors. Results suggest that the natural frequency and dynamic stiffness of the maglev vehicle would be obviously reduced with the eccentric distance, posing negative effects on the stability of HTS maglev.

Parametric Study of HTS Coil Quench Protection Strategies

NASA Astrophysics Data System (ADS)

Seibert, Joseph; Zarnstorff, Michael; Zhai, Yuhu

2016-10-01

Next generation fusion devices require high magnetic fields to adequately contain burning plasmas. Use of high temperature superconducting (HTS) coils to generate these magnetic fields would lower energy cost of operation as well as increase stability of the superconducting state compared to low temperature superconducting coils. However, use of HTS coils requires developing quench protection strategies to prevent damage to the coils. One technique involves the utilization of copper discs and other conductors mutually coupled to the HTS coil to quickly extract the current from the coil. Another technique allows conduction between HTS turns to reduce the current in the coil during quench. This project describes a parametric study of the HTS coil and resistive-conductor setup in order to determine limiting cases of the geometry in an attempt to optimize current extraction and coil protection during quench scenarios. This work was supported in part by the U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Science Undergraduate Laboratory Internship (SULI) program.

Development of REBCO HTS Magnet of Magnetic Bearing for Large Capacity Flywheel Energy Storage System

NASA Astrophysics Data System (ADS)

Mukoyama, Shinichi; Matsuoka, Taro; Furukawa, Makoto; Nakao, Kengo; Nagashima, Ken; Ogata, Masafumi; Yamashita, Tomohisa; Hasegawa, Hitoshi; Yoshizawa, Kazuhiro; Arai, Yuuki; Miyazaki, Kazuki; Horiuchi, Shinichi; Maeda, Tadakazu; Shimizu, Hideki

A flywheel energy storage system (FESS) is a promising electrical storage system that moderates fluctuation of electrical power from renewable energy sources. The FESS can charge and discharge the surplus electrical power repetitively with the rotating energy. Particularly, the FESS that utilizes a high temperature superconducting magnetic bearing (HTS bearing) is lower loss than conventional FESS that has mechanical bearing, and has property of longer life operation than secondary batteries. The HTS bearing consists of a HTS bulk and double-pancake coils used 2nd generation REBCO wires. In the development, the HTS double-pancake coils were fabricated and were provided for a levitation test to verify the possibility of the HTS bearing. We successfully confirmed the magnetic field was achieved to design value, and levitation force in the configuration of one YBCO bulk and five double pan-cake coils was obtained to a satisfactory force of 39.2 kN (4 tons).

Vibration measurements and analyses for a magnet superconductor levitated system

NASA Astrophysics Data System (ADS)

Wen, Zheng; Liu, Yu; Yang, Wenjiang; Qiu, Ming

2007-12-01

Magnetic levitation technology, having the characteristics of low cost and high quality, has been considered a preferable option for the next generation of launcher systems. A world-wide research design on the conceptual level has been carried out on the highly reusable space transportation systems by applying magnetic levitation to the launch assistance. Recently, a research plan has been implemented in our laboratory by constructing a scale-model suspension system with high temperature superconductor (HTS henceforth) bulks over a 7 m Nd-Fe-B permanent-magnet (PM henceforth) track for the launch assistance. An experimental platform was built to investigate the dynamic responses of the PM-HTS interaction at different field-cooled positions. The critical frequencies and amplitudes which lead to the instability of levitation drift were investigated. The stiffness and the vibration damping were also discussed at the zero-field-cooled position.

La0.7Sr0.3MnO3: A single, conductive-oxide buffer layer for the development of YBa2Cu3O7-δ coated conductors

NASA Astrophysics Data System (ADS)

Aytug, T.; Paranthaman, M.; Kang, B. W.; Sathyamurthy, S.; Goyal, A.; Christen, D. K.

2001-10-01

Coated conductor applications in power technologies require stabilization of the high-temperature superconducting (HTS) layers against thermal runaway. Conductive La0.7Sr0.3MnO3 (LSMO) has been epitaxially grown on biaxially textured Ni substrates as a single buffer layer. The subsequent epitaxial growth of YBa2Cu3O7-δ (YBCO) coatings by pulsed laser deposition yielded self-field critical current densities (Jc) of 0.5×106A/cm2 at 77 K, and provided good electrical connectivity over the entire structure (HTS+conductive-buffer+metal substrate). Property characterizations of YBCO/LSMO/Ni architecture revealed excellent crystallographic and morphological properties. These results have demonstrated that LSMO, used as a single, conductive buffer layer, may offer potential for use in fully stabilized YBCO coated conductors.

2G HTS wires made on 30 μm thick Hastelloy substrate

NASA Astrophysics Data System (ADS)

Sundaram, A.; Zhang, Y.; Knoll, A. R.; Abraimov, D.; Brownsey, P.; Kasahara, M.; Carota, G. M.; Nakasaki, R.; Cameron, J. B.; Schwab, G.; Hope, L. V.; Schmidt, R. M.; Kuraseko, H.; Fukushima, T.; Hazelton, D. W.

2016-10-01

REBCO (RE = rare earth) based high temperature superconducting (HTS) wires are now being utilized for the development of electric and electromagnetic devices for various industrial, scientific and medical applications. In the last several years, the increasing efforts in using the so-called second generation (2G) HTS wires for some of the applications require a further increase in their engineering current density (J e). The applications are those typically related to high magnetic fields where the higher J e of a REBCO wire, in addition to its higher irreversibility fields and higher mechanical strength, is already a major advantage over other superconducting wires. An effective way to increase the J e is to decrease the total thickness of a wire, for which using a thinner substrate becomes an obvious and attractive approach. By using our IBAD-MOCVD (ion beam assisted deposition-metal organic chemical vapor deposition) technology we have successfully made 2G HTS wires using a Hastelloy® C276 substrate that is only 30 μm in thickness. By using this thinner substrate instead of the typical 50 μm thick substrate and with a same critical current (I c), the J e of a wire can be increased by 30% to 45% depending on the copper stabilizer thickness. In this paper, we report the fabrication and characterization of the 2G HTS wires made on the 30 μm thick Hastelloy® C276 substrate. It was shown that with the optimization in the processing protocol, the surface of the thinner Hastelloy® C276 substrate can be readily electropolished to the quality needed for the deposition of the buffer stack. Same in the architecture as that on the standard 50 μm thick substrate, the buffer stack made on the 30 μm thick substrate showed an in-plane texture with a Δϕ of around 6.7° in the LaMnO3 cap layer. Low-temperature in-field transport measurement results suggest that the wires on the thinner substrate had achieved equivalent superconducting performance, most importantly the I c, as those on the 50 μm thick substrate. It is expected the 2G HTS wires made on the 30 μm thick Hastelloy® C276 substrate, the thinnest and with the highest J e to date, will greatly benefit such applications as high field magnets and high current cables.

Reflective HTS switch

DOEpatents

Martens, Jon S.; Hietala, Vincent M.; Hohenwarter, Gert K. G.

1994-01-01

A HTS switch includes a HTS conductor for providing a superconducting path for an electrical signal and an serpentine wire actuator for controllably heating a portion of the conductor sufficiently to cause that portion to have normal, and not superconducting, resistivity. Mass of the portion is reduced to decrease switching time.

Establishment of a novel whole animal HTS technology platform for melioidosis drug discovery.

PubMed

Lakshmanan, Umayal; Yap, Amelia; Fulwood, Justina; Yichun, Li; Hoon, Sim Siew; Lim, Jolander; Ting, Audrey; Sem, Xiao Hui; Kreisberg, Jason F; Tan, Patrick; Tan, Gladys; Flotow, Horst

2014-01-01

Melioidosis is a serious emerging endemic infectious disease caused by Burkholderia pseudomallei, a gram-negative pathogen. Septicemic melioidosis has a mortality rate of 50% even with treatment. Like other gram-negative bacteria, B. pseudomallei is resistant to a number of antibiotics and multi-drug resistant B. pseudomallei is beginning to be encountered in hospitals. There is a clear medical need to develop new treatment options to manage this disease. We used Burkholderia thailandensis (a BSL-2 class organism) to infect Caenorhabditis elegans and set up a surrogate whole animal infection model of melioidosis that we could run in a 384 microtitre plate and establish a whole animal HTS assay. We have optimized and validated this assay in a fluorescence-based format that can be run on our automated screening platforms. This assay has now been used to screen over 300,000 compounds from our small molecule library and we are in the process of characterizing the hits obtained and select compounds for further studies. We have thus established a biologically relevant assay technology platform to screen for antibacterial compounds and used this platform to identify new compounds that may find application in treating melioidosis infections.

Understanding microalgal species composition and contributions in Antarctic glacial melt water through rbcL high throughput sequencing

NASA Astrophysics Data System (ADS)

Barretto, K. M.; Kalmbach, A. J.; de la Torre, J. R.; Falcón, L. I.; Carpenter, E. J.

2016-02-01

The McMurdo Dry Valleys (MDV) in Antarctica present unique research opportunities, both because of the understudied biogeochemical impact of their microbial communities, and their sensitivity to climate change. Despite harsh desiccation, pH, and salinity stress, summer glacial melt water supports life in the MDV in the form of algal mats. These mat communities are complex in structure, with a network of dominant cyanobacteria interspersed with heterotrophic diazotrophs, smaller photoautotrophs, and thick extracellular polymeric substances. Due to their complexity, standard microscopy yields a limited understanding of community assemblages. Our previous high throughput sequencing (HTS) approaches focusing on 16S rRNA have profiled communities with understudied photosynthetic phyla such as Acidobacteria, Gemmatimonadetes, and Chloroflexi. To characterize these phototrophic communities, we are interested in (1) understanding their temporal dynamics and how the dominant cyanobacterial species influence community composition, (2) modeling how pH, nutrients, soil wetness, and temperature act as multivariate drivers of community composition, and (3) establishing a pipeline for HTS of the rbcL gene - which encodes the large subunit of the ubiquitous photosynthetic protein RuBisCO. Our initial screening of community DNA from MDV algal mats has shown the presence of Form IA, IB, and IC cbbL (an rbcL ortholog), and Form ID rbcL - indicating a relatively high degree of photoautotrophic diversity. Soil wetness drives anoxic conditions and we see that it shifts overall microbial composition - we expect photoautotrophs to respond similarly. We also expect photoautotrophic assemblages to shift with pH and soil nutrients. Our deep sequencing efforts suggest an inconsistency between indexing primers and algal DNA that could underestimate cyanobacterial and overestimate eukaryotic abundance. Resolving these issues with new approaches will allow us to more fully understand the dynamics of the MDV.

Who's for dinner? High-throughput sequencing reveals bat dietary differentiation in a biodiversity hotspot where prey taxonomy is largely undescribed.

PubMed

Burgar, Joanna M; Murray, Daithi C; Craig, Michael D; Haile, James; Houston, Jayne; Stokes, Vicki; Bunce, Michael

2014-08-01

Effective management and conservation of biodiversity requires understanding of predator-prey relationships to ensure the continued existence of both predator and prey populations. Gathering dietary data from predatory species, such as insectivorous bats, often presents logistical challenges, further exacerbated in biodiversity hot spots because prey items are highly speciose, yet their taxonomy is largely undescribed. We used high-throughput sequencing (HTS) and bioinformatic analyses to phylogenetically group DNA sequences into molecular operational taxonomic units (MOTUs) to examine predator-prey dynamics of three sympatric insectivorous bat species in the biodiversity hotspot of south-western Australia. We could only assign between 4% and 20% of MOTUs to known genera or species, depending on the method used, underscoring the importance of examining dietary diversity irrespective of taxonomic knowledge in areas lacking a comprehensive genetic reference database. MOTU analysis confirmed that resource partitioning occurred, with dietary divergence positively related to the ecomorphological divergence of the three bat species. We predicted that bat species' diets would converge during times of high energetic requirements, that is, the maternity season for females and the mating season for males. There was an interactive effect of season on female, but not male, bat species' diets, although small sample sizes may have limited our findings. Contrary to our predictions, females of two ecomorphologically similar species showed dietary convergence during the mating season rather than the maternity season. HTS-based approaches can help elucidate complex predator-prey relationships in highly speciose regions, which should facilitate the conservation of biodiversity in genetically uncharacterized areas, such as biodiversity hotspots. © 2013 John Wiley & Sons Ltd.

Reflective HTS switch

DOEpatents

Martens, J.S.; Hietala, V.M.; Hohenwarter, G.K.G.

1994-09-27

A HTS (High Temperature Superconductor) switch includes a HTS conductor for providing a superconducting path for an electrical signal and an serpentine wire actuator for controllably heating a portion of the conductor sufficiently to cause that portion to have normal, and not superconducting, resistivity. Mass of the portion is reduced to decrease switching time. 6 figs.

Efficient growth of HTS films with volatile elements

DOEpatents

Siegal, M.P.; Overmyer, D.L.; Dominguez, F.

1998-12-22

A system is disclosed for applying a volatile element-HTS layer, such as Tl-HTS, to a substrate in a multiple zone furnace, said method includes heating at higher temperature, in one zone of the furnace, a substrate and adjacent first source of Tl-HTS material, to sublimate Tl-oxide from the source to the substrate; and heating at lower temperature, in a separate zone of the furnace, a second source of Tl-oxide to replenish the first source of Tl-oxide from the second source. 3 figs.

Heat loss analysis-based design of a 12 MW wind power generator module having an HTS flux pump exciter

NASA Astrophysics Data System (ADS)

Sung, Hae-Jin; Go, Byeong-Soo; Jiang, Zhenan; Park, Minwon; Yu, In-Keun

2016-11-01

The development of an effective high-temperature superconducting (HTS) generator is currently a research focus; however, the reduction of heat loss of a large-scale HTS generator is a challenge. This study deals with a heat loss analysis-based design of a 12 MW wind power generator module having an HTS flux pump exciter. The generator module consists of an HTS rotor of the generator and an HTS flux pump exciter. The specifications of the module were described, and the detailed configuration of the module was illustrated. For the heat loss analysis of the module, the excitation loss of the flux pump exciter, eddy current loss of all of the structures in the module, radiation loss, and conduction loss of an HTS coil supporter were assessed using a 3D finite elements method program. In the case of the conduction loss, different types of the supporters were compared to find out the supporter of the lowest conduction loss in the module. The heat loss analysis results of the module were reflected in the design of the generator module and discussed in detail. The results will be applied to the design of large-scale superconducting generators for wind turbines including a cooling system.

Application of Titration-Based Screening for the Rapid Pilot Testing of High-Throughput Assays.

PubMed

Zhang, Ji-Hu; Kang, Zhao B; Ardayfio, Ophelia; Ho, Pei-i; Smith, Thomas; Wallace, Iain; Bowes, Scott; Hill, W Adam; Auld, Douglas S

2014-06-01

Pilot testing of an assay intended for high-throughput screening (HTS) with small compound sets is a necessary but often time-consuming step in the validation of an assay protocol. When the initial testing concentration is less than optimal, this can involve iterative testing at different concentrations to further evaluate the pilot outcome, which can be even more time-consuming. Quantitative HTS (qHTS) enables flexible and rapid collection of assay performance statistics, hits at different concentrations, and concentration-response curves in a single experiment. Here we describe the qHTS process for pilot testing in which eight-point concentration-response curves are produced using an interplate asymmetric dilution protocol in which the first four concentrations are used to represent the range of typical HTS screening concentrations and the last four concentrations are added for robust curve fitting to determine potency/efficacy values. We also describe how these data can be analyzed to predict the frequency of false-positives, false-negatives, hit rates, and confirmation rates for the HTS process as a function of screening concentration. By taking into account the compound pharmacology, this pilot-testing paradigm enables rapid assessment of the assay performance and choosing the optimal concentration for the large-scale HTS in one experiment. © 2013 Society for Laboratory Automation and Screening.

Analyzing older users' home telehealth services acceptance behavior-applying an Extended UTAUT model.

PubMed

Cimperman, Miha; Makovec Brenčič, Maja; Trkman, Peter

2016-06-01

Although telehealth offers an improved approach to providing healthcare services, its adoption by end users remains slow. With an older population as the main target, these traditionally conservative users pose a big challenge to the successful implementation of innovative telehealth services. The objective of this study was to develop and empirically test a model for predicting the factors affecting older users' acceptance of Home Telehealth Services (HTS). A survey instrument was administered to 400 participants aged 50 years and above from both rural and urban environments in Slovenia. Structural equation modeling was applied to analyze the causal effect of seven hypothesized predicting factors. HTS were introduced as a bundle of functionalities, representing future services that currently do not exist. This enabled users' perceptions to be measured on the conceptual level, rather than attitudes to a specific technical solution. Six relevant predictors were confirmed in older users' HTS acceptance behavior, with Performance Expectancy (r=0.30), Effort Expectancy (r=0.49), Facilitating Conditions (r=0.12), and Perceived Security (r=0.16) having a direct impact on behavioral intention to use HTS. In addition, Computer Anxiety is positioned as an antecedent of Effort Expectancy with a strong negative influence (r=-0.61), and Doctor's Opinion influence showed a strong impact on Performance Expectancy (r=0.31). The results also indicate Social Influence as an irrelevant predictor of acceptance behavior. The model of six predictors yielded 77% of the total variance explained in the final measured Behavioral Intention to Use HTS by older adults. The level at which HTS are perceived as easy to use and manage is the leading acceptance predictor in older users' HTS acceptance. Together with Perceived Usefulness and Perceived Security, these three factors represent the key influence on older people's HTS acceptance behavior. When promoting HTS, interventions should focus to portray it as secure. Marketing interventions should focus also on promoting HTS among health professionals, using them as social agents to frame the services as useful and beneficial. The important role of computer anxiety may result in a need to use different equipment such as a tablet computer to access HTS. Finally, this paper introduces important methodological guidelines for measuring perceptions on a conceptual level of future services that currently do not exist. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Cost analysis of two community-based HIV testing service modalities led by a Non-Governmental Organization in Cape Town, South Africa.

PubMed

Meehan, Sue-Ann; Beyers, Nulda; Burger, Ronelle

2017-12-02

In South Africa, the financing and sustainability of HIV services is a priority. Community-based HIV testing services (CB-HTS) play a vital role in diagnosis and linkage to HIV care for those least likely to utilise government health services. With insufficient estimates of the costs associated with CB-HTS provided by NGOs in South Africa, this cost analysis explored the cost to implement and provide services at two NGO-led CB-HTS modalities and calculated the costs associated with realizing key HIV outputs for each CB-HTS modality. The study took place in a peri-urban area where CB-HTS were provided from a stand-alone centre and mobile service. Using a service provider (NGO) perspective, all inputs were allocated by HTS modality with shared costs apportioned according to client volume or personnel time. We calculated the total cost of each HTS modality and the cost categories (personnel, capital and recurring goods/services) across each HTS modality. Costs were divided into seven pre-determined project components, used to examine cost drivers. HIV outputs were analysed for each HTS modality and the mean cost for each HIV output was calculated per HTS modality. The annual cost of the stand-alone and mobile modalities was $96,616 and $77,764 respectively, with personnel costs accounting for 54% of the total costs at the stand-alone. For project components, overheads and service provision made up the majority of the costs. The mean cost per person tested at stand-alone ($51) was higher than at the mobile ($25). Linkage to care cost at the stand-alone ($1039) was lower than the mobile ($2102). This study provides insight into the cost of an NGO led CB-HTS project providing HIV testing and linkage to care through two CB-HIV testing modalities. The study highlights; (1) the importance of including all applicable costs (including overheads) to ensure an accurate cost estimate that is representative of the full service implementation cost, (2) the direct link between test uptake and mean cost per person tested, and (3) the need for effective linkage to care strategies to increase linkage and thereby reduce the mean cost per person linked to HIV care.

Modelling ac ripple currents in HTS coated conductors

NASA Astrophysics Data System (ADS)

Xu, Zhihan; Grilli, Francesco

2015-10-01

Dc transmission using high temperature superconducting (HTS) coated conductors (CCs) offers a promising solution to the globally growing demand for effective, reliable and economic transmission of green energy up to the gigawatt level over very long distances. The credible estimation of the losses and thereby the heat dissipation involved, where ac ripples (introduced in rectification/ac-dc conversion) are viewed as a potential source of notable contribution, is highly essential for the rational design of practical HTS dc transmission cables and corresponding cryogenic systems to fulfil this demand. Here we report a targeted modelling study into the ac losses in a HTS CC subject to dc and ac ripple currents simultaneously, by solving Maxwell’s equations using the finite element method (FEM) in the commercial software package COMSOL. It is observed that the instantaneous loss exhibits only one peak per cycle in the HTS CC subject to sinusoidal ripples, given that the amplitude of the ac ripples is smaller than approximately 20% of that of the dc current. This is a distinct contrast to the usual observation of two peaks per cycle in a HTS CC subject to ac currents only. The unique mechanism is also revealed, which is directly associated with the finding that, around any local minima of the applied ac ripples, the critical state of -J c is never reached at the edges of the HTS CC, as it should be according to the Bean model. When running further into the longer term, it is discovered that the ac ripple loss of the HTS CC in full-wave rectification decays monotonically, at a speed which is found to be insensitive to the frequency of the applied ripples within our targeted situations, to a relatively low level of approximately 1.38 × 10-4 W m-1 in around 1.7 s. Comparison between this level and other typical loss contributions in a HTS dc cable implies that ac ripple currents in HTS CCs should only be considered as a minor source of dissipation in superconducting dc transmission.

web cellHTS2: a web-application for the analysis of high-throughput screening data.

PubMed

Pelz, Oliver; Gilsdorf, Moritz; Boutros, Michael

2010-04-12

The analysis of high-throughput screening data sets is an expanding field in bioinformatics. High-throughput screens by RNAi generate large primary data sets which need to be analyzed and annotated to identify relevant phenotypic hits. Large-scale RNAi screens are frequently used to identify novel factors that influence a broad range of cellular processes, including signaling pathway activity, cell proliferation, and host cell infection. Here, we present a web-based application utility for the end-to-end analysis of large cell-based screening experiments by cellHTS2. The software guides the user through the configuration steps that are required for the analysis of single or multi-channel experiments. The web-application provides options for various standardization and normalization methods, annotation of data sets and a comprehensive HTML report of the screening data analysis, including a ranked hit list. Sessions can be saved and restored for later re-analysis. The web frontend for the cellHTS2 R/Bioconductor package interacts with it through an R-server implementation that enables highly parallel analysis of screening data sets. web cellHTS2 further provides a file import and configuration module for common file formats. The implemented web-application facilitates the analysis of high-throughput data sets and provides a user-friendly interface. web cellHTS2 is accessible online at http://web-cellHTS2.dkfz.de. A standalone version as a virtual appliance and source code for platforms supporting Java 1.5.0 can be downloaded from the web cellHTS2 page. web cellHTS2 is freely distributed under GPL.

A predictive data-driven framework for endocrine prioritization: a triazole fungicide case study.

PubMed

Paul Friedman, Katie; Papineni, Sabitha; Marty, M Sue; Yi, Kun Don; Goetz, Amber K; Rasoulpour, Reza J; Kwiatkowski, Pat; Wolf, Douglas C; Blacker, Ann M; Peffer, Richard C

2016-10-01

The US Environmental Protection Agency Endocrine Disruptor Screening Program (EDSP) is a tiered screening approach to determine the potential for a chemical to interact with estrogen, androgen, or thyroid hormone systems and/or perturb steroidogenesis. Use of high-throughput screening (HTS) to predict hazard and exposure is shifting the EDSP approach to (1) prioritization of chemicals for further screening; and (2) targeted use of EDSP Tier 1 assays to inform specific data needs. In this work, toxicology data for three triazole fungicides (triadimefon, propiconazole, and myclobutanil) were evaluated, including HTS results, EDSP Tier 1 screening (and other scientifically relevant information), and EPA guideline mammalian toxicology study data. The endocrine-related bioactivity predictions from HTS and information that satisfied the EDSP Tier 1 requirements were qualitatively concordant. Current limitations in the available HTS battery for thyroid and steroidogenesis pathways were mitigated by inclusion of guideline toxicology studies in this analysis. Similar margins (3-5 orders of magnitude) were observed between HTS-predicted human bioactivity and exposure values and between in vivo mammalian bioactivity and EPA chronic human exposure estimates for these products' registered uses. Combined HTS hazard and human exposure predictions suggest low priority for higher-tiered endocrine testing of these triazoles. Comparison with the mammalian toxicology database indicated that this HTS-based prioritization would have been protective for any potential in vivo effects that form the basis of current risk assessment for these chemicals. This example demonstrates an effective, human health protective roadmap for EDSP evaluation of pesticide active ingredients via prioritization using HTS and guideline toxicology information.

A predictive data-driven framework for endocrine prioritization: a triazole fungicide case study

PubMed Central

Paul Friedman, Katie; Papineni, Sabitha; Marty, M. Sue; Yi, Kun Don; Goetz, Amber K.; Rasoulpour, Reza J.; Kwiatkowski, Pat; Wolf, Douglas C.; Blacker, Ann M.; Peffer, Richard C.

2016-01-01

Abstract The US Environmental Protection Agency Endocrine Disruptor Screening Program (EDSP) is a tiered screening approach to determine the potential for a chemical to interact with estrogen, androgen, or thyroid hormone systems and/or perturb steroidogenesis. Use of high-throughput screening (HTS) to predict hazard and exposure is shifting the EDSP approach to (1) prioritization of chemicals for further screening; and (2) targeted use of EDSP Tier 1 assays to inform specific data needs. In this work, toxicology data for three triazole fungicides (triadimefon, propiconazole, and myclobutanil) were evaluated, including HTS results, EDSP Tier 1 screening (and other scientifically relevant information), and EPA guideline mammalian toxicology study data. The endocrine-related bioactivity predictions from HTS and information that satisfied the EDSP Tier 1 requirements were qualitatively concordant. Current limitations in the available HTS battery for thyroid and steroidogenesis pathways were mitigated by inclusion of guideline toxicology studies in this analysis. Similar margins (3–5 orders of magnitude) were observed between HTS-predicted human bioactivity and exposure values and between in vivo mammalian bioactivity and EPA chronic human exposure estimates for these products’ registered uses. Combined HTS hazard and human exposure predictions suggest low priority for higher-tiered endocrine testing of these triazoles. Comparison with the mammalian toxicology database indicated that this HTS-based prioritization would have been protective for any potential in vivo effects that form the basis of current risk assessment for these chemicals. This example demonstrates an effective, human health protective roadmap for EDSP evaluation of pesticide active ingredients via prioritization using HTS and guideline toxicology information. PMID:27347635

26 CFR 52.4682-3 - Imported taxable products.

Code of Federal Regulations, 2012 CFR

2012-04-01

....4681-1(c)(5)) of VCRs. The HTS classification for the VCRs is 8528.10.40. VCRs classified under HTS... reference to the Table. The Table ODC weight specified for VCRs classified under HTS heading 8528.10.40 is 0... of nonmechanical amplification or switching devices such as tubes, transistors, and integrated...

26 CFR 52.4682-3 - Imported taxable products.

Code of Federal Regulations, 2014 CFR

2014-04-01

....4681-1(c)(5)) of VCRs. The HTS classification for the VCRs is 8528.10.40. VCRs classified under HTS... reference to the Table. The Table ODC weight specified for VCRs classified under HTS heading 8528.10.40 is 0... of nonmechanical amplification or switching devices such as tubes, transistors, and integrated...

Quench Detection and Protection for High Temperature Superconducting Transformers by Using the Active Power Method

NASA Astrophysics Data System (ADS)

Nanato, N.; Kobayashi, Y.

AC high temperature superconducting (HTS) coils have been developed for transformers, motors and so on. Quench detection and protection system are essential for safety operations of the AC HTS facilities. The balance voltage method is universally used for the quench detection and protection, however especially for AC operations, the method has risks in terms of high voltage sparks. Because the method needs a voltage tap soldered to a midpoint of the coil winding and the AC HTS facilities generally operate at high voltages and therefore high voltage sparks may occur at the midpoint with no insulation. We have proposed the active power method for the quench detection and protection. The method requires no voltage tap on the midpoint of the coil winding and therefore it has in-built effectiveness for the AC HTS facilities. In this paper, we show that the method can detect the quench in an HTS transformer and moreover our proposed quench protection circuits which consist of thyristors are simple and useful for the AC HTS facilities.

Influence of radius of cylinder HTS bulk on guidance force in a maglev vehicle system

NASA Astrophysics Data System (ADS)

Longcai, Zhang

2014-07-01

Bulk superconductors had great potential for various engineering applications, especially in a high-temperature superconducting (HTS) maglev vehicle system. In such a system, the HTS bulks were always exposed to AC external magnetic field, which was generated by the inhomogeneous surface magnetic field of the NdFeB guideway. In our previous work, it was observed that the guidance force of the YBCO bulk over the NdFeB guideway used in the HTS maglev vehicle system was decayed by the application of the AC external magnetic field. In this paper, we investigated the influence of the radius of the cylinder HTS bulk exposed to an AC magnetic field perturbation on the guidance force in the maglev vehicle system. From the results, it was found that the guidance force was stronger for the bulk with bigger radius and the guidance force decay rates of the bulks were approximately equal despite of the different radius in the maglev vehicle system. Therefore, in order to obtain higher guidance force in the maglev vehicle system, we could use the cylinder HTS bulks with the bigger radius.

Integration of HTS Cables in the Future Grid of the Netherlands

NASA Astrophysics Data System (ADS)

Zuijderduin, R.; Chevtchenko, O.; Smit, J. J.; Aanhaanen, G.; Melnik, I.; Geschiere, A.

Due to increasing power demand, the electricity grid of the Netherlands is changing. The future transmission grid will obtain electrical power generated by decentralized renewable sources, together with large scale generation units located at the coastal region. In this way electrical power has to be distributed and transmitted over longer distances from generation to end user. Potential grid issues like: amount of distributed power, grid stability and electrical loss dissipation merit particular attention. High temperature superconductors (HTS) can play an important role in solving these grid problems. Advantages to integrate HTS components at transmission voltages are numerous: more transmittable power together with less emissions, intrinsic fault current limiting capability, lower ac loss, better control of power flow, reduced footprint, less magnetic field emissions, etc. The main obstacle at present is the relatively high price of HTS conductor. However as the price goes down, initial market penetration of several HTS components (e.g.: cables, fault current limiters) is expected by year 2015. In the full paper we present selected ways to integrate EHV AC HTS cables depending on a particular future grid scenario in the Netherlands.

Age-related environmental gradients influence invertebrate distribution in the Prince Charles Mountains, East Antarctica.

PubMed

Czechowski, Paul; White, Duanne; Clarke, Laurence; McKay, Alan; Cooper, Alan; Stevens, Mark I

2016-12-01

The potential impact of environmental change on terrestrial Antarctic ecosystems can be explored by inspecting biodiversity patterns across large-scale gradients. Unfortunately, morphology-based surveys of Antarctic invertebrates are time-consuming and limited by the cryptic nature of many taxa. We used biodiversity information derived from high-throughput sequencing (HTS) to elucidate the relationship between soil properties and invertebrate biodiversity in the Prince Charles Mountains, East Antarctica. Across 136 analysed soil samples collected from Mount Menzies, Mawson Escarpment and Lake Terrasovoje, we found invertebrate distribution in the Prince Charles Mountains significantly influenced by soil salinity and/or sulfur content. Phyla Tardigrada and Arachnida occurred predominantly in low-salinity substrates with abundant nutrients, whereas Bdelloidea (Rotifera) and Chromadorea (Nematoda) were more common in highly saline substrates. A significant correlation between invertebrate occurrence, soil salinity and time since deglaciation indicates that terrain age indirectly influences Antarctic terrestrial biodiversity, with more recently deglaciated areas supporting greater diversity. Our study demonstrates the value of HTS metabarcoding to investigate environmental constraints on inconspicuous soil biodiversity across large spatial scales.

Age-related environmental gradients influence invertebrate distribution in the Prince Charles Mountains, East Antarctica

PubMed Central

White, Duanne; Clarke, Laurence; McKay, Alan; Cooper, Alan; Stevens, Mark I.

2016-01-01

The potential impact of environmental change on terrestrial Antarctic ecosystems can be explored by inspecting biodiversity patterns across large-scale gradients. Unfortunately, morphology-based surveys of Antarctic invertebrates are time-consuming and limited by the cryptic nature of many taxa. We used biodiversity information derived from high-throughput sequencing (HTS) to elucidate the relationship between soil properties and invertebrate biodiversity in the Prince Charles Mountains, East Antarctica. Across 136 analysed soil samples collected from Mount Menzies, Mawson Escarpment and Lake Terrasovoje, we found invertebrate distribution in the Prince Charles Mountains significantly influenced by soil salinity and/or sulfur content. Phyla Tardigrada and Arachnida occurred predominantly in low-salinity substrates with abundant nutrients, whereas Bdelloidea (Rotifera) and Chromadorea (Nematoda) were more common in highly saline substrates. A significant correlation between invertebrate occurrence, soil salinity and time since deglaciation indicates that terrain age indirectly influences Antarctic terrestrial biodiversity, with more recently deglaciated areas supporting greater diversity. Our study demonstrates the value of HTS metabarcoding to investigate environmental constraints on inconspicuous soil biodiversity across large spatial scales. PMID:28083092

Extreme MHC class I diversity in the sedge warbler (Acrocephalus schoenobaenus); selection patterns and allelic divergence suggest that different genes have different functions.

PubMed

Biedrzycka, Aleksandra; O'Connor, Emily; Sebastian, Alvaro; Migalska, Magdalena; Radwan, Jacek; Zając, Tadeusz; Bielański, Wojciech; Solarz, Wojciech; Ćmiel, Adam; Westerdahl, Helena

2017-07-05

Recent work suggests that gene duplications may play an important role in the evolution of immunity genes. Passerine birds, and in particular Sylvioidea warblers, have highly duplicated major histocompatibility complex (MHC) genes, which are key in immunity, compared to other vertebrates. However, reasons for this high MHC gene copy number are yet unclear. High-throughput sequencing (HTS) allows MHC genotyping even in individuals with extremely duplicated genes. This HTS data can reveal evidence of selection, which may help to unravel the putative functions of different gene copies, i.e. neofunctionalization. We performed exhaustive genotyping of MHC class I in a Sylvioidea warbler, the sedge warbler, Acrocephalus schoenobaenus, using the Illumina MiSeq technique on individuals from a wild study population. The MHC diversity in 863 genotyped individuals by far exceeds that of any other bird species described to date. A single individual could carry up to 65 different alleles, a large proportion of which are expressed (transcribed). The MHC alleles were of three different lengths differing in evidence of selection, diversity and divergence within our study population. Alleles without any deletions and alleles containing a 6 bp deletion showed characteristics of classical MHC genes, with evidence of multiple sites subject to positive selection and high sequence divergence. In contrast, alleles containing a 3 bp deletion had no sites subject to positive selection and had low divergence. Our results suggest that sedge warbler MHC alleles that either have no deletion, or contain a 6 bp deletion, encode classical antigen presenting MHC molecules. In contrast, MHC alleles containing a 3 bp deletion may encode molecules with a different function. This study demonstrates that highly duplicated MHC genes can be characterised with HTS and that selection patterns can be useful for revealing neofunctionalization. Importantly, our results highlight the need to consider the putative function of different MHC genes in future studies of MHC in relation to disease resistance and fitness.

Lattice parameters guide superconductivity in iron-arsenides

DOE PAGES

Konzen, Lance M. N.; Sefat, Athena S.

2017-01-12

The discovery of superconducting materials has led to their use in modern technological marvels, such as magnetic field sensors in MRI machines, powerful research magnets, and high-speed trains. Despite such applications, the uses of superconductors are not widespread due to high cooling costs. Since the discovery of Cu- and Fe-based high-temperature superconductors (HTS), numerous studies have tried to explain and understand the superconducting phenomenon. While no exact explanations are given, several trends are reported in relation to the materials basis in magnetism and spin excitations. In fact, most HTS have antiferromagnetic undoped ‘parent’ materials that undergo a superconducting transition uponmore » small chemical substitutions in them. As it is currently unclear which ‘dopants’ can favor of superconductivity, this manuscript investigates crystal structure changes upon chemical substitutions, to find clues in lattice parameters for the superconducting occurrence. We review the chemical substitution effects on the crystal lattice of iron-based materials (2008 to present). We note that (a) HTS compounds have nearly tetragonal structures with a-lattice parameter close to 4 Å, and (b) superconductivity can depend strongly on the c-lattice parameter changes with chemical substitution. For example, a decrease in c-lattice parameter is required to induce ‘in-plane’ superconductivity. The review of lattice parameter trends in iron-based superconductors presented here, should guide synthesis of new materials and give clues for superconductivity.« less

Operational characteristics of energy storage high temperature superconducting flywheels considering time dependent processes

NASA Astrophysics Data System (ADS)

Vajda, Istvan; Kohari, Zalan; Porjesz, Tamas; Benko, Laszlo; Meerovich, V.; Sokolovsky; Gawalek, W.

2002-08-01

Technical and economical feasibilities of short-term energy storage flywheels with high temperature superconducting (HTS) bearing are widely investigated. It is essential to reduce the ac losses caused by magnetic field variations in HTS bulk disks/rings (levitators) used in the magnetic bearings of flywheels. For the HTS bearings the calculation and measurement of the magnetic field distribution were performed. Effects like eccentricity, tilting were measured. Time dependency of the levitation force following a jumpwise movement of the permanent magnet was measured. The results were used to setup an engineering design algorithm for energy storage HTS flywheels. This algorithm was applied to an experimental HTS flywheel model with a disk type permanent magnet motor/generator unit designed and constructed by the authors. A conceptual design of the disk-type motor/generator with radial flux is shown.

Characteristic and magnetic field analysis of a high temperature superconductor axial-flux coreless induction maglev motor.

PubMed

Wei, Qin; Yu, Fan; Jin, Fang; Shuo, Li; Guoguo, Li; Gang, Lv

2012-04-01

A new high temperature superconductor axial-flux coreless maglev motor (HTS AFIM) is proposed, of which the primary windings are made of HTS tapes and the secondary is a non-magnetic conductor. The main works of this paper are the magnetic-field computation and characteristics analysis of HTS AFIM. For the first one, the reduction of magnetic fields near outer and inner radius of the HTS AFIM is solved by introducing the sub-loop electro-magnetic model along the radial position. For the second one, the AC losses of HTS coils are calculated. The relationships between the device's characteristics and device parameters are presented, and the results indicate that under certain frequency and current levitation device can output enough lift force. The conclusions are verified by finite element calculations.

Characteristic and magnetic field analysis of a high temperature superconductor axial-flux coreless induction maglev motor

PubMed Central

Wei, Qin; Yu, Fan; Jin, Fang; Shuo, Li; Guoguo, Li; Gang, Lv

2012-01-01

A new high temperature superconductor axial-flux coreless maglev motor (HTS AFIM) is proposed, of which the primary windings are made of HTS tapes and the secondary is a non-magnetic conductor. The main works of this paper are the magnetic-field computation and characteristics analysis of HTS AFIM. For the first one, the reduction of magnetic fields near outer and inner radius of the HTS AFIM is solved by introducing the sub-loop electro-magnetic model along the radial position. For the second one, the AC losses of HTS coils are calculated. The relationships between the device’s characteristics and device parameters are presented, and the results indicate that under certain frequency and current levitation device can output enough lift force. The conclusions are verified by finite element calculations. PMID:22393268

AC losses in horizontally parallel HTS tapes for possible wireless power transfer applications

NASA Astrophysics Data System (ADS)

Shen, Boyang; Geng, Jianzhao; Zhang, Xiuchang; Fu, Lin; Li, Chao; Zhang, Heng; Dong, Qihuan; Ma, Jun; Gawith, James; Coombs, T. A.

2017-12-01

This paper presents the concept of using horizontally parallel HTS tapes with AC loss study, and the investigation on possible wireless power transfer (WPT) applications. An example of three parallel HTS tapes was proposed, whose AC loss study was carried out both from experiment using electrical method; and simulation using 2D H-formulation on the FEM platform of COMSOL Multiphysics. The electromagnetic induction around the three parallel tapes was monitored using COMSOL simulation. The electromagnetic induction and AC losses generated by a conventional three turn coil was simulated as well, and then compared to the case of three parallel tapes with the same AC transport current. The analysis demonstrates that HTS parallel tapes could be potentially used into wireless power transfer systems, which could have lower total AC losses than conventional HTS coils.

Use of Cell Viability Assay Data Improves the Prediction Accuracy of Conventional Quantitative Structure–Activity Relationship Models of Animal Carcinogenicity

PubMed Central

Zhu, Hao; Rusyn, Ivan; Richard, Ann; Tropsha, Alexander

2008-01-01

Background To develop efficient approaches for rapid evaluation of chemical toxicity and human health risk of environmental compounds, the National Toxicology Program (NTP) in collaboration with the National Center for Chemical Genomics has initiated a project on high-throughput screening (HTS) of environmental chemicals. The first HTS results for a set of 1,408 compounds tested for their effects on cell viability in six different cell lines have recently become available via PubChem. Objectives We have explored these data in terms of their utility for predicting adverse health effects of the environmental agents. Methods and results Initially, the classification k nearest neighbor (kNN) quantitative structure–activity relationship (QSAR) modeling method was applied to the HTS data only, for a curated data set of 384 compounds. The resulting models had prediction accuracies for training, test (containing 275 compounds together), and external validation (109 compounds) sets as high as 89%, 71%, and 74%, respectively. We then asked if HTS results could be of value in predicting rodent carcinogenicity. We identified 383 compounds for which data were available from both the Berkeley Carcinogenic Potency Database and NTP–HTS studies. We found that compounds classified by HTS as “actives” in at least one cell line were likely to be rodent carcinogens (sensitivity 77%); however, HTS “inactives” were far less informative (specificity 46%). Using chemical descriptors only, kNN QSAR modeling resulted in 62.3% prediction accuracy for rodent carcinogenicity applied to this data set. Importantly, the prediction accuracy of the model was significantly improved (72.7%) when chemical descriptors were augmented by HTS data, which were regarded as biological descriptors. Conclusions Our studies suggest that combining NTP–HTS profiles with conventional chemical descriptors could considerably improve the predictive power of computational approaches in toxicology. PMID:18414635

Simulation and measurement of a Ka-band HTS MMIC Josephson junction mixer

NASA Astrophysics Data System (ADS)

Zhang, Ting; Pegrum, Colin; Du, Jia; Guo, Yingjie Jay

2017-01-01

We report modeling and simulation results for a Ka band high-temperature superconducting (HTS) monolithic microwave integrated circuit (MMIC) Josephson junction mixer. A Verilog-A model of a Josephson junction is established and imported into the system simulator to realize a full HTS MMIC circuit simulation containing the HTS passive circuit models. Impedance matching optimization between the junction and passive devices is investigated. Junction DC I-V characteristics, current and local oscillator bias conditions and mixing performance are simulated and compared with the experimental results. Good agreement is obtained between the simulation and measurement results.

Composite Materials

NASA Technical Reports Server (NTRS)

1988-01-01

Langley Research Center researchers invented an advanced polymer, a chemical compound formed by uniting many small molecules to create a complex molecule with different chemical properties. The material is a thermoplastic polyimide that resists solvents. Other polymers of this generic type are soluble in solvents, thus cannot be used where solvents are present. High Technology Services (HTS), Inc. licensed technology and is engaged in development and manufacture of high performance plastics, resins and composite materials. Techimer Materials Division is using technology for composite matrix resins that offer heat resistance and protection from radiation, electrical and chemical degradation. Applications of new polymer include molding resins, adhesives and matrix resins for fiber reinforced composites.

Use of Threshold of Toxicological Concern (TTC) with High Throughput Exposure Predictions as a Risk-Based Screening Approach of Several Thousand Commodity Chemicals (SOT Poster)

EPA Science Inventory

Although progress has been made with HTS (high throughput screening) in profiling biological activity (e.g., EPA’s ToxCast™), challenges arise interpreting HTS results in the context of adversity & converting HTS assay concentrations to equivalent human doses for the broad domain...

Probe molecules (PrM) approach in adverse outcome pathway (AOP) based high throughput screening (HTS): in vivo discovery for developing in vitro target methods

EPA Science Inventory

Efficient and accurate adverse outcome pathway (AOP) based high-throughput screening (HTS) methods use a systems biology based approach to computationally model in vitro cellular and molecular data for rapid chemical prioritization; however, not all HTS assays are grounded by rel...

An equiosmolar study on early intracranial physiology and long term outcome in severe traumatic brain injury comparing mannitol and hypertonic saline.

PubMed

Jagannatha, Aniruddha Tekkatte; Sriganesh, Kamath; Devi, Bhagavatula Indira; Rao, Ganne Sesha Umamaheswara

2016-05-01

The impact of hypertonic saline (HTS) on long term control of intracranial hypertension (ICH) is yet to be established. The current prospective randomized controlled study was carried out in 38 patients with severe traumatic brain injury (TBI). Over 450 episodes of refractory ICH were treated with equiosmolar boluses of 20% mannitol in 20 patients and 3.0% HTS in 18 subjects. Intracranial pressure (ICP) was monitored for 6days. ICP and cerebral perfusion pressure (CPP) were comparable between the groups. The mannitol group had a progressive increase in the ICP over the study period (p=0.01). A similar increase was not seen in the HTS group (p=0.1). The percentage time for which the ICP remained below a threshold of 20 mmHg on day6 was higher in the HTS group (63% versus 49%; p=0.3). The duration of inotrope requirement in the HTS group was less compared to the mannitol group (p=0.06). The slope of fall in ICP in response to a bolus dose at a given baseline value of ICP was higher with HTS compared to mannitol (p=0.0001). In-hospital mortality tended to be lower in the HTS group (3 versus 10; p=0.07) while mortality at 6 months was not different between the groups (6 versus 10; p=0.41). Dichotomized Glasgow Outcome Scale scores at 6months were comparable between the groups (p=0.21). To conclude, immediate physiological advantages seen with HTS over mannitol did not translate into long term benefit on ICP/CPP control or mortality of patients with TBI. Copyright © 2015 Elsevier Ltd. All rights reserved.

Potential use of routine databases in health technology assessment.

PubMed

Raftery, J; Roderick, P; Stevens, A

2005-05-01

To develop criteria for classifying databases in relation to their potential use in health technology (HT) assessment and to apply them to a list of databases of relevance in the UK. To explore the extent to which prioritized databases could pick up those HTs being assessed by the National Coordinating Centre for Health Technology Assessment (NCCHTA) and the extent to which these databases have been used in HT assessment. To explore the validation of the databases and their cost. Electronic databases. Key literature sources. Experienced users of routine databases. A 'first principles' examination of the data necessary for each type of HT assessment was carried out, supplemented by literature searches and a historical review. The principal investigators applied the criteria to the databases. Comments of the 'keepers' of the prioritized databases were incorporated. Details of 161 topics funded by the NHS R&D Health Technology Assessment (HTA) programme were reviewed iteratively by the principal investigators. Uses of databases in HTAs were identified by literature searches, which included the title of each prioritized database as a keyword. Annual reports of databases were examined and 'keepers' queried. The validity of each database was assessed using criteria based on a literature search and involvement by the authors in a national academic network. The costs of databases were established from annual reports, enquiries to 'keepers' of databases and 'guesstimates' based on cost per record. For assessing effectiveness, equity and diffusion, routine databases were classified into three broad groups: (1) group I databases, identifying both HTs and health states, (2) group II databases, identifying the HTs, but not a health state, and (3) group III databases, identifying health states, but not an HT. Group I datasets were disaggregated into clinical registries, clinical administrative databases and population-oriented databases. Group III were disaggregated into adverse event reporting, confidential enquiries, disease-only registers and health surveys. Databases in group I can be used not only to assess effectiveness but also to assess diffusion and equity. Databases in group II can only assess diffusion. Group III has restricted scope for assessing HTs, except for analysis of adverse events. For use in costing, databases need to include unit costs or prices. Some databases included unit cost as well as a specific HT. A list of around 270 databases was identified at the level of UK, England and Wales or England (over 1000 including Scotland, Wales and Northern Ireland). Allocation of these to the above groups identified around 60 databases with some potential for HT assessment, roughly half to group I. Eighteen clinical registers were identified as having the greatest potential although the clinical administrative datasets had potential mainly owing to their inclusion of a wide range of technologies. Only two databases were identified that could directly be used in costing. The review of the potential capture of HTs prioritized by the UK's NHS R&D HTA programme showed that only 10% would be captured in these databases, mainly drugs prescribed in primary care. The review of the use of routine databases in any form of HT assessment indicated that clinical registers were mainly used for national comparative audit. Some databases have only been used in annual reports, usually time trend analysis. A few peer-reviewed papers used a clinical register to assess the effectiveness of a technology. Accessibility is suggested as a barrier to using most databases. Clinical administrative databases (group Ib) have mainly been used to build population needs indices and performance indicators. A review of the validity of used databases showed that although internal consistency checks were common, relatively few had any form of external audit. Some comparative audit databases have data scrutinised by participating units. Issues around coverage and coding have, in general, received little attention. NHS funding of databases has been mainly for 'Central Returns' for management purposes, which excludes those databases with the greatest potential for HT assessment. Funding for databases was various, but some are unfunded, relying on goodwill. The estimated total cost of databases in group I plus selected databases from groups II and III has been estimated at pound 50 million or around 0.1% of annual NHS spend. A few databases with limited potential for HT assessment account for the bulk of spending. Suggestions for policy include clarification of responsibility for the strategic development of databases, improved resourcing, and issues around coding, confidentiality, ownership and access, maintenance of clinical support, optimal use of information technology, filling gaps and remedying deficiencies. Recommendations for researchers include closer policy links between routine data and R&D, and selective investment in the more promising databases. Recommended research topics include optimal capture and coding of the range of HTs, international comparisons of the role, funding and use of routine data in healthcare systems and use of routine database in trials and in modelling. Independent evaluations are recommended for information strategies (such as those around the National Service Frameworks and various collaborations) and for electronic patient and health records.

De novo transcriptome assembly for a non-model species, the blood-sucking bug Triatoma brasiliensis, a vector of Chagas disease.

PubMed

Marchant, A; Mougel, F; Almeida, C; Jacquin-Joly, E; Costa, J; Harry, M

2015-04-01

High throughput sequencing (HTS) provides new research opportunities for work on non-model organisms, such as differential expression studies between populations exposed to different environmental conditions. However, such transcriptomic studies first require the production of a reference assembly. The choice of sampling procedure, sequencing strategy and assembly workflow is crucial. To develop a reliable reference transcriptome for Triatoma brasiliensis, the major Chagas disease vector in Northeastern Brazil, different de novo assembly protocols were generated using various datasets and software. Both 454 and Illumina sequencing technologies were applied on RNA extracted from antennae and mouthparts from single or pooled individuals. The 454 library yielded 278 Mb. Fifteen Illumina libraries were constructed and yielded nearly 360 million RNA-seq single reads and 46 million RNA-seq paired-end reads for nearly 45 Gb. For the 454 reads, we used three assemblers, Newbler, CAP3 and/or MIRA and for the Illumina reads, the Trinity assembler. Ten assembly workflows were compared using these programs separately or in combination. To compare the assemblies obtained, quantitative and qualitative criteria were used, including contig length, N50, contig number and the percentage of chimeric contigs. Completeness of the assemblies was estimated using the CEGMA pipeline. The best assembly (57,657 contigs, completeness of 80 %, <1 % chimeric contigs) was a hybrid assembly leading to recommend the use of (1) a single individual with large representation of biological tissues, (2) merging both long reads and short paired-end Illumina reads, (3) several assemblers in order to combine the specific advantages of each.

Loss measurement and analysis for the prototype generator with HTS stator and permanent magnet rotor

NASA Astrophysics Data System (ADS)

Song, Peng; Qu, Timing; Yu, Xiaoyu; Li, Longnian; Gu, Chen; Li, Xiaohang; Wang, Dewen; Hu, Boping; Chen, Duxing; Han, Zhenghe

2013-11-01

A prototype HTS synchronous generator with a permanent magnet rotor and HTS armature windings was developed. The rated armature frequency is 10 Hz. The cryogenic Dewar is tightly surrounded outside the iron core. Both HTS coils and the iron core were cooled by using conduction cooling method. During the process of no-load running, the no-load loss power data were obtained through the torque measurement. The temperature evolution characteristics of the stator was measured by PT-100 temperature sensors. These results show that the no-load loss power at around 77 K are much larger than that at room temperature. The possible reason for the no-load loss increment is discussed. The ac loss power of one individual HTS coil used in this generator was also tested. Compared with the iron loss power, the ac loss power is rather small and could be neglected.

High temperature superconductors for magnetic suspension applications

NASA Technical Reports Server (NTRS)

Mcmichael, C. K.; Cooley, R. S.; Chen, Q. Y.; Ma, K. B.; Lamb, M. A.; Meng, R. L.; Chu, C. W.; Chu, W. K.

1994-01-01

High temperature superconductors (HTS) hold the promise for applications in magnetic levitation bearings, vibration damping, and torque coupling. Traditional magnetic suspension systems require active feedback and vibration controls in which power consumption and low frequency vibration are among the major engineering concerns. HTS materials have been demonstrated to be an enabling approach towards such problems due to their flux trapping properties. In our laboratory at TCSUH, we have been conducting a series of experiments to explore various mechanical applications using HTS. We have constructed a 30 lb. model flywheel levitated by a hybrid superconducting magnetic bearing (HSMB). We are also developing a levitated and vibration-dampled platform for high precision instrumentation. These applications would be ideal for space usages where ambient temperature is adequate for HTS to operate properly under greatly reduced cryogenic requirements. We will give a general overview of these potential applications and discuss the operating principles of the HTS devices we have developed.

Detecting and removing multiplicative spatial bias in high-throughput screening technologies.

PubMed

Caraus, Iurie; Mazoure, Bogdan; Nadon, Robert; Makarenkov, Vladimir

2017-10-15

Considerable attention has been paid recently to improve data quality in high-throughput screening (HTS) and high-content screening (HCS) technologies widely used in drug development and chemical toxicity research. However, several environmentally- and procedurally-induced spatial biases in experimental HTS and HCS screens decrease measurement accuracy, leading to increased numbers of false positives and false negatives in hit selection. Although effective bias correction methods and software have been developed over the past decades, almost all of these tools have been designed to reduce the effect of additive bias only. Here, we address the case of multiplicative spatial bias. We introduce three new statistical methods meant to reduce multiplicative spatial bias in screening technologies. We assess the performance of the methods with synthetic and real data affected by multiplicative spatial bias, including comparisons with current bias correction methods. We also describe a wider data correction protocol that integrates methods for removing both assay and plate-specific spatial biases, which can be either additive or multiplicative. The methods for removing multiplicative spatial bias and the data correction protocol are effective in detecting and cleaning experimental data generated by screening technologies. As our protocol is of a general nature, it can be used by researchers analyzing current or next-generation high-throughput screens. The AssayCorrector program, implemented in R, is available on CRAN. makarenkov.vladimir@uqam.ca. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

No-insulation multi-width winding technique for high temperature superconducting magnet.

PubMed

Hahn, Seungyong; Kim, Youngjae; Keun Park, Dong; Kim, Kwangmin; Voccio, John P; Bascuñán, Juan; Iwasa, Yukikazu

2013-10-21

We present a No-Insulation ( NI ) Multi-Width ( MW ) winding technique for an HTS (high temperature superconductor) magnet consisting of double-pancake (DP) coils. The NI enables an HTS magnet self-protecting and the MW minimizes the detrimental anisotropy in current-carrying capacity of HTS tape by assigning tapes of multiple widths to DP coils within a stack, widest tape to the top and bottom sections and the narrowest in the midplane section. This paper presents fabrication and test results of an NI-MW HTS magnet and demonstrates the unique features of the NI-MW technique: self-protecting and enhanced field performance, unattainable with the conventional technique.

Static and dynamic stability of the guidance force in a side-suspended HTS maglev system

NASA Astrophysics Data System (ADS)

Zhou, Dajin; Cui, Chenyu; Zhao, Lifeng; Zhang, Yong; Wang, Xiqing; Zhao, Yong

2017-02-01

The static and dynamic stability of the guidance force in a side-suspended HTS-PMG (permanent magnetic guideway) system were studied theoretically and experimentally. It is found that there are two types of guidance force that exist in the HTS-PMG system, which are sensitive to the levitation gap and the arrangement of YBCO bulks around the central axis of the PMG. An optimized YBCO array was used to stabilize the system, which enabled a side-suspended HTS-PMG maglev vehicle to run stably at 102 km h-1 on a circular test track with 6.5 m in diameter.

HTS cryogenic current comparator for non-invasive sensing of charged-particle beams

NASA Astrophysics Data System (ADS)

Hao, L.; Gallop, J. C.; Macfarlane, J. C.; Carr, C.

2002-03-01

The principle of the superconducting cryogenic direct-current comparator (CCC) is applied to the non-invasive sensing of charged-particle beams (ions, electrons). With the use of HTS components it is feasible to envisage applications, for example, in precision mass spectrometry, in real-time monitoring of ion-beam implantation currents and for the determination of the Faraday fundamental constant. We have developed a novel current concentrating technique using HTS thick-film material, to increase the sensitivity of the CCC. Recent simulations and experimental measurements of the flux and current concentration ratios, frequency response and linearity of a prototype HTS-CCC operating at 77 K are described.

Coupled Cryogenic Thermal and Electrical Models for Transient Analysis of Superconducting Power Devices with Integrated Cryogenic Systems

NASA Astrophysics Data System (ADS)

Satyanarayana, S.; Indrakanti, S.; Kim, J.; Kim, C.; Pamidi, S.

2017-12-01

Benefits of an integrated high temperature superconducting (HTS) power system and the associated cryogenic systems on board an electric ship or aircraft are discussed. A versatile modelling methodology developed to assess the cryogenic thermal behavior of the integrated system with multiple HTS devices and the various potential configurations are introduced. The utility and effectiveness of the developed modelling methodology is demonstrated using a case study involving a hypothetical system including an HTS propulsion motor, an HTS generator and an HTS power cable cooled by an integrated cryogenic helium circulation system. Using the methodology, multiple configurations are studied. The required total cooling power and the ability to maintain each HTS device at the required operating temperatures are considered for each configuration and the trade-offs are discussed for each configuration. Transient analysis of temperature evolution in the cryogenic helium circulation loop in case of a system failure is carried out to arrive at the required critical response time. The analysis was also performed for a similar liquid nitrogen circulation for an isobaric condition and the cooling capacity ratio is used to compare the relative merits of the two cryogens.

Nonlinear vibration behaviors of high-Tc superconducting bulks in an applied permanent magnetic array field

NASA Astrophysics Data System (ADS)

Li, Jipeng; Li, Haitao; Zheng, Jun; Zheng, Botian; Huang, Huan; Deng, Zigang

2017-06-01

The nonlinear vibration of high temperature superconducting (HTS) bulks in an applied permanent magnetic array (Halbach array) field, as a precondition for commercial application to HTS maglev train and HTS bearing, is systematically investigated. This article reports the actual vibration rules of HTS bulks from three aspects. First, we propose a new numerical model to simplify the calculation of levitation force. This model could provide precise simulations, especially the estimation of eigenfrequency. Second, an approximate analytic solution of the vibration of the HTS bulks is obtained by using the method of harmonic balance. Finally, to verify the results mentioned above, we measure the vertical vibration acceleration signals of an HTS maglev model, consisting of eight YBaCuO bulks, oscillating freely above a Halbach array with large displacement excitation. Higher order harmonic components, which indicate the nonlinear vibration phenomenon, are detected in the responses. All the three results are compared and agreed well with each other. This study combines the experimental and theoretical analyses and provides a deep understanding of the physical phenomenon of the nonlinear vibration and is meaningful for the vibration control of the relevant applications.

AC HTS Transmission Cable for Integration into the Future EHV Grid of the Netherlands

NASA Astrophysics Data System (ADS)

Zuijderduin, R.; Chevtchenko, O.; Smit, J. J.; Aanhaanen, G.; Melnik, I.; Geschiere, A.

Due to increasing power demand, the electricity grid of the Netherlands is changing. The future grid must be capable to transmit all the connected power. Power generation will be more decentralized like for instance wind parks connected to the grid. Furthermore, future large scale production units are expected to be installed near coastal regions. This creates some potential grid issues, such as: large power amounts to be transmitted to consumers from west to east and grid stability. High temperature superconductors (HTS) can help solving these grid problems. Advantages to integrate HTS components at Extra High Voltage (EHV) and High Voltage (HV) levels are numerous: more power with less losses and less emissions, intrinsic fault current limiting capability, better control of power flow, reduced footprint, etc. Today's main obstacle is the relatively high price of HTS. Nevertheless, as the price goes down, initial market penetration for several HTS components is expected by year 2015 (e.g.: cables, fault current limiters). In this paper we present a design of intrinsically compensated EHV HTS cable for future grid integration. Discussed are the parameters of such cable providing an optimal power transmission in the future network.

Design of conduction cooling system for a high current HTS DC reactor

NASA Astrophysics Data System (ADS)

Dao, Van Quan; Kim, Taekue; Le Tat, Thang; Sung, Haejin; Choi, Jongho; Kim, Kwangmin; Hwang, Chul-Sang; Park, Minwon; Yu, In-Keun

2017-07-01

A DC reactor using a high temperature superconducting (HTS) magnet reduces the reactor’s size, weight, flux leakage, and electrical losses. An HTS magnet needs cryogenic cooling to achieve and maintain its superconducting state. There are two methods for doing this: one is pool boiling and the other is conduction cooling. The conduction cooling method is more effective than the pool boiling method in terms of smaller size and lighter weight. This paper discusses a design of conduction cooling system for a high current, high temperature superconducting DC reactor. Dimensions of the conduction cooling system parts including HTS magnets, bobbin structures, current leads, support bars, and thermal exchangers were calculated and drawn using a 3D CAD program. A finite element method model was built for determining the optimal design parameters and analyzing the thermo-mechanical characteristics. The operating current and inductance of the reactor magnet were 1,500 A, 400 mH, respectively. The thermal load of the HTS DC reactor was analyzed for determining the cooling capacity of the cryo-cooler. The study results can be effectively utilized for the design and fabrication of a commercial HTS DC reactor.

Potential escalation of heat-related working costs with climate and socioeconomic changes in China

PubMed Central

Zhao, Yan; Sultan, Benjamin; Vautard, Robert; Braconnot, Pascale; Wang, Huijun J.; Ducharne, Agnes

2016-01-01

Global climate change will increase the frequency of hot temperatures, impairing health and productivity for millions of working people and raising labor costs. In mainland China, high-temperature subsidies (HTSs) are allocated to employees for each working day in extremely hot environments, but the potential heat-related increase in labor cost has not been evaluated so far. Here, we estimate the potential HTS cost in current and future climates under different scenarios of socioeconomic development and radiative forcing (Representative Concentration Pathway), taking uncertainties from the climate model structure and bias correction into account. On average, the total HTS in China is estimated at 38.6 billion yuan/y (US $6.22 billion/y) over the 1979–2005 period, which is equivalent to 0.2% of the gross domestic product (GDP). Assuming that the HTS standards (per employee per hot day) remain unchanged throughout the 21st century, the total HTS may reach 250 billion yuan/y in the 2030s and 1,000 billion yuan/y in 2100. We further show that, without specific adaptation, the increased HTS cost is mainly determined by population growth until the 2030s and climate change after the mid-21st century because of increasingly frequent hot weather. Accounting for the likely possibility that HTS standards follow the wages, the share of GDP devoted to HTS could become as high as 3% at the end of 21st century. PMID:27044089

Numerical study on AC loss reduction of stacked HTS tapes by optimal design of flux diverter

NASA Astrophysics Data System (ADS)

Liu, Guole; Zhang, Guomin; Jing, Liwei; Yu, Hui

2017-12-01

High temperature superconducting (HTS) coils are key parts of many AC applications, such as generators, superconducting magnetic energy storage and transformers. AC loss reduction in HTS coils is essential for the commercialization of these HTS devices. Magnetic material is generally used as the flux diverter in an effort to reduce the AC loss in HTS coils. To achieve the greatest reduction in the AC loss of the coils, the flux diverter should be made of a material with low loss and high saturated magnetic density, and the optimization of the geometric size and location of the flux diverter is required. In this paper, we chose Ni-alloy as the flux diverter, which can be processed into a specific shape and size. The influence of the shape and location of the flux diverter on the AC loss characteristics of stacked (RE)BCO tapes is investigated by use of a finite element method. Taking both the AC loss of the (RE)BCO coils and the ferromagnetic loss of the flux diverter into account, the optimal geometry of the flux diverter is obtained. It is found that when the applied current is at half the value of the critical current, the total loss of the HTS stack with the optimal flux diverter is only 18% of the original loss of the HTS stack without the flux diverter. Besides, the effect of the flux diverter on the critical current of the (RE)BCO stack is investigated.

High-throughput process development of an alternative platform for the production of virus-like particles in Escherichia coli.

PubMed

Ladd Effio, Christopher; Baumann, Pascal; Weigel, Claudia; Vormittag, Philipp; Middelberg, Anton; Hubbuch, Jürgen

2016-02-10

The production of safe vaccines against untreatable or new diseases has pushed the research in the field of virus-like particles (VLPs). Currently, a large number of commercial VLP-based human vaccines and vaccine candidates are available or under development. A promising VLP production route is the controlled in vitro assembly of virus proteins into capsids. In the study reported here, a high-throughput screening (HTS) procedure was implemented for the upstream process development of a VLP platform in bacterial cell systems. Miniaturized cultivations were carried out in 48-well format in the BioLector system (m2p-Labs, Germany) using an Escherichia coli strain with a tac promoter producing the murine polyomavirus capsid protein (VP1). The screening procedure incorporated micro-scale cultivations, HTS cell disruption by sonication and HTS-compatible analytics by capillary gel electrophoresis. Cultivation temperatures, shaking speeds, induction and medium conditions were varied to optimize the product expression in E. coli. The most efficient system was selected based on an evaluation of soluble and insoluble product concentrations as well as on the percentage of product in the total soluble protein fraction. The optimized system was scaled up to cultivation 2.5L shaker flask scale and purified using an anion exchange chromatography membrane adsorber, followed by a size exclusion chromatography polishing procedure. For proof of concept, purified VP1 capsomeres were assembled under defined buffer conditions into empty capsids and characterized using transmission electron microscopy (TEM). The presented HTS procedure allowed for a fast development of an efficient production process of VLPs in E. coli. Under optimized cultivation conditions, the VP1 product totalled up to 43% of the total soluble protein fraction, yielding 1.63 mg VP1 per mL of applied cultivation medium. The developed production process strongly promotes the murine polyoma-VLP platform, moving towards an industrially feasible technology for new chimeric vaccines. Copyright © 2015 Elsevier B.V. All rights reserved.

Cryogenic experiences during W7-X HTS-current lead tests

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

Richter, Thomas; Lietzow, Ralph

2014-01-29

The Karlsruhe Institute of Technology (KIT) was responsible for design, production and test of the High Temperature Superconductor (HTS) current leads (CL) for the stellerator Wendelstein 7-X (W7-X). 16 current leads were delivered. Detailed prototype tests as well as the final acceptance tests were performed at KIT, using a dedicated test cryostat assembled beside and connected to the main vacuum vessel of the TOSKA facility. A unique feature is the upside down orientation of the current leads due to the location of the power supplies in the basement of the experimental area of W7-X. The HTS-CL consists of three mainmore » parts: the cold end for the connection to the bus bar at 4.5 K, the HTS part operating in the temperature range from 4.5 K to 65 K and a copper heat exchanger (HEX) in the temperature range from 65 K to room temperature, which is cooled with 50 K helium. Therefore in TOSKA it is possible to cool test specimens simultaneously with helium at two different temperature levels. The current lead tests included different scenarios with currents up to 18.2 kA. In total, 10 cryogenic test campaigns with a total time of about 24 weeks were performed till beginning of 2013. The test facility as well as the 2 kW cryogenic plant of ITEP showed a very good reliability. However, during such a long and complex experimental campaign, one has to deal with failures, technical difficulties and incidents. The paper gives a summary of the test performance comprising the test preparation and operation. This includes the performance and reliability of the refrigerator and the test facility with reference to the process measuring and control system, the data acquisition system, as well as the building infrastructure.« less

Sensing Fissile Materials at Long Range

DTIC Science & Technology

2016-04-01

Adjusted Magnetic Design Working Point Parametrics ................................................ 21  B.  Use of  HTS  Monoliths or Permanent Magnets for...25  B.3 Applications of  HTS  bulk to cyclotrons. ....................................................................... 26  B.4...57  D.  HTS  Potential for cyclotrons

High throughput system for magnetic manipulation of cells, polymers, and biomaterials

PubMed Central

Spero, Richard Chasen; Vicci, Leandra; Cribb, Jeremy; Bober, David; Swaminathan, Vinay; O’Brien, E. Timothy; Rogers, Stephen L.; Superfine, R.

2008-01-01

In the past decade, high throughput screening (HTS) has changed the way biochemical assays are performed, but manipulation and mechanical measurement of micro- and nanoscale systems have not benefited from this trend. Techniques using microbeads (particles ∼0.1–10 μm) show promise for enabling high throughput mechanical measurements of microscopic systems. We demonstrate instrumentation to magnetically drive microbeads in a biocompatible, multiwell magnetic force system. It is based on commercial HTS standards and is scalable to 96 wells. Cells can be cultured in this magnetic high throughput system (MHTS). The MHTS can apply independently controlled forces to 16 specimen wells. Force calibrations demonstrate forces in excess of 1 nN, predicted force saturation as a function of pole material, and powerlaw dependence of F∼r−2.7±0.1. We employ this system to measure the stiffness of SR2+ Drosophila cells. MHTS technology is a key step toward a high throughput screening system for micro- and nanoscale biophysical experiments. PMID:19044357

Feasibility of introducing ferromagnetic materials to onboard bulk high-Tc superconductors to enhance the performance of present maglev systems

NASA Astrophysics Data System (ADS)

Deng, Zigang; Wang, Jiasu; Zheng, Jun; Zhang, Ya; Wang, Suyu

2013-02-01

Performance improvement is a long-term research task for the promotion of practical application of promising high-temperature superconducting (HTS) magnetic levitation (maglev) vehicle technologies. We studied the feasibility to enhance the performance of present HTS Maglev systems by introducing ferromagnetic materials to onboard bulk superconductors. The principle here is to make use of the high magnetic permeability of ferromagnetic materials to alter the flux distribution of the permanent magnet guideway for the enhancement of magnetic field density at the position of the bulk superconductors. Ferromagnetic iron plates were added to the upper surface of bulk superconductors and their geometric and positioning effects on the maglev performance were investigated experimentally. Results show that the guidance performance (stability) was enhanced greatly for a particular setup when compared to the present maglev system which is helpful in the application where large guidance forces are needed such as maglev tracks with high degrees of curves.

High Content Imaging (HCI) on Miniaturized Three-Dimensional (3D) Cell Cultures

PubMed Central

Joshi, Pranav; Lee, Moo-Yeal

2015-01-01

High content imaging (HCI) is a multiplexed cell staining assay developed for better understanding of complex biological functions and mechanisms of drug action, and it has become an important tool for toxicity and efficacy screening of drug candidates. Conventional HCI assays have been carried out on two-dimensional (2D) cell monolayer cultures, which in turn limit predictability of drug toxicity/efficacy in vivo; thus, there has been an urgent need to perform HCI assays on three-dimensional (3D) cell cultures. Although 3D cell cultures better mimic in vivo microenvironments of human tissues and provide an in-depth understanding of the morphological and functional features of tissues, they are also limited by having relatively low throughput and thus are not amenable to high-throughput screening (HTS). One attempt of making 3D cell culture amenable for HTS is to utilize miniaturized cell culture platforms. This review aims to highlight miniaturized 3D cell culture platforms compatible with current HCI technology. PMID:26694477

MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data

PubMed Central

Denis, Jean-Baptiste; Vandenbogaert, Mathias; Caro, Valérie

2016-01-01

The detection and characterization of emerging infectious agents has been a continuing public health concern. High Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies have proven to be promising approaches for efficient and unbiased detection of pathogens in complex biological samples, providing access to comprehensive analyses. As NGS approaches typically yield millions of putatively representative reads per sample, efficient data management and visualization resources have become mandatory. Most usually, those resources are implemented through a dedicated Laboratory Information Management System (LIMS), solely to provide perspective regarding the available information. We developed an easily deployable web-interface, facilitating management and bioinformatics analysis of metagenomics data-samples. It was engineered to run associated and dedicated Galaxy workflows for the detection and eventually classification of pathogens. The web application allows easy interaction with existing Galaxy metagenomic workflows, facilitates the organization, exploration and aggregation of the most relevant sample-specific sequences among millions of genomic sequences, allowing them to determine their relative abundance, and associate them to the most closely related organism or pathogen. The user-friendly Django-Based interface, associates the users’ input data and its metadata through a bio-IT provided set of resources (a Galaxy instance, and both sufficient storage and grid computing power). Galaxy is used to handle and analyze the user’s input data from loading, indexing, mapping, assembly and DB-searches. Interaction between our application and Galaxy is ensured by the BioBlend library, which gives API-based access to Galaxy’s main features. Metadata about samples, runs, as well as the workflow results are stored in the LIMS. For metagenomic classification and exploration purposes, we show, as a proof of concept, that integration of intuitive exploratory tools, like Krona for representation of taxonomic classification, can be achieved very easily. In the trend of Galaxy, the interface enables the sharing of scientific results to fellow team members. PMID:28451381

MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data.

PubMed

Correia, Damien; Doppelt-Azeroual, Olivia; Denis, Jean-Baptiste; Vandenbogaert, Mathias; Caro, Valérie

2015-01-01

The detection and characterization of emerging infectious agents has been a continuing public health concern. High Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies have proven to be promising approaches for efficient and unbiased detection of pathogens in complex biological samples, providing access to comprehensive analyses. As NGS approaches typically yield millions of putatively representative reads per sample, efficient data management and visualization resources have become mandatory. Most usually, those resources are implemented through a dedicated Laboratory Information Management System (LIMS), solely to provide perspective regarding the available information. We developed an easily deployable web-interface, facilitating management and bioinformatics analysis of metagenomics data-samples. It was engineered to run associated and dedicated Galaxy workflows for the detection and eventually classification of pathogens. The web application allows easy interaction with existing Galaxy metagenomic workflows, facilitates the organization, exploration and aggregation of the most relevant sample-specific sequences among millions of genomic sequences, allowing them to determine their relative abundance, and associate them to the most closely related organism or pathogen. The user-friendly Django-Based interface, associates the users' input data and its metadata through a bio-IT provided set of resources (a Galaxy instance, and both sufficient storage and grid computing power). Galaxy is used to handle and analyze the user's input data from loading, indexing, mapping, assembly and DB-searches. Interaction between our application and Galaxy is ensured by the BioBlend library, which gives API-based access to Galaxy's main features. Metadata about samples, runs, as well as the workflow results are stored in the LIMS. For metagenomic classification and exploration purposes, we show, as a proof of concept, that integration of intuitive exploratory tools, like Krona for representation of taxonomic classification, can be achieved very easily. In the trend of Galaxy, the interface enables the sharing of scientific results to fellow team members.

No-insulation multi-width winding technique for high temperature superconducting magnet

PubMed Central

Hahn, Seungyong; Kim, Youngjae; Keun Park, Dong; Kim, Kwangmin; Voccio, John P.; Bascuñán, Juan; Iwasa, Yukikazu

2013-01-01

We present a No-Insulation (NI) Multi-Width (MW) winding technique for an HTS (high temperature superconductor) magnet consisting of double-pancake (DP) coils. The NI enables an HTS magnet self-protecting and the MW minimizes the detrimental anisotropy in current-carrying capacity of HTS tape by assigning tapes of multiple widths to DP coils within a stack, widest tape to the top and bottom sections and the narrowest in the midplane section. This paper presents fabrication and test results of an NI-MW HTS magnet and demonstrates the unique features of the NI-MW technique: self-protecting and enhanced field performance, unattainable with the conventional technique. PMID:24255549

Design, Construction and Test of Cryogen-Free HTS Coil Structure

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

Hocker, H.; Anerella, M.; Gupta, R.

2011-03-28

This paper will describe design, construction and test results of a cryo-mechanical structure to study coils made with the second generation High Temperature Superconductor (HTS) for the Facility for Rare Isotope Beams (FRIB). A magnet comprised of HTS coils mounted in a vacuum vessel and conduction-cooled with Gifford-McMahon cycle cryocoolers is used to develop and refine design and construction techniques. The study of these techniques and their effect on operations provides a better understanding of the use of cryogen free magnets in future accelerator projects. A cryogen-free, superconducting HTS magnet possesses certain operational advantages over cryogenically cooled, low temperature superconductingmore » magnets.« less

Technical Challenges and Potential Solutions for Cross-Country Multi-Terminal Superconducting DC Power Cables

NASA Astrophysics Data System (ADS)

Al-Taie, A.; Graber, L.; Pamidi, S. V.

2017-12-01

Opportunities for applications of high temperature superconducting (HTS) DC power cables for long distance power transmission in increasing the reliability of the electric power grid and to enable easier integration of distributed renewable sources into the grid are discussed. The gaps in the technology developments both in the superconducting cable designs and cryogenic systems as well as power electronic devices are identified. Various technology components in multi-terminal high voltage DC power transmission networks and the available options are discussed. The potential of ongoing efforts in the development of superconducting DC transmission systems is discussed.

Design, development and calibration of HTS wire based LOX level sensor probe

NASA Astrophysics Data System (ADS)

Karunanithi, R.; Jacob, S.; Nadig, D. S.; Prasad, M. V. N.; Gour, A. S.; Gowthaman, M.; Deekshith, P.; Shrivastava, V.

2014-01-01

For space applications, the weight of the liquid level sensors are of major concern as they affect the payload fraction and hence the cost. An attempt is made to design and test a light weight High Temperature Superconductor (HTS) wire based liquid level sensor for Liquid Oxygen (LOX) tank used in the cryostage of the spacecraft. The total resistance value measured of the HTS wire is inversely proportional to the liquid level. A HTS wire (SF12100) of 12mm width and 2.76m length without copper stabilizer has been used in the level sensor. The developed HTS wire based LOX level sensor is calibrated against a discrete diode array type level sensor. Liquid Nitrogen (LN2) and LOX has been used as cryogenic fluid for the calibration purpose. The automatic data logging for the system has been done using LabVIEW11. The net weight of the developed sensor is less than 1 kg.

Chemical stability of high-temperature superconductors

NASA Technical Reports Server (NTRS)

Bansal, Narottam P.

1992-01-01

A review of the available studies on the chemical stability of the high temperature superconductors (HTS) in various environments was made. The La(1.8)Ba(0.2)CuO4 HTS is unstable in the presence of H2O, CO2, and CO. The YBa2Cu3O(7-x) superconductor is highly susceptible to degradation in different environments, especially water. The La(2-x)Ba(x)CuO4 and Bi-Sr-Ca-Cu-O HTS are relatively less reactive than the YBa2Cu3O(7-x). Processing of YBa2Cu3O(7-x) HTS in purified oxygen, rather than in air, using high purity noncarbon containing starting materials is recommended. Exposure of this HTS to the ambient atmosphere should also be avoided at all stages during processing and storage. Devices and components made out of these oxide superconductors would have to be protected with an impermeable coating of a polymer, glass, or metal to avoid deterioration during use.

Measurements and tests of HTS bulk material in resistive fault current limiters

NASA Astrophysics Data System (ADS)

Noe, M.; Juengst, K.-P.; Werfel, F. N.; Elschner, S.; Bock, J.; Wolf, A.; Breuer, F.

2002-08-01

The application of superconducting fault current limiters (SCFCL) depends highly on their technical and economical benefits. Therefore it is obvious that the main requirements on the SCFCL are a reliable, fail-safe and rapid current limitation, low losses, and an inexpensive production. As a potential candidate material we have investigated HTS bulk material in resistive fault current limiters. Our report focuses on the E- j-curves, the AC-losses and the quench behaviour of melt cast processed-BSCCO 2212 and melt textured polycrystalline-YBCO 123. Within a temperature range from 64 to 80 K E- j-curves and AC losses of HTS elements were measured. The measurement results show that HTS bulk material meets the SCFCL specifications. In order to avoid hot spots during limitation and to improve mechanical stability a metallic bypass is needed. First test results of the quench behaviour of HTS bulk material with metallic bypass demonstrate safe limitation up to the specified electrical field of 100 V/m.

Analysis and experimental study of wireless power transfer with HTS coil and copper coil as the intermediate resonators system

NASA Astrophysics Data System (ADS)

Wang, Xiufang; Nie, Xinyi; Liang, Yilang; Lu, Falong; Yan, Zhongming; Wang, Yu

2017-01-01

Intermediate resonator (repeater) between transmitter and receiver can significantly increase the distance of wireless power transfer (WPT) and the efficiency of wireless power transfer. The wireless power transfer via strongly coupled magnetic resonances with an high temperature superconducting (HTS) coil and copper coil as intermediate resonators was presented in this paper. The electromagnetic experiment system under different conditions with different repeating coils were simulated by finite element software. The spatial distribution patterns of magnetic induction intensity at different distances were plotted. In this paper, we examined transfer characteristics with HTS repeating coil and copper repeating coil at 77 K and 300 K, respectively. Simulation and experimental results show that HTS and copper repeating coil can effectively enhance the space magnetic induction intensity, which has significant effect on improving the transmission efficiency and lengthening transmission distance. We found that the efficiency and the distance of wireless power transfer system with an HTS coil as repeater is much higher by using of copper coil as repeater.

Transient analysis of an HTS DC power cable with an HVDC system

NASA Astrophysics Data System (ADS)

Dinh, Minh-Chau; Ju, Chang-Hyeon; Kim, Jin-Geun; Park, Minwon; Yu, In-Keun; Yang, Byeongmo

2013-11-01

The operational characteristics of a superconducting DC power cable connected to a highvoltage direct current (HVDC) system are mainly concerned with the HVDC control and protection system. To confirm how the cable operates with the HVDC system, verifications using simulation tools are needed. This paper presents a transient analysis of a high temperature superconducting (HTS) DC power cable in connection with an HVDC system. The study was conducted via the simulation of the HVDC system and a developed model of the HTS DC power cable using a real time digital simulator (RTDS). The simulation was performed with some cases of short circuits that may have caused system damage. The simulation results show that during the faults, the quench did not happen with the HTS DC power cable because the HVDC controller reduced some degree of the fault current. These results could provide useful data for the protection design of a practical HVDC and HTS DC power cable system.

Comparison of bioluminescent kinase assays using substrate depletion and product formation.

PubMed

Tanega, Cordelle; Shen, Min; Mott, Bryan T; Thomas, Craig J; MacArthur, Ryan; Inglese, James; Auld, Douglas S

2009-12-01

Assays for ATPases have been enabled for high-throughput screening (HTS) by employing firefly luciferase to detect the remaining ATP in the assay. However, for any enzyme assay, measurement of product formation is a more sensitive assay design. Recently, technologies that allow detection of the ADP product from ATPase reactions have been described using fluorescent methods of detection. We describe here the characterization of a bioluminescent assay that employs firefly luciferase in a coupled-enzyme assay format to enable detection of ADP levels from ATPase assays (ADP-Glo, Promega Corp.). We determined the performance of the ADP-Glo assay in 1,536-well microtiter plates using the protein kinase Clk4 and a 1,352 member kinase focused combinatorial library. The ADP-Glo assay was compared to the Clk4 assay performed using a bioluminescence ATP-depletion format (Kinase-Glo, Promega Corp). We performed this analysis using quantitative HTS (qHTS) where we determined potency values for all library members and identified approximately 300 compounds with potencies ranging from as low as 50 nM to >10 microM, yielding a robust dataset for the comparison. Both assay formats showed high performance (Z'-factors approximately 0.9) and showed a similar potency distribution for the actives. We conclude that the bioluminescence ADP detection assay system is a viable generic alternative to the widely used ATP-depletion assay for ATPases and discuss the advantages and disadvantages of both approaches.

Using In Vitro High-Throughput Screening Data for Predicting ...

EPA Pesticide Factsheets

Today there are more than 80,000 chemicals in commerce and the environment. The potential human health risks are unknown for the vast majority of these chemicals as they lack human health risk assessments, toxicity reference values and risk screening values. We aim to use computational toxicology and quantitative high throughput screening (qHTS) technologies to fill these data gaps, and begin to prioritize these chemicals for additional assessment. By coupling qHTS data with adverse outcome pathways (AOPs) we can use ontologies to make predictions about potential hazards and to identify those assays which are sufficient to infer these same hazards. Once those assays are identified, we can use bootstrap natural spline-based metaregression to integrate the evidence across multiple replicates or assays (if a combination of assays are together necessary to be sufficient). In this pilot, we demonstrate how we were able to identify that benzo[k]fluoranthene (B[k]F) may induce DNA damage and steatosis using qHTS data and two separate AOPs. We also demonstrate how bootstrap natural spline-based metaregression can be used to integrate the data across multiple assay replicates to generate a concentration-response curve. We used this analysis to calculate an internal point of departure of 0.751µM and risk-specific concentrations of 0.378µM for both 1:1,000 and 1:10,000 additive risk for B[k]F induced DNA damage based on the p53 assay. Based on the available evidence, we

Automation of Data Analysis Programs Used in the Cryogenic Characterization of Superconducting Microwave Resonators

NASA Technical Reports Server (NTRS)

Creason, A. S.; Miranda, F. A.

1996-01-01

Knowledge of the microwave properties at cryogenic temperatures of components fabricated using High-Temperature-Superconductors (HTS) is useful in the design of HTS-based microwave circuits. Therefore, fast and reliable characterization techniques have been developed to study the aforementioned properties. In this paper, we discuss computer analysis techniques employed in the cryogenic characterization of HTS-based resonators. The revised data analysis process requires minimal user input. and organizes the data in a form that is easily accessible by the user for further examination. These programs retrieve data generated during the cryogenic characterization at microwave frequencies of HTS based resonators and use it to calculate parameters such as the loaded and unloaded quality factors (Q and Q(sub o), respectively), the resonant frequency (f(sub o)), and the coupling coefficient (k), which are important quantities in the evaluation of HTS resonators. While the data are also stored for further use, the programs allow the user to obtain a graphical representation of any of the measured parameters as a function of temperature soon after the completion of the cryogenic measurement cycle. Although these programs were developed to study planar HTS-based resonators operating in the reflection mode, they could also be used in the cryogenic characterization of two ports (i.e., reflection/transmission) resonators.

A New Training for Older Adults Using Combined Neuromuscular Electrical Stimulation and Volitional Contraction: A Pilot Study.

PubMed

Takano, Yoshio; Matsuse, Hiroo; Tsukada, Yuuya; Omoto, Masayuki; Hashida, Ryuki; Shiba, Naoto

2016-01-01

The hybrid training system (HTS) resists the motion of a volitionally contracting agonist muscle using force generated by its electrically stimulated antagonist. We have developed a new training method using the principle of HTS. This study was designed to evaluate the effect of HTS with electrical stimulation on muscle strength and physical function by comparing it against training without electrical stimulation in older adults. 16 subjects were randomly divided into two groups: the squat and single leg lift training (control, CTR) group, and the CTR with HTS training group. Some electrical stimulation was applied to the quadriceps and hamstring muscles in the HTS group. The subjects performed training for 25 min per session 3 times a week for 12 weeks. At points before and after the research maximal isokinetic torque, knee-flexors (KFT) and knee-extensors (KET), a one-leg standing test (OLT), a functional reach test (FRT), a 10-meter maximal gait time (10MGT) and Timed up & go test (TUG) were conducted. None of the subjects had any injuries during the study period. TUG significantly improved after the training period in both the HTS group (7.15 sec to 6.01 sec P = 0.01) and in the CTR.

Knowledge, attitudes, and normative beliefs as predictors of hookah smoking initiation: a longitudinal study of university students.

PubMed

Sidani, Jaime E; Shensa, Ariel; Barnett, Tracey E; Cook, Robert L; Primack, Brian A

2014-06-01

While cross-sectional studies have shown that hookah tobacco smoking (HTS) is an increasingly popular behavior among university students, little is known about factors associated with initiation. This study sought to determine associations between knowledge, attitudes, and normative beliefs and initiation of HTS among university students. Data were from a prospective longitudinal cohort study of 569 randomly selected first- and second-year university students. Online questionnaires that were developed in accordance with our composite theoretical model were completed in September 2010 and April 2011. About one-seventh (13%) of participants initiated HTS by follow-up. Positive attitudes and favorable normative beliefs were associated with increased adjusted odds of initiation (AOR = 4.12, 95% CI = 2.56, 6.59; and AOR = 2.01, 95% CI = 1.35, 2.99, respectively), while negative attitudes were associated with decreased adjusted odds (AOR = 0.62, 95% CI = 0.48, 0.80). Correct knowledge regarding toxicants associated with HTS was not significantly associated with initiation. While positive attitudes and favorable normative beliefs are associated with initiation of HTS in a cohort of never-users, increased knowledge about toxins is not associated with lower initiation. It may be particularly valuable for educational interventions to attempt to alter positive attitudes and normative beliefs related to HTS.

Use of high-throughput in vitro toxicity screening data in cancer hazard evaluations by IARC Monograph Working Groups

PubMed Central

Chiu, Weihsueh A.; Guyton, Kathryn Z.; Martin, Matthew T.; Reif, David M.; Rusyn, Ivan

2017-01-01

Evidence regarding carcinogenic mechanisms serves a critical role in International Agency for Research on Cancer (IARC) Monograph evaluations. Three recent IARC Working Groups pioneered inclusion of the US Environmental Protection Agency (EPA) ToxCast program high-throughput screening (HTS) data to supplement other mechanistic evidence. In Monograph V110, HTS profiles were compared between perfluorooctanoic acid (PFOA) and prototypical activators across multiple nuclear receptors. For Monograph V112 -113, HTS assays were mapped to 10 key characteristics of carcinogens identified by an IARC expert group, and systematically considered as an additional mechanistic data stream. Both individual assay results and ToxPi-based rankings informed mechanistic evaluations. Activation of multiple nuclear receptors in HTS assays showed that PFOA targets peroxisome proliferator activated and other receptors. ToxCast assays substantially covered 5 of 10 key characteristics, corroborating literature evidence of “induces oxidative stress” and “alters cell proliferation, cell death or nutrient supply” and filling gaps for “modulates receptor-mediated effects.” Thus, ToxCast HTS data were useful both in evaluating specific mechanistic hypotheses and in the overall evaluation of mechanistic evidence. However, additional HTS assays are needed to provide more comprehensive coverage of the 10 key characteristics of carcinogens that form the basis of current IARC mechanistic evaluations. PMID:28738424

Use of high-throughput in vitro toxicity screening data in cancer hazard evaluations by IARC Monograph Working Groups.

PubMed

Chiu, Weihsueh A; Guyton, Kathryn Z; Martin, Matthew T; Reif, David M; Rusyn, Ivan

2018-01-01

Evidence regarding carcinogenic mechanisms serves a critical role in International Agency for Research on Cancer (IARC) Monograph evaluations. Three recent IARC Working Groups pioneered inclusion of the US Environmental Protection Agency (EPA) ToxCast program high-throughput screening (HTS) data to supplement other mechanistic evidence. In Monograph V110, HTS profiles were compared between perfluorooctanoic acid (PFOA) and prototypical activators across multiple nuclear receptors. For Monograph V112-113, HTS assays were mapped to 10 key characteristics of carcinogens identified by an IARC expert group, and systematically considered as an additional mechanistic data stream. Both individual assay results and ToxPi-based rankings informed mechanistic evaluations. Activation of multiple nuclear receptors in HTS assays showed that PFOA targets not only peroxisome proliferator activated receptors, but also other receptors. ToxCast assays substantially covered 5 of 10 key characteristics, corroborating literature evidence of "induces oxidative stress" and "alters cell proliferation, cell death or nutrient supply" and filling gaps for "modulates receptor-mediated effects." Thus, ToxCast HTS data were useful both in evaluating specific mechanistic hypotheses and in contributing to the overall evaluation of mechanistic evidence. However, additional HTS assays are needed to provide more comprehensive coverage of the 10 key characteristics of carcinogens that form the basis of current IARC mechanistic evaluations.

Ictal semiology in hippocampal versus extrahippocampal temporal lobe epilepsy.

PubMed

Gil-Nagel, A; Risinger, M W

1997-01-01

We have analysed retrospectively the clinical features and electroencephalograms in 35 patients with complex partial seizures of temporal lobe origin who were seizure-free after epilepsy surgery. Two groups were differentiated for statistical analysis: 16 patients had hippocampal temporal lobe seizures (HTS) and 19 patients had extrahippocampal temporal lobe seizures (ETS) associated with a small tumour of the lateral or inferior temporal cortex. All patients in the HTS group had ictal onset verified with intracranial recordings (depth or subdural electrodes). In the ETS group, extrahippocampal onset was verified with intracranial recordings in eight patients and assumed, because of failure of a previous amygdalohippocampectomy, in one patient. Historical information, ictal semiology and ictal EEG of typical seizures were analysed in each patient. The occurrence of early and late oral automatisms and dystonic posturing of an upper extremity was analysed separately. A prior history of febrile convulsions was obtained in 13 HTS patients (81.3%) but in none with ETS (P < 0.0001, Fisher's exact test). An epigastric aura preceded seizures in five patients with HTS (31.3%) and none with ETS (P = 0.0135, Fisher's exact test), while an aura with experiential content was recalled by nine patients with ETS (47.4%) and none with HTS (P = 0.0015), Fisher's exact test). Early oral automatisms occurred in 11 patients with HTS (68.8%) and in two with ETS (10.5%) (P = 0.0005, Fisher's exact test). Early motor involvement of the contralateral upper extremity without oral automatisms occurred in three patients with HTS (18.8%) and in 10 with ETS (52.6%) (P = 0.0298, Fisher's exact test). Arrest reaction, vocalization, speech, facial grimace, postictal cough, late oral automatisms and late motor involvement of the contralateral arm and hand occurred with similar frequency in both groups. These observations show that the early clinical features of HTS and ETS are different.

Diagnostic value and cost-benefit analysis of 24 hours ambulatory blood pressure monitoring in primary care in Portugal

PubMed Central

2013-01-01

Background Hypertensive patients (HTs) are usually attended in primary care (PC). We aimed to assess the diagnostic accuracy and cost-benefit ratio of 24-hour ambulatory blood pressure monitoring (ABPM) in all newly diagnosed hypertensive patients (HTs) attended in PC. Methods In a cross-sectional study ABPM was recorded in all 336 never treated HTs (Office BP ≥140 and/or ≥ 90 mm Hg) that were admitted during 16 months. Since benefits from drug treatment in white-coat hypertension (WCH) remain unproven, a cost benefit estimation of a general use of ABPM (vs absence of ABPM) in HTs was calculated comparing the cost of usual medical assistance of HTs only diagnosed in office with that based both on refraining from drug treatment all subjects identified as WCH and on the reduction by half of the frequency of biochemical exams and doctor visits. Results Women were 56%, age 51 ± 14 years and BMI 27 ± 4 Kg/m2. Out of these, 206 were considered as true HTs, daytime ABPM ≥ 135 and/or ≥85 mm Hg and 130 (38,7%) were identified as having white coat hypertension (WCH), daytime ABPM <135/85 mm Hg. Versus HTs, WCH group showed higher percentage of women (68% vs 51%) and lower values of an index composed by the association of cardiovascular risk factors. We estimated that with ABPM total medical expenses can be reduced by 23% (157.500 euros) with a strategy based on ABPM for 1000 patients followed for 2 years. Conclusions In PC, the widespread use of ABPM in newly diagnosed HTs increases diagnostic accuracy of hypertension, improves cardiovascular risk stratification, reduces health expenses showing a highly favourable benefit-cost ratio vs a strategy without ABPM. PMID:23937261

Evaluation of DC electric field distribution of PPLP specimen based on the measurement of electrical conductivity in LN2

NASA Astrophysics Data System (ADS)

Hwang, Jae-Sang; Seong, Jae-Kyu; Shin, Woo-Ju; Lee, Jong-Geon; Cho, Jeon-Wook; Ryoo, Hee-Suk; Lee, Bang-Wook

2013-11-01

High temperature superconducting (HTS) cable has been paid much attention due to its high efficiency and high current transportation capability, and it is also regarded as eco-friendly power cable for the next generation. Especially for DC HTS cable, it has more sustainable and stable properties compared to AC HTS cable due to the absence of AC loss in DC HTS cable. Recently, DC HTS cable has been investigated competitively all over the world, and one of the key components of DC HTS cable to be developed is a cable joint box considering HVDC environment. In order to achieve the optimum insulation design of the joint box, analysis of DC electric field distribution of the joint box is a fundamental process to develop DC HTS cable. Generally, AC electric field distribution depends on relative permittivity of dielectric materials but in case of DC, electrical conductivity of dielectric material is a dominant factor which determines electric field distribution. In this study, in order to evaluate DC electric field characteristics of the joint box for DC HTS cable, polypropylene laminated paper (PPLP) specimen has been prepared and its DC electric field distribution was analyzed based on the measurement of electrical conductivity of PPLP in liquid nitrogen (LN2). Electrical conductivity of PPLP in LN2 has not been reported yet but it should be measured for DC electric field analysis. The experimental works for measuring electrical conductivity of PPLP in LN2 were presented in this paper. Based on the experimental works, DC electric field distribution of PPLP specimen was fully analyzed considering the steady state and the transient state of DC. Consequently, it was possible to determine the electric field distribution characteristics considering different DC applying stages including DC switching on, DC switching off and polarity reversal conditions.

Bolts from Orion: Destroying Mobile Surface-to-Air Missile Systems with Lethal Autonomous Aircraft

DTIC Science & Technology

2016-07-01

era SAMs that had been upgraded by Ukrainian contractors . During the operation, Russian aircraft’s 10 electronic countermeasures could not...main SEAD asset is the F-16 CJ equipped with the HARM targeting system ( HTS ). The HTS can autonomously locate and identify threat radars and pass...targeting information to the HARMs before launch. The HTS can also provide targeting 13 information to global positioning system (GPS) guided

High temperature superconductor analog electronics for millimeter-wavelength communications

NASA Technical Reports Server (NTRS)

Romanofsky, R. R.; Bhasin, K. B.

1991-01-01

The performance of high temperature superconductor (HTS) passive microwave circuits up to X-band was encouraging when compared to their metallic counterparts. The extremely low surface resistance of HTS films up to about 10 GHz enables a reduction in loss by as much as 100 times compared to copper when both materials are kept at about 77 K. However, a superconductor's surface resistance varies in proportion to the frequency squared. Consequently, the potential benefit of HTS materials to millimeter-wave communications requires careful analysis. A simple ring resonator was used to evaluate microstrip losses at Ka-band. Additional promising components were investigated such as antennas and phase shifters. Prospects for HTS to favorable impact millimeter-wave communications systems are discussed.

Dynamic motion modes of high temperature superconducting maglev on a 45-m long ring test line

NASA Astrophysics Data System (ADS)

Lei, W. Y.; Qian, N.; Zheng, J.; Jin, L. W.; Zhang, Y.; Deng, Z. G.

2017-10-01

With the development of high temperature superconducting (HTS) maglev, studies on the running stability have become more and more significant to ensure the operation safety. An experimental HTS maglev vehicle was tested on a 45-m long ring test line under the speed from 4 km/h to 20 km/h. The lateral and vertical acceleration signals of each cryostat were collected by tri-axis accelerometers in real time. By analyzing the phase relationship of acceleration signals on the four cryostats, several typical motion modes of the HTS maglev vehicle, including lateral, yaw, pitch and heave motions were observed. This experimental finding is important for the next improvement of the HTS maglev system.

sRNAtoolboxVM: Small RNA Analysis in a Virtual Machine.

PubMed

Gómez-Martín, Cristina; Lebrón, Ricardo; Rueda, Antonio; Oliver, José L; Hackenberg, Michael

2017-01-01

High-throughput sequencing (HTS) data for small RNAs (noncoding RNA molecules that are 20-250 nucleotides in length) can now be routinely generated by minimally equipped wet laboratories; however, the bottleneck in HTS-based research has shifted now to the analysis of such huge amount of data. One of the reasons is that many analysis types require a Linux environment but computers, system administrators, and bioinformaticians suppose additional costs that often cannot be afforded by small to mid-sized groups or laboratories. Web servers are an alternative that can be used if the data is not subjected to privacy issues (what very often is an important issue with medical data). However, in any case they are less flexible than stand-alone programs limiting the number of workflows and analysis types that can be carried out.We show in this protocol how virtual machines can be used to overcome those problems and limitations. sRNAtoolboxVM is a virtual machine that can be executed on all common operating systems through virtualization programs like VirtualBox or VMware, providing the user with a high number of preinstalled programs like sRNAbench for small RNA analysis without the need to maintain additional servers and/or operating systems.

Evaluation of the Combined Application of Neuromuscular Electrical Stimulation and Volitional Contractions on Thigh Muscle Strength, Knee Pain and Physical Performance in Women at Risk for Knee Osteoarthritis: A Randomized Controlled Trial.

PubMed

Rabe, Kaitlin G; Matsuse, Hiroo; Jackson, Anthony; Segal, Neil A

2018-05-28

Knee osteoarthritis (OA) is a leading cause of disability that is associated with quadriceps weakness. However, strengthening in people with or with risk factors for knee OA can be poorly tolerated. To assess the efficacy of a twelve-week low-load exercise program, using a hybrid training system (HTS) that utilizes the combination of neuromuscular electrical stimulation and volitional contractions, for improving thigh muscle strength, knee pain and physical performance in women with or with risk factors for knee OA. Randomized, single-blind, controlled trial SETTING: Exercise training laboratory PARTICIPANTS: Forty-two women, age 44-85 years, with risk factors for knee OA INTERVENTIONS: Participants randomized to 12 weeks of biweekly low-load resistance training either with HTS or on an isokinetic dynamometer (control). Maximum isokinetic knee extensor torque. Secondary measures included: maximum isokinetic knee flexor torque, knee pain (KOOS), and timed 20-meter walk and chair-stand tests. HTS and control both resulted in muscle strengthening, reduced knee pain and improved physical performance. HTS group quadriceps and hamstring strength increased by 0.06±0.04 Nm/kg (p>.05) and 0.05±0.02 Nm/kg (p=.02), respectively. Control group quadriceps and hamstring strength increased by 0.03±0.04 Nm/kg (p>.05) and 0.06±0.02 Nm/kg (p=.009), respectively. Knee pain improved by 11.9±11.5 points (p<.001) for the HTS group and 14.1±15.4 points (p=.001) for the control group. 20-meter walk time decreased by 1.60±2.04 seconds (p=.005) and 0.95±1.2 seconds (p=.004), and chair stand time decreased by 4.8±10.0 seconds (p>.05) and 1.9±4.7 seconds (p>.05) in the HTS and control groups, respectively. These results did not differ statistically between HTS and control groups. These results suggest HTS is effective for improving pain and physical performance in women with risk factors for knee OA. However, HTS does not appear to be superior to low-load resistance training for improving muscle strength, pain or physical function. Copyright © 2018 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

Use of in Vitro HTS-Derived Concentration–Response Data as Biological Descriptors Improves the Accuracy of QSAR Models of in Vivo Toxicity

PubMed Central

Sedykh, Alexander; Zhu, Hao; Tang, Hao; Zhang, Liying; Richard, Ann; Rusyn, Ivan; Tropsha, Alexander

2011-01-01

Background Quantitative high-throughput screening (qHTS) assays are increasingly being used to inform chemical hazard identification. Hundreds of chemicals have been tested in dozens of cell lines across extensive concentration ranges by the National Toxicology Program in collaboration with the National Institutes of Health Chemical Genomics Center. Objectives Our goal was to test a hypothesis that dose–response data points of the qHTS assays can serve as biological descriptors of assayed chemicals and, when combined with conventional chemical descriptors, improve the accuracy of quantitative structure–activity relationship (QSAR) models applied to prediction of in vivo toxicity end points. Methods We obtained cell viability qHTS concentration–response data for 1,408 substances assayed in 13 cell lines from PubChem; for a subset of these compounds, rodent acute toxicity half-maximal lethal dose (LD50) data were also available. We used the k nearest neighbor classification and random forest QSAR methods to model LD50 data using chemical descriptors either alone (conventional models) or combined with biological descriptors derived from the concentration–response qHTS data (hybrid models). Critical to our approach was the use of a novel noise-filtering algorithm to treat qHTS data. Results Both the external classification accuracy and coverage (i.e., fraction of compounds in the external set that fall within the applicability domain) of the hybrid QSAR models were superior to conventional models. Conclusions Concentration–response qHTS data may serve as informative biological descriptors of molecules that, when combined with conventional chemical descriptors, may considerably improve the accuracy and utility of computational approaches for predicting in vivo animal toxicity end points. PMID:20980217

ARQiv-HTS, a versatile whole-organism screening platform enabling in vivo drug discovery at high-throughput rates

PubMed Central

White, David T; Eroglu, Arife Unal; Wang, Guohua; Zhang, Liyun; Sengupta, Sumitra; Ding, Ding; Rajpurohit, Surendra K; Walker, Steven L; Ji, Hongkai; Qian, Jiang; Mumm, Jeff S

2017-01-01

The zebrafish has emerged as an important model for whole-organism small-molecule screening. However, most zebrafish-based chemical screens have achieved only mid-throughput rates. Here we describe a versatile whole-organism drug discovery platform that can achieve true high-throughput screening (HTS) capacities. This system combines our automated reporter quantification in vivo (ARQiv) system with customized robotics, and is termed ‘ARQiv-HTS’. We detail the process of establishing and implementing ARQiv-HTS: (i) assay design and optimization, (ii) calculation of sample size and hit criteria, (iii) large-scale egg production, (iv) automated compound titration, (v) dispensing of embryos into microtiter plates, and (vi) reporter quantification. We also outline what we see as best practice strategies for leveraging the power of ARQiv-HTS for zebrafish-based drug discovery, and address technical challenges of applying zebrafish to large-scale chemical screens. Finally, we provide a detailed protocol for a recently completed inaugural ARQiv-HTS effort, which involved the identification of compounds that elevate insulin reporter activity. Compounds that increased the number of insulin-producing pancreatic beta cells represent potential new therapeutics for diabetic patients. For this effort, individual screening sessions took 1 week to conclude, and sessions were performed iteratively approximately every other day to increase throughput. At the conclusion of the screen, more than a half million drug-treated larvae had been evaluated. Beyond this initial example, however, the ARQiv-HTS platform is adaptable to almost any reporter-based assay designed to evaluate the effects of chemical compounds in living small-animal models. ARQiv-HTS thus enables large-scale whole-organism drug discovery for a variety of model species and from numerous disease-oriented perspectives. PMID:27831568

US effort on HTS power transformers

NASA Astrophysics Data System (ADS)

Mehta, S.

2011-11-01

Waukesha Electric Systems has been working in HTS power transformers development program under the auspices of US Government Department of Energy since 1994. This presentation will describe various milestones for this program and program history along with the lessons learned along the way. Our motivations for working on this development program based on man benefits offered by HTS power transformers to power delivery systems will be discussed. Based on various issues encountered during execution of many HTS projects, DOE has set up an independent program review process that is lead by team of experts. This team reviews are integral part of all DOE HTS projects. Success of all projects would be greatly enhanced by identifying critical issues early in the program. Requiring appropriate actions to mitigate the issues before processing further will lead to proactive interrogation and incorporation of expert's ideas in the project plans. Working of this review process will be also described in this presentation. Waukesha Electric Systems team including: Superpower-Inc, Oak Ridge National Laboratory, University of Houston Center for Superconductivity and Southern California Edison company was awarded a cost share grant by US Government in 2010 for development of a fault current limiting HTS power transformer. This multi year's program will require design, manufacture, installation, and monitoring of a 28 MVA tree phase transformer installed at Irvine CA. Smart Grid demonstration site. Transformer specifications along with requirements for fault current limiting and site requirement will be discussed. Design and development of various sub systems in support of this program including: HTS conductor performance specification, Dielectric system design approach, Dewar development for containing phase assemblies, cryo-cooling system design approach, etc. will be described. Finally; overall program schedule, critical milestone events, test plans and progress to date will be reported.

Performance of the BG1Luc ER TA method in a qHTS format.

PubMed

Ceger, Patricia; Allen, David; Huang, Ruili; Xia, Menghang; Casey, Warren

2015-01-01

In 2012, the BG1Luc4E2 estrogen receptor (ER) transactivation (TA) method (BG1Luc ER TA) was accepted by U.S. regulatory agencies and the Organisation for Economic Co-operation and Development to detect substances with ER agonist activity. The method is now part of the Tier 1 testing battery in the Environmental Protection Agency's Endocrine Disruptor Screening Program. The BG1Luc ER TA method uses the BG1 ovarian cell line that endogenously expresses full-length ER (α and β) and is stably transfected with a plasmid containing four estrogen responsive elements upstream of a luciferase reporter gene. To allow increased throughput and testing efficiency, the BG1Luc ER TA ("BG1 manual") method was adapted for quantitative high-throughput screening (BG1 qHTS) in the U.S. Tox21 testing program. The BG1 qHTS test method was used to test approximately 10,000 chemicals three times each, and concentration-response data (n=15) were analyzed to evaluate test method performance. The balanced accuracy of the BG1 qHTS test method (97% [32/33]) was determined by comparing results to ER TA performance standards for the BG1 manual method. Concordance between the BG1 manual and qHTS methods was 92% (57/62) when calculated for a larger set of non-reference chemicals tested in both methods. These data demonstrate that the performance of the BG1 qHTS is similar to the currently accepted BG1 manual method, thereby establishing the utility of the BG1 qHTS method for identifying ER active environmental chemicals.

HTS flux concentrator for non-invasive sensing of charged particle beams

NASA Astrophysics Data System (ADS)

Hao, L.; Gallop, J. C.; Macfarlane, J. C.; Carr, C.; Donaldson, G. B.

2001-12-01

The principle of the superconducting cryogenic current comparator (CCC) is applied to the non-invasive sensing of charged-particle beams (ions, electrons). With the use of HTS components it is feasible to envisage applications, for example, in precision mass spectrometry and real-time monitoring of ion-beam implantation currents. Recent simulations and experimental measurements of the flux concentration ratio, frequency response and linearity of a prototype HTS-CCC operating at 77 K are described.

Progress in American Superconductor's HTS wire and optimization for fault current limiting systems

NASA Astrophysics Data System (ADS)

Malozemoff, Alexis P.

2016-11-01

American Superconductor has developed composite coated conductor tape-shaped wires using high temperature superconductor (HTS) on a flexible substrate with laminated metal stabilizer. Such wires enable many applications, each requiring specific optimization. For example, coils for HTS rotating machinery require increased current density J at 25-50 K. A collaboration with Argonne, Brookhaven and Los Alamos National Laboratories and several universities has increased J using an optimized combination of precipitates and ion irradiation defects in the HTS. Major commercial opportunities also exist to enhance electric power grid resiliency by linking substations with distribution-voltage HTS power cables [10]. Such links provide alternative power sources if one substation's transmission-voltage power is compromised. But they must also limit fault currents which would otherwise be increased by such distribution-level links. This can be done in an HTS cable, exploiting the superconductor-to-resistive transition when current exceeds the wires' critical J. A key insight is that such transitions are usually nonuniform; so the wire must be designed to prevent localized hot spots from damaging the wire or even generating gas bubbles in the cable causing dielectric breakdown. Analysis shows that local heating can be minimized by increasing the composite tape's total thickness, decreasing its total resistance in the normal state and decreasing its critical J. This conflicts with other desirable wire characteristics. Optimization of these conflicting requirements is discussed.

Knowledge, Attitudes, and Normative Beliefs as Predictors of Hookah Smoking Initiation: A Longitudinal Study of University Students

PubMed Central

2014-01-01

Introduction: While cross-sectional studies have shown that hookah tobacco smoking (HTS) is an increasingly popular behavior among university students, little is known about factors associated with initiation. This study sought to determine associations between knowledge, attitudes, and normative beliefs and initiation of HTS among university students. Methods: Data were from a prospective longitudinal cohort study of 569 randomly selected first- and second-year university students. Online questionnaires that were developed in accordance with our composite theoretical model were completed in September 2010 and April 2011. Results: About one-seventh (13%) of participants initiated HTS by follow-up. Positive attitudes and favorable normative beliefs were associated with increased adjusted odds of initiation (AOR = 4.12, 95% CI = 2.56, 6.59; and AOR = 2.01, 95% CI = 1.35, 2.99, respectively), while negative attitudes were associated with decreased adjusted odds (AOR = 0.62, 95% CI = 0.48, 0.80). Correct knowledge regarding toxicants associated with HTS was not significantly associated with initiation. Conclusions: While positive attitudes and favorable normative beliefs are associated with initiation of HTS in a cohort of never-users, increased knowledge about toxins is not associated with lower initiation. It may be particularly valuable for educational interventions to attempt to alter positive attitudes and normative beliefs related to HTS. PMID:24323574

Use of in Vitro HTS-Derived Concentration-Response Data as ...

EPA Pesticide Factsheets

Background: Quantitative high-throughput screening (qHTS) assays are increasingly being employed to inform chemical hazard identification. Hundreds of chemicals have been tested in dozens of cell lines across extensive concentration ranges by the National Toxicology Program in collaboration with the NIH Chemical Genomics Center. Objectives: To test a hypothesis that dose-response data points of the qHTS assays can serve as biological descriptors of assayed chemicals and, when combined with conventional chemical descriptors, may improve the accuracy of Quantitative Structure-Activity Relationship (QSAR) models applied to prediction of in vivo toxicity endpoints. Methods and Results: The cell viability qHTS concentration-response data for 1,408 substances assayed in 13 cell lines were obtained from PubChem; for a subset of these compounds rodent acute toxicity LD50 data were also available. The classification k Nearest Neighbor and Random Forest QSAR methods were employed for modeling LD50 data using either chemical descriptors alone (conventional models) or in combination with biological descriptors derived from the concentration-response qHTS data (hybrid models). Critical to our approach was the use of a novel noise-filtering algorithm to treat qHTS data. We show that both the external classification accuracy and coverage (i.e., fraction of compounds in the external set that fall within the applicability domain) of the hybrid QSAR models was superior to convent

Identification of Novel Pathogenicity Loci in Clostridium perfringens Strains That Cause Avian Necrotic Enteritis

PubMed Central

Parreira, Valeria R.; Marri, Pradeep R.; Rosey, Everett L.; Gong, Joshua; Songer, J. Glenn; Vedantam, Gayatri; Prescott, John F.

2010-01-01

Type A Clostridium perfringens causes poultry necrotic enteritis (NE), an enteric disease of considerable economic importance, yet can also exist as a member of the normal intestinal microbiota. A recently discovered pore-forming toxin, NetB, is associated with pathogenesis in most, but not all, NE isolates. This finding suggested that NE-causing strains may possess other virulence gene(s) not present in commensal type A isolates. We used high-throughput sequencing (HTS) technologies to generate draft genome sequences of seven unrelated C. perfringens poultry NE isolates and one isolate from a healthy bird, and identified additional novel NE-associated genes by comparison with nine publicly available reference genomes. Thirty-one open reading frames (ORFs) were unique to all NE strains and formed the basis for three highly conserved NE-associated loci that we designated NELoc-1 (42 kb), NELoc-2 (11.2 kb) and NELoc-3 (5.6 kb). The largest locus, NELoc-1, consisted of netB and 36 additional genes, including those predicted to encode two leukocidins, an internalin-like protein and a ricin-domain protein. Pulsed-field gel electrophoresis (PFGE) and Southern blotting revealed that the NE strains each carried 2 to 5 large plasmids, and that NELoc-1 and -3 were localized on distinct plasmids of sizes ∼85 and ∼70 kb, respectively. Sequencing of the regions flanking these loci revealed similarity to previously characterized conjugative plasmids of C. perfringens. These results provide significant insight into the pathogenetic basis of poultry NE and are the first to demonstrate that netB resides in a large, plasmid-encoded locus. Our findings strongly suggest that poultry NE is caused by several novel virulence factors, whose genes are clustered on discrete pathogenicity loci, some of which are plasmid-borne. PMID:20532244

Identification of novel pathogenicity loci in Clostridium perfringens strains that cause avian necrotic enteritis.

PubMed

Lepp, Dion; Roxas, Bryan; Parreira, Valeria R; Marri, Pradeep R; Rosey, Everett L; Gong, Joshua; Songer, J Glenn; Vedantam, Gayatri; Prescott, John F

2010-05-24

Type A Clostridium perfringens causes poultry necrotic enteritis (NE), an enteric disease of considerable economic importance, yet can also exist as a member of the normal intestinal microbiota. A recently discovered pore-forming toxin, NetB, is associated with pathogenesis in most, but not all, NE isolates. This finding suggested that NE-causing strains may possess other virulence gene(s) not present in commensal type A isolates. We used high-throughput sequencing (HTS) technologies to generate draft genome sequences of seven unrelated C. perfringens poultry NE isolates and one isolate from a healthy bird, and identified additional novel NE-associated genes by comparison with nine publicly available reference genomes. Thirty-one open reading frames (ORFs) were unique to all NE strains and formed the basis for three highly conserved NE-associated loci that we designated NELoc-1 (42 kb), NELoc-2 (11.2 kb) and NELoc-3 (5.6 kb). The largest locus, NELoc-1, consisted of netB and 36 additional genes, including those predicted to encode two leukocidins, an internalin-like protein and a ricin-domain protein. Pulsed-field gel electrophoresis (PFGE) and Southern blotting revealed that the NE strains each carried 2 to 5 large plasmids, and that NELoc-1 and -3 were localized on distinct plasmids of sizes approximately 85 and approximately 70 kb, respectively. Sequencing of the regions flanking these loci revealed similarity to previously characterized conjugative plasmids of C. perfringens. These results provide significant insight into the pathogenetic basis of poultry NE and are the first to demonstrate that netB resides in a large, plasmid-encoded locus. Our findings strongly suggest that poultry NE is caused by several novel virulence factors, whose genes are clustered on discrete pathogenicity loci, some of which are plasmid-borne.

The essential roles of chemistry in high-throughput screening triage

PubMed Central

Dahlin, Jayme L; Walters, Michael A

2015-01-01

It is increasingly clear that academic high-throughput screening (HTS) and virtual HTS triage suffers from a lack of scientists trained in the art and science of early drug discovery chemistry. Many recent publications report the discovery of compounds by screening that are most likely artifacts or promiscuous bioactive compounds, and these results are not placed into the context of previous studies. For HTS to be most successful, it is our contention that there must exist an early partnership between biologists and medicinal chemists. Their combined skill sets are necessary to design robust assays and efficient workflows that will weed out assay artifacts, false positives, promiscuous bioactive compounds and intractable screening hits, efforts that ultimately give projects a better chance at identifying truly useful chemical matter. Expertise in medicinal chemistry, cheminformatics and purification sciences (analytical chemistry) can enhance the post-HTS triage process by quickly removing these problematic chemotypes from consideration, while simultaneously prioritizing the more promising chemical matter for follow-up testing. It is only when biologists and chemists collaborate effectively that HTS can manifest its full promise. PMID:25163000

Thermal Insulation Performance of Flexible Piping for Use in HTS Power Cables

NASA Technical Reports Server (NTRS)

Fesmire, James E.; Augustynowicz, S. D.; Demko, J. A.; Thompson, Karen (Technical Monitor)

2001-01-01

High-temperature superconducting (HTS) cables that typically operate at temperatures below 80 K are being developed for power transmission. The practical application of HTS power cables will require the use of flexible piping to contain the cable and the liquid nitrogen coolant. A study of thermal performance of multilayer insulation (MLI) was conducted in geometries representing both rigid and flexible piping. This experimental study performed at the Cryogenics Test Laboratory of NASA Kennedy Space Center provides a framework for the development of cost-effective, efficient thermal insulation systems that will support these long-distance flexible lines containing HTS power cables. The overall thermal performance of the insulation system for a rigid configuration and for a flexible configuration, simulating a flexible HTS power cable, was determined by the steady-state liquid nitrogen boiloff method under the full range of vacuum levels. Two different cylindrically rolled material systems were tested: a standard MLI and a layered composite insulation (LCI). Comparisons of ideal MLI, MLI on rigid piping, and MLI between flexible piping are presented.

Large-scale HTS bulks for magnetic application

NASA Astrophysics Data System (ADS)

Werfel, Frank N.; Floegel-Delor, Uta; Riedel, Thomas; Goebel, Bernd; Rothfeld, Rolf; Schirrmeister, Peter; Wippich, Dieter

2013-01-01

ATZ Company has constructed about 130 HTS magnet systems using high-Tc bulk magnets. A key feature in scaling-up is the fabrication of YBCO melts textured multi-seeded large bulks with three to eight seeds. Except of levitation, magnetization, trapped field and hysteresis, we review system engineering parameters of HTS magnetic linear and rotational bearings like compactness, cryogenics, power density, efficiency and robust construction. We examine mobile compact YBCO bulk magnet platforms cooled with LN2 and Stirling cryo-cooler for demonstrator use. Compact cryostats for Maglev train operation contain 24 pieces of 3-seed bulks and can levitate 2500-3000 N at 10 mm above a permanent magnet (PM) track. The effective magnetic distance of the thermally insulated bulks is 2 mm only; the stored 2.5 l LN2 allows more than 24 h operation without refilling. 34 HTS Maglev vacuum cryostats are manufactured tested and operate in Germany, China and Brazil. The magnetic levitation load to weight ratio is more than 15, and by group assembling the HTS cryostats under vehicles up to 5 t total loads levitated above a magnetic track is achieved.

Assessment of High Temperature Superconducting (HTS) electric motors for rotorcraft propulsion

NASA Technical Reports Server (NTRS)

Doernbach, Jay

1990-01-01

The successful development of high temperature superconductors (HTS) could have a major impact on future aeronautical propulsion and aeronautical flight vehicle systems. Applications of high temperature superconductors have been envisioned for several classes of aeronautical systems, including subsonic and supersonic transports, hypersonic aircraft, V/STOL aircraft, rotorcraft and solar powered aircraft. The potential of HTS electric motors and generators for providing primary shaft power for rotorcraft propulsion is examined. Three different sized production helicopters were investigated; namely, the Bell Jet Ranger, the Sikorsky Black Hawk and the Sikorsky Super Stallion. These rotorcraft have nominal horsepower ratings of 500, 3600, and 13400 respectively. Preliminary results indicated that an all-electric HTS drive system produces an improvement in rotorcraft Takeoff Gross Weight (TOGW) for those rotorcraft with power ratings above 2000 horsepower. The predicted TOGW improvements are up to 9 percent for the medium-sized Sikorsky Black Hawk and up to 20 percent for the large-sized Sikorsky Super Stallion. The small-sized Bell Jet Ranger, however, experienced a penalty in TOGW with the all-electric HTS drive system.

Influence of experimental methods on crossing in magnetic force-gap hysteresis curve of HTS maglev system

NASA Astrophysics Data System (ADS)

Lu, Yiyun; Qin, Yujie; Dang, Qiaohong; Wang, Jiasu

2010-12-01

The crossing in magnetic levitation force-gap hysteresis curve of melt high-temperature superconductor (HTS) vs. NdFeB permanent magnet (PM) was experimentally studied. One HTS bulk and PM was used in the experiments. Four experimental methods were employed combining of high/low speed of movement of PM with/without heat insulation materials (HIM) enclosed respectively. Experimental results show that crossing of the levitation force-gap curve is related to experimental methods. A crossing occurs in the magnetic force-gap curve while the PM moves approaching to and departing from the sample with high or low speed of movement without HIM enclosed. When the PM is enclosed with HIM during the measurement procedures, there is no crossing in the force-gap curve no matter high speed or low speed of movement of the PM. It was found experimentally that, with the increase of the moving speed of the PM, the maximum magnitude of levitation force of the HTS increases also. The results are interpreted based on Maxwell theories and flux flow-creep models of HTS.

HTS-Net: An integrated regulome-interactome approach for establishing network regulation models in high-throughput screenings

PubMed Central

Rioualen, Claire; Da Costa, Quentin; Chetrit, Bernard; Charafe-Jauffret, Emmanuelle; Ginestier, Christophe

2017-01-01

High-throughput RNAi screenings (HTS) allow quantifying the impact of the deletion of each gene in any particular function, from virus-host interactions to cell differentiation. However, there has been less development for functional analysis tools dedicated to RNAi analyses. HTS-Net, a network-based analysis program, was developed to identify gene regulatory modules impacted in high-throughput screenings, by integrating transcription factors-target genes interaction data (regulome) and protein-protein interaction networks (interactome) on top of screening z-scores. HTS-Net produces exhaustive HTML reports for results navigation and exploration. HTS-Net is a new pipeline for RNA interference screening analyses that proves better performance than simple gene rankings by z-scores, by re-prioritizing genes and replacing them in their biological context, as shown by the three studies that we reanalyzed. Formatted input data for the three studied datasets, source code and web site for testing the system are available from the companion web site at http://htsnet.marseille.inserm.fr/. We also compared our program with existing algorithms (CARD and hotnet2). PMID:28949986

Characteristics on electodynamic suspension simulator with HTS levitation magnet

NASA Astrophysics Data System (ADS)

Lee, J.; Bae, D. K.; Sim, K.; Chung, Y. D.; Lee, Y.-S.

2009-10-01

High- Tc superconducting (HTSC) electrodynamic suspension (EDS) system basically consists of the HTSC levitation magnet and the ground conductor. The levitation force of EDS system is forms by the interaction between the moving magnetic field produced by the onboard levitation magnet and the induced magnetic field produced by eddy current in the ground conductor. This paper deals with the characteristics of the EDS simulators with high- Tc superconducting (HTS) levitation magnet. Two EDS simulator systems, rotating type EDS simulator and static type EDS simulator, were studied in this paper. The rotating type EDS simulator consists of a HTS levitation magnet and a 1.5 m diameter rotating ground conductor, a motor, the supporting structure and force measuring devices. In the static type EDS simulator, instead of moving magnetic field, AC current was applied to the fixed HTS levitation magnet to induce the eddy current. The static type EDS simulator consists of a HTS levitation magnet, a ground conductor, force measuring devices and supporting structure. The double-pancake type HTSC levitation magnet was designed, manufactured and tested in the EDS simulator.

Multilayer Approach for Characterization of Bacterial Diversity in a Marginal Sea: From Surface to Seabed

NASA Technical Reports Server (NTRS)

Ivana, Babic; Maja, Mucko; Ivica, Vilibic; Hrvoje, Mihanovic; Reffaella, Casotti; Zrinka, Ljubesic; Ivona, Cetinic; Cecilia, Balestra; Ines, Petric; Suncica, Bosak;

Development of a 600 kJ HTS SMES

NASA Astrophysics Data System (ADS)

Seong, K. C.; Kim, H. J.; Kim, S. H.; Sim, K. D.; Sohn, M. H.; Lee, E. Y.; Park, S. J.; Hahn, S. Y.; Park, M. W.

2008-09-01

This paper describes an overview of development on a 600 kJ high-temperature superconducting magnetic energy storage (HTS SMES). Our final goal will be the commercialization of MJ class HTS SMES system for the increase of power quality within 5 years. Hence, for this purpose, we have developed the research and development in 3 years. The purpose of this research is to develop a pilot system, which can protect the sensitivity loads from a momentary power interruption or a voltage sag.

Dynamic Field and Current Distributions in Multifilamentary YBa2Cu3O7-delta Thin Films with Magnetic Coupling (POSTPRINT)

DTIC Science & Technology

2010-03-01

INTRODUCTION The separation of high-temperature superconducting HTS tapes into filaments is a viable approach to reduce ac and hysteretic losses in...generation HTS coated conductors. However, ac losses of finely striated tapes can still be larger than desired as predicted by analytical expressions.6...necessitates an in-depth understanding of the flux and current dynamics in multifilamentary HTS structures as both depend strongly on temperature and history of

Development of a Magneto-Resistive Angular Position Sensor for Space Mechanisms

NASA Technical Reports Server (NTRS)

Hahn, Robert; Schmidt, Tilo; Seifart, Klaus; Olberts, Bastian; Romera, Fernando

2016-01-01

Magnetic microsystems in the form of magneto-resistive (MR) sensors are firmly established in automobiles and industrial applications. They are used to measure travel, angle, electrical current, or magnetic fields. MR technology opens up new sensor possibilities in space applications and can be an enabling technology for optimal performance, high robustness and long lifetime at reasonable costs. In some science missions, the technology is already applied, however, the designs are proprietary and case specific, for instance in case of the angular sensors used for JPL/NASA's Mars rover Curiosity [1]. Since 2013 HTS GmbH and Sensitec GmbH have teamed up to develop and qualify a standardized yet flexible to use MR angular sensor for space mechanisms. Starting with a first assessment study and market survey performed under ESA contract, a very strong industry interest in novel, contactless position measurement means was found. Currently a detailed and comprehensive development program is being performed by HTS and Sensitec. The objective of this program is to advance the sensor design up to Engineering Qualification Model level and to perform qualification testing for a representative space application. The paper briefly reviews the basics of magneto-resistive effects and possible sensor applications and describes the key benefits of MR angular sensors with reference to currently operational industrial and space applications. The key applications and specification are presented and the preliminary baseline mechanical and electrical design will be discussed. An outlook on the upcoming development and test stages as well as the qualification program will be provided.

Comparison of the effects of 7.2% hypertonic saline and 20% mannitol on whole blood coagulation and platelet function in dogs with suspected intracranial hypertension - a pilot study.

PubMed

Yozova, Ivayla D; Howard, Judith; Henke, Diana; Dirkmann, Daniel; Adamik, Katja N

2017-06-19

Hyperosmolar therapy with either mannitol or hypertonic saline (HTS) is commonly used in the treatment of intracranial hypertension (ICH). In vitro data indicate that both mannitol and HTS affect coagulation and platelet function in dogs. The aim of this study was to compare the effects of 20% mannitol and 7.2% HTS on whole blood coagulation using rotational thromboelastometry (ROTEM®) and platelet function using a platelet function analyzer (PFA®) in dogs with suspected ICH. Thirty client-owned dogs with suspected ICH needing osmotherapy were randomized to receive either 20% mannitol (5 ml/kg IV over 15 min) or 7.2% HTS (4 ml/kg IV over 5 min). ROTEM® (EXTEM® and FIBTEM® assays) and PFA® analyses (collagen/ADP cartridges) were performed before (T 0 ), as well as 5 (T 5 ), 60 (T 60 ) and 120 (T 120 ) minutes after administration of HTS or mannitol. Data at T 5 , T 60 and T 120 were analyzed as a percentage of values at T 0 for comparison between groups, and as absolute values for comparison between time points, respectively. No significant difference was found between the groups for the percentage change of any parameter at any time point except for FIBTEM® clotting time. Within each group, no significant difference was found between time points for any parameter except for FIBTEM® clotting time in the HTS group, and EXTEM® and FIBTEM® maximum clot firmness in the mannitol group. Median ROTEM® values lay within institutional reference intervals in both groups at all time points, whereas median PFA® values were above the reference intervals at T 5 (both groups) and T 60 (HTS group). Using currently recommended doses, mannitol and HTS do not differ in their effects on whole blood coagulation and platelet function in dogs with suspected ICH. Moreover, no relevant impairment of whole blood coagulation was found following treatment with either solution, whereas a short-lived impairment of platelet function was found after both solutions.

23.4% saline decreases brain tissue volume in severe hepatic encephalopathy as assessed by a quantitative computed tomography marker

PubMed Central

Liotta, Eric M; Lizza, Bryan D; Romanova, Anna L; Guth, James C; Berman, Michael D; Carroll, Timothy J; Francis, Brandon; Ganger, Daniel; Ladner, Daniela P; Maas, Matthew B; Naidech, Andrew M

2016-01-01

Objective Cerebral edema is common in severe hepatic encephalopathy and may be life-threatening. Bolus 23.4% hypertonic saline (HTS) improves surveillance neuromonitoring scores, although its mechanism of action is not clearly established. We investigated the hypothesis that bolus HTS decreases cerebral edema in severe hepatic encephalopathy utilizing a quantitative technique to measure brain and CSF volume changes. Design Retrospective analysis of serial computed tomography (CT) scans and clinical data for a case-control series was performed. Setting Intensive care units of a tertiary care hospital. Patients Patients with severe hepatic encephalopathy treated with 23.4% HTS and control patients who did not receive 23.4% HTS. Methods We used clinically obtained CT scans to measure volumes of the ventricles, intracranial CSF, and brain using a previously validated semi-automated technique (Analyze Direct; Overland Park, KS). Volumes before and after 23.4% HTS were compared with Wilcoxon signed-rank test. Associations between total CSF volume, ventricular volume, serum sodium, and Glasgow Coma Scale Scores were assessed using Spearman correlation. Results Eleven patients with 18 administrations of 23.4% HTS met inclusion criteria. Total CSF (median 47.6 [35.1–69.4] to 61.9 [47.7–87.0] mL, p<0.001) and ventricular volumes (median 8.0 [6.9–9.5] to 9.2 [7.8–11.9] mL, p=0.002) increased and Glasgow Coma Scale Scores improved (median 4 [3–6] to 7 [6–9], p=0.008) after 23.4% HTS. In contrast, total CSF and ventricular volumes decreased in untreated control patients. Serum sodium increase was associated with increase in total CSF volume (r=0.83, p<0.001) and change in total CSF volume was associated with ventricular volume change (r=0.86, p<0.001). Conclusions Total CSF and ventricular volumes increased after 23.4% HTS, consistent with a reduction in brain tissue volume. Total CSF and ventricular volume change may be useful quantitative measures to assess cerebral edema in severe hepatic encephalopathy. PMID:26308431

Low Cost Cryocoolers for High Temperature Superconductor Communication Filters

NASA Technical Reports Server (NTRS)

Brown, Davina

1998-01-01

This final report describes the work performed by a consortium of Industry and Government to develop low cost cryocoolers. The specific application was for low cost commercial based high temperature superconductor communication filters. This program was initiated in January 1995 and resulted in the successful demonstration of an HTS filter dewar cooled by a low cost pulse tube cryocooler. Further development of this cryocooler technology is proceeding through various contracts underway and proposed at this time.

Development of a Scintillation Proximity Assay (SPA) Based, High Throughput Screening Feasible Method for the Identification of PDE12 Activity Modulators.

PubMed

Mang, Samuel; Bucher, Hannes; Nickolaus, Peter

2016-01-01

The scintillation proximity assay (SPA) technology has been widely used to establish high throughput screens (HTS) for a range of targets in the pharmaceutical industry. PDE12 (aka. 2'- phosphodiesterase) has been published to participate in the degradation of oligoadenylates that are involved in the establishment of an antiviral state via the activation of ribonuclease L (RNAse-L). Degradation of oligoadenylates by PDE12 terminates these antiviral activities, leading to decreased resistance of cells for a variety of viral pathogens. Therefore inhibitors of PDE12 are discussed as antiviral therapy. Here we describe the use of the yttrium silicate SPA bead technology to assess inhibitory activity of compounds against PDE12 in a homogeneous, robust HTS feasible assay using tritiated adenosine-P-adenylate ([3H]ApA) as substrate. We found that the used [3H]ApA educt, was not able to bind to SPA beads, whereas the product [3H]AMP, as known before, was able to bind to SPA beads. This enables the measurement of PDE12 activity on [3H]ApA as a substrate using a wallac microbeta counter. This method describes a robust and high throughput capable format in terms of specificity, commonly used compound solvents, ease of detection and assay matrices. The method could facilitate the search for PDE12 inhibitors as antiviral compounds.

Plate-fin Heat-exchangers for a 10 kW Brayton Cryocooler and a 1 km HTS Cable

NASA Astrophysics Data System (ADS)

Chang, Ho-Myung; Gwak, Kyung Hyun; Jung, Seyong; Yang, Hyung Suk; Hwang, Si-Dole

Plate-fin heat exchangers (PFHX) are designed and fabricated for a cryogenic cooling system, serving for a 10 kW Brayton cryocooler and a 1 km HTS transmission cable under development in Korea. To achieve compactness and thermal efficiency at the same time, a recuperative HX for Brayton cycle and a sub-cooling HX of liquid nitrogen for HTS cable are designed as integrated parts. A key design feature is focused on the coldest part of sub-cooling HX, where the streams of liquid nitrogen and refrigerant (helium gas) are arranged as two-pass cross-flow so that the risk of freeze-out of liquid nitrogen can be reduced. Details of hardware PFHX design are presented and discussed towards its immediate application to the HTS cable system.

1 MVA HTS-2G Generator for Wind Turbines

NASA Astrophysics Data System (ADS)

Kovalev, K. L.; Poltavets, V. N.; Ilyasov, R. I.; Verzhbitsky, L. G.; Kozub, S. S.

2017-10-01

The calculation, design simulations and design performance of 1 MVA HTS-2G (second-generation high-temperature superconductor) Generator for Wind Turbines were done in 2013-2014 [1]. The results of manufacturing and testing of 1 MVA generator are presented in the article. HTS-2G field coils for the rotor were redesigned, fabricated and tested. The tests have shown critical current of the coils, 41-45 A (self field within the ferromagnetic core, T = 77 K), which corresponds to the current of short samples at self field. Application of the copper inner frame on the pole has improved internal cooling conditions of HTS coil windings and reduced the magnetic field in the area, thereby increased the critical current value. The original construction of the rotor with a rotating cryostat was developed, which decreases the thermal in-flow to the rotor. The stator of 1 MW HTS-2G generator has been manufactured. In order to improve the specific weight of the generator, the wave (harmonic drive) multiplier was used, which provides increasing RPM from 15 RPM up to 600 RPM. The total mass of the multiplier and generator is significantly smaller compared to traditional direct-drive wind turbines generators [2-7]. Parameters of the multiplier and generator were chosen based on the actual parameters of wind turbines, namely: 15 RPM, power is 1 MVA. The final test of the assembled synchronous generator with HTS-2G field coils for Wind Turbines with output power 1 MVA was completed during 2015.

Robotic liquid handling and automation in epigenetics.

PubMed

Gaisford, Wendy

2012-10-01

Automated liquid-handling robots and high-throughput screening (HTS) are widely used in the pharmaceutical industry for the screening of large compound libraries, small molecules for activity against disease-relevant target pathways, or proteins. HTS robots capable of low-volume dispensing reduce assay setup times and provide highly accurate and reproducible dispensing, minimizing variation between sample replicates and eliminating the potential for manual error. Low-volume automated nanoliter dispensers ensure accuracy of pipetting within volume ranges that are difficult to achieve manually. In addition, they have the ability to potentially expand the range of screening conditions from often limited amounts of valuable sample, as well as reduce the usage of expensive reagents. The ability to accurately dispense lower volumes provides the potential to achieve a greater amount of information than could be otherwise achieved using manual dispensing technology. With the emergence of the field of epigenetics, an increasing number of drug discovery companies are beginning to screen compound libraries against a range of epigenetic targets. This review discusses the potential for the use of low-volume liquid handling robots, for molecular biological applications such as quantitative PCR and epigenetics.

Test results of a 20 kA high temperature superconductor current lead using REBCO tapes

NASA Astrophysics Data System (ADS)

Heller, R.; Fietz, W. H.; Gröner, F.; Heiduk, M.; Hollik, M.; Lange, C.; Lietzow, R.

2018-05-01

The Karlsruhe Institute of Technology has developed a 20 kA high temperature superconductor (HTS) current lead (CL) using the second generation material REBCO, as industry worldwide concentrate on the production of this material. The aim was to demonstrate the possibility of replacing the Bi-2223/AgAu tapes by REBCO tapes, while for easy comparison of results, all other components are copies of the 20 kA HTS CL manufactured for the satellite tokamak JT-60SA. After the manufacture of all CL components including the newly developed REBCO module, the assembly of the CL has been executed at KIT and an experiment has been carried out in the CuLTKa test facility where the REBCO CL was installed and connected to a JT-60SA CL via a superconducting bus bar. The experiment covers steady state operation up to 20 kA, pulsed operation, measurement of the heat load at 4.5 K end, loss-of-flow-accident simulations, and quench performance studies. Here the results of these tests are reported and directly compared to those of the JT-60SA CL.

Design versions of HTS three-phase cables with the minimized value of AC losses

NASA Astrophysics Data System (ADS)

Altov, V. A.; Balashov, N. N.; Degtyarenko, P. N.; Ivanov, S. S.; Kopylov, S. I.; Lipa, DA; Samoilenkov, S. V.; Sytnikov, V. E.; Zheltov, V. V.

2018-03-01

Design versions of HTS three-phase cables consisting of 2G HTS tapes have been investigated by the numerical simulation method with the aim of AC losses minimization. Two design versions of cables with the coaxial and extended rectangular cross-section shape are considered – the non-sectioned and sectioned one. In the latter each cable phase consists of sections connected in parallel. The optimal dimensions of sections and order of their alteration are chosen by appropriate calculations. The model used takes into account the current distribution between the sections and its non-uniformity within each single HTS tape as well. The following characteristics are varied: design version, dimension, positioning of extra copper layer in a cable, design of HTS tapes themselves and their mutual position. The dependence of AC losses on the latter two characteristics is considered in details, and the examples of cable designs optimized by the total set of characteristics for the medium class of voltages (10 – 60 kV) are given. At the critical current JC=5.1 кA per phase and current amplitudes lower than 0.85JC, the level of total AC losses does not exceed the natural cryostat heat losses.

1 ATM subcooled liquid nitrogen cryogenic system with GM-refrigerator for a HTS power transformer

NASA Astrophysics Data System (ADS)

Yoshida, S.; Ohashi, K.; Umeno, T.; Suzuki, Y.; Kamioka, Y.; Kimura, H.; Tsutsumi, K.; Iwakuma, M.; Funaki, K.; Bhono, T.; Yagi, Y.

2002-05-01

A subcooled liquid nitrogen cryogenic system with GM-refrigerators was developed. The system was operated successfully in a commercial distribution power grid for three consecutive weeks without additional liquid nitrogen supply. The system consists of two main units. One is a HTS transformer unit and the HTS transformer is installed in a G-FRP cryostat. The other one is a pump unit. The pump unit has a liquid nitrogen pump and two GM-refrigerators of 290 W at 64 K for 50 Hz operation in a stainless steel dewar. The refrigerator cold heads are immersed in liquid nitrogen and produce directly subcooled liquid nitrogen in the pump unit. Those two units are connected by transfer-tubes and 1 atmosphere (0.1 MPa) subcooled liquid nitrogen is circulated through the system. In the field test, the refrigerators were operated at 60 Hz and it took 12 hours to cool the transformer down to 70 K and 26 hours to 66 K. The refrigerator cold heads were controlled not to be below 64 K during operation. In spite of a heat generation by the HTS transformer, the subcooled liquid nitrogen temperature in the HTS transformer unit was kept lower than 68 K.

Screening for angiogenic inhibitors in zebrafish to evaluate a predictive model for developmental vascular toxicity.

PubMed

Tal, Tamara; Kilty, Claire; Smith, Andrew; LaLone, Carlie; Kennedy, Brendán; Tennant, Alan; McCollum, Catherine W; Bondesson, Maria; Knudsen, Thomas; Padilla, Stephanie; Kleinstreuer, Nicole

2017-06-01

Chemically-induced vascular toxicity during embryonic development may cause a wide range of adverse effects. To identify putative vascular disrupting chemicals (pVDCs), a predictive pVDC signature was constructed from 124 U.S. EPA ToxCast high-throughput screening (HTS) assays and used to rank 1060 chemicals for their potential to disrupt vascular development. Thirty-seven compounds were selected for targeted testing in transgenic Tg(kdrl:EGFP) and Tg(fli1:EGFP) zebrafish embryos to identify chemicals that impair developmental angiogenesis. We hypothesized that zebrafish angiogenesis toxicity data would correlate with human cell-based and cell-free in vitro HTS ToxCast data. Univariate statistical associations used to filter HTS data based on correlations with zebrafish angiogenic inhibition in vivo revealed 132 total significant associations, 33 of which were already captured in the pVDC signature, and 689 non-significant assay associations. Correlated assays were enriched in cytokine and extracellular matrix pathways. Taken together, the findings indicate the utility of zebrafish assays to evaluate an HTS-based predictive toxicity signature and also provide an experimental basis for expansion of the pVDC signature with novel HTS assays. Published by Elsevier Inc.

An active magnetic bearing with high T(sub c) superconducting coils and ferromagnetic cores

NASA Technical Reports Server (NTRS)

Brown, G. V.; Dirusso, E.; Provenza, A. J.

1995-01-01

A proof-of-feasibility demonstration showed that high-T(sub c) superconductor (HTS) coils can be used in a high-load, active magnetic bearing in LN2. A homopolar radial bearing with commercially wound HTS (Bi 2223) bias and control coils produced over 890 N (200 lb) radial load capacity (measured non-rotatings) and supported a shaft to 14,000 rpm. The goal was to show that HTS coils can operate stably with ferromagnetic cores in a feedback controlled system at a current density similar to that for Cu in LN2. The bias coil, wound with non-twisted, multifilament HTS conductor, dissipated negligible power for its direct current. The control coils, wound with monofilament HTS sheathed in Ag, dissipated negligible power for direct current. AC losses increased rapidly with frequency and quadratically with AC amplitude. Above about 2 Hz, the effective resistance of the control coils exceeds that of the silver which is in electrical parallel with the oxide superconductor. These results show that twisted multifilament conductor is not needed for stable levitation but may be desired to reduce control power for sizable dynamic loads.

Heat Transfer Search Algorithm for Non-convex Economic Dispatch Problems

NASA Astrophysics Data System (ADS)

Hazra, Abhik; Das, Saborni; Basu, Mousumi

2018-06-01

This paper presents Heat Transfer Search (HTS) algorithm for the non-linear economic dispatch problem. HTS algorithm is based on the law of thermodynamics and heat transfer. The proficiency of the suggested technique has been disclosed on three dissimilar complicated economic dispatch problems with valve point effect; prohibited operating zone; and multiple fuels with valve point effect. Test results acquired from the suggested technique for the economic dispatch problem have been fitted to that acquired from other stated evolutionary techniques. It has been observed that the suggested HTS carry out superior solutions.

Heat Transfer Search Algorithm for Non-convex Economic Dispatch Problems

NASA Astrophysics Data System (ADS)

Hazra, Abhik; Das, Saborni; Basu, Mousumi

2018-03-01

This paper presents Heat Transfer Search (HTS) algorithm for the non-linear economic dispatch problem. HTS algorithm is based on the law of thermodynamics and heat transfer. The proficiency of the suggested technique has been disclosed on three dissimilar complicated economic dispatch problems with valve point effect; prohibited operating zone; and multiple fuels with valve point effect. Test results acquired from the suggested technique for the economic dispatch problem have been fitted to that acquired from other stated evolutionary techniques. It has been observed that the suggested HTS carry out superior solutions.

Unexpected biodiversity of ciliates in marine samples from below the photic zone.

PubMed

Grattepanche, Jean-David; Santoferrara, Luciana F; McManus, George B; Katz, Laura A

2016-08-01

Marine microbial eukaryotes play critical roles in planktonic food webs and have been described as most diverse in the photic zone where productivity is high. We used high-throughput sequencing (HTS) to analyse the spatial distribution of planktonic ciliate diversity from shallow waters (<30 m depth) to beyond the continental shelf (>800 m depth) along a 163 km transect off the coast of New England, USA. We focus on ciliates in the subclasses Oligotrichia and Choreotrichia (class Spirotrichea), as these taxa are major components of marine food webs. We did not observe the decrease of diversity below the photic zone expected based on productivity and previous analyses. Instead, we saw an increase of diversity with depth. We also observed that the ciliate communities assessed by HTS cluster by depth layer and degree of water column stratification, suggesting that community assembly is driven by environmental factors. Across our samples, abundant OTUs tend to match previously characterized morphospecies while rare OTUs are more often undescribed, consistent with the idea that species in the rare biosphere remain to be characterized by microscopy. Finally, samples taken below the photic zone also reveal the prevalence of two uncharacterized (i.e. lacking sequenced morphospecies) clades - clusters X1 and X2 - that are enriched within the nano-sized fraction (2-10 μm) and are defined by deletions within the region of the SSU-rDNA analysed here. Together, these data reinforce that we still have much to learn about microbial diversity in marine ecosystems, especially in deep-waters that may be a reservoir for rare species and uncharacterized taxa. © 2016 John Wiley & Sons Ltd.

Screening of phospholipase A activity and its production by new actinomycete strains cultivated by solid-state fermentation.

PubMed

Sutto-Ortiz, Priscila; Camacho-Ruiz, María de Los Angeles; Kirchmayr, Manuel R; Camacho-Ruiz, Rosa María; Mateos-Díaz, Juan Carlos; Noiriel, Alexandre; Carrière, Frédéric; Abousalham, Abdelkarim; Rodríguez, Jorge A

2017-01-01

Novel microbial phospholipases A (PLAs) can be found in actinomycetes which have been poorly explored as producers of this activity. To investigate microbial PLA production, efficient methods are necessary such as high-throughput screening (HTS) assays for direct search of PLAs in microbial cultures and cultivation conditions to promote this activity. About 200 strains isolated with selected media for actinomycetes and mostly belonging to Streptomyces (73%) and Micromonospora (10%) genus were first screened on agar-plates containing the fluorophore rhodamine 6G and egg yolk phosphatidylcholine (PC) to detect strains producing phospholipase activity. Then, a colorimetric HTS assay for general PLA activity detection (cHTS-PLA) using enriched PC (≈60%) as substrate and cresol red as indicator was developed and applied; this cHTS-PLA assay was validated with known PLAs. For the first time, actinomycete strains were cultivated by solid-state fermentation (SSF) using PC as inductor and sugar-cane bagasse as support to produce high PLA activity (from 207 to 2,591 mU/g of support). Phospholipase activity of the enzymatic extracts from SSF was determined using the implemented cHTS-PLA assay and the PC hydrolysis products obtained, were analyzed by TLC showing the presence of lyso-PC. Three actinomycete strains of the Streptomyces genus that stood out for high accumulation of lyso-PC, were selected and analyzed with the specific substrate 1,2-α-eleostearoyl- sn -glycero-3-phosphocholine (EEPC) in order to confirm the presence of PLA activity in their enzymatic extracts. Overall, the results obtained pave the way toward the HTS of PLA activity in crude microbial enzymatic extracts at a larger scale. The cHTS-PLA assay developed here can be also proposed as a routine assay for PLA activity determination during enzyme purification,directed evolution or mutagenesis approaches. In addition, the production of PLA activity by actinomycetes using SSF allow find and produce novel PLAs with potential applications in biotechnology.

Screening of phospholipase A activity and its production by new actinomycete strains cultivated by solid-state fermentation

PubMed Central

Sutto-Ortiz, Priscila; Camacho-Ruiz, María de los Angeles; Kirchmayr, Manuel R.; Camacho-Ruiz, Rosa María; Mateos-Díaz, Juan Carlos; Noiriel, Alexandre; Carrière, Frédéric; Abousalham, Abdelkarim

2017-01-01

Novel microbial phospholipases A (PLAs) can be found in actinomycetes which have been poorly explored as producers of this activity. To investigate microbial PLA production, efficient methods are necessary such as high-throughput screening (HTS) assays for direct search of PLAs in microbial cultures and cultivation conditions to promote this activity. About 200 strains isolated with selected media for actinomycetes and mostly belonging to Streptomyces (73%) and Micromonospora (10%) genus were first screened on agar-plates containing the fluorophore rhodamine 6G and egg yolk phosphatidylcholine (PC) to detect strains producing phospholipase activity. Then, a colorimetric HTS assay for general PLA activity detection (cHTS-PLA) using enriched PC (≈60%) as substrate and cresol red as indicator was developed and applied; this cHTS-PLA assay was validated with known PLAs. For the first time, actinomycete strains were cultivated by solid-state fermentation (SSF) using PC as inductor and sugar-cane bagasse as support to produce high PLA activity (from 207 to 2,591 mU/g of support). Phospholipase activity of the enzymatic extracts from SSF was determined using the implemented cHTS-PLA assay and the PC hydrolysis products obtained, were analyzed by TLC showing the presence of lyso-PC. Three actinomycete strains of the Streptomyces genus that stood out for high accumulation of lyso-PC, were selected and analyzed with the specific substrate 1,2-α-eleostearoyl-sn-glycero-3-phosphocholine (EEPC) in order to confirm the presence of PLA activity in their enzymatic extracts. Overall, the results obtained pave the way toward the HTS of PLA activity in crude microbial enzymatic extracts at a larger scale. The cHTS-PLA assay developed here can be also proposed as a routine assay for PLA activity determination during enzyme purification,directed evolution or mutagenesis approaches. In addition, the production of PLA activity by actinomycetes using SSF allow find and produce novel PLAs with potential applications in biotechnology. PMID:28695068

Structural modeling of HTS tapes and cables

NASA Astrophysics Data System (ADS)

Allen, N. C.; Chiesa, L.; Takayasu, M.

2016-12-01

Structural finite element analysis (FEA) has been used as an insightful tool to investigate the electromechanical behavior of HTS REBCO tapes and twisted stacked-tape cables under tension, torsion, bending and combined loads. A novel technique was developed for modeling the layered composite structure of the 2G tapes with structural solid-shell elements in ANSYS®. The FEA models produced detailed strain information for the REBCO superconducting layer which was then paired with an analytical model to predict the critical current performance of the 2G HTS tapes under various loads. Two commercially available HTS tapes (SuperPower and SuNAM) under tension, torsion and combined tension-torsion were first analyzed with FEA and compared with available experimental results at 77 K. A sharp critical current degradation was experienced at the yield strength of the tapes under tension and below a 100 mm twist-pitch under torsion. Combined tension-torsion loads had a more gradual degradation of critical current for twist-pitches of 115 mm or shorter but had a negligible difference compared to pure tension for longer twist-pitches. Using the structural solid-shell technique for modeling 2G tapes in ANSYS®, an FEA methodology for simulating full scale three-dimensional HTS stacked-tape cables under pure bending was created. A model of a Twisted-Stacked Tape Cable (TSTC), a configuration first proposed at MIT, was initially developed and then adapted to the slotted-core HTS Cable-In-Conduit Conductor produced by the ENEA laboratory in Italy. The numerical axial strain of the HTS REBCO tapes within the cables as calculated by FEA were found to agree with an analytical model for two cases: perfect-slip (frictionless) and no-slip (bonded). The ENEA CICC model was also compared with recent experimental critical current data at 77 K and was found to match best using a low friction coefficient of 0.02 indicating that the tapes within the cable freely slide with respect to each other helping to reduce the axial strain during bending.

Insights and Perspectives on Emerging Inputs to Weight of Evidence Determinations for Food Safety: Workshop Proceedings

PubMed Central

Bialk, Heidi; Llewellyn, Craig; Kretser, Alison; Canady, Richard; Lane, Richard; Barach, Jeffrey

2013-01-01

This workshop aimed to elucidate the contribution of computational and emerging in vitro methods to the weight of evidence used by risk assessors in food safety assessments. The following issues were discussed: using in silico and high-throughput screening (HTS) data to confirm the safety of approved food ingredients, applying in silico and HTS data in the process of assessing the safety of a new food ingredient, and utilizing in silico and HTS data in communicating the safety of food ingredients while enhancing the public’s trust in the food supply. Perspectives on integrating computational modeling and HTS assays as well as recommendations for optimizing predictive methods for risk assessment were also provided. Given the need to act quickly or proceed cautiously as new data emerge, this workshop also focused on effectively identifying a path forward in communicating in silico and in vitro data. PMID:24296863

Numerical calculation of primary slot leakage inductance of a Single-sided HTS linear induction motor used for linear metro

NASA Astrophysics Data System (ADS)

Li, Dong; Wen, Yinghong; Li, Weili; Fang, Jin; Cao, Junci; Zhang, Xiaochen; Lv, Gang

2017-03-01

In the paper, the numerical method calculating asymmetric primary slot leakage inductances of Single-sided High-Temperature Superconducting (HTS) Linear Induction Motor (HTS LIM) is presented. The mathematical and geometric models of three-dimensional nonlinear transient electromagnetic field are established and the boundary conditions are also given. The established model is solved by time-stepping Finite Element Method (FEM). Then, the three-phase asymmetric primary slot leakage inductances under different operation conditions are calculated by using the obtained electromagnetic field distribution. The influences of the special effects such as longitudinal end effects, transversal edge effects, etc. on the primary slot leakage inductance are investigated. The presented numerical method is validated by experiments carried out on a 3.5 kW prototype with copper wires which has the same structures with the HTS LIM.

The effect of temperature on pinning mechanisms in HTS composites

NASA Astrophysics Data System (ADS)

Sotnikova, A. P.; Rudnev, I. A.

2016-09-01

Pinning mechanism in samples of second generation tapes (2G) of high-temperature superconductors (HTS) was studied The critical current and the pinning force were calculated from the magnetization curves measured in the temperature range of 4.2 - 77 K in magnetic fields up to 14 Tesla using vibration sample magnetometer. To determine the pinning mechanism the dependences of pinning force on magnetic field were constructed according to the Dew-Hughes model and Kramer's rule. The obtained dependences revealed a significant influence of the temperature on effectiveness of different types of pinning. At low temperatures the 2G HTS tapes of different manufacturers demonstrated an equal efficiency of the pinning centers but with temperature increase the differences in pinning mechanisms as well as in properties and effectiveness of the pinning centers become obvious. The influence of the pinning mechanism on the energy losses in HTS tapes was shown.

Nuisance Compounds, PAINS Filters, and Dark Chemical Matter in the GSK HTS Collection.

PubMed

Chakravorty, Subhas J; Chan, James; Greenwood, Marie Nicole; Popa-Burke, Ioana; Remlinger, Katja S; Pickett, Stephen D; Green, Darren V S; Fillmore, Martin C; Dean, Tony W; Luengo, Juan I; Macarrón, Ricardo

2018-07-01

High-throughput screening (HTS) hits include compounds with undesirable properties. Many filters have been described to identify such hits. Notably, pan-assay interference compounds (PAINS) has been adopted by the community as the standard term to refer to such filters, and very useful guidelines have been adopted by the American Chemical Society (ACS) and subsequently triggered a healthy scientific debate about the pitfalls of draconian use of filters. Using an inhibitory frequency index, we have analyzed in detail the promiscuity profile of the whole GlaxoSmithKline (GSK) HTS collection comprising more than 2 million unique compounds that have been tested in hundreds of screening assays. We provide a comprehensive analysis of many previously published filters and newly described classes of nuisance structures that may serve as a useful source of empirical information to guide the design or growth of HTS collections and hit triaging strategies.

Electrical and thermal characteristics of Bi2212/Ag HTS coils for conduction-cooled SMES

NASA Astrophysics Data System (ADS)

Hayakawa, N.; Noguchi, S.; Kurupakorn, C.; Kojima, H.; Endo, F.; Hirano, N.; Nagaya, S.; Okubo, H.

2006-06-01

In this paper, we investigated the electrical and thermal performance of conduction-cooled Bi2212/Ag HTS coils with 4K-GM cryocooler system. First, we measured the critical current Ic for different ambient temperatures T0 at 4.2 K - 40 K. Experimental results revealed that Ic increased with the decrease in T0 and was saturated at T0 < 10 K. We carried out thermal analysis considering heat generation, conduction and transfer under conduction-cooling condition, and reproduced the electrical and thermal characteristics of the conduction-cooled HTS coil, taking account of temperature dependence of specific heat and thermal conductivity of the materials. We also measured the temperature rise of Bi2212/Ag HTS coil for different continuous current levels at T0 = 4.8 K. Experimental results revealed the criterion of thermal runaway, which was discussed in terms of heat generation and propagation in the test coil.

Further development of high temperature-resistant graphite fiber coupling agents

NASA Technical Reports Server (NTRS)

Griffin, R. N.

1976-01-01

Potential coupling agents for graphite fibers were screened by their effect on the weight losses of Thornel 300, HMS, and HTS fibers at 588K for 200 and 400 hours. Unidirectional laminates were made from HMS and HTS fibers, untreated, and treated with each of the seven coupling agents. The matrix of all laminates was PMR polyimide (PMR-PR). On the basis of the best overall retention of elevated temperature interlaminar shear strength after 200 hours at 588K, composite weight after 200 hours at 588K, and fiber weight after 400 hours at 588K, ventromer T-1 applied from aqueous solution and pyrolyzed PPQ were selected for further evaluation as coupling agents for HTS fiber while ventromer T-2 and pyrolyzed PPQ were selected as coupling agents for HMS fiber. It was shown that pyrolyzed PPQ as a coupling agent improves the oxidative stability of HTS/PMR-PI composites.

Operation of a 500 MHz high temperature superconducting NMR: towards an NMR spectrometer operating beyond 1 GHz.

PubMed

Yanagisawa, Y; Nakagome, H; Tennmei, K; Hamada, M; Yoshikawa, M; Otsuka, A; Hosono, M; Kiyoshi, T; Takahashi, M; Yamazaki, T; Maeda, H

2010-04-01

We have begun a project to develop an NMR spectrometer that operates at frequencies beyond 1 GHz (magnetic field strength in excess of 23.5 T) using a high temperature superconductor (HTS) innermost coil. As the first step, we developed a 500 MHz NMR with a Bi-2223 HTS innermost coil, which was operated in external current mode. The temporal magnetic field change of the NMR magnet after the coil charge was dominated by (i) the field fluctuation due to a DC power supply and (ii) relaxation in the screening current in the HTS tape conductor; effect (i) was stabilized by the 2H field-frequency lock system, while effect (ii) decreased with time due to relaxation of the screening current induced in the HTS coil and reached 10(-8)(0.01 ppm)/h on the 20th day after the coil charge, which was as small as the persistent current mode of the NMR magnet. The 1D (1)H NMR spectra obtained by the 500 MHz LTS/HTS magnet were nearly equivalent to those obtained by the LTS NMR magnet. The 2D-NOESY, 3D-HNCO and 3D-HNCACB spectra were achieved for ubiquitin by the 500 MHz LTS/HTS magnet; their quality was closely equivalent to that achieved by a conventional LTS NMR. Based on the results of numerical simulation, the effects of screening current-induced magnetic field changes are predicted to be harmless for the 1.03 GHz NMR magnet system. 2010 Elsevier Inc. All rights reserved.

Cryopreservation of isolated primary rat hepatocytes: enhanced survival and long-term hepatospecific function.

PubMed

Sosef, Meindert N; Baust, John M; Sugimachi, Keishi; Fowler, Alex; Tompkins, Ronald G; Toner, Mehmet

2005-01-01

To investigate the long-term effect of cryopreservation on hepatocyte function, as well as attempt to improve cell viability and function through the utilization of the hypothermic preservation solution, HypoThermosol (HTS), as the carrier solution. Advances in the field of bioartificial liver support have led to an increasing demand for successful, efficient means of cryopreservation of hepatocytes. Fresh rat hepatocytes were cryopreserved in suspension in culture media (Media-cryo group) or HTS (HTS-cryo group), both supplemented with 10% DMSO. Following storage up to 2 months in liquid nitrogen, cells were thawed and maintained in a double collagen gel culture for 14 days. Hepatocyte yield and viability were assessed up to 14 days postthaw. Serial measurements of albumin secretion, urea synthesis, deethylation of ethoxyresorufin (CYT P450 activity), and responsiveness to stimulation with interleukin-6 (IL-6) were performed. Immediate postthaw viability was 60% in Media-cryo and 79% in HTS-cryo, in comparison with control (90%). Albumin secretion, urea synthesis and CYT P450 activity yielded 33%, 55%, and 59% in Media-cryo and 71%, 80%, and 88% in HTS-cryo, respectively, compared with control (100%). Assessment of cellular response to IL-6 following cryopreservation revealed a similar pattern of up-regulation in fibrinogen production and suppression of albumin secretion compared with nonfrozen controls. This study demonstrates that isolated rat hepatocytes cryopreserved using HTS showed high viability, long-term hepatospecific function, and response to cytokine challenge. These results may represent an important step forward to the utilization of cryopreserved isolated hepatocytes in bioartificial liver devices.

Lateral motion stability of high-temperature superconducting maglev systems derived from a nonlinear guidance force hysteretic model

NASA Astrophysics Data System (ADS)

Li, Haitao; Deng, Zigang; Jin, Li’an; Li, Jipeng; Li, Yanxing; Zheng, Jun

2018-07-01

High-temperature superconducting (HTS) maglev, owning to the capability of passive stabilization, is potentially promising for high-speed transportation. The guidance force of bulk HTS materials above a permanent magnetic guideway has a nonlinear response due to the hysteresis effect. As a kind of rail transit, when the vehicle runs along the track, the curve and other disturbances will cause vibrations to the vehicle system. These physical factors will pose dynamic loads on the components, reducing structural reliability as well as affecting the ride comfort. The lateral motion, as an important part of the vehicle system dynamics, needs to be studied in the pursuit of HTS maglev realization. In this paper, we first measured the guidance forces of HTS bulks under different motion conditions, and analyzed the relationship between the lateral displacement, the movement velocity and the guidance force. Then, a mathematical model was built based on these experimental data. The key feature of this mathematical model is that it can describe the hysteresis characteristic of the guidance force. Based on this model, we investigated the lateral motion stability of the HTS levitation system, and found three singular points, one stable focus point, and two unstable saddle points. Lastly, a phase portrait was proposed to indicate the safe working region of the HTS maglev vehicle where the vehicle can automatically return to its equilibrium position. These experimental and simulation results are important to clarify the lateral motion stability under external disturbance or shock, and provide a reference basis for the design of levitation systems.

Novel model of stator design to reduce the mass of superconducting generators

NASA Astrophysics Data System (ADS)

Kails, Kevin; Li, Quan; Mueller, Markus

2018-05-01

High temperature superconductors (HTS), with much higher current density than conventional copper wires, make it feasible to develop very powerful and compact power generators. Thus, they are considered as one promising solution for large (10 + MW) direct-drive offshore wind turbines due to their low tower head mass. However, most HTS generator designs are based on a radial topology, which requires an excessive amount of HTS material and suffers from cooling and reliability issues. Axial flux machines on the other hand offer higher torque/volume ratios than the radial machines, which makes them an attractive option where space and transportation becomes an issue. However, their disadvantage is heavy structural mass. In this paper a novel stator design is introduced for HTS axial flux machines which enables a reduction in their structural mass. The stator is for the first time designed with a 45° angle that deviates the air gap closing forces into the vertical direction reducing the axial forces. The reduced axial forces improve the structural stability and consequently simplify their structural design. The novel methodology was then validated through an existing design of the HTS axial flux machine achieving a ∼10% mass reduction from 126 tonnes down to 115 tonnes. In addition, the air gap flux density increases due to the new claw pole shapes improving its power density from 53.19 to 61.90 W kg‑1. It is expected that the HTS axial flux machines designed with the new methodology offer a competitive advantage over other proposed superconducting generator designs in terms of cost, reliability and power density.

Trends and exceptions of physical properties on antibacterial activity for Gram-positive and Gram-negative pathogens.

PubMed

Brown, Dean G; May-Dracka, Tricia L; Gagnon, Moriah M; Tommasi, Ruben

2014-12-11

To better understand the difficulties surrounding the identification of novel antibacterial compounds from corporate screening collections, physical properties of ∼3200 antibacterial project compounds with whole cell activity against Gram-negative or Gram-positive pathogens were profiled and compared to actives found from high throughput (HTS) screens conducted on both biochemical and phenotypic bacterial targets. The output from 23 antibacterial HTS screens illustrated that when compared to the properties of the antibacterial project compounds, the HTS actives were significantly more hydrophobic than antibacterial project compounds (typically 2-4 log units higher), and furthermore, for 14/23 HTS screens, the average clogD was higher than the screening collection average (screening collection clogD = 2.45). It was found that the consequences of this were the following: (a) lead identification programs often further gained hydrophobic character with increased biochemical potency, making the separation even larger between the physicochemical properties of known antibacterial agents and the HTS active starting point, (b) the probability of plasma protein binding and cytotoxicity are often increased, and (c) cell-based activity in Gram-negative bacteria was severely limited or, if present, demonstrated significant efflux. Our analysis illustrated that compounds least susceptible to efflux were those which were highly polar and small in MW or very large and typically zwitterionic. Hydrophobicity was often the dominant driver for HTS actives but, more often than not, precluded whole cell antibacterial activity. However, simply designing polar compounds was not sufficient for antibacterial activity and pointed to a lack of understanding of complex and specific bacterial penetration mechanisms.

High-Throughput Pharmacokinetics for Environmental Chemicals (SOT)

EPA Science Inventory

High throughput screening (HTS) promises to allow prioritization of thousands of environmental chemicals with little or no in vivo information. For bioactivity identified by HTS, toxicokinetic (TK) models are essential to predict exposure thresholds below which no significant bio...

Using information from historical high-throughput screens to predict active compounds.

PubMed

Riniker, Sereina; Wang, Yuan; Jenkins, Jeremy L; Landrum, Gregory A

2014-07-28

Modern high-throughput screening (HTS) is a well-established approach for hit finding in drug discovery that is routinely employed in the pharmaceutical industry to screen more than a million compounds within a few weeks. However, as the industry shifts to more disease-relevant but more complex phenotypic screens, the focus has moved to piloting smaller but smarter chemically/biologically diverse subsets followed by an expansion around hit compounds. One standard method for doing this is to train a machine-learning (ML) model with the chemical fingerprints of the tested subset of molecules and then select the next compounds based on the predictions of this model. An alternative approach would be to take advantage of the wealth of bioactivity information contained in older (full-deck) screens using so-called HTS fingerprints, where each element of the fingerprint corresponds to the outcome of a particular assay, as input to machine-learning algorithms. We constructed HTS fingerprints using two collections of data: 93 in-house assays and 95 publicly available assays from PubChem. For each source, an additional set of 51 and 46 assays, respectively, was collected for testing. Three different ML methods, random forest (RF), logistic regression (LR), and naïve Bayes (NB), were investigated for both the HTS fingerprint and a chemical fingerprint, Morgan2. RF was found to be best suited for learning from HTS fingerprints yielding area under the receiver operating characteristic curve (AUC) values >0.8 for 78% of the internal assays and enrichment factors at 5% (EF(5%)) >10 for 55% of the assays. The RF(HTS-fp) generally outperformed the LR trained with Morgan2, which was the best ML method for the chemical fingerprint, for the majority of assays. In addition, HTS fingerprints were found to retrieve more diverse chemotypes. Combining the two models through heterogeneous classifier fusion led to a similar or better performance than the best individual model for all assays. Further validation using a pair of in-house assays and data from a confirmatory screen--including a prospective set of around 2000 compounds selected based on our approach--confirmed the good performance. Thus, the combination of machine-learning with HTS fingerprints and chemical fingerprints utilizes information from both domains and presents a very promising approach for hit expansion, leading to more hits. The source code used with the public data is provided.

Prospects on the application of HTS SQUID magnetometry to nondestructive evaluation (NDE)

NASA Astrophysics Data System (ADS)

Weinstock, H.

1993-04-01

In light of recent advances in the fabrication of low-noise HTS SQUIDs, a review is presented on the use of LTS SQUID magnetometry for nondestructive evaluation (NDE). Examples are given on applications relating to defects in steel, subsurface cracks in aircraft frames, and voids in non-metallic structures. HTS SQUIDs may make a significant difference in the acceptance of these applications because sensing coils will be closer to a sample under test, there will be greater instrument portability and the problem of bringing liquid helium to remote locations will be eliminated.

Microwave signal-processing applications of HTS films

NASA Astrophysics Data System (ADS)

Adam, J. D.; Wagner, G. R.

1990-01-01

The low surface resistance (Rs) of high-temperature superconductors (HTS) will lead to the development of passive microwave devices for application in radar, electronic warfare, and satellite systems with performance significantly better than achieved with normal conductors. In particular, delay line based devices such as phase shifters, convolvers, and correlators will have low lossses and multi-GHz bandwidths. Low-loss filters which presently occupy cubic feet in waveguide will be fabricated in compact microstrip or stripline, and ultra-high Q resonators which currently require liquid helium refrigeration will be operated at around 77 K. Measurement of Rs of HTS is important both for device design and for optimization of the film growth process. Several approaches have been developed which provide data over a wide range of frequency and temperature, including stripline, cacity, and dielectric resonator techniques. HTS films for microwave applications should have at least Rs(HTS(

Evaluation of Impermeant, DNA-Binding Dye Fluorescence as a Real-Time Readout of Eukaryotic Cell Toxicity in a High Throughput Screening Format

PubMed Central

Chiaraviglio, Lucius

2014-01-01

Abstract Interpretation of high throughput screening (HTS) data in cell-based assays may be confounded by cytotoxic properties of screening compounds. Therefore, assessing cell toxicity in real time during the HTS process itself would be highly advantageous. Here, we investigate the potential of putatively impermeant, fluorescent, DNA-binding dyes to give cell toxicity readout during HTS. Amongst 19 DNA-binding dyes examined, three classes were identified that were (1) permeant, (2) cytotoxic, or (3) neither permeant nor cytotoxic during 3-day incubation with a macrophage cell line. In the last class, four dyes (SYTOX Green, CellTox Green, GelGreen, and EvaGreen) gave highly robust cytotoxicity data in 384-well screening plates. As proof of principle, successful combination with a luminescence-based assay in HTS format was demonstrated. Here, both intracellular growth of Legionella pneumophila (luminescence) and host cell viability (SYTOX Green exclusion) were assayed in the same screening well. Incorporation of membrane-impermeant, DNA-binding, fluorescent dyes in HTS assays should prove useful by allowing evaluation of cytotoxicity in real time, eliminating reagent addition steps and effort associated with endpoint cell viability analysis, and reducing the need for follow-up cytotoxicity screening. PMID:24831788

Enhanced quench propagation in 2G-HTS coils co-wound with stainless steel or anodised aluminium tapes

NASA Astrophysics Data System (ADS)

Núñez-Chico, A. B.; Martínez, E.; Angurel, L. A.; Navarro, R.

2016-08-01

Early quench detection and thermal stability of superconducting coils are of great relevance for practical applications. Magnets made with second generation high temperature superconducting (2G-HTS) tapes present low quench propagation velocities and therefore slow voltage development and high local temperature rises, which may cause irreversible damage. Since quench propagation depends on the anisotropy of the thermal conductivity, this may be used to achieve an improvement of the thermal stability and robustness of 2G-HTS coils. On pancake type coils, the thermal conductivity along the tapes (coil’s azimuthal direction) is mostly fixed by the 2G-HTS tape characteristics, so that the reduction of anisotropy relies on the improvement of the radial thermal conductivity, which depends on the used materials between superconducting tapes, as well as on the winding and impregnation processes. In this contribution, we have explored two possibilities for such anisotropy reduction: by using anodised aluminium or stainless steel tapes co-wound with the 2G-HTS tapes. For all the analysed coils, critical current distribution, minimum quench energy values and both tangential and radial quench propagation velocities at different temperatures and currents are reported and compared with the results of similar coils co-wound with polyimide (Kapton®) tapes.

Effects of Multicomponent Exercise on Functional and Cognitive Parameters of Hypertensive Patients: A Quasi-Experimental Study

PubMed Central

Feriani, Daniele Jardim; Gonçalves, Ivan de Oliveira; Asano, Ricardo Yukio; Aguiar, Samuel da Silva; Uchida, Marco Carlos

2017-01-01

Purpose. The present study aimed to investigate the impact of a 6-month multicomponent exercise program (MCEP) on physical function and cognitive parameters of normotensive (NTS) and hypertensive (HTS) older patients and verify if age can influence the adaptations in response to the exercise. Methods. A total of 218 subjects, 101 NTS and 117 HTS, were recruited and underwent functional and cognitive evaluations before and after six months of a MCEP. The program of exercise was performed twice a week, for 26 weeks. The physical exercises were thought to mimic the activities of daily living and, therefore, aggregated functional and walking exercises. Exercise sessions were performed at moderate intensity. Results. Data indicated that HTS and NST patients showed a similar increase in the performance of walking speed test and one-leg stand test after the MCEP. Regarding age, results did not show differences in the magnitude of adaptations between old and young HTS and NTS patients. Conclusions. Data of the present study indicated that a 6-month MCEP was able to increase equally balance and mobility in NTS and HTS patients. Moreover, data demonstrated that aging did not seem to impair the capacity to adapt in response to exercise in both groups. PMID:28409030

Epitaxy of mercury-based high temperature superconducting films on oxide and metal substrates

NASA Astrophysics Data System (ADS)

Xie, Yi-Yuan

High-Tc superconducting (HTS) cuprates are highly anisotropic thus epitaxy along certain crystalline directions is essential to realize high-current-carrying capability at temperatures above 77 K. Hg-based HTS (Hg-HTS) cuprates have the record-high Tc up to 135 K, therefore are of great interest for fundamental research and practical applications. However, growth Of epitaxial Hg-HTS films is extremely difficult in conventional thermal-reaction process since Hg is highly volatile. Motivated by this, we first developed a cation-exchange process for growing epitaxial Hg-HTS films, which involves two steps: selection of precursor matrices with predesigned structure and composition followed by cation-exchange processing. New materials are formed via "atomic surgery" on an existing structure rather than thermal reaction among amorphous oxides in conventional process, thus the structural features of the precursor are inherited by the new material. Using epitaxial Tl-based HTS films as precursor and annealing them in Hg-vapor, epitaxial Hg-HTS films with superior quality have been obtained. This success encouraged us to develop epitaxy on metal tapes for coated conductors and On large-area wafers for electronic devices. For coated conductors, we addressed three critical issues: epitaxy on metal substrates, enhancement of in-field Jcs and scale-up in thickness and length. First, using a fabrication scheme that combines two processes: cation-exchange and fast-temperature-ramping-annealing, epitaxial HgBa2CaCu2O6+delta films were grown on rolling-assisted-biaxially-textured Ni substrates buffered with CeO 2/YSZ/CeO2 for the first time. We fabricated HgBa2CaCu 2O6+delta coated conductors with Tc = 122--124 K and self-field Jc > 1 x 106A/cm2 at 92 K which are record-high for HTS coated conductors. Second, we demonstrated improved in-field J cs via overdoping HgBa2CaCu 2O6+delta films (by means Of charge "overdoped"), heavy-ion-irradiation and substrate engineering. Finally, thick HgBa 2CaCu2O6+delta films show high I c, and spool process also shows potential in middle-length tape fabrication. These results make Hg-HTS films good candidates as power transmission wires/tapes. For large-area epitaxy, ½ inch x ½ inch HgBa2CaCu 2O6+delta films were synthesized on LaAlO3(100) with uniform and high Tcs and Jc s. A new crucible Hg-annealing technique that requires neither vacuum nor torch-sealing has been invented, promising for large-area wafers and long tapes/wires. So far HgBa2CaCu2O6+delta films with good quality have been reproducibly fabricated using this new technique.

Applications of Biophysics in High-Throughput Screening Hit Validation.

PubMed

Genick, Christine Clougherty; Barlier, Danielle; Monna, Dominique; Brunner, Reto; Bé, Céline; Scheufler, Clemens; Ottl, Johannes

2014-06-01

For approximately a decade, biophysical methods have been used to validate positive hits selected from high-throughput screening (HTS) campaigns with the goal to verify binding interactions using label-free assays. By applying label-free readouts, screen artifacts created by compound interference and fluorescence are discovered, enabling further characterization of the hits for their target specificity and selectivity. The use of several biophysical methods to extract this type of high-content information is required to prevent the promotion of false positives to the next level of hit validation and to select the best candidates for further chemical optimization. The typical technologies applied in this arena include dynamic light scattering, turbidometry, resonance waveguide, surface plasmon resonance, differential scanning fluorimetry, mass spectrometry, and others. Each technology can provide different types of information to enable the characterization of the binding interaction. Thus, these technologies can be incorporated in a hit-validation strategy not only according to the profile of chemical matter that is desired by the medicinal chemists, but also in a manner that is in agreement with the target protein's amenability to the screening format. Here, we present the results of screening strategies using biophysics with the objective to evaluate the approaches, discuss the advantages and challenges, and summarize the benefits in reference to lead discovery. In summary, the biophysics screens presented here demonstrated various hit rates from a list of ~2000 preselected, IC50-validated hits from HTS (an IC50 is the inhibitor concentration at which 50% inhibition of activity is observed). There are several lessons learned from these biophysical screens, which will be discussed in this article. © 2014 Society for Laboratory Automation and Screening.

Using In Vitro High-Throughput Screening Data for Predicting Benzo[k]Fluoranthene Human Health Hazards.

PubMed

Burgoon, Lyle D; Druwe, Ingrid L; Painter, Kyle; Yost, Erin E

2017-02-01

Today there are more than 80,000 chemicals in commerce and the environment. The potential human health risks are unknown for the vast majority of these chemicals as they lack human health risk assessments, toxicity reference values, and risk screening values. We aim to use computational toxicology and quantitative high-throughput screening (qHTS) technologies to fill these data gaps, and begin to prioritize these chemicals for additional assessment. In this pilot, we demonstrate how we were able to identify that benzo[k]fluoranthene may induce DNA damage and steatosis using qHTS data and two separate adverse outcome pathways (AOPs). We also demonstrate how bootstrap natural spline-based meta-regression can be used to integrate data across multiple assay replicates to generate a concentration-response curve. We used this analysis to calculate an in vitro point of departure of 0.751 μM and risk-specific in vitro concentrations of 0.29 μM and 0.28 μM for 1:1,000 and 1:10,000 risk, respectively, for DNA damage. Based on the available evidence, and considering that only a single HSD17B4 assay is available, we have low overall confidence in the steatosis hazard identification. This case study suggests that coupling qHTS assays with AOPs and ontologies will facilitate hazard identification. Combining this with quantitative evidence integration methods, such as bootstrap meta-regression, may allow risk assessors to identify points of departure and risk-specific internal/in vitro concentrations. These results are sufficient to prioritize the chemicals; however, in the longer term we will need to estimate external doses for risk screening purposes, such as through margin of exposure methods. © 2016 Society for Risk Analysis.

A 1 kA-class cryogen-free critical current characterization system for superconducting coated conductors.

PubMed

Strickland, N M; Hoffmann, C; Wimbush, S C

2014-11-01

A cryogenic electrical transport measurement system is described that is particularly designed to meet the requirements for routine and effective characterization of commercial second generation high-temperature superconducting (HTS) wires in the form of coated conductors based on YBa2Cu3O7. Specific design parameters include a base temperature of 20 K, an applied magnetic field capability of 8 T (provided by a HTS split-coil magnet), and a measurement current capacity approaching 1 kA. The system accommodates samples up to 12 mm in width (the widest conductor size presently commercially available) and 40 mm long, although this is not a limiting size. The sample is able to be rotated freely with respect to the magnetic field direction about an axis parallel to the current flow, producing field angle variations in the standard maximum Lorentz force configuration. The system is completely free of liquid cryogens for both sample cooling and magnet cool-down and operation. Software enables the system to conduct a full characterization of the temperature, magnetic field, and field angle dependence of the critical current of a sample without any user interaction. The system has successfully been used to measure a wide range of experimental and commercially-available superconducting wire samples sourced from different manufacturers across the full range of operating conditions. The system encapsulates significant advances in HTS magnet design and efficient cryogen-free cooling technologies together with the capability for routine and automated high-current electrical transport measurements at cryogenic temperatures. It will be of interest to both research scientists investigating superconductor behavior and commercial wire manufacturers seeking to accurately characterize the performance of their product under all desired operating conditions.

Design and Test Results of Superconducting Magnet for Heavy-Ion Rotating Gantry

NASA Astrophysics Data System (ADS)

Takayama, S.; Koyanagi, K.; Miyazaki, H.; Takami, S.; Orikasa, T.; Ishii, Y.; Kurusu, T.; Iwata, Y.; Noda, K.; Obana, T.; Suzuki, K.; Ogitsu, T.; Amemiya, N.

2017-07-01

Heavy-ion radiotherapy has a high curative effect in cancer treatment and also can reduce the burden on patients. These advantages have been generally recognized. Furthermore, a rotating gantry can irradiate a tumor with ions from any direction without changing the position of the patient. This can reduce the physical dose on normal cells, and is thus commonly used in proton radiotherapy. However, because of the high magnetic rigidity of carbon ions, the weight of the rotating gantry for heavy-ion therapy is about three-times heavier than those used for proton cancer therapy, according to our estimation. To overcome this issue, we developed a small and lightweight rotating gantry in collaboration with the National Institute of Radiological Sciences (NIRS). The compact rotating gantry was composed of ten low-temperature superconducting (LTS) magnets that were designed from the viewpoint of beam optics. These LTS magnets have a surface-winding coil-structure and provide both dipole and quadrupole fields. The maximum dipole and quadrupole magnetic field of the magnets were 2.88 T and 9.3 T/m, respectively. The rotating gantry was installed at NIRS, and beam commissioning is in progress to achieve the required beam quality. In the three years since 2013, in a project supported by the Ministry of Economy, Trade and Industry (METI) and the Japan Agency for Medical Research and Development (AMED), we have been developing high-temperature superconducting (HTS) magnets with the aim of a further size reduction of the rotating gantry. To develop fundamental technologies for designing and fabricating HTS magnets, a model magnet was manufactured. The model magnet was composed of 24 saddle-shaped HTS coils and generated a magnetic field of 1.2 T. In the presentation, recent progress in this research will be reported.

Development and Validation of a Computational Model for Androgen Receptor Activity

PubMed Central

2016-01-01

Testing thousands of chemicals to identify potential androgen receptor (AR) agonists or antagonists would cost millions of dollars and take decades to complete using current validated methods. High-throughput in vitro screening (HTS) and computational toxicology approaches can more rapidly and inexpensively identify potential androgen-active chemicals. We integrated 11 HTS ToxCast/Tox21 in vitro assays into a computational network model to distinguish true AR pathway activity from technology-specific assay interference. The in vitro HTS assays probed perturbations of the AR pathway at multiple points (receptor binding, coregulator recruitment, gene transcription, and protein production) and multiple cell types. Confirmatory in vitro antagonist assay data and cytotoxicity information were used as additional flags for potential nonspecific activity. Validating such alternative testing strategies requires high-quality reference data. We compiled 158 putative androgen-active and -inactive chemicals from a combination of international test method validation efforts and semiautomated systematic literature reviews. Detailed in vitro assay information and results were compiled into a single database using a standardized ontology. Reference chemical concentrations that activated or inhibited AR pathway activity were identified to establish a range of potencies with reproducible reference chemical results. Comparison with existing Tier 1 AR binding data from the U.S. EPA Endocrine Disruptor Screening Program revealed that the model identified binders at relevant test concentrations (<100 μM) and was more sensitive to antagonist activity. The AR pathway model based on the ToxCast/Tox21 assays had balanced accuracies of 95.2% for agonist (n = 29) and 97.5% for antagonist (n = 28) reference chemicals. Out of 1855 chemicals screened in the AR pathway model, 220 chemicals demonstrated AR agonist or antagonist activity and an additional 174 chemicals were predicted to have potential weak AR pathway activity. PMID:27933809

Interactive modeling-synthesis-characterization approach towards controllable in situ self-assembly of artificial pinning centers in RE-123 films

NASA Astrophysics Data System (ADS)

Wu, Judy; Shi, Jack

2017-10-01

Raising critical current density J c in high temperature superconductors (HTSs) is an important strategy towards performance-cost balanced HTS technology for commercialization. The development of strong nanoscale artificial pinning centers (APCs) in HTS, such as YBa2Cu3O7 or RE-123 in general, represents one of the most exciting progressions in HTS material research in the last decade. Significantly raised J c has been demonstrated in APC/RE-123 nanocomposites by enhanced pinning on magnetic vortices in magnetic fields towards that demanded in practical applications. Among other processes, strain-mediated self-organization has been explored extensively for in situ formation of the APCs based on fundamental physics design rules. The desire in controlling the morphology, dimension, orientation, and concentration of APCs has led to a fundamental question on how strains interact in determining APCs at a macroscopic scale. Answering this question demands an interactive modeling-synthesis-characterization approach towards a thorough understanding of fundamental physics governing the strain-mediated self-organization of the APCs in the APC/RE-123 nanocomposites. Such an understanding is the key for a leap forward from the traditionally empirical method to materials-by-design to enable an optimal APC landscape to be achieved in epitaxial films of APC/YBCO nanocomposites under a precise guidance of fundamental physics. The paper intends to provide a review of recent progress made in the controllable generation of APCs using the interactive modeling-synthesis-characterization approach. The emphasis will be given to the understanding so far achieved using such an approach on the collective effect of the strain field on the morphology, dimension, and orientation of APCs in epitaxial APC/RE-123 nanocomposite films.

Magnetic imaging of antiferromagnetic and superconducting phases in R bxF e2 -yS e2 crystals

NASA Astrophysics Data System (ADS)

Hazi, J.; Mousavi, T.; Dudin, P.; van der Laan, G.; Maccherozzi, F.; Krzton-Maziopa, A.; Pomjakushina, E.; Conder, K.; Speller, S. C.

2018-02-01

High-temperature superconducting (HTS) cuprate materials, with the ability to carry large electrical currents with no resistance at easily reachable temperatures, have stimulated enormous scientific and industrial interest since their discovery in the 1980's. However, technological applications of these promising compounds have been limited by their chemical and microstructural complexity and the challenging processing strategies required for the exploitation of their extraordinary properties. The lack of theoretical understanding of the mechanism for superconductivity in these HTS materials has also hindered the search for new superconducting systems with enhanced performance. The unexpected discovery in 2008 of HTS iron-based compounds has provided an entirely new family of materials for studying the crucial interplay between superconductivity and magnetism in unconventional superconductors. Alkali-metal-doped iron selenide (AxF e2 -yS e2 , A =alkali metal ) compounds are of particular interest owing to the coexistence of superconductivity at relatively high temperatures with antiferromagnetism. Intrinsic phase separation on the mesoscopic scale is also known to occur in what were intended to be single crystals of these compounds, making it difficult to interpret bulk property measurements. Here, we use a combination of two advanced microscopy techniques to provide direct evidence of the magnetic properties of the individual phases. First, x-ray linear dichroism studies in a photoelectron emission microscope, and supporting multiplet calculations, indicate that the matrix (majority) phase is antiferromagnetic whereas the minority phase is nonmagnetic at room temperature. Second, cryogenic magnetic force microscopy demonstrates unambiguously that superconductivity occurs only in the minority phase. The correlation of these findings with previous microstructural studies and bulk measurements paves the way for understanding the intriguing electronic and magnetic properties of these compounds.

Alternating current loss characteristics in (bismuth,lead)SCCO and yttrium barium copper oxide superconducting tapes

NASA Astrophysics Data System (ADS)

Nguyen, Doan Ngoc

Alternating current (AC) loss and current carrying capacity are two of the most crucial considerations in large-scale power applications of high temperature superconducting (HTS) conductors. AC losses result in an increased thermal load for cooling machines, and thus increased operating costs. Furthermore, AC losses can stimulate quenching phenomena or at least decrease the stability margin for superconducting devices. Thus, understanding AC losses is essential for the development of HTS AC applications. The main focus of this dissertation is to make reliable total AC loss measurements and interpret the experimental results in a theoretical framework. With a specially designed magnet, advanced total AC loss measurement system in liquid nitrogen (77 K) has been successfully built. Both calorimetric and electromagnetic methods were employed to confirm the validity of the measured results and to have a more thorough understanding of AC loss in HTS conductors. The measurement is capable of measuring total AC loss in HTS tapes over a wide range of frequency and amplitude of transport current and magnetic field. An accurate phase control technique allows measurement of total AC loss with any phase difference between the transport current and magnetic field by calorimetric method. In addition, a novel total AC loss measurement system with variable temperatures from 30 K to 100 K was successfully built and tested. Understanding the dependence of AC losses on temperature will enable optimization of the operating temperature and design of HTS devices. As a part of the dissertation, numerical calculations using Brandt's model were developed to study electrodynamics and total AC loss in HTS conductors. In the calculations, the superconducting electrical behavior is assumed to follow a power-law model. In general, the practical properties of conductors, including field-dependence of critical current density Jc, n-value and non-uniform distribution of Jc, can be accounted for in the numerical calculations. The numerical calculations are also capable of investigating eddy current loss in the stabilizer and ferromagnetic loss in the substrate of YBa2Cu3O 7-delta (YBCO) coated conductor. AC loss characteristics and electrodynamics in several (Bi,Pb)2 Sr2Ca2Cu3Ox (Bi-2223) and YBCO tapes were studied experimentally and numerically. It was found that AC loss behavior Ax in HTS tapes is strongly affected by the sample parameters such as cross-section, structure, dimensions, critical current distribution as well as by operation parameters including temperature, frequency, the phase difference between transport current and magnetic field, the orientation of magnetic field. The Ni-5%W substrate in YBCO conductors generates some ferromagnetic loss but this loss component is significantly reduced by a small parallel DC magnetic field. At a given AC magnetic field B0, there is a temperature Tmax at which the magnetization loss is maximum. The design of HTS devices needs to be optimized to avoid operating at that temperature. In general, the total AC loss in HTS tapes is still high for many power device applications, especially for those that present a rather high AC applied magnetic field. The development of low loss conductors is therefore crucial for HTS large-scale applications.

Computational toxicology and in silico modeling of embryogenesis

EPA Science Inventory

High-throughput screening (HTS) is providing a rich source of in vitro data for predictive toxicology. ToxCast™ HTS data presently covers 1060 broad-use chemicals and captures >650 in vitro features for diverse biochemical and receptor binding activities, multiplexed reporter gen...

20180312 - Mechanistic Modeling of Developmental Defects through Computational Embryology (SOT)

EPA Science Inventory

Significant advances in the genome sciences, in automated high-throughput screening (HTS), and in alternative methods for testing enable rapid profiling of chemical libraries for quantitative effects on diverse cellular activities. While a surfeit of HTS data and information is n...

Pathway Profiling and Tissue Modeling Using ToxCast HTS Data

EPA Science Inventory

High-throughput screening (HTS) and high-content screening (HCS) assays are providing data-rich studies to probe and profile the direct cellular effects of thousands of chemical compounds in commerce or potentially entering the environment. In vitro profiling may compare unknown ...

Palm-size miniature superconducting bulk magnet

NASA Astrophysics Data System (ADS)

Saho, Norihide; Matsuda, Kazuya; Nishijima, Noriyo

The development of a small, light, powerful and energy-efficient superconducting magnet has been desired in order to realize better efficiency and manipulability in guiding magnetic nano-particles, magnetic organic cells and other items to the right place. This study focuses on the development of a high-temperature superconducting (HTS) bulk magnet characterized by comparatively low leak magnetism despite a relatively high magnetic field. On this basis, the authors developed a palm-sized superconducting bulk magnet, which is the world's smallest, lightest, and lowest power consuming, as well as a new technology to effectively magnetize such a bulk magnet in a compact Stirling-cycle cryocooler (magnet C) with a pre-magnetized HTS bulk magnet (magnet B) in a compact cryocooler. This technology is demonstrated in two steps. In the first step, magnet B is magnetized using a superconducting solenoid magnet with a high magnetic field (magnet A) via the field cooling method. In the second step, magnet C is magnetized in the high magnetic field of magnet B. The prototype magnet C weighs 1.8 kg, and measures 235 × 65 × 115 mm (L × W × H). Magnet B was magnetized to 4.9 T using a 5 T magnet, and the target, magnet C, was magnetized using magnet B so that its maximum trapped magnetic flux density reached the value of 3.15 T. The net power consumption in a steady cooling state was 23 W, which is very low and comparable to that of a laptop computer.

Ultrahigh field NMR and MRI: Science at a crossroads. Report on a jointly-funded NSF, NIH and DOE workshop, held on November 12-13, 2015 in Bethesda, Maryland, USA

NASA Astrophysics Data System (ADS)

Polenova, Tatyana; Budinger, Thomas F.

2016-05-01

Magnetic resonance plays a central role in academic, industrial and medical research. NMR is widely used for characterizing the structure, chemistry and dynamic properties of new materials, chemicals and pharmaceuticals, in both the liquid and solid phases. NMR also provides detailed functional information on biological macromolecules and their assemblies, in vitro, in membranes and even in whole cells. In vivo, MRI/S are used for clinical diagnosis and prognosis of disease, for non-invasive studies of human physiology and metabolism in general, and for evaluating brain function, in particular. MRI/S is also a key technology for imaging small organisms at the cellular level, monitoring catalysis in chemical reactors and other scientific areas where non-destructive characterizations of structure and dynamics in complex systems are needed. At the heart of all the MR methods are strong, stable and homogeneous magnets built from low-temperature superconductors (LTS), which are essential to these experiments. Further developments in NMR/MRI are hampered because the ultimate limit of the attainable field strengths of persistent LTS magnets has now been reached. Fortunately, recent breakthroughs in new high-temperature superconductors (HTS) and hybrid LTS/HTS magnet technologies promise to greatly increase the achievable field strength of NMR magnets and to decrease the operational complexity of high field human MRI infrastructures, thereby enabling new applications at the forefront of modern multidisciplinary research.

A miniaturized HTS microwave receiver front-end subsystem for radar and communication applications

NASA Astrophysics Data System (ADS)

Bian, Yongbo; Guo, Jin; Gao, Changzheng; Li, Chunguang; Li, Hong; Wang, Jia; Cui, Bin; He, Xiaofeng; Li, Chao; Li, Na; Li, Guoqiang; Zhang, Qiang; Zhang, Xueqiang; Meng, Jibao; He, Yusheng

2010-08-01

This paper presents a miniaturized high performance high temperature superconducting (HTS) microwave receiver front-end subsystem, which uses a mini stirling cryocooler to cool a high selective HTS filter and a low noise amplifier (LNA). The HTS filter was miniaturized by using specially designed compact resonators and fabricating with double-sided YBCO films on LAO substrate which has a relatively high permittivity. The LNA was specially designed to work at cryogenic temperature with noise figure of 0.27 dB at 71 K. The mini cryocooler, which is widely used in infrared detectors, has a smaller size (60 mm × 80 mm × 100 mm) and a lighter weight (340 g) than the stirling cryocoolers commonly used in other HTS filter subsystem. The whole front-end subsystem, including a HTS filter, a LNA, a cryocooler and the vacuum chamber, has a size of only φ120 mm × 175 mm and a weight of only 3.3 kg. The microwave devices inside the subsystem are working at 71.8 K with a consumed cooling power of 0.325 W. The center frequency of this subsystem is 925.2 MHz and the bandwidth is 2.7 MHz (which is a fractional bandwidth of 0.2%), with the gain of 19.75 dB at center frequency and the return loss better than -18.11 dB in the pass band. The stop band rejection is more than 60 dB and the skirt slope is exceeding 120 dB MHz -1. The noise figure of this subsystem is less than 0.8 dB. This front-end subsystem can be used in radars and communication systems conveniently due to it’s compact size and light weight.

A Systematic Review of Randomized Controlled Trials Comparing Hypertonic Sodium Solutions and Mannitol for Traumatic Brain Injury: Implications for Emergency Department Management.

PubMed

Burgess, Sarah; Abu-Laban, Riyad B; Slavik, Richard S; Vu, Erik N; Zed, Peter J

2016-04-01

To comparatively evaluate hypertonic sodium (HTS) and mannitol in patients following acute traumatic brain injury (TBI) on the outcomes of all-cause mortality, neurological disability, intracranial pressure (ICP) change from baseline, ICP treatment failure, and serious adverse events. PubMed, EMBASE, CENTRAL, Cochrane Database of Systematic Reviews, ClinicalTrials.gov, and WHO ICTRP (World Health Organization International Clinical Trials Registry Platform) were searched (inception to November 2015) using hypertonic saline solutions, sodium chloride, mannitol, osmotic diuretic, traumatic brain injury, brain injuries, and head injury. Searches were limited to humans. Clinical practice guidelines and bibliographies were reviewed. Prospective, randomized trials comparing HTS and mannitol in adults (≥16 years) with severe TBI (Glasgow Coma Scale score ≤8) and elevated ICP were included. ICP elevation, ICP reduction, and treatment failure were defined using study definitions. Of 326 articles screened, 7 trials enrolling a total of 191 patients met inclusion criteria. Studies were underpowered to detect a significant difference in mortality or neurological outcomes. Due to significant heterogeneity and differences in reporting ICP change from baseline, this outcome was not meta-analyzed. No difference between HTS and mannitol was observed for mean ICP reduction; however, risk of ICP treatment failure favored HTS (risk ratio [RR] = 0.39; 95% CI = 0.18-0.81). Serious adverse events were not reported. Based on limited data, clinically important differences in mortality, neurological outcomes, and ICP reduction were not observed between HTS or mannitol in the management of severe TBI. HTS appears to lead to fewer ICP treatment failures. © The Author(s) 2016.

An active homopolar magnetic bearing with high temperature superconductor (HTS) coils and ferromagnetic cores

NASA Technical Reports Server (NTRS)

Brown, G. V.; Dirusso, E.; Provenza, A. J.

1995-01-01

A proof-of-feasibility demonstration showed that high temperature superconductor (HTS) coils can be used in a high-load, active magnetic bearing in liquid nitrogen. A homopolar radial bearing with commercially wound HTS (Bi 2223) bias and control coils produced over 200 lb (890 N) radial load capacity (measured non-rotating) and supported a shaft to 14000 rpm. The goal was to show that HTS coils can operate stably with ferromagnetic cores in a feedback controlled system at a current density similar to that in Cu in liquid nitrogen. Design compromises permitted use of circular coils with rectangular cross section. Conductor improvements will eventually permit coil shape optimization, higher current density and higher bearing load capacity. The bias coil, wound with non-twisted, multifilament HTS conductor, required negligible power to carry its direct current. The control coils were wound with monofilament HTS sheathed in Ag. These dissipated negligible power for direct current (i.e. for steady radial load components). When an alternating current (AC) was added, the AC component dissipated power which increased rapidly with frequency and quadratically with AC amplitude. In fact at frequencies above about 2 hz, the effective resistance of the control coil conductor actually exceeds that of the silver which is in electrical parallel with the oxide superconductor. This is at least qualitatively understandable in the context of a Bean-type model of flux and current penetration into a Type II superconductor. Fortunately the dynamic currents required for bearing stability are of small amplitude. These results show that while twisted multifilament conductor is not needed for stable levitation, twisted multifilaments will be required to reduce control power for sizable dynamic loads, such as those due to unbalance.

Development of a compact HTS lead unit for the SC correction coils of the SuperKEKB final focusing magnet system

NASA Astrophysics Data System (ADS)

Zong, Zhanguo; Ohuchi, Norihito; Tsuchiya, Kiyosumi; Arimoto, Yasushi

2016-09-01

Forty-three superconducting (SC) correction coils with maximum currents of about 60 A are installed in the SuperKEKB final focusing magnet system. Current leads to energize the SC correction coils should have an affordable heat load and fit the spatial constraints in the service cryostat where the current leads are installed. To address the requirements, design optimization of individual lead was performed with vapor cooled current lead made of a brass material, and a compact unit was designed to accommodate eight current leads together in order to be installed with one port in the service cryostat. The 2nd generation high temperature SC (HTS) tape was adopted and soldered at the cold end of the brass current lead to form a hybrid HTS lead structure. A prototype of the compact lead unit with HTS tape was constructed and tested with liquid helium (LHe) environment. This paper presents a cryogenic measurement system to simulate the real operation conditions in the service cryostat, and analysis of the experimental results. The measured results showed excellent agreement with the theoretical analysis and numerical simulation. In total, 11 sets of the compact HTS lead units were constructed for the 43 SC correction coils at KEK. One set from the mass production was tested in cryogenic conditions, and exhibited the same performance as the prototype. The compact HTS lead unit can feed currents to four SC correction coils simultaneously with the simple requirement of controlling and monitoring helium vapor flow, and has a heat load of about 0.762 L/h in terms of LHe consumption.

AOPs and Biomarkers: Bridging High Throughput Screening and Regulatory Decision Making

EPA Science Inventory

As high throughput screening (HTS) plays a larger role in toxicity testing, camputational toxicology has emerged as a critical component in interpreting the large volume of data produced. Computational models designed to quantify potential adverse effects based on HTS data will b...

Metabolism Retrofit Strategies for ToxCast Assays (BOSC)

EPA Science Inventory

The EPA’s ToxCast program utilizes a wide variety of high-throughput screening assays (HTS) to assess chemical perturbations of molecular and cellular endpoints. A limitation of many HTS assays used for toxicity assessment is the lack of xenobiotic metabolism (XM) which precludes...

Superconductor-Magnet Bearings With Inherent Stability and Velocity-Independent Drag Torque

NASA Technical Reports Server (NTRS)

Lee, Eun-Jeong; Ma, Ki Bui; Wilson, Thomas L.; Chu, Wei-Kan

1999-01-01

A hybrid superconductor magnet bearing system has been developed based on passive magnetic levitation and the flux pinning effect of high-temperature superconductivity. The rationale lies in the unique capability of a high-temperature superconductor (HTS) to enhance system stability passively without power consumption. Characterization experiments have been conducted to understand its dynamic behavior and to estimate the required motor torque for its driving system design. These experiments show that the hybrid HTS-magnet bearing system has a periodic oscillation of drag torque due mainly to the nonuniform magnetic field density of permanent magnets. Furthermore, such a system also suffers from a small superimposed periodic oscillation introduced by the use of multiple HTS disks rather than a uniform annulus of HTS material. The magnitude of drag torque is velocity independent and very small. These results make this bearing system appealing for high-speed application. Finally, design guidelines for superconducting bearing systems are suggested based on these experimental results.

Magnetic superelevation design of Halbach permanent magnet guideway for high-temperature superconducting maglev

NASA Astrophysics Data System (ADS)

Lei, Wuyang; Qian, Nan; Zheng, Jun; Huang, Huan; Zhang, Ya; Deng, Zigang

2017-07-01

To improve the curve negotiating ability of high-temperature superconducting (HTS) maglev system, a special structure of magnetic superelevation for double-pole Halbach permanent magnet guideway (PMG) was designed. The most significant feature of this design is the asymmetrical PMG that forms a slanting magnetic field without affecting the smoothness of the PMG surface. When HTS maglev vehicle runs through curves with magnetic superelevation, the vehicle will slant due to asymmetry in magnetic field and the flux-pinning effect of onboard HTS bulks. At the same time, one component of the levitation force provides a part of the centripetal force that reduces lateral acceleration of the vehicle and thus enhances its curve negotiating ability. Furthermore, the slant angle of magnetic superelevation can be adjusted by changing the materials and the thickness of the added permanent magnets. This magnetic superelevation method, together with orographic uplift, can be applied to different requirements of PMG designs. Besides, the applicability of this method would benefit future development of high-speed HTS maglev system.

Structures of human thymidylate synthase R163K with dUMP, FdUMP and glutathione show asymmetric ligand binding

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

Gibson, Lydia M.; Celeste, Lesa R.; Lovelace, Leslie L.

Thymidylate synthase (TS) is a well validated target in cancer chemotherapy. Here, a new crystal form of the R163K variant of human TS (hTS) with five subunits per asymmetric part of the unit cell, all with loop 181-197 in the active conformation, is reported. This form allows binding studies by soaking crystals in artificial mother liquors containing ligands that bind in the active site. Using this approach, crystal structures of hTS complexes with FdUMP and dUMP were obtained, indicating that this form should facilitate high-throughput analysis of hTS complexes with drug candidates. Crystal soaking experiments using oxidized glutathione revealed thatmore » hTS binds this ligand. Interestingly, the two types of binding observed are both asymmetric. In one subunit of the physiological dimer covalent modification of the catalytic nucleophile Cys195 takes place, while in another dimer a noncovalent adduct with reduced glutathione is formed in one of the active sites.« less

Abbott Physicochemical Tiering (APT)--a unified approach to HTS triage.

PubMed

Cox, Philip B; Gregg, Robert J; Vasudevan, Anil

2012-07-15

The selection of the highest quality chemical matter from high throughput screening (HTS) is the ultimate aim of any triage process. Typically there are many hundreds or thousands of hits capable of modulating a given biological target in HTS with a wide range of physicochemical properties that should be taken into consideration during triage. Given the multitude of physicochemical properties that define drug-like space, a system needs to be in place that allows for a rapid selection of chemical matter based on a prioritized range of these properties. With this goal in mind, we have developed a tool, coined Abbott Physicochemical Tiering (APT) that enables hit prioritization based on ranges of these important physicochemical properties. This tool is now used routinely at Abbott to help prioritize hits out of HTS during the triage process. Herein we describe how this tool was developed and validated using Abbott internal high throughput ADME data (HT-ADME). Copyright © 2012 Elsevier Ltd. All rights reserved.

Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa 2 Cu 3 O 7 - δ Coated Conductors

DOE PAGES

Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.; ...

2016-01-01

The ability of high-temperature superconductors (HTSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. The development and further improvement of HTS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. We present a critical current analysis of a real HTS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa 2Cu 3O 7-δ. This methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsiblemore » for the high-current-carrying-capacity characteristic of commercial HTS wires. Finally, our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HTS wire designs.« less

Cycle Design of Reverse Brayton Cryocooler for HTS Cable Cooling Using Exergy Analysis

NASA Astrophysics Data System (ADS)

Gupta, Sudeep Kumar; Ghosh, Parthasarathi

2017-02-01

The reliability and price of cryogenic refrigeration play an important role in the successful commercialization of High Temperature Superconducting (HTS) cables. For cooling HTS cable, sub-cooled liquid nitrogen (LN2) circulation system is used. One of the options to maintain LN2 in its sub-cooled state is by providing refrigeration with the help of Reverse Brayton Cryo-cooler (RBC). The refrigeration requirement is 10 kW for continuously sub-cooling LN2 from 72 K to 65 K for cooling 1 km length of HTS cable [1]. In this paper, a parametric evaluation of RBC for sub-cooling LN2 has been performed using helium as a process fluid. Exergy approach has been adopted for this analysis. A commercial process simulator, Aspen HYSYS® V8.6 has been used for this purpose. The critical components have been identified and their exergy destruction and exergy efficiency have been obtained for a given heat load condition.

Side-suspended High-Tc Superconducting Maglev Prototype Vehicle Running at a High Speed in an Evacuated Circular Test Track

NASA Astrophysics Data System (ADS)

Zhou, Dajin; Zhao, Lifeng; Cui, Chenyu; Zhang, Yong; Guo, Jianqiang; Zhao, Yong

2017-07-01

High-T c superconductor (HTS) and permanent magnetic guideway (PMG) based maglev train is intensively studied in China, Japan, Germany and Brazil, mainly through static or vibration test. Amongst these studies, only a few of reports are available for the direct and effective assessment on the dynamic performance of the HTS maglev vehicle by running on a straight or circular PMG track. The highest running speed of these experiments is lower than 50 km/h. In this paper, a side-suspended HTS permanent magnetic guideway maglev system was proposed and constructed in order to increase the running speed in a circular track. By optimizing the arrangement of YBCO bulks besides the PMG, the side-suspended HTS maglev prototype vehicle was successfully running stably at a speed as high as 150 km/h in a circular test track with 6.5 m in diameter, and in an evacuated tube environment, in which the pressure is 5 × 103 Pa.

Simulation of the Vortex Dynamics in a Real Pinning Landscape of YBa 2 Cu 3 O 7 - δ Coated Conductors

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

Sadovskyy, I. A.; Koshelev, A. E.; Glatz, A.

The ability of high-temperature superconductors (HTSs) to carry very large currents with almost no dissipation makes them irreplaceable for high-power applications. The development and further improvement of HTS-based cables require an in-depth understanding of the superconducting vortex dynamics in the presence of complex pinning landscapes. We present a critical current analysis of a real HTS sample in a magnetic field by combining state-of-the-art large-scale Ginzburg-Landau simulations with reconstructive three-dimensional scanning-transmission-electron-microscopy tomography of the pinning landscape in Dy-doped YBa 2Cu 3O 7-δ. This methodology provides a unique look at the vortex dynamics in the presence of a complex pinning landscape responsiblemore » for the high-current-carrying-capacity characteristic of commercial HTS wires. Finally, our method demonstrates very good functional and quantitative agreement of the critical current between simulation and experiment, providing a new predictive tool for HTS wire designs.« less

Numerical studies on the force characteristic of superconducting linear synchronous motor with HTS bulk magnet

NASA Astrophysics Data System (ADS)

Tang, Junjie; Li, Jing; Li, Xiang; Han, Le

2018-03-01

High temperature superconductor (HTS) bulks have significant potential use in linear motor application act as quasi-permanent magnet to replace traditional magnets. Force characteristic between HTS bulk magnet and traveling magnetic field was investigated with numerical simulation and experimental measurement in this paper. Influences of bulk height and number on the force characteristic were studied by the finite element model considering the nonlinear E-J relationship. Study was also made on addition of a back iron plate to the bulk magnet. Besides, force characteristic of bulk was compared with the permanent magnet results. The small initial decrease of the thrust could be explained by inside superconducting current redistribution. It was found that efficiency of linear motor did not increase by adding more bulk magnets. The bulk magnet will be remagnetized instead of erasing trapped field with the increase of the traveling magnetic field strength. The conclusions are helpful in prediction and design the linear motor with HTS bulk magnet.

The design and testing of a cooling system using mixed solid cryogen for a portable superconducting magnetic energy storage system

NASA Astrophysics Data System (ADS)

Kim, K. L.; Song, J. B.; Choi, J. H.; Kim, S. H.; Y Koh, D.; Seong, K. C.; Chang, H. M.; Lee, H. G.

2010-12-01

A cooling system that uses solid nitrogen (SN2) as an effective heat capacity enhancer was recently introduced to enhance the thermal stability of the HTS SMES. Since SN2 has a large enthalpy with minimal weight, it enables a portable system by increasing the recooling to recooling time period (RRTP). However, contact between the SN2 and HTS SMES magnet can be broken by repeated thermal disturbances (thermal 'dry-out' phenomena). Therefore, it is essential to improve thermal contact to allow full use of the heat capacity of SN2. This study evaluated the effect of using a mixture containing SN2 and a small amount of a liquid cryogen as a cooling system in the HTS SMES system. The performance of the cooling system was evaluated using the mixed cryogen and compared with that of SN2 alone. In addition, the role of liquid neon (Ne) as a heat exchanger between SN2 and the HTS SMES magnet is discussed.

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

PubMed

Hach, Faraz; Sarrafi, Iman; Hormozdiari, Farhad; Alkan, Can; Eichler, Evan E; Sahinalp, S Cenk

2014-07-01

High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such as structural variation detection, where it is important to report multiple mapping loci for each read. For this purpose we introduce mrsFAST-Ultra, a fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of HTS reads very efficiently. mrsFAST-Ultra improves mrsFAST, our first cache oblivious read aligner capable of handling multi-mapping reads, through new and compact index structures that reduce not only the overall memory usage but also the number of CPU operations per alignment. In fact the size of the index generated by mrsFAST-Ultra is 10 times smaller than that of mrsFAST. As importantly, mrsFAST-Ultra introduces new features such as being able to (i) obtain the best mapping loci for each read, and (ii) return all reads that have at most n mapping loci (within an error threshold), together with these loci, for any user specified n. Furthermore, mrsFAST-Ultra is SNP-aware, i.e. it can map reads to reference genome while discounting the mismatches that occur at common SNP locations provided by db-SNP; this significantly increases the number of reads that can be mapped to the reference genome. Notice that all of the above features are implemented within the index structure and are not simple post-processing steps and thus are performed highly efficiently. Finally, mrsFAST-Ultra utilizes multiple available cores and processors and can be tuned for various memory settings. Our results show that mrsFAST-Ultra is roughly five times faster than its predecessor mrsFAST. In comparison to newly enhanced popular tools such as Bowtie2, it is more sensitive (it can report 10 times or more mappings per read) and much faster (six times or more) in the multi-mapping mode. Furthermore, mrsFAST-Ultra has an index size of 2GB for the entire human reference genome, which is roughly half of that of Bowtie2. mrsFAST-Ultra is open source and it can be accessed at http://mrsfast.sourceforge.net. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Development and test of a 100 kVA superconducting transformer operated at 77 K

NASA Astrophysics Data System (ADS)

Kummeth, P.; Schlosser, R.; Massek, P.; Schmidt, H.; Albrecht, C.; Breitfelder, D.; Neumüller, H.-W.

2000-05-01

High-temperature superconducting (HTS) transformers are very promising candidates for application in electrical power engineering. Their main advantages are reduced size, weight, better efficiency and reduced potential fire and environmental hazards. We have designed, constructed and tested a 100 kVA HTS power transformer operated at 77 K. The nominal primary and secondary currents (voltages) are 18 A (5.6 kV) and 92 A (1.1 kV), respectively. No-load tests, short-circuit tests and load tests proved repeatedly that the transformer has the rated capacity. HTS winding losses of 20.6 W and iron losses of 403 W were measured.

Development of Y-Ba-Cu-O Superconductors for Magnetic Bearings

NASA Technical Reports Server (NTRS)

Selvamanickam, V.; Pfaffenbach, K.; Sokolowski, R. S.; Zhang, Y.; Salama, K.

1996-01-01

The material requirements, material manufacturing and magnetic properties that are relevant to fabrication of High Temperature Superconductor (HTS) magnetic bearings have been discussed. It is found that the seeded-melt-texturing method can be used to fabricate the single domain material that is required to achieve the best magnetic properties. Trapped-field mapping has been used as a non-destructive tool to determine the single-domain nature of the HTS material and quantity of the HTS disks. Both the trapped field and the levitation force of the Y-Ba-Cu-O disks are found to be strongly sensitive to the oxygen content.

Flux pumping for non-insulated and metal-insulated HTS coils

NASA Astrophysics Data System (ADS)

Ma, Jun; Geng, Jianzhao; Coombs, T. A.

2018-01-01

High-temperature superconducting (HTS) coils wound from coated conductors without turn-to-turn insulation (non-insulated (NI) coils) have been proven with excellent electrical and thermal performances. However, the slow charging of NI coils has been a long-lasting problem. In this work, we explore using a transformer-rectifier HTS flux pump to charge an NI coil and a metal-insulated coil. The charging performance comparison is made between different coils. Comprehensive study is done to thoroughly understand the electrical-magnetic transience in charging these coils. We will show that the low-voltage high-current flux pump is especially suitable for charging NI coils with very low characteristic resistance.

The Development and Demonstration of a 360m/10 kA HTS DC Power Cable

NASA Astrophysics Data System (ADS)

Xiao, Liye

With the quick development of renewable energy, it is expected that the electric power from renewable energy would be the dominant one for the future power grid. Due to the specialty of the renewable energy, the HVDC power transmission would be very useful for the transmission of electric power from renewable energy. DC power cable made of High Tc Superconductor (HTS) would be a possible alternative for the construction of HVDC power transmission system. In this chapter, we report the development and demonstration of a 360 m/10 kA HTS DC power cable and the test results.

Nanomaterial (NM) bioactivity profiling by ToxCast high-throughput screening (HTS)

EPA Science Inventory

Rapidly increasing numbers of new NMs and their uses demand efficient tests of NM bioactivity for safety assessment. The EPA’s ToxCast program uses HTS assays to prioritize for targeted testing, identify biological pathways affected, and aid in linking NM properties and potential...

Superconducting multiport antenna arrays

NASA Astrophysics Data System (ADS)

Chaloupka, H.

1993-10-01

Applications of HTS to radiating elements and beam-forming networks of multibeam and/or multifrequency arrays are discussed. This includes radiating elements which meet special requirements with respect to size and frequency response. Realized versions of both a three-port HTS array and a 4 x 4 Butler matrix are presented.

Development of a tiered screening strategy for a molecular-initiating event: thyroperoxidase inhibition (SOT)

EPA Science Inventory

Adverse outcome pathway (AOP) analyses illustrate that some molecular-initiating events (MIEs) for thyroid disruption, including thyroperoxidase (TPO) inhibition, are not evaluated by current ToxCast/Tox21 high-throughput screening (HTS) assays. A novel HTS assay for TPO inhibiti...

Incorporating Population Variability and Susceptible Subpopulations into Dosimetry for High-Throughput Toxicity Testing

EPA Science Inventory

Momentum is growing worldwide to use in vitro high-throughput screening (HTS) to evaluate human health effects of chemicals. However, the integration of dosimetry into HTS assays and incorporation of population variability will be essential before its application in a risk assess...

Retrofit Strategies for Incorporating Xenobiotic Metabolism into High Throughput Screening Assays (EMGS)

EPA Science Inventory

The US EPA’s ToxCast program is designed to assess chemical perturbations of molecular and cellular endpoints using a variety of high-throughput screening (HTS) assays. However, existing HTS assays have limited or no xenobiotic metabolism which could lead to a mischaracterization...

Dynamic levitation performance of Gd-Ba-Cu-O and Y-Ba-Cu-O bulk superconductors under a varying external magnetic field

NASA Astrophysics Data System (ADS)

Liao, Hengpei; Zheng, Jun; Jin, Liwei; Huang, Huan; Deng, Zigang; Shi, Yunhua; Zhou, Difan; Cardwell, David A.

2018-07-01

We report that the dynamic levitation force of bulk high temperature superconductors (HTS) in motion attenuates when exposed to an inhomogeneous magnetic field. This phenomenon has significant potential implications for the long-term stability and running performance of HTS in maglev applications. In order to suppress the attenuation of the levitation force associated with fluctuations in magnetic field, we compare the dynamic levitation performance of single grain Y-Ba-Cu-O (YBCO) and Gd-Ba-Cu-O (GdBCO) bulk superconductors with relatively high critical current densities. A bespoke HTS maglev dynamic measurement system (SCML-03) incorporating a rotating circular permanent magnet guideway was employed to simulate the movement of HTS in a varying magnetic field at different frequencies (i.e. speed of rotation). The attenuation of the levitation force during dynamic operation, which is key parameter for effective maglev operation, has been evaluated experimentally. It is found that GdBCO bulk superconductors that exhibit superior levitation force properties are more able to resist the attenuation of levitation force compared with YBCO bulk materials under the same operating conditions. This investigation indicates clearly that GdBCO bulk superconductors can play an important role in suppressing attenuation of the levitation force, therefore improving the long-term levitation performance under dynamic operating conditions. This result is potentially significant in the design and application of HTS in maglev systems.